From rphellan2210 at gmail.com  Sat Aug  1 20:08:17 2015
From: rphellan2210 at gmail.com (Renzo Ph)
Date: Sat, 1 Aug 2015 21:08:17 -0300
Subject: [ITK] Gradient vector of gradient vector
Message-ID: <CAOvLtO5j_Ricxtq=AamXHi_XHtv+AnTcbThWU6jiOjNnqoHkjg@mail.gmail.com>

Hi there,

Is it possible to get the Matrix (as a vector of vectors) that results
after calculating the second derivative (gradient of the gradient) of an
scalar image. I know that the VectorGradientMagnitudeImageFilter can
calculate the magnitude of those vectors, but I need the vectors themselves.

Thanks.
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From tevain at telecom-paristech.fr  Mon Aug  3 04:51:31 2015
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 3 Aug 2015 10:51:31 +0200 (CEST)
Subject: [ITK] Gradient vector of gradient vector
In-Reply-To: <CAOvLtO5j_Ricxtq=AamXHi_XHtv+AnTcbThWU6jiOjNnqoHkjg@mail.gmail.com>
References: <CAOvLtO5j_Ricxtq=AamXHi_XHtv+AnTcbThWU6jiOjNnqoHkjg@mail.gmail.com>
Message-ID: <2002819194.88193670.1438591891015.JavaMail.zimbra@enst.fr>

Hello,

It seems to me that what you want is the directional components of the second derivative, right ?
If so, maybe you could take the first derivative by any mean of your choice, and then use a Sobel in each direction to have each component of your vectors.
For example, if you're working on 2D data, run a Sobel on X direction (e.g. SobelX) then Y direction (e.g. SobelY), the vector you look for will be [SobelX(x,y),SobelY(x,y)].
For this you could use :
http://www.itk.org/Doxygen/html/classitk_1_1SobelOperator.html
with
http://www.itk.org/Doxygen/html/classitk_1_1ConvolutionImageFilter.html

If your question is "Is there an one-shot filter" to do so : not to my knowledge.

Hope this helps

Tim

----- Mail original -----
De: "Renzo Ph" <rphellan2210 at gmail.com>
?: community at itk.org
Envoy?: Dimanche 2 Ao?t 2015 02:08:17
Objet: [ITK] Gradient vector of gradient vector

Hi there, 

Is it possible to get the Matrix (as a vector of vectors) that results after calculating the second derivative (gradient of the gradient) of an scalar image. I know that the VectorGradientMagnitudeImageFilter can calculate the magnitude of those vectors, but I need the vectors themselves. 

Thanks. 

_______________________________________________
Community mailing list
Community at itk.org
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From c.spanakis83 at gmail.com  Mon Aug  3 06:14:20 2015
From: c.spanakis83 at gmail.com (Constantinus Spanakis)
Date: Mon, 3 Aug 2015 13:14:20 +0300
Subject: [ITK] X3D to dicom
Message-ID: <CAOZihbd_o+Ni+sBC2WpH+qewV7_4r-gXRgp92Xr_QRCEz0ew2A@mail.gmail.com>

Hello. When we want to visualize the human body (or a part of it) in
3D, we convert a dicom series into an x3d file. Is it possible to do
the reverse, i.e extract dicom files from x3d using ITK?

From matt.mccormick at kitware.com  Mon Aug  3 09:37:24 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 3 Aug 2015 09:37:24 -0400
Subject: [ITK] X3D to dicom
In-Reply-To: <CAOZihbd_o+Ni+sBC2WpH+qewV7_4r-gXRgp92Xr_QRCEz0ew2A@mail.gmail.com>
References: <CAOZihbd_o+Ni+sBC2WpH+qewV7_4r-gXRgp92Xr_QRCEz0ew2A@mail.gmail.com>
Message-ID: <CALzTN-RuTtVUg1beFg=HkeyGdoKRoKdCoYn+d5H0fc077Ybo=Q@mail.gmail.com>

Hello Constantinus,

Due to modality-specific tags, the task of writing dicom files is
especially difficult, and we could use improved support.  There are
some previous discussions on the list that can be found. However, see
this example:

  http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html

and this resource:

 http://gdcm.sourceforge.net/wiki/index.php/Writing_DICOM

for a starting point.

HTH,
Matt

On Mon, Aug 3, 2015 at 6:14 AM, Constantinus Spanakis
<c.spanakis83 at gmail.com> wrote:
> Hello. When we want to visualize the human body (or a part of it) in
> 3D, we convert a dicom series into an x3d file. Is it possible to do
> the reverse, i.e extract dicom files from x3d using ITK?
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

From kolin9105 at gmail.com  Mon Aug  3 11:41:24 2015
From: kolin9105 at gmail.com (meikolin saimara)
Date: Mon, 3 Aug 2015 22:41:24 +0700
Subject: [ITK] my task
Message-ID: <CAEiw7u7DE0zenniRGnoL+LhyPbKFyaC5eXUXRifSnS3BxzTeuA@mail.gmail.com>

 Hi everyone!
I'm working on a project right now and my tasks are:
how to segment brain tumors and get a brain tumor volume or extent of brain
tumors without visualization only using the ITK and using Dicom file

I found it difficult to separate so far with the surrounding brain tumor
segmentation method.

If anyone could help with this , I would appreciate it.
Thank you!
this is my first time to use itk
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From matt.mccormick at kitware.com  Mon Aug  3 11:57:50 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 3 Aug 2015 11:57:50 -0400
Subject: [ITK] my task
In-Reply-To: <CAEiw7u7DE0zenniRGnoL+LhyPbKFyaC5eXUXRifSnS3BxzTeuA@mail.gmail.com>
References: <CAEiw7u7DE0zenniRGnoL+LhyPbKFyaC5eXUXRifSnS3BxzTeuA@mail.gmail.com>
Message-ID: <CALzTN-Sba2kL4Ju6qbviqjz7Gh=QJ+sAQB5v=f4mHisEah3tiw@mail.gmail.com>

Hi there,

Welcome to ITK!

There are many different approaches depending on your image data.  It
is recommended to start by reading the ITK Software Guide [1]. Then,
look at articles in the Insight Journal [2]

Matt

[1] http://itk.org/ITK/help/documentation.html

[2] http://insight-journal.org/search/?search=brain

On Mon, Aug 3, 2015 at 11:41 AM, meikolin saimara <kolin9105 at gmail.com> wrote:
> Hi everyone!
> I'm working on a project right now and my tasks are:
> how to segment brain tumors and get a brain tumor volume or extent of brain
> tumors without visualization only using the ITK and using Dicom file
>
> I found it difficult to separate so far with the surrounding brain tumor
> segmentation method.
>
> If anyone could help with this , I would appreciate it.
> Thank you!
> this is my first time to use itk
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From kolin9105 at gmail.com  Mon Aug  3 13:22:26 2015
From: kolin9105 at gmail.com (meikolin saimara)
Date: Tue, 4 Aug 2015 00:22:26 +0700
Subject: [ITK] (no subject)
Message-ID: <CAEiw7u4yWRXaHY5Pkmb9TNEVF1CTJ37cGrUfNyp34=dDYonsUg@mail.gmail.com>

how to build Skull-stripping in itk
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From matt.mccormick at kitware.com  Mon Aug  3 13:28:45 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 3 Aug 2015 13:28:45 -0400
Subject: [ITK] (no subject)
In-Reply-To: <CAEiw7u4yWRXaHY5Pkmb9TNEVF1CTJ37cGrUfNyp34=dDYonsUg@mail.gmail.com>
References: <CAEiw7u4yWRXaHY5Pkmb9TNEVF1CTJ37cGrUfNyp34=dDYonsUg@mail.gmail.com>
Message-ID: <CALzTN-RChbFQq_DsGthaG8Ck=ZHv6sWGi5=m1hbCUgYc9A4wrA@mail.gmail.com>

Hi,

The Skull Stripper Insight Journal [1] article has been been
integrated into ITK as Remote Module [2].  To build the code, set

  Module_SkullStrip

to ON in your CMake configuration. The code [3] corresponding to this
article [4] that also uses the code may be helpful.

Hope this helps,
Matt

[1] http://insight-journal.org/browse/publication/859

[2] http://www.itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules

[3] https://github.com/InsightSoftwareConsortium/ITKFrontierNeuroinformatics2013

[4] http://journal.frontiersin.org/article/10.3389/fninf.2014.00013/abstract

On Mon, Aug 3, 2015 at 1:22 PM, meikolin saimara <kolin9105 at gmail.com> wrote:
> how to build Skull-stripping in itk
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From olivier.comtois at polymtl.ca  Mon Aug  3 17:30:13 2015
From: olivier.comtois at polymtl.ca (Olivier Comtois)
Date: Mon, 03 Aug 2015 21:30:13 +0000
Subject: [ITK] [ITK-users] Generating a warping field
	with	ThinPlateSplineKernelTransform
Message-ID: <20150803213013.Horde.k-Tn9jq9s3NiK8P8YzGdJrX@www.imp.polymtl.ca>


Hi everyone,

I am trying to use ThinPlateSplineKernelTransform in order to produce  
a warping field. I am closely following the example in  
Examples/RegistrationITKv4/ThinPlateSplineWarp.cxx however, the field  
and image outputted this way is completely wrong.

I am trying to straighten a set of point (the spinal cord). I have a  
source set of points which is a set of points alongside of the spinal  
cord and a corresponding set of points which is a set of points taken  
from a straightened spinal cord.These points are landmarks on the  
image. The problem is the output image is still curved and not  
anywhere close the target landmarks.

Thank you in advance,

Olivier

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From kolin9105 at gmail.com  Tue Aug  4 02:29:40 2015
From: kolin9105 at gmail.com (meikolin saimara)
Date: Tue, 4 Aug 2015 13:29:40 +0700
Subject: [ITK] (no subject)
Message-ID: <CAEiw7u6EeJvXbK4MrL6uBAkVt0fivOMPshCOe6ykERZtX6wcXw@mail.gmail.com>

how to calculate pixel value black and white of image?
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From jhlegarreta at vicomtech.org  Tue Aug  4 03:02:48 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Tue, 4 Aug 2015 09:02:48 +0200
Subject: [ITK] (no subject)
In-Reply-To: <CAEiw7u6EeJvXbK4MrL6uBAkVt0fivOMPshCOe6ykERZtX6wcXw@mail.gmail.com>
References: <CAEiw7u6EeJvXbK4MrL6uBAkVt0fivOMPshCOe6ykERZtX6wcXw@mail.gmail.com>
Message-ID: <CAAKhGh-rBU7DoEDCfHPMr5EnPQfQXUBjBiODVEQgs1ctS3MY8Q@mail.gmail.com>

Hi Meikolin,
assuming you have an itk::Image, and that you correctly specify the pixel
index whose value you are requiring, you can do:

ImageType::PixelType value = image->GetPixel(index);

You can have a look at section 4.1.3 of the ITK software guide [1] for
further details.

HTH,
JON HAITZ


[1] http://www.itk.org/ItkSoftwareGuide.pdf



On 4 August 2015 at 08:29, meikolin saimara <kolin9105 at gmail.com> wrote:

> how to calculate pixel value black and white of image?
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From marco.dev.open at gmail.com  Tue Aug  4 08:04:33 2015
From: marco.dev.open at gmail.com (Marco Dev)
Date: Tue, 4 Aug 2015 16:34:33 +0430
Subject: [ITK] [ITK-dev] converting metaimage format to nrrd
Message-ID: <CAKcUdn411XXGpsrXhFpWbBNvcAD+K6JW=_GMaqHdjxSjnJBniQ@mail.gmail.com>

Hi dears,
Is way to convert metaimage (.mhd and .raw )format to .nrrd format ?
Thanks in advance.
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From tevain at telecom-paristech.fr  Tue Aug  4 08:30:17 2015
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Tue, 4 Aug 2015 14:30:17 +0200 (CEST)
Subject: [ITK] [ITK-dev] converting metaimage format to nrrd
In-Reply-To: <CAKcUdn411XXGpsrXhFpWbBNvcAD+K6JW=_GMaqHdjxSjnJBniQ@mail.gmail.com>
References: <CAKcUdn411XXGpsrXhFpWbBNvcAD+K6JW=_GMaqHdjxSjnJBniQ@mail.gmail.com>
Message-ID: <1455192097.88872168.1438691417531.JavaMail.zimbra@enst.fr>

Hello,

Have you tried what is suggested here :
http://www.cmake.org/Wiki/Getting_Started_with_the_NRRD_Format  ?

Tim

----- Mail original -----
De: "Marco Dev" <marco.dev.open at gmail.com>
?: insight-developers at itk.org, vtkusers at vtk.org
Envoy?: Mardi 4 Ao?t 2015 14:04:33
Objet: [ITK] [ITK-dev] converting metaimage format to nrrd

Hi dears, 
Is way to convert metaimage (.mhd and .raw )format to .nrrd format ? 
Thanks in advance. 


_______________________________________________
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From matt.mccormick at kitware.com  Tue Aug  4 10:21:21 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 4 Aug 2015 10:21:21 -0400
Subject: [ITK] [ITK-dev] converting metaimage format to nrrd
In-Reply-To: <CAKcUdn411XXGpsrXhFpWbBNvcAD+K6JW=_GMaqHdjxSjnJBniQ@mail.gmail.com>
References: <CAKcUdn411XXGpsrXhFpWbBNvcAD+K6JW=_GMaqHdjxSjnJBniQ@mail.gmail.com>
Message-ID: <CALzTN-SfFLj4i0Dy9488AYQv66df1H0uAphbwb_wpmKsOecP7g@mail.gmail.com>

Hi Marco,

This example may be useful:

  http://itk.org/ITKExamples/src/IO/ImageBase/ConvertFileFormats/Documentation.html

HTH,
Matt

On Tue, Aug 4, 2015 at 8:04 AM, Marco Dev <marco.dev.open at gmail.com> wrote:
> Hi dears,
> Is way to convert metaimage (.mhd and .raw )format to .nrrd format ?
> Thanks in advance.
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
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From siavashk at ece.ubc.ca  Tue Aug  4 17:13:16 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Tue, 4 Aug 2015 14:13:16 -0700 (MST)
Subject: [ITK] [ITK-users] Generating a warping field with
 ThinPlateSplineKernelTransform
In-Reply-To: <20150803213013.Horde.k-Tn9jq9s3NiK8P8YzGdJrX@www.imp.polymtl.ca>
References: <20150803213013.Horde.k-Tn9jq9s3NiK8P8YzGdJrX@www.imp.polymtl.ca>
Message-ID: <1438722796207-35972.post@n7.nabble.com>

Having your exact code (on the small chance that it differs from the
example), your data, and the argument list would help in debugging your
problem. But in the mean time, you can try the following to see where the
problem lies:

1. If you write out the defomation field and view it in the context of your
volume in a 3rd party software (e.g., Paraview), what would you see? Would
it make sense in terms of smoothness and direction?

2. Is the deformed volume (output of itk::ResmapleImageFilter) different
compared to the input volume? In other words, is the resampler doing
anything?

3. If you invert the deformation field, would your deformed volume be the
output that you expect? You can do this by swapping source and target
landmarks.

Siavash



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Generating-a-warping-field-with-ThinPlateSplineKernelTransform-tp35971p35972.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From siavashk at ece.ubc.ca  Tue Aug  4 17:53:46 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Tue, 4 Aug 2015 14:53:46 -0700 (MST)
Subject: [ITK] [ITK-users] 3D/2D registration with
 itkRayCastInterpolateImageFunction
In-Reply-To: <b0b244228f0c4cc9a2d55169deff2cd3@vprd-opci0018.b-com.local>
References: <b0b244228f0c4cc9a2d55169deff2cd3@vprd-opci0018.b-com.local>
Message-ID: <1438725226436-35973.post@n7.nabble.com>

Is the metric decreasing? (i.e. similarity value) It could be that everything
is correct, it is just that you have an ill-posed problem. If the metric is
decreasing, it could be that you are converging to a local minimum.

Siavash



--
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Sent from the ITK - Users mailing list archive at Nabble.com.
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From lasso at queensu.ca  Tue Aug  4 18:38:37 2015
From: lasso at queensu.ca (Andras Lasso)
Date: Tue, 4 Aug 2015 22:38:37 +0000
Subject: [ITK] [ITK-users] Generating a warping field with
 ThinPlateSplineKernelTransform
In-Reply-To: <1438722796207-35972.post@n7.nabble.com>
References: <20150803213013.Horde.k-Tn9jq9s3NiK8P8YzGdJrX@www.imp.polymtl.ca>
 <1438722796207-35972.post@n7.nabble.com>
Message-ID: <CY1PR0701MB1613B15AF8B413FC7C21C855D8760@CY1PR0701MB1613.namprd07.prod.outlook.com>

You can also load non-linear transforms into 3D Slicer for interactive visualization, application to your images, comparing fixed/moving/registered images, etc. You can also invert, compose, decompose transforms, apply it to marked points, segmented surfaces, etc.

See some examples here:
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

Paraview is very good but not for analyzing transforms: it can only load exported displacement fields (but for that you would need to be sure that your region of interest is correct and you lose information when you sample the field), it only supports axis-aligned images, and dense vector field visualization has been broken in recent versions (I haven't checked the latest version).

Andras

-----Original Message-----
From: Community [mailto:community-bounces at itk.org] On Behalf Of Siavash Khallaghi
Sent: Tuesday, August 4, 2015 5:13 PM
To: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] Generating a warping field with ThinPlateSplineKernelTransform

Having your exact code (on the small chance that it differs from the example), your data, and the argument list would help in debugging your problem. But in the mean time, you can try the following to see where the problem lies:

1. If you write out the defomation field and view it in the context of your volume in a 3rd party software (e.g., Paraview), what would you see? Would it make sense in terms of smoothness and direction?

2. Is the deformed volume (output of itk::ResmapleImageFilter) different compared to the input volume? In other words, is the resampler doing anything?

3. If you invert the deformation field, would your deformed volume be the output that you expect? You can do this by swapping source and target landmarks.

Siavash



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Generating-a-warping-field-with-ThinPlateSplineKernelTransform-tp35971p35972.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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http://www.itk.org/Wiki/ITK_FAQ

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_____________________________________
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From marco.dev.open at gmail.com  Wed Aug  5 06:11:59 2015
From: marco.dev.open at gmail.com (Marco Dev)
Date: Wed, 5 Aug 2015 14:41:59 +0430
Subject: [ITK] [ITK-dev] converting metaimage format to nrrd
In-Reply-To: <CALzTN-SfFLj4i0Dy9488AYQv66df1H0uAphbwb_wpmKsOecP7g@mail.gmail.com>
References: <CAKcUdn411XXGpsrXhFpWbBNvcAD+K6JW=_GMaqHdjxSjnJBniQ@mail.gmail.com>
 <CALzTN-SfFLj4i0Dy9488AYQv66df1H0uAphbwb_wpmKsOecP7g@mail.gmail.com>
Message-ID: <CAKcUdn6RiBqXAV7ccKqrhRMMo8-qu-MbnbkU7zzCST7hFbj-Fw@mail.gmail.com>

Thanks about your help .

On Tue, Aug 4, 2015 at 6:51 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Marco,
>
> This example may be useful:
>
>
> http://itk.org/ITKExamples/src/IO/ImageBase/ConvertFileFormats/Documentation.html
>
> HTH,
> Matt
>
> On Tue, Aug 4, 2015 at 8:04 AM, Marco Dev <marco.dev.open at gmail.com>
> wrote:
> > Hi dears,
> > Is way to convert metaimage (.mhd and .raw )format to .nrrd format ?
> > Thanks in advance.
> >
> >
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-developers
> >
>
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From kolin9105 at gmail.com  Wed Aug  5 11:12:14 2015
From: kolin9105 at gmail.com (meikolin saimara)
Date: Wed, 5 Aug 2015 22:12:14 +0700
Subject: [ITK] (no subject)
Message-ID: <CAEiw7u6yhD6D0N6uoiK4BVUcC2V-mVPo+wQJ76KMMaMX0cvE-Q@mail.gmail.com>

Hello There
I had problems with my thesis where I was very difficult to separate the
brain tumor with the outer circumference of the brain or skull.
if I can define a brain tumor I want to also calculate the volume of a brain
tumor through a pixel value.
I use the method of segmentation threshold without using visualization only
ITK and I use dicom image.
can you help me
pleaz...
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From jhlegarreta at vicomtech.org  Wed Aug  5 12:31:19 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 5 Aug 2015 18:31:19 +0200
Subject: [ITK] (no subject)
In-Reply-To: <CAEiw7u6yhD6D0N6uoiK4BVUcC2V-mVPo+wQJ76KMMaMX0cvE-Q@mail.gmail.com>
References: <CAEiw7u6yhD6D0N6uoiK4BVUcC2V-mVPo+wQJ76KMMaMX0cvE-Q@mail.gmail.com>
Message-ID: <CAAKhGh--UifPmdtkCDKjmPrxV-cpbAmfMtRFv5x_HJq7SibPnQ@mail.gmail.com>

Hi Meikolin,
if you count the number of voxels your tumour has, knowing the volume would
imply multiplying the number of voxels by the resolution of your input
dataset in all three dimensions.
You can get the resolution of your image as

ImageType::SpacingType spacing =  myImage->GetSpacing();

HTH,
JON HAITZ



On 5 August 2015 at 17:12, meikolin saimara <kolin9105 at gmail.com> wrote:

> Hello There
> I had problems with my thesis where I was very difficult to separate the
> brain tumor with the outer circumference of the brain or skull.
> if I can define a brain tumor I want to also calculate the volume of a
> brain tumor through a pixel value.
> I use the method of segmentation threshold without using visualization
> only ITK and I use dicom image.
> can you help me
> pleaz...
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From david.m.welch at gmail.com  Wed Aug  5 12:51:12 2015
From: david.m.welch at gmail.com (David Welch)
Date: Wed, 05 Aug 2015 11:51:12 -0500
Subject: [ITK] [ITK-dev] converting metaimage format to nrrd
In-Reply-To: <CAKcUdn6RiBqXAV7ccKqrhRMMo8-qu-MbnbkU7zzCST7hFbj-Fw@mail.gmail.com>
References: <CAKcUdn411XXGpsrXhFpWbBNvcAD+K6JW=_GMaqHdjxSjnJBniQ@mail.gmail.com>
 <CALzTN-SfFLj4i0Dy9488AYQv66df1H0uAphbwb_wpmKsOecP7g@mail.gmail.com>
 <CAKcUdn6RiBqXAV7ccKqrhRMMo8-qu-MbnbkU7zzCST7hFbj-Fw@mail.gmail.com>
Message-ID: <EB732195-359C-44D9-B275-1388C6B34542@urthecast.com>

These pages are also a lot of help:

http://www.cmake.org/Wiki/Getting_Started_with_the_NRRD_Format
http://teem.sourceforge.net/nrrd/format.html

Cheers,
Dave

From:  Marco Dev
Date:  Wednesday, August 5, 2015 at 5:11 AM
To:  Matt McCormick
Cc:  "vtkusers at vtk.org", ITK
Subject:  Re: [ITK-dev] converting metaimage format to nrrd

Thanks about your help .

On Tue, Aug 4, 2015 at 6:51 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
Hi Marco,

This example may be useful:

  http://itk.org/ITKExamples/src/IO/ImageBase/ConvertFileFormats/Documentation.html

HTH,
Matt

On Tue, Aug 4, 2015 at 8:04 AM, Marco Dev <marco.dev.open at gmail.com> wrote:
> Hi dears,
> Is way to convert metaimage (.mhd and .raw )format to .nrrd format ?
> Thanks in advance.
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>


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_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
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Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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Follow this link to subscribe/unsubscribe:
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From siavashk at ece.ubc.ca  Wed Aug  5 18:01:54 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Wed, 5 Aug 2015 15:01:54 -0700 (MST)
Subject: [ITK] [ITK-users] translate: units
In-Reply-To: <1438696937794-7587643.post@n2.nabble.com>
References: <1438696937794-7587643.post@n2.nabble.com>
Message-ID: <1438812114032-7587647.post@n2.nabble.com>

They are in physical units, i.e. mm. This is because geometric
transformations are always done in physical space in ITK. 

Siavash



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/translate-units-tp7587643p7587647.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

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From matt.mccormick at kitware.com  Thu Aug  6 00:34:22 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 6 Aug 2015 00:34:22 -0400
Subject: [ITK] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-RqTnNpZ-3WwrME8MkkDsCGSwX6tBbcrFb_go1c5ga2qQ@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

 https://plus.google.com/u/1/events/c06hvrqf6uihp4b0h3h0qu0df2o


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/u/1/events/cm1b6rc5sfq201r8map9uher4b0



For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From tevain at telecom-paristech.fr  Thu Aug  6 04:05:20 2015
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Thu, 6 Aug 2015 10:05:20 +0200 (CEST)
Subject: [ITK] (no subject)
In-Reply-To: <CAAKhGh--UifPmdtkCDKjmPrxV-cpbAmfMtRFv5x_HJq7SibPnQ@mail.gmail.com>
References: <CAEiw7u6yhD6D0N6uoiK4BVUcC2V-mVPo+wQJ76KMMaMX0cvE-Q@mail.gmail.com>
 <CAAKhGh--UifPmdtkCDKjmPrxV-cpbAmfMtRFv5x_HJq7SibPnQ@mail.gmail.com>
Message-ID: <790273056.89749731.1438848320436.JavaMail.zimbra@enst.fr>

Hi,

To complete Jon suggestion, you could easily acces the volume (in voxels) of your segmentation with a ShapeLabelMap:
http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html
It labels each binary object of an image and compute some features on it.
You can acces the volume with:
ShapeLabelFilter->GetOutput()->GetLabelObject(*Label of your segmentation*)->GetNumberOfPixels();

Tim

----- Mail original -----
De: "Jon Haitz Legarreta" <jhlegarreta at vicomtech.org>
?: "meikolin saimara" <kolin9105 at gmail.com>
Cc: community at itk.org
Envoy?: Mercredi 5 Ao?t 2015 18:31:19
Objet: Re: [ITK] (no subject)

Hi Meikolin, 
if you count the number of voxels your tumour has, knowing the volume would imply multiplying the number of voxels by the resolution of your input dataset in all three dimensions. 
You can get the resolution of your image as 
ImageType::SpacingType spacing = ?myImage->GetSpacing(); 
HTH, 
JON HAITZ 



On 5 August 2015 at 17:12, meikolin saimara < kolin9105 at gmail.com > wrote: 



Hello There 
I had problems with my thesis where I was very difficult to separate the brain tumor with the outer circumference of the brain or skull . 
if I can define a brain tumor I want to also calculate the volume of a brain tumor through a pixel value . 
I use the method of segmentation threshold without using visualization only ITK and I use dicom image. 
can you help me 
pleaz... 

_______________________________________________ 
Community mailing list 
Community at itk.org 
http://public.kitware.com/mailman/listinfo/community 



_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community

From matt.mccormick at kitware.com  Thu Aug  6 10:28:47 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 6 Aug 2015 10:28:47 -0400
Subject: [ITK] [ITK-dev] Ubuntu 14 Test failure bisect results
In-Reply-To: <8EC6E57A-1ED3-4909-A1AA-81EA4E83DFA5@mail.nih.gov>
References: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov>
 <CALzTN-TJD+Zxzk-5yawApDAVxD7R2Q26ExfRnfbOaZmw9KUeuw@mail.gmail.com>
 <8EC6E57A-1ED3-4909-A1AA-81EA4E83DFA5@mail.nih.gov>
Message-ID: <CALzTN-RiC-0Q+UUw6L9BGsAp8Fh5eDynNDZ7SoGaTaqz0JQsVA@mail.gmail.com>

Hi Brad,

I have been doing some Experimental builds on the dashboard.  So far,
the test failures are repeatable with GCC / Binutils in Ubuntu 14.04
with BUILD_SHARED_LIBS OFF, but not BUILD_SHARED_LIBS ON.  I am
working on a patch... :-)

Thanks,
Matt

On Thu, Aug 6, 2015 at 9:33 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Matt,
>
> What were the results of this experiment? It'd be nice to clean up the release branch of these failing tests.
>
> And I want to steal the correct solution for SimpleITK too :)
>
> Brad
>
> On Jul 31, 2015, at 3:29 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>
>> Hi Brad,
>>
>> Thanks for investigating and getting great information out of git bisect.
>>
>> I developed the patch on Gentoo with GCC 4.8.4 / binutils 2.24, and I
>> have not seen any issues.  The eldorado builds on the dashboard are
>> all Ubuntu 14.04.2, too.  I will start an Experimental build with
>> BUILD_SHARED_LIBS set on eldorado to be sure it can be reproduced.
>>
>> Thanks,
>> Matt
>>
>> On Fri, Jul 31, 2015 at 1:03 PM, Bradley Lowekamp
>> <blowekamp at mail.nih.gov> wrote:
>>> Matt,
>>>
>>> I was digging into these test failures:
>>>
>>> https://open.cdash.org/viewTest.php?onlyfailed&buildid=3932451
>>>
>>> Here are the results of the git bisect:
>>>
>>> 674acdb2dd5546b7045f7253c84e4f9f237405e8 is the first bad commit
>>> commit 674acdb2dd5546b7045f7253c84e4f9f237405e8
>>> Author: Matt McCormick <matt.mccormick at kitware.com>
>>> Date:   Sun May 31 21:00:55 2015 -0400
>>>
>>>    ENH: Use gold linker on Linux with GCC.
>>>
>>>
>>>
>>>    The gold linker is approximately three times as fast as the default
>>> linker.
>>>    Enable it with GCC 4.8 and newer where it was tested. The gold linker
>>> only
>>>    works with ELF executables, so it is only enabled for Linux.
>>>
>>>
>>>
>>>    Timing tests:
>>>
>>>
>>>
>>>    Static libs link time:
>>>
>>>
>>>
>>>      ld:      452 sec
>>>      ld-gold: 179 sec
>>>
>>>
>>>
>>>    Shared libs link time, wrapping enabled:
>>>
>>>
>>>
>>>      ld:      164 sec
>>>      ld-gold: 48 sec
>>>
>>>
>>>
>>>    Change-Id: Ic8d9b5132ad6b71e5f100b5436615d6a8fac3e5c
>>>
>>> Disabling ld-gold seems to fix the problem.
>>>
>>> Versions:
>>>
>>> blowekamp at lhcp-vm-ubu14:~/ITK$ gcc --version
>>> gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4
>>> Copyright (C) 2013 Free Software Foundation, Inc.
>>> This is free software; see the source for copying conditions.  There is NO
>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>>>
>>> blowekamp at lhcp-vm-ubu14:~/ITK$ ld --version
>>> GNU ld (GNU Binutils for Ubuntu) 2.24
>>> Copyright 2013 Free Software Foundation, Inc.
>>> This program is free software; you may redistribute it under the terms of
>>> the GNU General Public License version 3 or (at your option) a later
>>> version.
>>> This program has absolutely no warranty.
>>>
>>> blowekamp at lhcp-vm-ubu14:~/ITK$ lsb_release -a
>>> No LSB modules are available.
>>> Distributor ID: Ubuntu
>>> Description: Ubuntu 14.04.2 LTS
>>> Release: 14.04
>>> Codename: trusty
>>>
>>>
>>> Currently we have a check for using gold with > 4.8.3:
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L206
>>>
>>> But looking at this change:
>>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e
>>>
>>> We should have know about these related test failures:
>>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e
>>>
>>> So what do you recall about what versions of GCC ld-gold works on?
>>>
>>> Thanks,
>>> Brad
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-developers

From blowekamp at mail.nih.gov  Thu Aug  6 09:33:36 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 06 Aug 2015 09:33:36 -0400
Subject: [ITK] [ITK-dev] Ubuntu 14 Test failure bisect results
In-Reply-To: <CALzTN-TJD+Zxzk-5yawApDAVxD7R2Q26ExfRnfbOaZmw9KUeuw@mail.gmail.com>
References: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov>
 <CALzTN-TJD+Zxzk-5yawApDAVxD7R2Q26ExfRnfbOaZmw9KUeuw@mail.gmail.com>
Message-ID: <8EC6E57A-1ED3-4909-A1AA-81EA4E83DFA5@mail.nih.gov>

Matt,

What were the results of this experiment? It'd be nice to clean up the release branch of these failing tests.

And I want to steal the correct solution for SimpleITK too :)

Brad

On Jul 31, 2015, at 3:29 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> Hi Brad,
> 
> Thanks for investigating and getting great information out of git bisect.
> 
> I developed the patch on Gentoo with GCC 4.8.4 / binutils 2.24, and I
> have not seen any issues.  The eldorado builds on the dashboard are
> all Ubuntu 14.04.2, too.  I will start an Experimental build with
> BUILD_SHARED_LIBS set on eldorado to be sure it can be reproduced.
> 
> Thanks,
> Matt
> 
> On Fri, Jul 31, 2015 at 1:03 PM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
>> Matt,
>> 
>> I was digging into these test failures:
>> 
>> https://open.cdash.org/viewTest.php?onlyfailed&buildid=3932451
>> 
>> Here are the results of the git bisect:
>> 
>> 674acdb2dd5546b7045f7253c84e4f9f237405e8 is the first bad commit
>> commit 674acdb2dd5546b7045f7253c84e4f9f237405e8
>> Author: Matt McCormick <matt.mccormick at kitware.com>
>> Date:   Sun May 31 21:00:55 2015 -0400
>> 
>>    ENH: Use gold linker on Linux with GCC.
>> 
>> 
>> 
>>    The gold linker is approximately three times as fast as the default
>> linker.
>>    Enable it with GCC 4.8 and newer where it was tested. The gold linker
>> only
>>    works with ELF executables, so it is only enabled for Linux.
>> 
>> 
>> 
>>    Timing tests:
>> 
>> 
>> 
>>    Static libs link time:
>> 
>> 
>> 
>>      ld:      452 sec
>>      ld-gold: 179 sec
>> 
>> 
>> 
>>    Shared libs link time, wrapping enabled:
>> 
>> 
>> 
>>      ld:      164 sec
>>      ld-gold: 48 sec
>> 
>> 
>> 
>>    Change-Id: Ic8d9b5132ad6b71e5f100b5436615d6a8fac3e5c
>> 
>> Disabling ld-gold seems to fix the problem.
>> 
>> Versions:
>> 
>> blowekamp at lhcp-vm-ubu14:~/ITK$ gcc --version
>> gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4
>> Copyright (C) 2013 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.  There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>> 
>> blowekamp at lhcp-vm-ubu14:~/ITK$ ld --version
>> GNU ld (GNU Binutils for Ubuntu) 2.24
>> Copyright 2013 Free Software Foundation, Inc.
>> This program is free software; you may redistribute it under the terms of
>> the GNU General Public License version 3 or (at your option) a later
>> version.
>> This program has absolutely no warranty.
>> 
>> blowekamp at lhcp-vm-ubu14:~/ITK$ lsb_release -a
>> No LSB modules are available.
>> Distributor ID: Ubuntu
>> Description: Ubuntu 14.04.2 LTS
>> Release: 14.04
>> Codename: trusty
>> 
>> 
>> Currently we have a check for using gold with > 4.8.3:
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L206
>> 
>> But looking at this change:
>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e
>> 
>> We should have know about these related test failures:
>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e
>> 
>> So what do you recall about what versions of GCC ld-gold works on?
>> 
>> Thanks,
>> Brad
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 

_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From blowekamp at mail.nih.gov  Thu Aug  6 10:37:29 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 06 Aug 2015 10:37:29 -0400
Subject: [ITK] [ITK-users] SimpleITK: Pass Image from C++ to Python
In-Reply-To: <558EA415.8050409@gmx.net>
References: <558EA415.8050409@gmx.net>
Message-ID: <5D940348-9F6D-441B-93F4-2730E61E6A55@mail.nih.gov>

Hello Klaus,

Sorry for the very delayed response.

I would like to know more about your application requirements.

I have implemented an initial prorotype of a public method in the _SimpleITK Python library which allows conversions from the SWIG PyObject to the SimpleITK Image class. This should allow pulling Image objects created in Python SimpleITK  into a C++ application. A similar method can be created to go the other way too.

I believe this is the interface you need, and just wanted to verify your requirements.

Here is the proof of concept branch:
https://github.com/blowekamp/SimpleITK/commits/AddCXXConvertInterfaceToPythonLibrary


HTH,
Brad


On Jun 27, 2015, at 9:24 AM, Klaus <drechsler at gmx.net> wrote:

> Hi,
> 
> I have a C++ application which I use to do all major image processing
> stuff, UI and so on.  I embedded python as scripting language to quickly
> test new ideas. Currently I am using temporary files and pass file paths
> back and forth as a quick and dirty solution to pass images from one
> language to the other.  However, I would like to directly pass a sitk
> (or itk) image from c++ as parameter to a python method/function call.
> 
> Is there a straight forward (and efficient) way to achieve this?
> 
> Thank you!
> 
> Klaus
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
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From olivier.comtois at polymtl.ca  Thu Aug  6 11:53:32 2015
From: olivier.comtois at polymtl.ca (Olivier Comtois)
Date: Thu, 06 Aug 2015 15:53:32 +0000
Subject: [ITK] [ITK-users] Generating a warping field
	with	ThinPlateSplineKernelTransform
In-Reply-To: <mailman.13.1438790405.4557.insight-users@itk.org>
Message-ID: <20150806155332.Horde.prSADUXzWlTSvqlZxJd62Rs@www.imp.polymtl.ca>

Thank you for your reply Siavash,

Here is my code :

It differs from the example in that I take my landmark points from 2  
files (one for the source landmarks and another for the target). The  
source landmarks come from the segmentation of a curved spinal cord  
while the straight ones come from a template (which is straightened).

std::vector<double> ReadLabelValueFromFile(std::string filename) {
	std::ifstream file(filename.c_str());
	string line;
	char* token;
	std::vector<double> result;
	std::vector<double>::iterator it;

	it = result.begin();
	if (file.is_open()) {
		while (file.good()) {
			getline(file, line);
			char * charLine = new char[line.length() + 1];
			strcpy(charLine, line.c_str());
			token = std::strtok(charLine, ",");
			while (token != NULL) {
				result.push_back(std::atof(token));
				token = strtok(NULL, ",");
			}
			delete[] charLine;
		}
		file.close();
	} else {
		throw std::runtime_error(std::string("Cannot open file : ") + filename);
	}
	return result;
}

void GetRealValuePointSetFromFile(itk::ThinPlateSplineKernelTransform<  
double, 3>::PointSetType::Pointer &source,
		itk::ThinPlateSplineKernelTransform< double,  
3>::PointSetType::Pointer &destination,
		string curvedFilename, string straightFilename) {
	//define variables needed for this function
	string line;
	string token;
	std::vector<double> straightValues;
	std::vector<double> curvedValues;

	//fetching coordinates from files
	try {
		straightValues = ReadLabelValueFromFile(straightFilename);
		curvedValues = ReadLabelValueFromFile(curvedFilename);
		//check if not empty
		if (curvedValues.size() == 0) {
			throw std::runtime_error(
					"No value found in the curved labels text file.");
		}
		if (straightValues.size() == 0) {
			throw std::runtime_error(
					"No value found in straight the labels text file.");
		}
		if ((straightValues.size() % 3) != 0) {
			throw std::runtime_error(
					"The straight file size must be divisible by 3 (since there is 3  
dimensions to the image)");
		}
		if ((curvedValues.size() % 3) != 0) {
			throw std::runtime_error(
					"The curved file size must be divisible by 3 (since there is 3  
dimensions to the image)");
		}
		if (straightValues.size() != curvedValues.size()) {
			throw std::runtime_error(
					"Curved and Straight files do not have the same size.");
		}
	} catch (const std::exception &e) {
		throw;
	}

	//Produce the Straight points
	typedef double Realtype;
	typedef itk::ThinPlateSplineKernelTransform< double, ImageDimension>  
TransformType;
	typedef TransformType::PointSetType PointSetType;

	std::vector<double>::iterator itS = straightValues.begin();
	std::vector<double>::iterator itC = curvedValues.begin();
	typedef PointSetType::PointIdentifier PointIdType;
	PointIdType id = itk::NumericTraits< PointIdType >::ZeroValue();

	while (itS != straightValues.end()) {
		typedef itk::Point<double, ImageDimension> PointType;
		PointType pS;
		PointType pC;
		for (int i = 0; i < 3; i++) {
			pS[i] = *itS;
			pC[i] = *itC;
			itS++;
			itC++;
		}
		//Place points in the point sets
		source->SetPoint(id, pC);
		source->SetPointData(id, id);
		destination->SetPoint(id, pS);
		destination->SetPointData(id, id);
		id++;
	}
	printf("RETURNING POINT VALUES");
	return;

}

int LandmarkBasedWithTextDisplacementFieldTransformInitializer(int  
argc, char *argv[]) {


	////////////////////////////////////////////////////////////////////////////////////////////
	/*CREATING USEFUL TYPES*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nCREATING USEFUL TYPES\n");
	typedef double RealType;
	typedef unsigned int LabelType;
	typedef itk::Image<LabelType, ImageDimension> LabelImageType;
	typedef itk::Image<RealType, ImageDimension> RealImageType;
	typedef itk::Vector<RealType, ImageDimension> VectorType;
	typedef itk::Vector< double, ImageDimension > FieldVectorType;
	typedef itk::ResampleImageFilter<LabelImageType, LabelImageType>  
ResamplerType;
	typedef itk::LinearInterpolateImageFunction<LabelImageType, RealType  
 > InterpolatorType;
	typedef itk::ImageFileWriter< LabelImageType >  DeformedImageWriterType;
	typedef itk::Image< FieldVectorType,  ImageDimension > DisplacementFieldType;
	typedef itk::ImageFileWriter< DisplacementFieldType > FieldWriterType;
	typedef itk::ThinPlateSplineKernelTransform< RealType,  
ImageDimension> TransformType;
	typedef itk::ImageFileReader<LabelImageType> ImageReaderType;
	typedef TransformType::PointSetType PointSetType;
	typedef PointSetType::PointIdentifier PointIdType;
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*LOADING FIXED IMAGE*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nLOADING DESTINATION IMAGE\n");

	ImageReaderType::Pointer destinationReader = ImageReaderType::New();
	destinationReader->SetFileName(argv[2]);
	destinationReader->Update();
	LabelImageType::Pointer destinationImage = destinationReader->GetOutput();
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*LOADING MOVING IMAGE*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nLOADING SOURCE IMAGE\n");

	ImageReaderType::Pointer sourceReader = ImageReaderType::New();
	sourceReader->SetFileName(argv[1]);
	sourceReader->Update();
	LabelImageType::Pointer sourceImage = sourceReader->GetOutput();
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*INIT IMAGE CONTAINERS*/
	////////////////////////////////////////////////////////////////////////////////////////////
	typedef itk::PointSet<RealType, ImageDimension> RealPointSetType;
	PointSetType::Pointer destinationPts = PointSetType::New();
	PointSetType::Pointer sourcePts = PointSetType::New();
	RegistrationType::Pointer registration = RegistrationType::New();

	destinationPts->Initialize();
	sourcePts->Initialize();
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*IMPORTING LANDMARKS FROM TEXT FILES*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nIMPORTING LANDMARKS FROM TEXT FILES\n");
	if (string(argv[3]).compare("") != 0) {
		if (string(argv[4]).compare("") != 0) {
			try {
				string sourceFilename = argv[3];
				string destinationFilename = argv[4];
				GetRealValuePointSetFromFile(sourcePts, destinationPts,  
sourceFilename, destinationFilename);
			} catch (exception &e) {
				throw;
			}
		} else
			throw std::runtime_error(
					"Both arguments the straight and curved file must be specified");
	} else
		throw std::runtime_error(
				"A file must be specified in order to take input real labels.");
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*DEFINING KERNEL TRANSFORM*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nDEFINING KERNEL TRANSFORM\n");
	TransformType::Pointer tps = TransformType::New();

	tps->SetSourceLandmarks(sourcePts);
	tps->SetTargetLandmarks(destinationPts);
	tps->ComputeWMatrix();
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*DEFINING RESAMPLER TO EXECUTE TRANSFORM*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nDEFINING RESAMPLER\n");
	LabelImageType::ConstPointer inputImage = sourceReader->GetOutput();

	LabelImageType::SpacingType spacing = destinationImage->GetSpacing();
	LabelImageType::PointType   origin  = destinationImage->GetOrigin();
	LabelImageType::DirectionType direction  = destinationImage->GetDirection();
	LabelImageType::RegionType region =  
destinationImage->GetLargestPossibleRegion();
	LabelImageType::SizeType   size =  region.GetSize();
	cout << spacing <<std::endl;
	cout << origin <<std::endl;
	cout << direction <<std::endl;
	cout << region <<std::endl;
	cout << size <<std::endl;



	if (argc > 6)
	{
		ResamplerType::Pointer resampler = ResamplerType::New();
		InterpolatorType::Pointer interpolator = InterpolatorType::New();
		resampler->SetInterpolator( interpolator );
		resampler->SetOutputSpacing( spacing );
		resampler->SetOutputDirection( direction );
		resampler->SetOutputOrigin(  origin  );
		resampler->SetSize( size );
		resampler->SetTransform( tps );

		resampler->SetOutputStartIndex(  region.GetIndex() );
		resampler->SetInput( sourceReader->GetOutput() );
		////////////////////////////////////////////////////////////////////////////////////////////

		DeformedImageWriterType::Pointer deformedImageWriter =  
DeformedImageWriterType::New();
		deformedImageWriter->SetInput( resampler->GetOutput() );
		deformedImageWriter->SetFileName( argv[6] );

		try
		{
		   deformedImageWriter->Update();
		}
		catch( itk::ExceptionObject & excp )
		{
		   std::cerr << "Exception thrown " << std::endl;
		   std::cerr << excp << std::endl;
		   return EXIT_FAILURE;
		}
	}

	////////////////////////////////////////////////////////////////////////////////////////////
	/*DEFINING FIELD*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nDEFINING FIELD\n");
     DisplacementFieldType::Pointer field = DisplacementFieldType::New();
     field->SetRegions( region );
     field->SetOrigin( origin );
     field->SetDirection( direction );
     field->SetSpacing( spacing );
     field->Allocate();

	cout << field->GetLargestPossibleRegion() <<std::endl;
	cout << field->GetOrigin() <<std::endl;
	cout << field->GetDirection() <<std::endl;
	cout << field->GetSpacing() <<std::endl;
	cout << field->GetLargestPossibleRegion().GetSize() <<std::endl;
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*APPLYING TRANSFORM TO POINTS*/
	////////////////////////////////////////////////////////////////////////////////////////////
     printf("\nAPPLYING TRANSFORM TO POINTS\n");
     typedef itk::ImageRegionIterator< DisplacementFieldType > FieldIterator;
     FieldIterator fi( field, region );
     fi.GoToBegin();
     TransformType::InputPointType  point1;
     TransformType::OutputPointType point2;
     DisplacementFieldType::IndexType index;

     FieldVectorType displacement;
     int fieldCount
     while( ! fi.IsAtEnd() )
     {
	  index = fi.GetIndex();
	  field->TransformIndexToPhysicalPoint( index, point1 );
	  point2 = tps->TransformPoint( point1 );

	  for ( int i = 0;i < ImageDimension;i++)
	  {
		displacement[i] = point2[i] - point1[i];
	  }
	  fi.Set( displacement );
	  ++fi;
     }
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*GENERATING FIELD FILE*/
	////////////////////////////////////////////////////////////////////////////////////////////
     //Write computed deformation field
     printf("\nGENERATING FIELD FILE\n");
     FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
     fieldWriter->SetFileName( argv[5] );
     fieldWriter->SetInput( field );
     try
       {
       fieldWriter->Update();
       }
     catch( itk::ExceptionObject & excp )
       {
       std::cerr << "Exception thrown " << std::endl;
       std::cerr << excp << std::endl;
       return EXIT_FAILURE;
       }
     return EXIT_SUCCESS;
	////////////////////////////////////////////////////////////////////////////////////////////

}


insight-users-request at itk.org a ?crit?:

> Send Insight-users mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Insight-users digest..."
>
>
> Today's Topics:
>
>    1. Re: Generating a warping field with
>       ThinPlateSplineKernelTransform (Siavash Khallaghi)
>    2. Re: 3D/2D registration with
>       itkRayCastInterpolateImageFunction (Siavash Khallaghi)
>    3. Re: [ITK] Generating a warping field with
>       ThinPlateSplineKernelTransform (Andras Lasso)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 4 Aug 2015 14:13:16 -0700 (MST)
> From: Siavash Khallaghi <siavashk at ece.ubc.ca>
> To: insight-users at itk.org
> Subject: Re: [ITK-users] Generating a warping field with
> 	ThinPlateSplineKernelTransform
> Message-ID: <1438722796207-35972.post at n7.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Having your exact code (on the small chance that it differs from the
> example), your data, and the argument list would help in debugging your
> problem. But in the mean time, you can try the following to see where the
> problem lies:
>
> 1. If you write out the defomation field and view it in the context of your
> volume in a 3rd party software (e.g., Paraview), what would you see? Would
> it make sense in terms of smoothness and direction?
>
> 2. Is the deformed volume (output of itk::ResmapleImageFilter) different
> compared to the input volume? In other words, is the resampler doing
> anything?
>
> 3. If you invert the deformation field, would your deformed volume be the
> output that you expect? You can do this by swapping source and target
> landmarks.
>
> Siavash
>
>
>
> --
> View this message in context:  
> http://itk-users.7.n7.nabble.com/ITK-users-Generating-a-warping-field-with-ThinPlateSplineKernelTransform-tp35971p35972.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 4 Aug 2015 14:53:46 -0700 (MST)
> From: Siavash Khallaghi <siavashk at ece.ubc.ca>
> To: insight-users at itk.org
> Subject: Re: [ITK-users] 3D/2D registration with
> 	itkRayCastInterpolateImageFunction
> Message-ID: <1438725226436-35973.post at n7.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Is the metric decreasing? (i.e. similarity value) It could be that everything
> is correct, it is just that you have an ill-posed problem. If the metric is
> decreasing, it could be that you are converging to a local minimum.
>
> Siavash
>
>
>
> --
> View this message in context:  
> http://itk-users.7.n7.nabble.com/ITK-users-3D-2D-registration-with-itkRayCastInterpolateImageFunction-tp35970p35973.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 4 Aug 2015 22:38:37 +0000
> From: Andras Lasso <lasso at queensu.ca>
> To: Siavash Khallaghi <siavashk at ece.ubc.ca>, "insight-users at itk.org"
> 	<insight-users at itk.org>
> Subject: Re: [ITK-users] [ITK] Generating a warping field with
> 	ThinPlateSplineKernelTransform
> Message-ID:
> 	<CY1PR0701MB1613B15AF8B413FC7C21C855D8760 at CY1PR0701MB1613.namprd07.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> You can also load non-linear transforms into 3D Slicer for  
> interactive visualization, application to your images, comparing  
> fixed/moving/registered images, etc. You can also invert, compose,  
> decompose transforms, apply it to marked points, segmented surfaces,  
> etc.
>
> See some examples here:
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms
>
> Paraview is very good but not for analyzing transforms: it can only  
> load exported displacement fields (but for that you would need to be  
> sure that your region of interest is correct and you lose  
> information when you sample the field), it only supports  
> axis-aligned images, and dense vector field visualization has been  
> broken in recent versions (I haven't checked the latest version).
>
> Andras
>
> -----Original Message-----
> From: Community [mailto:community-bounces at itk.org] On Behalf Of  
> Siavash Khallaghi
> Sent: Tuesday, August 4, 2015 5:13 PM
> To: insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] Generating a warping field with  
> ThinPlateSplineKernelTransform
>
> Having your exact code (on the small chance that it differs from the  
> example), your data, and the argument list would help in debugging  
> your problem. But in the mean time, you can try the following to see  
> where the problem lies:
>
> 1. If you write out the defomation field and view it in the context  
> of your volume in a 3rd party software (e.g., Paraview), what would  
> you see? Would it make sense in terms of smoothness and direction?
>
> 2. Is the deformed volume (output of itk::ResmapleImageFilter)  
> different compared to the input volume? In other words, is the  
> resampler doing anything?
>
> 3. If you invert the deformation field, would your deformed volume  
> be the output that you expect? You can do this by swapping source  
> and target landmarks.
>
> Siavash
>
>
>
> --
> View this message in context:  
> http://itk-users.7.n7.nabble.com/ITK-users-Generating-a-warping-field-with-ThinPlateSplineKernelTransform-tp35971p35972.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at  
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
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>
>
> ------------------------------
>
> End of Insight-users Digest, Vol 136, Issue 2
> *********************************************



_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
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From matt.mccormick at kitware.com  Thu Aug  6 12:10:43 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 6 Aug 2015 12:10:43 -0400
Subject: [ITK] [ITK-dev] Ubuntu 14 Test failure bisect results
In-Reply-To: <CALzTN-RiC-0Q+UUw6L9BGsAp8Fh5eDynNDZ7SoGaTaqz0JQsVA@mail.gmail.com>
References: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov>
 <CALzTN-TJD+Zxzk-5yawApDAVxD7R2Q26ExfRnfbOaZmw9KUeuw@mail.gmail.com>
 <8EC6E57A-1ED3-4909-A1AA-81EA4E83DFA5@mail.nih.gov>
 <CALzTN-RiC-0Q+UUw6L9BGsAp8Fh5eDynNDZ7SoGaTaqz0JQsVA@mail.gmail.com>
Message-ID: <CALzTN-S0Kg-rpmG2qDxk15AYbL_e8Wy1jnh5vzfudTwC9=QxEw@mail.gmail.com>

Here is the patch:

  http://review.source.kitware.com/#/c/20068/

Interestingly, the test failures are not repeatable on Gentoo with the
same versions of GCC / binutils.

Matt

On Thu, Aug 6, 2015 at 10:28 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Hi Brad,
>
> I have been doing some Experimental builds on the dashboard.  So far,
> the test failures are repeatable with GCC / Binutils in Ubuntu 14.04
> with BUILD_SHARED_LIBS OFF, but not BUILD_SHARED_LIBS ON.  I am
> working on a patch... :-)
>
> Thanks,
> Matt
>
> On Thu, Aug 6, 2015 at 9:33 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> Matt,
>>
>> What were the results of this experiment? It'd be nice to clean up the release branch of these failing tests.
>>
>> And I want to steal the correct solution for SimpleITK too :)
>>
>> Brad
>>
>> On Jul 31, 2015, at 3:29 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>
>>> Hi Brad,
>>>
>>> Thanks for investigating and getting great information out of git bisect.
>>>
>>> I developed the patch on Gentoo with GCC 4.8.4 / binutils 2.24, and I
>>> have not seen any issues.  The eldorado builds on the dashboard are
>>> all Ubuntu 14.04.2, too.  I will start an Experimental build with
>>> BUILD_SHARED_LIBS set on eldorado to be sure it can be reproduced.
>>>
>>> Thanks,
>>> Matt
>>>
>>> On Fri, Jul 31, 2015 at 1:03 PM, Bradley Lowekamp
>>> <blowekamp at mail.nih.gov> wrote:
>>>> Matt,
>>>>
>>>> I was digging into these test failures:
>>>>
>>>> https://open.cdash.org/viewTest.php?onlyfailed&buildid=3932451
>>>>
>>>> Here are the results of the git bisect:
>>>>
>>>> 674acdb2dd5546b7045f7253c84e4f9f237405e8 is the first bad commit
>>>> commit 674acdb2dd5546b7045f7253c84e4f9f237405e8
>>>> Author: Matt McCormick <matt.mccormick at kitware.com>
>>>> Date:   Sun May 31 21:00:55 2015 -0400
>>>>
>>>>    ENH: Use gold linker on Linux with GCC.
>>>>
>>>>
>>>>
>>>>    The gold linker is approximately three times as fast as the default
>>>> linker.
>>>>    Enable it with GCC 4.8 and newer where it was tested. The gold linker
>>>> only
>>>>    works with ELF executables, so it is only enabled for Linux.
>>>>
>>>>
>>>>
>>>>    Timing tests:
>>>>
>>>>
>>>>
>>>>    Static libs link time:
>>>>
>>>>
>>>>
>>>>      ld:      452 sec
>>>>      ld-gold: 179 sec
>>>>
>>>>
>>>>
>>>>    Shared libs link time, wrapping enabled:
>>>>
>>>>
>>>>
>>>>      ld:      164 sec
>>>>      ld-gold: 48 sec
>>>>
>>>>
>>>>
>>>>    Change-Id: Ic8d9b5132ad6b71e5f100b5436615d6a8fac3e5c
>>>>
>>>> Disabling ld-gold seems to fix the problem.
>>>>
>>>> Versions:
>>>>
>>>> blowekamp at lhcp-vm-ubu14:~/ITK$ gcc --version
>>>> gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4
>>>> Copyright (C) 2013 Free Software Foundation, Inc.
>>>> This is free software; see the source for copying conditions.  There is NO
>>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>>>>
>>>> blowekamp at lhcp-vm-ubu14:~/ITK$ ld --version
>>>> GNU ld (GNU Binutils for Ubuntu) 2.24
>>>> Copyright 2013 Free Software Foundation, Inc.
>>>> This program is free software; you may redistribute it under the terms of
>>>> the GNU General Public License version 3 or (at your option) a later
>>>> version.
>>>> This program has absolutely no warranty.
>>>>
>>>> blowekamp at lhcp-vm-ubu14:~/ITK$ lsb_release -a
>>>> No LSB modules are available.
>>>> Distributor ID: Ubuntu
>>>> Description: Ubuntu 14.04.2 LTS
>>>> Release: 14.04
>>>> Codename: trusty
>>>>
>>>>
>>>> Currently we have a check for using gold with > 4.8.3:
>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L206
>>>>
>>>> But looking at this change:
>>>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e
>>>>
>>>> We should have know about these related test failures:
>>>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e
>>>>
>>>> So what do you recall about what versions of GCC ld-gold works on?
>>>>
>>>> Thanks,
>>>> Brad
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>
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From lasso at queensu.ca  Thu Aug  6 13:33:09 2015
From: lasso at queensu.ca (Andras Lasso)
Date: Thu, 6 Aug 2015 17:33:09 +0000
Subject: [ITK] [ITK-users] Generating a
	warping	field	with	ThinPlateSplineKernelTransform
In-Reply-To: <20150806155332.Horde.prSADUXzWlTSvqlZxJd62Rs@www.imp.polymtl.ca>
References: <mailman.13.1438790405.4557.insight-users@itk.org>
 <20150806155332.Horde.prSADUXzWlTSvqlZxJd62Rs@www.imp.polymtl.ca>
Message-ID: <CY1PR0701MB16139E52CB1BABD72EFBDB32D8740@CY1PR0701MB1613.namprd07.prod.outlook.com>

Have you tested if the registration works well with those landmarks? I would suggest to first experiment with the registration in an interactive environment where you can see the registration result in real-time as you define/move landmarks (for example, http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/LandmarkRegistration). After you've figured out how many landmarks, at what distance, what configuration are needed for a good-quality alignment you can dive into coding your own implementation.

Andras

-----Original Message-----
From: Community [mailto:community-bounces at itk.org] On Behalf Of Olivier Comtois
Sent: Thursday, August 06, 2015 11:54 AM
To: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] Generating a warping field with ThinPlateSplineKernelTransform

Thank you for your reply Siavash,

Here is my code :

It differs from the example in that I take my landmark points from 2 files (one for the source landmarks and another for the target). The source landmarks come from the segmentation of a curved spinal cord while the straight ones come from a template (which is straightened).

std::vector<double> ReadLabelValueFromFile(std::string filename) {
	std::ifstream file(filename.c_str());
	string line;
	char* token;
	std::vector<double> result;
	std::vector<double>::iterator it;

	it = result.begin();
	if (file.is_open()) {
		while (file.good()) {
			getline(file, line);
			char * charLine = new char[line.length() + 1];
			strcpy(charLine, line.c_str());
			token = std::strtok(charLine, ",");
			while (token != NULL) {
				result.push_back(std::atof(token));
				token = strtok(NULL, ",");
			}
			delete[] charLine;
		}
		file.close();
	} else {
		throw std::runtime_error(std::string("Cannot open file : ") + filename);
	}
	return result;
}

void GetRealValuePointSetFromFile(itk::ThinPlateSplineKernelTransform<
double, 3>::PointSetType::Pointer &source,
		itk::ThinPlateSplineKernelTransform< double,  
3>::PointSetType::Pointer &destination,
		string curvedFilename, string straightFilename) {
	//define variables needed for this function
	string line;
	string token;
	std::vector<double> straightValues;
	std::vector<double> curvedValues;

	//fetching coordinates from files
	try {
		straightValues = ReadLabelValueFromFile(straightFilename);
		curvedValues = ReadLabelValueFromFile(curvedFilename);
		//check if not empty
		if (curvedValues.size() == 0) {
			throw std::runtime_error(
					"No value found in the curved labels text file.");
		}
		if (straightValues.size() == 0) {
			throw std::runtime_error(
					"No value found in straight the labels text file.");
		}
		if ((straightValues.size() % 3) != 0) {
			throw std::runtime_error(
					"The straight file size must be divisible by 3 (since there is 3 dimensions to the image)");
		}
		if ((curvedValues.size() % 3) != 0) {
			throw std::runtime_error(
					"The curved file size must be divisible by 3 (since there is 3 dimensions to the image)");
		}
		if (straightValues.size() != curvedValues.size()) {
			throw std::runtime_error(
					"Curved and Straight files do not have the same size.");
		}
	} catch (const std::exception &e) {
		throw;
	}

	//Produce the Straight points
	typedef double Realtype;
	typedef itk::ThinPlateSplineKernelTransform< double, ImageDimension> TransformType;
	typedef TransformType::PointSetType PointSetType;

	std::vector<double>::iterator itS = straightValues.begin();
	std::vector<double>::iterator itC = curvedValues.begin();
	typedef PointSetType::PointIdentifier PointIdType;
	PointIdType id = itk::NumericTraits< PointIdType >::ZeroValue();

	while (itS != straightValues.end()) {
		typedef itk::Point<double, ImageDimension> PointType;
		PointType pS;
		PointType pC;
		for (int i = 0; i < 3; i++) {
			pS[i] = *itS;
			pC[i] = *itC;
			itS++;
			itC++;
		}
		//Place points in the point sets
		source->SetPoint(id, pC);
		source->SetPointData(id, id);
		destination->SetPoint(id, pS);
		destination->SetPointData(id, id);
		id++;
	}
	printf("RETURNING POINT VALUES");
	return;

}

int LandmarkBasedWithTextDisplacementFieldTransformInitializer(int
argc, char *argv[]) {


	////////////////////////////////////////////////////////////////////////////////////////////
	/*CREATING USEFUL TYPES*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nCREATING USEFUL TYPES\n");
	typedef double RealType;
	typedef unsigned int LabelType;
	typedef itk::Image<LabelType, ImageDimension> LabelImageType;
	typedef itk::Image<RealType, ImageDimension> RealImageType;
	typedef itk::Vector<RealType, ImageDimension> VectorType;
	typedef itk::Vector< double, ImageDimension > FieldVectorType;
	typedef itk::ResampleImageFilter<LabelImageType, LabelImageType> ResamplerType;
	typedef itk::LinearInterpolateImageFunction<LabelImageType, RealType  > InterpolatorType;
	typedef itk::ImageFileWriter< LabelImageType >  DeformedImageWriterType;
	typedef itk::Image< FieldVectorType,  ImageDimension > DisplacementFieldType;
	typedef itk::ImageFileWriter< DisplacementFieldType > FieldWriterType;
	typedef itk::ThinPlateSplineKernelTransform< RealType,  
ImageDimension> TransformType;
	typedef itk::ImageFileReader<LabelImageType> ImageReaderType;
	typedef TransformType::PointSetType PointSetType;
	typedef PointSetType::PointIdentifier PointIdType;
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*LOADING FIXED IMAGE*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nLOADING DESTINATION IMAGE\n");

	ImageReaderType::Pointer destinationReader = ImageReaderType::New();
	destinationReader->SetFileName(argv[2]);
	destinationReader->Update();
	LabelImageType::Pointer destinationImage = destinationReader->GetOutput();
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*LOADING MOVING IMAGE*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nLOADING SOURCE IMAGE\n");

	ImageReaderType::Pointer sourceReader = ImageReaderType::New();
	sourceReader->SetFileName(argv[1]);
	sourceReader->Update();
	LabelImageType::Pointer sourceImage = sourceReader->GetOutput();
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*INIT IMAGE CONTAINERS*/
	////////////////////////////////////////////////////////////////////////////////////////////
	typedef itk::PointSet<RealType, ImageDimension> RealPointSetType;
	PointSetType::Pointer destinationPts = PointSetType::New();
	PointSetType::Pointer sourcePts = PointSetType::New();
	RegistrationType::Pointer registration = RegistrationType::New();

	destinationPts->Initialize();
	sourcePts->Initialize();
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*IMPORTING LANDMARKS FROM TEXT FILES*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nIMPORTING LANDMARKS FROM TEXT FILES\n");
	if (string(argv[3]).compare("") != 0) {
		if (string(argv[4]).compare("") != 0) {
			try {
				string sourceFilename = argv[3];
				string destinationFilename = argv[4];
				GetRealValuePointSetFromFile(sourcePts, destinationPts, sourceFilename, destinationFilename);
			} catch (exception &e) {
				throw;
			}
		} else
			throw std::runtime_error(
					"Both arguments the straight and curved file must be specified");
	} else
		throw std::runtime_error(
				"A file must be specified in order to take input real labels.");
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*DEFINING KERNEL TRANSFORM*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nDEFINING KERNEL TRANSFORM\n");
	TransformType::Pointer tps = TransformType::New();

	tps->SetSourceLandmarks(sourcePts);
	tps->SetTargetLandmarks(destinationPts);
	tps->ComputeWMatrix();
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*DEFINING RESAMPLER TO EXECUTE TRANSFORM*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nDEFINING RESAMPLER\n");
	LabelImageType::ConstPointer inputImage = sourceReader->GetOutput();

	LabelImageType::SpacingType spacing = destinationImage->GetSpacing();
	LabelImageType::PointType   origin  = destinationImage->GetOrigin();
	LabelImageType::DirectionType direction  = destinationImage->GetDirection();
	LabelImageType::RegionType region =  
destinationImage->GetLargestPossibleRegion();
	LabelImageType::SizeType   size =  region.GetSize();
	cout << spacing <<std::endl;
	cout << origin <<std::endl;
	cout << direction <<std::endl;
	cout << region <<std::endl;
	cout << size <<std::endl;



	if (argc > 6)
	{
		ResamplerType::Pointer resampler = ResamplerType::New();
		InterpolatorType::Pointer interpolator = InterpolatorType::New();
		resampler->SetInterpolator( interpolator );
		resampler->SetOutputSpacing( spacing );
		resampler->SetOutputDirection( direction );
		resampler->SetOutputOrigin(  origin  );
		resampler->SetSize( size );
		resampler->SetTransform( tps );

		resampler->SetOutputStartIndex(  region.GetIndex() );
		resampler->SetInput( sourceReader->GetOutput() );
		////////////////////////////////////////////////////////////////////////////////////////////

		DeformedImageWriterType::Pointer deformedImageWriter = DeformedImageWriterType::New();
		deformedImageWriter->SetInput( resampler->GetOutput() );
		deformedImageWriter->SetFileName( argv[6] );

		try
		{
		   deformedImageWriter->Update();
		}
		catch( itk::ExceptionObject & excp )
		{
		   std::cerr << "Exception thrown " << std::endl;
		   std::cerr << excp << std::endl;
		   return EXIT_FAILURE;
		}
	}

	////////////////////////////////////////////////////////////////////////////////////////////
	/*DEFINING FIELD*/
	////////////////////////////////////////////////////////////////////////////////////////////
	printf("\nDEFINING FIELD\n");
     DisplacementFieldType::Pointer field = DisplacementFieldType::New();
     field->SetRegions( region );
     field->SetOrigin( origin );
     field->SetDirection( direction );
     field->SetSpacing( spacing );
     field->Allocate();

	cout << field->GetLargestPossibleRegion() <<std::endl;
	cout << field->GetOrigin() <<std::endl;
	cout << field->GetDirection() <<std::endl;
	cout << field->GetSpacing() <<std::endl;
	cout << field->GetLargestPossibleRegion().GetSize() <<std::endl;
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*APPLYING TRANSFORM TO POINTS*/
	////////////////////////////////////////////////////////////////////////////////////////////
     printf("\nAPPLYING TRANSFORM TO POINTS\n");
     typedef itk::ImageRegionIterator< DisplacementFieldType > FieldIterator;
     FieldIterator fi( field, region );
     fi.GoToBegin();
     TransformType::InputPointType  point1;
     TransformType::OutputPointType point2;
     DisplacementFieldType::IndexType index;

     FieldVectorType displacement;
     int fieldCount
     while( ! fi.IsAtEnd() )
     {
	  index = fi.GetIndex();
	  field->TransformIndexToPhysicalPoint( index, point1 );
	  point2 = tps->TransformPoint( point1 );

	  for ( int i = 0;i < ImageDimension;i++)
	  {
		displacement[i] = point2[i] - point1[i];
	  }
	  fi.Set( displacement );
	  ++fi;
     }
	////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////
	/*GENERATING FIELD FILE*/
	////////////////////////////////////////////////////////////////////////////////////////////
     //Write computed deformation field
     printf("\nGENERATING FIELD FILE\n");
     FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
     fieldWriter->SetFileName( argv[5] );
     fieldWriter->SetInput( field );
     try
       {
       fieldWriter->Update();
       }
     catch( itk::ExceptionObject & excp )
       {
       std::cerr << "Exception thrown " << std::endl;
       std::cerr << excp << std::endl;
       return EXIT_FAILURE;
       }
     return EXIT_SUCCESS;
	////////////////////////////////////////////////////////////////////////////////////////////

}


insight-users-request at itk.org a ?crit?:

> Send Insight-users mailing list submissions to
> 	insight-users at itk.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://public.kitware.com/mailman/listinfo/insight-users
> or, via email, send a message with subject or body 'help' to
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> When replying, please edit your Subject line so it is more specific 
> than "Re: Contents of Insight-users digest..."
>
>
> Today's Topics:
>
>    1. Re: Generating a warping field with
>       ThinPlateSplineKernelTransform (Siavash Khallaghi)
>    2. Re: 3D/2D registration with
>       itkRayCastInterpolateImageFunction (Siavash Khallaghi)
>    3. Re: [ITK] Generating a warping field with
>       ThinPlateSplineKernelTransform (Andras Lasso)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 4 Aug 2015 14:13:16 -0700 (MST)
> From: Siavash Khallaghi <siavashk at ece.ubc.ca>
> To: insight-users at itk.org
> Subject: Re: [ITK-users] Generating a warping field with
> 	ThinPlateSplineKernelTransform
> Message-ID: <1438722796207-35972.post at n7.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Having your exact code (on the small chance that it differs from the 
> example), your data, and the argument list would help in debugging 
> your problem. But in the mean time, you can try the following to see 
> where the problem lies:
>
> 1. If you write out the defomation field and view it in the context of 
> your volume in a 3rd party software (e.g., Paraview), what would you 
> see? Would it make sense in terms of smoothness and direction?
>
> 2. Is the deformed volume (output of itk::ResmapleImageFilter) 
> different compared to the input volume? In other words, is the 
> resampler doing anything?
>
> 3. If you invert the deformation field, would your deformed volume be 
> the output that you expect? You can do this by swapping source and 
> target landmarks.
>
> Siavash
>
>
>
> --
> View this message in context:  
> http://itk-users.7.n7.nabble.com/ITK-users-Generating-a-warping-field-
> with-ThinPlateSplineKernelTransform-tp35971p35972.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 4 Aug 2015 14:53:46 -0700 (MST)
> From: Siavash Khallaghi <siavashk at ece.ubc.ca>
> To: insight-users at itk.org
> Subject: Re: [ITK-users] 3D/2D registration with
> 	itkRayCastInterpolateImageFunction
> Message-ID: <1438725226436-35973.post at n7.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Is the metric decreasing? (i.e. similarity value) It could be that 
> everything is correct, it is just that you have an ill-posed problem. 
> If the metric is decreasing, it could be that you are converging to a local minimum.
>
> Siavash
>
>
>
> --
> View this message in context:  
> http://itk-users.7.n7.nabble.com/ITK-users-3D-2D-registration-with-itk
> RayCastInterpolateImageFunction-tp35970p35973.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 4 Aug 2015 22:38:37 +0000
> From: Andras Lasso <lasso at queensu.ca>
> To: Siavash Khallaghi <siavashk at ece.ubc.ca>, "insight-users at itk.org"
> 	<insight-users at itk.org>
> Subject: Re: [ITK-users] [ITK] Generating a warping field with
> 	ThinPlateSplineKernelTransform
> Message-ID:
> 	
> <CY1PR0701MB1613B15AF8B413FC7C21C855D8760 at CY1PR0701MB1613.namprd07.pro
> d.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> You can also load non-linear transforms into 3D Slicer for interactive 
> visualization, application to your images, comparing 
> fixed/moving/registered images, etc. You can also invert, compose, 
> decompose transforms, apply it to marked points, segmented surfaces, 
> etc.
>
> See some examples here:
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modul
> es/Transforms
>
> Paraview is very good but not for analyzing transforms: it can only 
> load exported displacement fields (but for that you would need to be 
> sure that your region of interest is correct and you lose information 
> when you sample the field), it only supports axis-aligned images, and 
> dense vector field visualization has been broken in recent versions (I 
> haven't checked the latest version).
>
> Andras
>
> -----Original Message-----
> From: Community [mailto:community-bounces at itk.org] On Behalf Of 
> Siavash Khallaghi
> Sent: Tuesday, August 4, 2015 5:13 PM
> To: insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] Generating a warping field with 
> ThinPlateSplineKernelTransform
>
> Having your exact code (on the small chance that it differs from the 
> example), your data, and the argument list would help in debugging 
> your problem. But in the mean time, you can try the following to see 
> where the problem lies:
>
> 1. If you write out the defomation field and view it in the context of 
> your volume in a 3rd party software (e.g., Paraview), what would you 
> see? Would it make sense in terms of smoothness and direction?
>
> 2. Is the deformed volume (output of itk::ResmapleImageFilter) 
> different compared to the input volume? In other words, is the 
> resampler doing anything?
>
> 3. If you invert the deformation field, would your deformed volume be 
> the output that you expect? You can do this by swapping source and 
> target landmarks.
>
> Siavash
>
>
>
> --
> View this message in context:  
> http://itk-users.7.n7.nabble.com/ITK-users-Generating-a-warping-field-
> with-ThinPlateSplineKernelTransform-tp35971p35972.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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> Community mailing list
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>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
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>
> ------------------------------
>
> End of Insight-users Digest, Vol 136, Issue 2
> *********************************************



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From siavashk at ece.ubc.ca  Thu Aug  6 14:07:59 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Thu, 6 Aug 2015 11:07:59 -0700 (MST)
Subject: [ITK] [ITK-users] Generating a
	warping	field	with	ThinPlateSplineKernelTransform
In-Reply-To: <CY1PR0701MB16139E52CB1BABD72EFBDB32D8740@CY1PR0701MB1613.namprd07.prod.outlook.com>
References: <20150803213013.Horde.k-Tn9jq9s3NiK8P8YzGdJrX@www.imp.polymtl.ca>
 <20150806155332.Horde.prSADUXzWlTSvqlZxJd62Rs@www.imp.polymtl.ca>
 <CY1PR0701MB16139E52CB1BABD72EFBDB32D8740@CY1PR0701MB1613.namprd07.prod.outlook.com>
Message-ID: <1438884479871-7587651.post@n2.nabble.com>

Olivier, I did not see anything that was obviously wrong in your code when I
was reading through it. 

I also agree with Andras on this. It could be that your code is correct, but
your parameters e.g. number of landmarks) are not suitable for generating a
quality deformation field. Might I also suggest that you look into the
corresponding  Slicer module
<http://slicer-users.65878.n3.nabble.com/Thin-plate-spline-transform-support-added-td4028422.html> 
(http://slicer-users.65878.n3.nabble.com/Thin-plate-spline-transform-support-added-td4028422.html)
and see if it is suitable for your purposes?

Siavash



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Generating-a-warping-field-with-ThinPlateSplineKernelTransform-tp7587642p7587651.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
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From broysam at Central.UH.EDU  Fri Aug  7 11:19:36 2015
From: broysam at Central.UH.EDU (Roysam, Badri)
Date: Fri, 7 Aug 2015 10:19:36 -0500
Subject: [ITK] Post-doc position
Message-ID: <D1EA36B8.EB17B%broysam@central.uh.edu>

Dear Friends,

The University of Houston has an opening for a post-doctoral researcher in the area of biological image analysis. We are especially interested in a candidate with expertise in cell segmentation, tracking, multivariate data analysis, data mining, machine learning, and parallel/GPU implementation of image analysis algorithms.

The ideal candidate will have a solid understanding of image analysis algorithms (especially cell segmentation and movement tracking), multivariate data analysis, machine learning, and programming in C/C++, Python, and MATLAB. Prior experience with working with biologists is a big plus. Experience with open source toolkits like ITK, VTK, multi-threaded (OpenMP) and/or GPU implementation, and graphical interface development tools are desirable.

The University of Houston is located in a park-like campus close to the Texas Medical Center, the largest in the world, and NASA. The Carnegie Foundation recognized UH as a public research university with very high research activity. Houston is a thriving city with an internationally diverse population, first-rate recreational opportunities, excellent schools, and affordable housing.

The University of Houston is an equal opportunity/affirmative action employer.  Minorities, women, veterans, and persons with disabilities are encouraged to apply. The University of Houston is an ADVANCE institution, one of a select group of universities funded by NSF in support of our commitment to increase diversity and the participation and advancement of women in STEM.

Please send your application to Professor Badri Roysam (broysam at uh.edu).

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From keansum at gmail.com  Fri Aug  7 23:05:07 2015
From: keansum at gmail.com (Kean Sum Ooi)
Date: Sat, 8 Aug 2015 11:05:07 +0800
Subject: [ITK] VTK 4.2 build failed VolumeRayCastMapper_CastRays not declared
Message-ID: <CAM0-uyXx6Jah0OSEJVfscsCs8N4w=ReFpZEUFJQEHD+2GUTiqw@mail.gmail.com>

I am trying to install ITKApps with VTK 4.2 as instructed from following
the instructions at: http://www.itk.org/Wiki/ITK/Insight_Applications

However when I try to build VTK 4.2, it fails at the make stage:
$ make -j2
/home/guest/installScripts/VTK/Rendering/vtkVolumeRayCastMapper.cxx: In
member function ?virtual void vtkVolumeRayCastMapper::Render(vtkRenderer*,
vtkVolume*)?:
/home/guest/installScripts/VTK/Rendering/vtkVolumeRayCastMapper.cxx:523:38:
error: ?VolumeRayCastMapper_CastRays? was not declared in this scope
     this->Threader->SetSingleMethod( VolumeRayCastMapper_CastRays,

So may I please ask is there something we have to do before we can
successfully compile VTK 4.2?

I have building from both the VTK-4.2-LatestRelease.tar.gz and by checking
out v4.2.0 from git with the same results.

Thank you,
Best regards,
Sum
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From bill.lorensen at gmail.com  Sat Aug  8 08:32:27 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Sat, 8 Aug 2015 08:32:27 -0400
Subject: [ITK] VTK 4.2 build failed VolumeRayCastMapper_CastRays not
	declared
In-Reply-To: <CAM0-uyXx6Jah0OSEJVfscsCs8N4w=ReFpZEUFJQEHD+2GUTiqw@mail.gmail.com>
References: <CAM0-uyXx6Jah0OSEJVfscsCs8N4w=ReFpZEUFJQEHD+2GUTiqw@mail.gmail.com>
Message-ID: <CADZJ4hPZyKPDaSLGPxegnXLtHEz3CcNW25uRp+GX5+A9mPhmeg@mail.gmail.com>

Those are old instructions. They will have to be updated. VTK4.2 is
really old. Try building the apps with VTK5.10.

Follow these instructions:
http://www.itk.org/ITK/resources/applications.html


On Fri, Aug 7, 2015 at 11:05 PM, Kean Sum Ooi <keansum at gmail.com> wrote:
> I am trying to install ITKApps with VTK 4.2 as instructed from following the
> instructions at: http://www.itk.org/Wiki/ITK/Insight_Applications
>
> However when I try to build VTK 4.2, it fails at the make stage:
> $ make -j2
> /home/guest/installScripts/VTK/Rendering/vtkVolumeRayCastMapper.cxx: In
> member function ?virtual void vtkVolumeRayCastMapper::Render(vtkRenderer*,
> vtkVolume*)?:
> /home/guest/installScripts/VTK/Rendering/vtkVolumeRayCastMapper.cxx:523:38:
> error: ?VolumeRayCastMapper_CastRays? was not declared in this scope
>      this->Threader->SetSingleMethod( VolumeRayCastMapper_CastRays,
>
> So may I please ask is there something we have to do before we can
> successfully compile VTK 4.2?
>
> I have building from both the VTK-4.2-LatestRelease.tar.gz and by checking
> out v4.2.0 from git with the same results.
>
> Thank you,
> Best regards,
> Sum
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>



-- 
Unpaid intern in BillsBasement at noware dot com

From bakkari.abdelkhalek at hotmail.fr  Mon Aug 10 08:39:00 2015
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Mon, 10 Aug 2015 13:39:00 +0100
Subject: [ITK] =?cp1256?q?Adding_button_for_ITK_snap=FE?=
Message-ID: <DUB129-W715B23BD35E43C80FA106883700@phx.gbl>

Hi!I am trying to add button for ITK Snap containing an ITK code source for the action of each button.Could any one help me; please.Thank you in advance.
Abdelkhalek BakkariPh.D candidate in Computer Science 		 	   		  
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From matt.mccormick at kitware.com  Mon Aug 10 09:19:15 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 10 Aug 2015 09:19:15 -0400
Subject: [ITK] =?utf-8?q?=5BITK-users=5D_Adding_button_for_ITK_snap?=
	=?utf-8?b?4oCP?=
In-Reply-To: <DUB129-W715B23BD35E43C80FA106883700@phx.gbl>
References: <DUB129-W715B23BD35E43C80FA106883700@phx.gbl>
Message-ID: <CALzTN-TLsX4Er4O24QoVMx+dtcjD7K=gZKDxL-9zZA0VpzKCEA@mail.gmail.com>

Hi,

ITK-SNAP is now based off Qt for its GUI widgets.  For more information,
see the Qt docs.  Also, specific messages on the ITK-SNAP mailing lists:

  http://www.itksnap.org/pmwiki/pmwiki.php?n=Main.HomePage

may generate the best support.

HTH,
Matt

On Mon, Aug 10, 2015 at 8:39 AM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

>
> Hi!
>
> I am trying to add button for ITK Snap containing an ITK code source for
> the action of each button.
> Could any one help me; please.
> Thank you in advance.
>
> Abdelkhalek Bakkari
> Ph.D candidate in Computer Science
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From kolin9105 at gmail.com  Mon Aug 10 09:29:10 2015
From: kolin9105 at gmail.com (meikolin saimara)
Date: Mon, 10 Aug 2015 20:29:10 +0700
Subject: [ITK] (no subject)
Message-ID: <CAEiw7u4LoA1KSs1rWP-wetzMhPwFgcH-d4UwSbS05jaOhmS+qA@mail.gmail.com>

hi everyone.
can u give me source code for how to get black voxel or black pixel value
from this picture to measure the volume of brain tumor.
the tumor is big large circle.
pleaz..
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From fisidoro at ethz.ch  Mon Aug 10 10:32:24 2015
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Mon, 10 Aug 2015 14:32:24 +0000
Subject: [ITK] [ITK-users] general info ICP implementation
Message-ID: <50B858FB5F53124F9E32314E5C1B40943511F43B@MBX214.d.ethz.ch>

I am trying to figure out how ICP is implemented in ITK. The general approach consists in iterating two steps: first compute the correspondences and then find the best transform with the current correspondences by using a close formula.

However in the ITK implementation I can't see this approach, plus LevenbergMarquardt alrgorithm is used instead of close formula to determine the transform. I know a special version of LevenbergMarquardt-ICP algorithm has been proposed in the following paper, however I can't see how the ITK implementation follows this proposed method (the ITK implementation seems to me very generic like any other optimization problem). Where should I look for?

Paper: "Robust registration of 2D and 3D point sets" Fitzgibbon 2003.

Thank you very much.
Fabio

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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

From kolin9105 at gmail.com  Mon Aug 10 10:37:19 2015
From: kolin9105 at gmail.com (meikolin saimara)
Date: Mon, 10 Aug 2015 21:37:19 +0700
Subject: [ITK] (no subject)
Message-ID: <CAEiw7u5H-CXBkGL-wUtMgFY=pxhx8aQGxm8KQULZMQ6-v18zgQ@mail.gmail.com>

how to creat new program in itk??
pleaz give me step by step how to create it??

My configuration is:

-        OS: Windows 7 32 bits

-        ITK 4.6.1
-        Visual 2008
pleaz..
thx before..
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From matt.mccormick at kitware.com  Mon Aug 10 10:46:21 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 10 Aug 2015 10:46:21 -0400
Subject: [ITK] (no subject)
In-Reply-To: <CAEiw7u5H-CXBkGL-wUtMgFY=pxhx8aQGxm8KQULZMQ6-v18zgQ@mail.gmail.com>
References: <CAEiw7u5H-CXBkGL-wUtMgFY=pxhx8aQGxm8KQULZMQ6-v18zgQ@mail.gmail.com>
Message-ID: <CALzTN-TL8Ju3380D30QT6OmRfc3B6EiDLmjFLwQpwZp3N2e-Fg@mail.gmail.com>

Hello,

Please see the first part of The ITK Software Guide [1] for guidance
on how to get started.

HTH,
Matt

[1] http://itk.org/ITK/help/documentation.html

On Mon, Aug 10, 2015 at 10:37 AM, meikolin saimara <kolin9105 at gmail.com> wrote:
> how to creat new program in itk??
> pleaz give me step by step how to create it??
>
> My configuration is:
>
> -        OS: Windows 7 32 bits
>
> -        ITK 4.6.1
>
> -        Visual 2008
> pleaz..
> thx before..
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From kolin9105 at gmail.com  Mon Aug 10 13:08:59 2015
From: kolin9105 at gmail.com (meikolin saimara)
Date: Tue, 11 Aug 2015 00:08:59 +0700
Subject: [ITK] (no subject)
Message-ID: <CAEiw7u6_0bHXz9D_mM9Kgpp9=DxbHWeVZ8HceZJzj__oEGWM4Q@mail.gmail.com>

hi every one..
did you have source code or libray to separete skull and tumor for this
case without visualization just used itk not the other.
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From todd.jensen at ieee.org  Mon Aug 10 13:18:04 2015
From: todd.jensen at ieee.org (Todd Jensen)
Date: Mon, 10 Aug 2015 12:18:04 -0500
Subject: [ITK] GDCM version in ITK 4.8
In-Reply-To: <mailman.4156.1439226541.10520.community@itk.org>
References: <mailman.4156.1439226541.10520.community@itk.org>
Message-ID: <5964757B-846F-4152-8C6E-A773995741B3@ieee.org>

The latest version of GDCM on SourceForge is 2.4.4 (http://sourceforge.net/projects/gdcm/files/ <http://sourceforge.net/projects/gdcm/files/>), but in ITK 4.8 it looks like a newer version is available according to the GDCM source there (InsightToolkit-4.8.0/Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt):

set(GDCM_MAJOR_VERSION 2)
set(GDCM_MINOR_VERSION 5)
set(GDCM_BUILD_VERSION 0)

Is this the latest stable released version now?
 


Todd Jensen, PhD
Jensen Informatics LLC
http://www.linkedin.com/in/toddjensen <http://www.linkedin.com/in/toddjensen>
todd at jenseninformatics.com



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From matt.mccormick at kitware.com  Mon Aug 10 14:37:01 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 10 Aug 2015 14:37:01 -0400
Subject: [ITK] GDCM version in ITK 4.8
In-Reply-To: <5964757B-846F-4152-8C6E-A773995741B3@ieee.org>
References: <mailman.4156.1439226541.10520.community@itk.org>
 <5964757B-846F-4152-8C6E-A773995741B3@ieee.org>
Message-ID: <CALzTN-TCqd8ACsZYT_=FSSPMBKRs2aBQftgnqnEBz+zScYDH0g@mail.gmail.com>

Hi Todd,

Yes, internally, ITK has included the GDCM Git master branch.  This is
ahead of the currently released version. After the release of GDCM
2.6.0, we will switch to GDCM Git release branch.

Thanks,
Matt

On Mon, Aug 10, 2015 at 1:18 PM, Todd Jensen <todd.jensen at ieee.org> wrote:
> The latest version of GDCM on SourceForge is 2.4.4
> (http://sourceforge.net/projects/gdcm/files/), but in ITK 4.8 it looks like
> a newer version is available according to the GDCM source there
> (InsightToolkit-4.8.0/Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt):
>
> set(GDCM_MAJOR_VERSION 2)
> set(GDCM_MINOR_VERSION 5)
> set(GDCM_BUILD_VERSION 0)
>
> Is this the latest stable released version now?
>
>
>
> Todd Jensen, PhD
> Jensen Informatics LLC
> http://www.linkedin.com/in/toddjensen
> todd at jenseninformatics.com
>
>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From kolin9105 at gmail.com  Tue Aug 11 11:30:13 2015
From: kolin9105 at gmail.com (meikolin saimara)
Date: Tue, 11 Aug 2015 22:30:13 +0700
Subject: [ITK] (no subject)
Message-ID: <CAEiw7u4dsZhiCUcyzZ8xLK7rVGN0bZ3m70BEw9WybX9800N0Yw@mail.gmail.com>

hi every one
I need your help how to show a number of pixel from image threshold ??
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From christophe.vandijck at kuleuven.be  Wed Aug 12 09:27:34 2015
From: christophe.vandijck at kuleuven.be (christophevd)
Date: Wed, 12 Aug 2015 06:27:34 -0700 (MST)
Subject: [ITK] [ITK-users] Multi-threading in pointsettopointsetmetric
Message-ID: <1439386054435-35985.post@n7.nabble.com>

Hi all,

To my knowledge, there is no multi-thread support for
pointsettopointsetmetric classes such as the euclideandistancepointmetric. 

Will this become available in upcoming releases? 

Regards,

Christophe




--
View this message in context: http://itk-users.7.n7.nabble.com/Multi-threading-in-pointsettopointsetmetric-tp35985.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

From ntustison at gmail.com  Wed Aug 12 10:35:52 2015
From: ntustison at gmail.com (Nicholas Tustison)
Date: Wed, 12 Aug 2015 07:35:52 -0700
Subject: [ITK] [ITK-users] Multi-threading in pointsettopointsetmetric
In-Reply-To: <1439386054435-35985.post@n7.nabble.com>
References: <1439386054435-35985.post@n7.nabble.com>
Message-ID: <38C7F2DA-EBE7-4A10-9C0F-5F0F5E75450F@gmail.com>

Have you looked at the v4 versions?  e.g., 

http://www.itk.org/Doxygen/html/classitk_1_1PointSetToPointSetMetricv4.html

> On Aug 12, 2015, at 6:27 AM, christophevd <christophe.vandijck at kuleuven.be> wrote:
> 
> Hi all,
> 
> To my knowledge, there is no multi-thread support for
> pointsettopointsetmetric classes such as the euclideandistancepointmetric. 
> 
> Will this become available in upcoming releases? 
> 
> Regards,
> 
> Christophe
> 
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Multi-threading-in-pointsettopointsetmetric-tp35985.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

From Christophe.VanDijck at kuleuven.be  Wed Aug 12 10:42:57 2015
From: Christophe.VanDijck at kuleuven.be (Christophe Van Dijck)
Date: Wed, 12 Aug 2015 16:42:57 +0200
Subject: [ITK] [ITK-users] Multi-threading in pointsettopointsetmetric
In-Reply-To: <38C7F2DA-EBE7-4A10-9C0F-5F0F5E75450F@gmail.com>
References: <1439386054435-35985.post@n7.nabble.com>
 <38C7F2DA-EBE7-4A10-9C0F-5F0F5E75450F@gmail.com>
Message-ID: <001101d0d50d$2e317a30$8a946e90$@kuleuven.be>

Hi Nicholas,

Thanks for the quick reply. I did had a look at them. The thing is that I
want to use those metrics in the pointsettopointsetregistrationmethod.
Correct me if I'm wrong, but this registration method assumes the old
pointsettopointsetmetrics and a multivalued optimizer. A v4 version of this
registration method is maybe still in development, I don't know...

Regards,
Christione

-----Original Message-----
From: Nicholas Tustison [mailto:ntustison at gmail.com] 
Sent: woensdag 12 augustus 2015 16:36
To: christophevd
Cc: insight-users at itk.org
Subject: Re: [ITK-users] Multi-threading in pointsettopointsetmetric

Have you looked at the v4 versions?  e.g., 

http://www.itk.org/Doxygen/html/classitk_1_1PointSetToPointSetMetricv4.html

> On Aug 12, 2015, at 6:27 AM, christophevd
<christophe.vandijck at kuleuven.be> wrote:
> 
> Hi all,
> 
> To my knowledge, there is no multi-thread support for 
> pointsettopointsetmetric classes such as the euclideandistancepointmetric.
> 
> Will this become available in upcoming releases? 
> 
> Regards,
> 
> Christophe
> 
> 
> 
> 
> --
> View this message in context: 
> http://itk-users.7.n7.nabble.com/Multi-threading-in-pointsettopointset
> metric-tp35985.html Sent from the ITK - Users mailing list archive at 
> Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

From ntustison at gmail.com  Wed Aug 12 12:01:57 2015
From: ntustison at gmail.com (Nicholas Tustison)
Date: Wed, 12 Aug 2015 09:01:57 -0700
Subject: [ITK] [ITK-users] Multi-threading in pointsettopointsetmetric
In-Reply-To: <001101d0d50d$2e317a30$8a946e90$@kuleuven.be>
References: <1439386054435-35985.post@n7.nabble.com>
 <38C7F2DA-EBE7-4A10-9C0F-5F0F5E75450F@gmail.com>
 <001101d0d50d$2e317a30$8a946e90$@kuleuven.be>
Message-ID: <9103909A-6192-4F07-8C35-DB2354408742@gmail.com>

There isn?t a point-set only registration method for the v4 classes.
However, the ImageRegistrationMethodv4 class

http://www.itk.org/Doxygen/html/classitk_1_1ImageRegistrationMethodv4.html <http://www.itk.org/Doxygen/html/classitk_1_1ImageRegistrationMethodv4.html>

will accommodate 1) images only, 2) point sets only, or 3) images
and point sets.

Nick


> On Aug 12, 2015, at 7:42 AM, Christophe Van Dijck <Christophe.VanDijck at kuleuven.be> wrote:
> 
> Hi Nicholas,
> 
> Thanks for the quick reply. I did had a look at them. The thing is that I
> want to use those metrics in the pointsettopointsetregistrationmethod.
> Correct me if I'm wrong, but this registration method assumes the old
> pointsettopointsetmetrics and a multivalued optimizer. A v4 version of this
> registration method is maybe still in development, I don't know...
> 
> Regards,
> Christione
> 
> -----Original Message-----
> From: Nicholas Tustison [mailto:ntustison at gmail.com] 
> Sent: woensdag 12 augustus 2015 16:36
> To: christophevd
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] Multi-threading in pointsettopointsetmetric
> 
> Have you looked at the v4 versions?  e.g., 
> 
> http://www.itk.org/Doxygen/html/classitk_1_1PointSetToPointSetMetricv4.html
> 
>> On Aug 12, 2015, at 6:27 AM, christophevd
> <christophe.vandijck at kuleuven.be> wrote:
>> 
>> Hi all,
>> 
>> To my knowledge, there is no multi-thread support for 
>> pointsettopointsetmetric classes such as the euclideandistancepointmetric.
>> 
>> Will this become available in upcoming releases? 
>> 
>> Regards,
>> 
>> Christophe
>> 
>> 
>> 
>> 
>> --
>> View this message in context: 
>> http://itk-users.7.n7.nabble.com/Multi-threading-in-pointsettopointset
>> metric-tp35985.html Sent from the ITK - Users mailing list archive at 
>> Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at 
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 

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From matt.mccormick at kitware.com  Wed Aug 12 16:08:05 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 12 Aug 2015 16:08:05 -0400
Subject: [ITK] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-QGaUD=1uyoqmSWPeb+QVRyDhX1RrsKG+r0-oZJYf9cGg@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/u/1/events/cr2j0kl1sgtjj5lvvp1l66mggf4



On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/u/1/events/cg6evue74hf0tkplf758g3ao6ck



For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From fotosentido at gmail.com  Wed Aug 12 17:36:24 2015
From: fotosentido at gmail.com (Marcos)
Date: Wed, 12 Aug 2015 23:36:24 +0200
Subject: [ITK] [ITK-users] Unresolved external symbol
Message-ID: <CAA24WvEfh0NedOi9uyvUSuUneapMRvfZk4-h==fKVh-WCuj0QA@mail.gmail.com>

Hi,

I compiled and installed successfully ITK 4.8 and VTK, with Visual Studio
2013 and Qt5.

Now I'm trying to compile a simple Hello World (with the ITK headers and
include dirs in the .pro file in Qt Creator) and I'm getting:

itkgdcmMSFF-4.8.lib(gdcmJPEGLSCodec.obj):-1: error: LNK2019: unresolved
external symbol _JpegLsEncode referenced in function "private: bool
__thiscall gdcm::JPEGLSCodec::CodeFrameIntoBuffer(char *,unsigned
int,unsigned int &,char const *,unsigned int)"
(?CodeFrameIntoBuffer at JPEGLSCodec@gdcm@@AAE_NPADIAAIPBDI at Z)

and similar errores relating all of them itkgdcmMSFF-4.8.lib.

Sometimes it specifies gdcmJPEGLSCodec.obj, sometimes gdcmJPEG2000Codec.obj.

I didn't check Module_ITKOpenJPEG in Cmake configure, but everything was
fine with compilation and installing.

If I omit adding itkgdcmMSFF-4.8.lib, it shows the same errors with
ITKIOGDCM-4.8.lib

I don't understand why is so hard to start using this library. I spend more
time configuring than developing.

Any ideas?

Thank you.
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From matt.mccormick at kitware.com  Wed Aug 12 17:39:16 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 12 Aug 2015 17:39:16 -0400
Subject: [ITK] [ITK-users] Unresolved external symbol
In-Reply-To: <CAA24WvEfh0NedOi9uyvUSuUneapMRvfZk4-h==fKVh-WCuj0QA@mail.gmail.com>
References: <CAA24WvEfh0NedOi9uyvUSuUneapMRvfZk4-h==fKVh-WCuj0QA@mail.gmail.com>
Message-ID: <CALzTN-QEvv_qvEpash+eOzx9iX4jZNQVxTssLu+pcfy-V9CwHQ@mail.gmail.com>

Hello,

It is recommended to use CMake CMakeLists.txt instead of Qt .pro files
to build your project.  You will have much less difficulty. Note that
QtCreator also supports CMake, and CMake has very good support for
working with Qt.

HTH,
Matt

On Wed, Aug 12, 2015 at 5:36 PM, Marcos <fotosentido at gmail.com> wrote:
> Hi,
>
> I compiled and installed successfully ITK 4.8 and VTK, with Visual Studio
> 2013 and Qt5.
>
> Now I'm trying to compile a simple Hello World (with the ITK headers and
> include dirs in the .pro file in Qt Creator) and I'm getting:
>
> itkgdcmMSFF-4.8.lib(gdcmJPEGLSCodec.obj):-1: error: LNK2019: unresolved
> external symbol _JpegLsEncode referenced in function "private: bool
> __thiscall gdcm::JPEGLSCodec::CodeFrameIntoBuffer(char *,unsigned
> int,unsigned int &,char const *,unsigned int)"
> (?CodeFrameIntoBuffer at JPEGLSCodec@gdcm@@AAE_NPADIAAIPBDI at Z)
>
> and similar errores relating all of them itkgdcmMSFF-4.8.lib.
>
> Sometimes it specifies gdcmJPEGLSCodec.obj, sometimes gdcmJPEG2000Codec.obj.
>
> I didn't check Module_ITKOpenJPEG in Cmake configure, but everything was
> fine with compilation and installing.
>
> If I omit adding itkgdcmMSFF-4.8.lib, it shows the same errors with
> ITKIOGDCM-4.8.lib
>
> I don't understand why is so hard to start using this library. I spend more
> time configuring than developing.
>
> Any ideas?
>
> Thank you.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
_____________________________________
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From siavashk at ece.ubc.ca  Wed Aug 12 17:10:31 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Wed, 12 Aug 2015 14:10:31 -0700 (MST)
Subject: [ITK] [ITK-users] Unresolved external symbol
In-Reply-To: <CAA24WvEfh0NedOi9uyvUSuUneapMRvfZk4-h==fKVh-WCuj0QA@mail.gmail.com>
References: <CAA24WvEfh0NedOi9uyvUSuUneapMRvfZk4-h==fKVh-WCuj0QA@mail.gmail.com>
Message-ID: <1439413831608-35991.post@n7.nabble.com>

Hi Marcos,

Could you please provide us with your CMakeLists.txt file? It could be that
you forgot to add

TARGET_LINK_LIBRARIES(ProjectName ${ITK_LIBRARIES})

to your CMakeLists.txt.

Siavash



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Unresolved-external-symbol-tp35989p35991.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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http://www.kitware.com/products/protraining.php

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From matt.mccormick at kitware.com  Wed Aug 12 18:18:09 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 12 Aug 2015 18:18:09 -0400
Subject: [ITK] [ITK-users] Unresolved external symbol
In-Reply-To: <CAA24WvGcbML54rRzFWFVTGq98yjiz1=OSq2jk+Ek_DMO4VfYsQ@mail.gmail.com>
References: <CAA24WvEfh0NedOi9uyvUSuUneapMRvfZk4-h==fKVh-WCuj0QA@mail.gmail.com>
 <CALzTN-QEvv_qvEpash+eOzx9iX4jZNQVxTssLu+pcfy-V9CwHQ@mail.gmail.com>
 <CAA24WvGcbML54rRzFWFVTGq98yjiz1=OSq2jk+Ek_DMO4VfYsQ@mail.gmail.com>
Message-ID: <CALzTN-Sc66MChr1Y3x5_C+DE5DR38DSRUxaTztr069yHzbrm7w@mail.gmail.com>

Hi Marcos,

CMake also has a Visual Studio generator.  Use CMake to generate the
Visual Studio project file.

A good place to start is the Configuring and Building ITK section of
The ITK Software Guide [1].

Hope this helps,
Matt

[1] http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html

On Wed, Aug 12, 2015 at 5:47 PM, Marcos <fotosentido at gmail.com> wrote:
> Thank you for your answer, I just couln't find a clear and direct tutorial
> for getting started an ITK/VTK project with a CMakeLists.txt example. A lot
> of generic Cmake tutorials or installing guides (I did that already). I
> looked into ITK wiki too.
>
> Any practical example to just start?
>
> With Qt5, the configuration for this file has changed, so some Qt4 examples
> are confusing.
>
> I'm spending too much before starting coding, it's .
> And I'm going to need debugging. I was trying to code in Visual Studio
> (thanks to the Qt plugin), but with that error I can't even start in Qt
> Creator.
>
> Thank you.
>
> 2015-08-12 23:39 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>> Hello,
>>
>> It is recommended to use CMake CMakeLists.txt instead of Qt .pro files
>> to build your project.  You will have much less difficulty. Note that
>> QtCreator also supports CMake, and CMake has very good support for
>> working with Qt.
>>
>> HTH,
>> Matt
>>
>> On Wed, Aug 12, 2015 at 5:36 PM, Marcos <fotosentido at gmail.com> wrote:
>> > Hi,
>> >
>> > I compiled and installed successfully ITK 4.8 and VTK, with Visual
>> > Studio
>> > 2013 and Qt5.
>> >
>> > Now I'm trying to compile a simple Hello World (with the ITK headers and
>> > include dirs in the .pro file in Qt Creator) and I'm getting:
>> >
>> > itkgdcmMSFF-4.8.lib(gdcmJPEGLSCodec.obj):-1: error: LNK2019: unresolved
>> > external symbol _JpegLsEncode referenced in function "private: bool
>> > __thiscall gdcm::JPEGLSCodec::CodeFrameIntoBuffer(char *,unsigned
>> > int,unsigned int &,char const *,unsigned int)"
>> > (?CodeFrameIntoBuffer at JPEGLSCodec@gdcm@@AAE_NPADIAAIPBDI at Z)
>> >
>> > and similar errores relating all of them itkgdcmMSFF-4.8.lib.
>> >
>> > Sometimes it specifies gdcmJPEGLSCodec.obj, sometimes
>> > gdcmJPEG2000Codec.obj.
>> >
>> > I didn't check Module_ITKOpenJPEG in Cmake configure, but everything was
>> > fine with compilation and installing.
>> >
>> > If I omit adding itkgdcmMSFF-4.8.lib, it shows the same errors with
>> > ITKIOGDCM-4.8.lib
>> >
>> > I don't understand why is so hard to start using this library. I spend
>> > more
>> > time configuring than developing.
>> >
>> > Any ideas?
>> >
>> > Thank you.
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>> >
>
>
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From fanglongwei2014 at ia.ac.cn  Wed Aug 12 21:22:30 2015
From: fanglongwei2014 at ia.ac.cn (=?GBK?B?t73B+s6w?=)
Date: Thu, 13 Aug 2015 09:22:30 +0800 (GMT+08:00)
Subject: [ITK] some questions about "itkMutualInformatinImageMetric" code
Message-ID: <81ddd7.1e548.14f24a6b8cb.Coremail.fanglongwei2014@ia.ac.cn>




hello, everyone

      i am working on 2d/3d registration, and i revise the 'intensitybased2d3dregistration' code which provided by the ITK. i change the metric methods 'itkGradientDifferenceImageToMetric.h' with 'itkMutualInformatinImageMetric'. However, there comes a bug, the program always set 'm_DerivativeCalculator->IsInsideBuffer(mappedPoint)' to false, all points derivatives are set to zero. why comes this bug, does anyone know how to resolve this and help me? thanks in advance.

longwei





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From marco.dev.open at gmail.com  Thu Aug 13 02:47:37 2015
From: marco.dev.open at gmail.com (Marco Dev)
Date: Thu, 13 Aug 2015 11:17:37 +0430
Subject: [ITK] [ITK-dev] converting coordinate system
Message-ID: <CAKcUdn62pe3OU9hwYMqbwGjq81GQs=RGT9xkD_Jdwh6u101hPA@mail.gmail.com>

Hi dears,
I have some itk image filter for translating from image coordinate system
to world coordinate system
Means I want to convert Dicom image position and another tag information
such as pixel spacing orientation to world coordinate for Itk coordinate
these are difference in position
How can do this convert
Thanks in advance
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From fisidoro at ethz.ch  Thu Aug 13 04:06:10 2015
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Thu, 13 Aug 2015 08:06:10 +0000
Subject: [ITK] [ITK-users] IterativeClosestPoint2 example: how to get
	better	results
Message-ID: <50B858FB5F53124F9E32314E5C1B409435126779@MBX114.d.ethz.ch>

I am trying to use the IterativeClosestPoint2 example on the fixed and moving point sets in attachment (called "src" and "dest" point sets).

The ground truth is "properly ordered dest = Transform(src)", where:

Euler angles:  (0.349065850398866, 0.349065850398866, 0.349065850398866)
Translations: (4.1335200571234, 5.90820985238168, 7.04748773837622)

(the dest_point set in attachment is randomly reshuffled)

>>> If I use srx = fixed, dest = moving, the registration results is:

Euler angles:  (-0.327201, -0.36953, -0.47291)
Translations: (-6.28471, -2.64212, -1.50835)

>>> If I use dest = fixed, src = moving, the registration results is:

Euler angles:  (0.44595, 0.20655, 0.36423)
Translations: (6.28471, 2.64212, 1.50835)



Question 1):

Given that "properly ordered dest = Transform(src)", according to the guide src should be the fixed point set. Am I wrong?

Question 2):

I am not happy with the results, given that there is no additional noise (the underlined values refer to error angles of up to 8 degrees and 3 mm errors). I am surprised because there is no additional noise to the data, so I would expect an accurate registration. Are my results normal? How could I improve the results? Should I change the optimizer, or the transform?


Please help, thank you.
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From Olivier.Commowick at inria.fr  Thu Aug 13 09:35:19 2015
From: Olivier.Commowick at inria.fr (Olivier Commowick)
Date: Thu, 13 Aug 2015 15:35:19 +0200
Subject: [ITK] [ITK-users] Symmetric eigen analysis discrepancy
Message-ID: <F80D6ED3-0AD2-466C-85BA-38C9DE1AC316@inria.fr>

Hello all,

I have been experiencing a problem when using the itk SymmetricEigenAnalysis class in ITK. When using this class, it sometimes produces NaN eigenvalues/vectors. On the contrary, the vnl_symmetric_eigensystem doesn?t seem to have a problem (and neither does matlab). Looking at the documentation, it seems both use QL decomposition but not implemented in the same place. In addition, the vnl one is said to be not thread safe, although it?s the one working for me.

In fact, I have isolated one 3x3 matrix for which I always have the problem. 

A = 
[7.503107128706855667859804009212206062302e-53 1.870107888834986371214720644344813262375e-52 -8.662047753682068190087788895125120421821e-27;
1.870107888834986371214720644344813262375e-52 4.661140319458029838073740773908360767728e-52 -2.15896741973055935210319454393408888029e-26;
-8.662047753682068190087788895125120421821e-27 -2.15896741973055935210319454393408888029e-26 1]

It?s a weird one I know, but again vnl (and matlab) works great on it. Would there be anyone who knows the QL decomposition code enough to help me understand and possibly correct the ITK class so that it does the same as the VNL one ?

Thanks a lot in advance.

---

Olivier Commowick, Ph.D.
Research Scientist
INRIA Rennes - Bretagne Atlantique, VISAGES Team
Campus de Beaulieu
35042 Rennes
FRANCE

Phone: +33 2 99 84 25 92
Email: Olivier.Commowick at inria.fr
Web: http://olivier.commowick.org/





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From arnaudgelas at gmail.com  Thu Aug 13 11:40:53 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 13 Aug 2015 17:40:53 +0200
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on
	Ubuntu	14.04
Message-ID: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>

Hi all,

I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I get
the following link error

[2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1

[...]

lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
'itk::VideoIOBase::VideoIOBase()'
lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
'itk::VideoIOBase::~VideoIOBase()'
lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const'
lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
'typeinfo for itk::VideoIOBase'
collect2: error: ld returned 1 exit status

I have checked these methods are implemented in itkVideoIOBase.cxx...

Any idea?

Thanks
Arnaud
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From ond at semanchuk.com  Thu Aug 13 11:22:06 2015
From: ond at semanchuk.com (Philip Semanchuk)
Date: Thu, 13 Aug 2015 11:22:06 -0400
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
	(command line too long)
Message-ID: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>

Hi, 
I?m new to CMake and SimpleITK, and I?m trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I?m using the ?SuperBuild? instructions from here:
http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself

I?m running into a problem where a build.make file creates a shell command that?s almost 5400 characters long. This leads to:
NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long

The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).

Since I?m new to CMake and SimpleITK, I?m a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I?m in the wrong place, would someone be kind enough to guide me elsewhere?

I can post my build config and steps if that would help. 

Thanks
Philip

From ond at semanchuk.com  Thu Aug 13 12:19:07 2015
From: ond at semanchuk.com (Philip Semanchuk)
Date: Thu, 13 Aug 2015 12:19:07 -0400
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
	(command line too long)
In-Reply-To: <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
Message-ID: <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>


> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> 
> Hello,
> 
> What version of CMake and Visual Studio are you using?

CMake 3.3.0. I?m using Microsoft Visual C++ for Python 2.7. That's not Visual Studio ? it?s not an IDE. It?s just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008. 


> What is your build and source path?

Build path is c:\Users\me\sitkb
Source path is C:\Users\me\SimpleITK-0.9.0


> Also know which Super build target that's causing the problem would be helpful too.

The U1095 error comes here:
[ 84%] Performing configure step for 'SimpleITK'


> 
> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld?.

Thanks for the suggestion. I?m aware that long paths can contribute to overly-long command lines (I?ve run into that problem earlier in this build process). I don?t think they're the culprits here, though. 

The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don?t control (e.g. lots of references to "C:/Program Files (x86)?). 

If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command. 

Thanks for your willingness to help. I appreciate it!

Philip


> 
> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
> 
>> Hi, 
>> I?m new to CMake and SimpleITK, and I?m trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I?m using the ?SuperBuild? instructions from here:
>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>> 
>> I?m running into a problem where a build.make file creates a shell command that?s almost 5400 characters long. This leads to:
>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>> 
>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>> 
>> Since I?m new to CMake and SimpleITK, I?m a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I?m in the wrong place, would someone be kind enough to guide me elsewhere?
>> 
>> I can post my build config and steps if that would help. 
>> 
>> Thanks
>> Philip
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
> 


From matt.mccormick at kitware.com  Thu Aug 13 12:41:01 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 13 Aug 2015 12:41:01 -0400
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
Message-ID: <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>

Hi Arnaud,

Is this with building the examples with the superbuild?  I think I was
getting this error, too.  Here is a patch that should address it:

  http://review.source.kitware.com/#/c/20077/

Thanks,
Matt

On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Hi all,
>
> I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I get
> the following link error
>
> [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1
>
> [...]
>
> lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> 'itk::VideoIOBase::VideoIOBase()'
> lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> 'itk::VideoIOBase::~VideoIOBase()'
> lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const'
> lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> 'typeinfo for itk::VideoIOBase'
> collect2: error: ld returned 1 exit status
>
> I have checked these methods are implemented in itkVideoIOBase.cxx...
>
> Any idea?
>
> Thanks
> Arnaud
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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>
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From blowekamp at mail.nih.gov  Thu Aug 13 11:53:14 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 13 Aug 2015 11:53:14 -0400
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
 (command line too long)
In-Reply-To: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
Message-ID: <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>

Hello,

What version of CMake and Visual Studio are you using?

What is your build and source path?

Also know which Super build target that's causing the problem would be helpful too.

Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld".

Brad

On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:

> Hi, 
> I?m new to CMake and SimpleITK, and I?m trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I?m using the ?SuperBuild? instructions from here:
> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
> 
> I?m running into a problem where a build.make file creates a shell command that?s almost 5400 characters long. This leads to:
> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
> 
> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
> 
> Since I?m new to CMake and SimpleITK, I?m a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I?m in the wrong place, would someone be kind enough to guide me elsewhere?
> 
> I can post my build config and steps if that would help. 
> 
> Thanks
> Philip
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From blowekamp at mail.nih.gov  Thu Aug 13 12:36:51 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 13 Aug 2015 12:36:51 -0400
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
 (command line too long)
In-Reply-To: <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
 <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
Message-ID: <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>

OK,

Your Visual Studio should be based on VS 2008 then.

You could try commenting out this line:
https://github.com/SimpleITK/SimpleITK/blob/1b1745da326bbb67e1752b3edbde344d15712032/SuperBuild/SuperBuild.cmake#L359

The will remove passing all the language variables on the command line to the SimpleITK sub-project. But they will still be in the initial CMakeCache. This will remove the ability to update the variables in the sub project from the superbuild. 

I'll investigate further, to determine if there is a better long-term solution.

HTH,
Brad

On Aug 13, 2015, at 12:19 PM, Philip Semanchuk <ond at semanchuk.com> wrote:

> 
>> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> 
>> Hello,
>> 
>> What version of CMake and Visual Studio are you using?
> 
> CMake 3.3.0. I?m using Microsoft Visual C++ for Python 2.7. That's not Visual Studio ? it?s not an IDE. It?s just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008. 
> 
> 
>> What is your build and source path?
> 
> Build path is c:\Users\me\sitkb
> Source path is C:\Users\me\SimpleITK-0.9.0
> 
> 
>> Also know which Super build target that's causing the problem would be helpful too.
> 
> The U1095 error comes here:
> [ 84%] Performing configure step for 'SimpleITK'
> 
> 
>> 
>> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld?.
> 
> Thanks for the suggestion. I?m aware that long paths can contribute to overly-long command lines (I?ve run into that problem earlier in this build process). I don?t think they're the culprits here, though. 
> 
> The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don?t control (e.g. lots of references to "C:/Program Files (x86)?). 
> 
> If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command. 
> 
> Thanks for your willingness to help. I appreciate it!
> 
> Philip
> 
> 
>> 
>> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
>> 
>>> Hi, 
>>> I?m new to CMake and SimpleITK, and I?m trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I?m using the ?SuperBuild? instructions from here:
>>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>>> 
>>> I?m running into a problem where a build.make file creates a shell command that?s almost 5400 characters long. This leads to:
>>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>>> 
>>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>>> 
>>> Since I?m new to CMake and SimpleITK, I?m a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I?m in the wrong place, would someone be kind enough to guide me elsewhere?
>>> 
>>> I can post my build config and steps if that would help. 
>>> 
>>> Thanks
>>> Philip
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>> 
> 


From davis.vigneault at gmail.com  Thu Aug 13 13:55:04 2015
From: davis.vigneault at gmail.com (DVigneault)
Date: Thu, 13 Aug 2015 10:55:04 -0700 (MST)
Subject: [ITK] [ITK-users] Do any of the mesh file formats store CellData?
Message-ID: <1439488504178-7587666.post@n2.nabble.com>

All--

Do any of the mesh file formats supported by ITK store CellData information? 
I've done a test where I've (a) created a mesh, (b) associated a value with
each cell, (c) written it to file, (d) read it back in, and (e) attempted to
read the associated value.  I did this for each file format.  When I ask for
the cell's data, .vtk and .gii formats return uninitialized data, whereas
.obj, .byu, .fcv, .fsa, .fsb, and .off segfault.

I looked through itk::MeshFileWriter to see whether there were an option
(such as WriteCellDataOn()), and there is a method WriteCellData() [1], but
it is protected.  Looking at the header files of some of the individual
writer objects (itkVTKPolyDataMeshIO, itkOBJMeshIO, etc), it looks like the
WriteCellData(void *buffer) method is abstract.

[1]
http://www.itk.org/Doxygen/html/classitk_1_1MeshFileWriter.html#a1819df60ed20493f64a84c1728ddf26b

I've pasted below the test program, in case the problem is due to a mistake
I've made there.

Best, and thanks!

--Davis

#include "itkMesh.h"
#include "itkMeshFileReader.h"
#include "itkMeshFileWriter.h"
#include "itkRegularSphereMeshSource.h"

const unsigned int Dimension = 3;
typedef float      TCoordinate;

typedef itk::Mesh< TCoordinate, Dimension >   TMesh;
typedef itk::RegularSphereMeshSource< TMesh > TSphere;
typedef itk::MeshFileReader< TMesh >          TMeshReader;
typedef itk::MeshFileWriter< TMesh >          TMeshWriter;

int main( int argc, char* argv[] )
{

  auto sphere = TSphere::New();
  sphere->Update();

  auto mesh = sphere->GetOutput();
  double value = 10;
  for (unsigned int i = 0; i < mesh->GetNumberOfCells(); ++i)
    mesh->SetCellData( i, value);
  std::cout << mesh->GetCellData()->ElementAt(0) << std::endl; // 10

  auto meshWriter = TMeshWriter::New();
  meshWriter->SetFileName( argv[1] );
  meshWriter->SetInput( mesh );
  meshWriter->Update();

  auto reader = TMeshReader::New();
  reader->SetFileName( argv[1] );
  reader->ReadPointData();
  reader->Update();

  float value2;
  auto mesh2 = reader->GetOutput();
  mesh2->SetCellData(0, value2);
  mesh2->GetCellData()->ElementAt(0);
  std::cout << value2 << std::endl; // Segfault or uninitialized

  return EXIT_SUCCESS;

}




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Do-any-of-the-mesh-file-formats-store-CellData-tp7587666.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
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From lasso at queensu.ca  Thu Aug 13 13:40:39 2015
From: lasso at queensu.ca (Andras Lasso)
Date: Thu, 13 Aug 2015 17:40:39 +0000
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
 (command line too long)
In-Reply-To: <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
 <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
 <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
Message-ID: <CY1PR0701MB1613BBA7C0EBC03D0604278ED87D0@CY1PR0701MB1613.namprd07.prod.outlook.com>

CMake uses a response file to pass parameters to the compiler to avoid any issues with limited command line length.

Unfortunately, it seems that CMake does not use files for passing parameters to CMake.exe for configuring external projects. This should be probably fixed in CMake (add support for response files in CMake.exe and use that in ExternalProject).

Also, CMake cannot do anything about custom commands, so if you create a custom command that may construct a long command line then it'll eventually fail (see for example "random" Python wrapping issues here: https://github.com/commontk/CTK/issues/525#issuecomment-67269513).

You should be able to see in the build log or the generated .vcproj file if the long command line is generated by CMake's ExternalProject or by some other add_custom_command.

Andras

-----Original Message-----
From: Community [mailto:community-bounces at itk.org] On Behalf Of Bradley Lowekamp
Sent: Thursday, August 13, 2015 12:37 PM
To: Philip Semanchuk <ond at semanchuk.com>
Cc: community at itk.org
Subject: Re: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095 (command line too long)

OK,

Your Visual Studio should be based on VS 2008 then.

You could try commenting out this line:
https://github.com/SimpleITK/SimpleITK/blob/1b1745da326bbb67e1752b3edbde344d15712032/SuperBuild/SuperBuild.cmake#L359

The will remove passing all the language variables on the command line to the SimpleITK sub-project. But they will still be in the initial CMakeCache. This will remove the ability to update the variables in the sub project from the superbuild. 

I'll investigate further, to determine if there is a better long-term solution.

HTH,
Brad

On Aug 13, 2015, at 12:19 PM, Philip Semanchuk <ond at semanchuk.com> wrote:

> 
>> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> 
>> Hello,
>> 
>> What version of CMake and Visual Studio are you using?
> 
> CMake 3.3.0. I'm using Microsoft Visual C++ for Python 2.7. That's not Visual Studio - it's not an IDE. It's just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008. 
> 
> 
>> What is your build and source path?
> 
> Build path is c:\Users\me\sitkb
> Source path is C:\Users\me\SimpleITK-0.9.0
> 
> 
>> Also know which Super build target that's causing the problem would be helpful too.
> 
> The U1095 error comes here:
> [ 84%] Performing configure step for 'SimpleITK'
> 
> 
>> 
>> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld".
> 
> Thanks for the suggestion. I'm aware that long paths can contribute to overly-long command lines (I've run into that problem earlier in this build process). I don't think they're the culprits here, though. 
> 
> The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don't control (e.g. lots of references to "C:/Program Files (x86)"). 
> 
> If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command. 
> 
> Thanks for your willingness to help. I appreciate it!
> 
> Philip
> 
> 
>> 
>> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
>> 
>>> Hi, 
>>> I'm new to CMake and SimpleITK, and I'm trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I'm using the "SuperBuild" instructions from here:
>>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>>> 
>>> I'm running into a problem where a build.make file creates a shell command that's almost 5400 characters long. This leads to:
>>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>>> 
>>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>>> 
>>> Since I'm new to CMake and SimpleITK, I'm a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I'm in the wrong place, would someone be kind enough to guide me elsewhere?
>>> 
>>> I can post my build config and steps if that would help. 
>>> 
>>> Thanks
>>> Philip
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>> 
> 

_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community

From mohammedrashadkm at gmail.com  Thu Aug 13 14:55:19 2015
From: mohammedrashadkm at gmail.com (Rashad M)
Date: Thu, 13 Aug 2015 20:55:19 +0200
Subject: [ITK] [ITK-dev] regarding
	ImageFileReader::GenerateOutputInformation()
Message-ID: <CANNqv9fxcUOACxh2EcXkQAE6hpcn=uJuYgtxcMwp3wRkYF8s1g@mail.gmail.com>

Hello all,

The documentation of   itk::ProcessObject::GenerateOutputInformation( )
 says
Generate the information describing the output data. [1]. The
GenerateOutputInformation()
in itkImageFileReader first create all instances of ImageIO and setup
direction, spacing, etc..

If I understand correctly, the GenerateOutputInformation in the image file
reader is  called by UpdateOutputInformation( )

To my question,
If I call reader->UpdateOutputInformation() for first time it calls
reader->GenerateOutputInformation() as described in docs[2].

Now If I have a second call to reader->UpdateOutputInformation( ) ?

Will it again go to GenerateOutputInformation() and createAllInstances of
imageio , do the same thing again!

In itkProcessObject.cxx, there is the below documentation

   * Call GenerateOutputInformation for subclass specific information.
   * Since UpdateOutputInformation propagates all the way up the pipeline,
   * we need to be careful here to call GenerateOutputInformation only if
   * necessary. Otherwise, we may cause this source to be modified which
   * will cause it to execute again on the next update.

How can I prevent it from calling it again in class sub class of
itk::ImageSource?

[1]
http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#abe61fb6b7de8c443e7af1561bd722736


-- 
Regards,
   Rashad
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From blowekamp at mail.nih.gov  Thu Aug 13 15:11:32 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 13 Aug 2015 15:11:32 -0400
Subject: [ITK] [ITK-dev] regarding
	ImageFileReader::GenerateOutputInformation()
In-Reply-To: <CANNqv9fxcUOACxh2EcXkQAE6hpcn=uJuYgtxcMwp3wRkYF8s1g@mail.gmail.com>
References: <CANNqv9fxcUOACxh2EcXkQAE6hpcn=uJuYgtxcMwp3wRkYF8s1g@mail.gmail.com>
Message-ID: <3284837D-9DD6-48A1-A65D-5ED81EC1A95B@mail.nih.gov>

Hello Rashad,

If you call ImageFileReader::UpdateOutputInformation() 2 times is "should" only call GenerateOutputInformation once.

The key to this behavior is the management of the timestamps in the process object classes done here [1].

What is required for this to work correctly is that the only the correct object get modified in these pipeline methods. When an object is modified the timestamp should be updated, and downstream processes get marked as out of date.

The best way to make sure your ImageSource does not get call twice is to write a test, that makes sure the process object's MTime does not change in GenerateOutputInformation call.

HTH,
Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/9f88e4e3b388ee2f1c1c006ae36de0613d305284/Modules/Core/Common/src/itkProcessObject.cxx#L1431-L1542

On Aug 13, 2015, at 2:55 PM, Rashad M <mohammedrashadkm at gmail.com> wrote:

> Hello all,
> 
> The documentation of   itk::ProcessObject::GenerateOutputInformation( )  says
> Generate the information describing the output data. [1]. The GenerateOutputInformation() in itkImageFileReader first create all instances of ImageIO and setup direction, spacing, etc.. 
> 
> If I understand correctly, the GenerateOutputInformation in the image file reader is  called by UpdateOutputInformation( )
> 
> To my question, 
> If I call reader->UpdateOutputInformation() for first time it calls 
> reader->GenerateOutputInformation() as described in docs[2]. 
> 
> Now If I have a second call to reader->UpdateOutputInformation( ) ?
> 
> Will it again go to GenerateOutputInformation() and createAllInstances of imageio , do the same thing again!
> 
> In itkProcessObject.cxx, there is the below documentation
> 
>    * Call GenerateOutputInformation for subclass specific information.
>    * Since UpdateOutputInformation propagates all the way up the pipeline,
>    * we need to be careful here to call GenerateOutputInformation only if
>    * necessary. Otherwise, we may cause this source to be modified which
>    * will cause it to execute again on the next update.
> 
> How can I prevent it from calling it again in class sub class of itk::ImageSource?
> 
> [1]http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#abe61fb6b7de8c443e7af1561bd722736
> 
> 
> -- 
> Regards,
>    Rashad
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
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> 
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From matt.mccormick at kitware.com  Thu Aug 13 16:59:17 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 13 Aug 2015 16:59:17 -0400
Subject: [ITK] [ITK-users] Symmetric eigen analysis discrepancy
In-Reply-To: <F80D6ED3-0AD2-466C-85BA-38C9DE1AC316@inria.fr>
References: <F80D6ED3-0AD2-466C-85BA-38C9DE1AC316@inria.fr>
Message-ID: <CALzTN-Stue7A1WrwjYP-gPj=6GgnSUNRhb2u0oYddBO8CQmyzg@mail.gmail.com>

Hi Olivier,

Those are some pretty small numbers ;-).  Thanks for sharing your experiences.

It may be necessary to build both ITK and vnl/netlib instances with
debugging symbols and walk through them in a debugger to see where the
deviation occurs.

As always, patches are welcome :-)

Thanks,
Matt

On Thu, Aug 13, 2015 at 9:35 AM, Olivier Commowick
<Olivier.Commowick at inria.fr> wrote:
> Hello all,
>
> I have been experiencing a problem when using the itk SymmetricEigenAnalysis class in ITK. When using this class, it sometimes produces NaN eigenvalues/vectors. On the contrary, the vnl_symmetric_eigensystem doesn?t seem to have a problem (and neither does matlab). Looking at the documentation, it seems both use QL decomposition but not implemented in the same place. In addition, the vnl one is said to be not thread safe, although it?s the one working for me.
>
> In fact, I have isolated one 3x3 matrix for which I always have the problem.
>
> A =
> [7.503107128706855667859804009212206062302e-53 1.870107888834986371214720644344813262375e-52 -8.662047753682068190087788895125120421821e-27;
> 1.870107888834986371214720644344813262375e-52 4.661140319458029838073740773908360767728e-52 -2.15896741973055935210319454393408888029e-26;
> -8.662047753682068190087788895125120421821e-27 -2.15896741973055935210319454393408888029e-26 1]
>
> It?s a weird one I know, but again vnl (and matlab) works great on it. Would there be anyone who knows the QL decomposition code enough to help me understand and possibly correct the ITK class so that it does the same as the VNL one ?
>
> Thanks a lot in advance.
>
> ---
>
> Olivier Commowick, Ph.D.
> Research Scientist
> INRIA Rennes - Bretagne Atlantique, VISAGES Team
> Campus de Beaulieu
> 35042 Rennes
> FRANCE
>
> Phone: +33 2 99 84 25 92
> Email: Olivier.Commowick at inria.fr
> Web: http://olivier.commowick.org/
>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
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From matt.mccormick at kitware.com  Thu Aug 13 18:08:38 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 13 Aug 2015 18:08:38 -0400
Subject: [ITK] [ITK-users] IterativeClosestPoint2 example: how to get
	better	results
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409435126779@MBX114.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435126779@MBX114.d.ethz.ch>
Message-ID: <CALzTN-T6MeG=j6dZzgUTni6PgSX+U4W3t1mVUmJG__6VeWh_kA@mail.gmail.com>

Hello,

On Thu, Aug 13, 2015 at 4:06 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> I am trying to use the IterativeClosestPoint2 example on the fixed and
> moving point sets in attachment (called ?src? and ?dest? point sets).
>
>
>
> The ground truth is ?properly ordered dest = Transform(src)?, where:
>
>
>
> Euler angles:  (0.349065850398866, 0.349065850398866, 0.349065850398866)
>
> Translations: (4.1335200571234, 5.90820985238168, 7.04748773837622)
>
>
>
> (the dest_point set in attachment is randomly reshuffled)
>
>
>
>>>> If I use srx = fixed, dest = moving, the registration results is:
>
>
>
> Euler angles:  (-0.327201, -0.36953, -0.47291)
>
> Translations: (-6.28471, -2.64212, -1.50835)
>
>
>
>>>> If I use dest = fixed, src = moving, the registration results is:
>
>
>
> Euler angles:  (0.44595, 0.20655, 0.36423)
>
> Translations: (6.28471, 2.64212, 1.50835)
>
>
>
>
>
>
>
> Question 1):
>
>
>
> Given that ?properly ordered dest = Transform(src)?, according to the guide
> src should be the fixed point set. Am I wrong?
>

This is a bit confusing because it is different from transforms with
images, but the src should be the moving point set.  See:

  http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkEuclideanDistancePointMetric.hxx;h=af1b04e91ed9126777134db3dfca6ef05810fc60;hb=HEAD#l87


> Question 2):
>
>
>
> I am not happy with the results, given that there is no additional noise
> (the underlined values refer to error angles of up to 8 degrees and 3 mm
> errors). I am surprised because there is no additional noise to the data, so
> I would expect an accurate registration. Are my results normal? How could I
> improve the results? Should I change the optimizer, or the transform?

Could the code be shared that generated the inputs?

Thanks,
Matt
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From matt.mccormick at kitware.com  Thu Aug 13 18:13:24 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 13 Aug 2015 18:13:24 -0400
Subject: [ITK] [ITK-dev] converting coordinate system
In-Reply-To: <CAKcUdn62pe3OU9hwYMqbwGjq81GQs=RGT9xkD_Jdwh6u101hPA@mail.gmail.com>
References: <CAKcUdn62pe3OU9hwYMqbwGjq81GQs=RGT9xkD_Jdwh6u101hPA@mail.gmail.com>
Message-ID: <CALzTN-QNLu9O7tm1qMpedJntPgLd+FDgz+XcEbRyqnnKsPh_VQ@mail.gmail.com>

Hello,

All computations in ITK are done in the world coordinate system, i.e.
the physical coordinates.  To convert an image coordinate, i.e. the
index coordinates, use the TransformIndexToPhysicalPoint [1] method on
itk::Image.  This takes into account image orientation and spacing.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#ab003313ba1a078d89a832dc0a35d2efa

On Thu, Aug 13, 2015 at 2:47 AM, Marco Dev <marco.dev.open at gmail.com> wrote:
> Hi dears,
> I have some itk image filter for translating from image coordinate system to
> world coordinate system
> Means I want to convert Dicom image position and another tag information
> such as pixel spacing orientation to world coordinate for Itk coordinate
> these are difference in position
> How can do this convert
> Thanks in advance
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
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From siavashk at ece.ubc.ca  Thu Aug 13 17:46:40 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Thu, 13 Aug 2015 14:46:40 -0700 (MST)
Subject: [ITK] [ITK-users] IterativeClosestPoint2 example: how to get
 better results
In-Reply-To: <CALzTN-T6MeG=j6dZzgUTni6PgSX+U4W3t1mVUmJG__6VeWh_kA@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409435126779@MBX114.d.ethz.ch>
 <CALzTN-T6MeG=j6dZzgUTni6PgSX+U4W3t1mVUmJG__6VeWh_kA@mail.gmail.com>
Message-ID: <1439502400763-35998.post@n7.nabble.com>

ICP is notorious for its small capture range and suesceptibility to
noise/local minima. This is why soft correspondence schemes to point cloud
registration have been developed that generally have a larger capture range
(e.g. see  CPD <http://arxiv.org/pdf/0905.2635.pdf>   and  GMM-FEM
<http://dx.doi.org/10.1109/TMI.2015.2440253>  ). It could be that the code
is fine, but ICP fails to converge to the true solution.

Siavash


D'Isidoro  Fabio wrote
>> I am not happy with the results, given that there is no additional noise
>> (the underlined values refer to error angles of up to 8 degrees and 3 mm
>> errors). I am surprised because there is no additional noise to the data,
>> so
>> I would expect an accurate registration. Are my results normal? How could
>> I
>> improve the results? Should I change the optimizer, or the transform? 





--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-IterativeClosestPoint2-example-how-to-get-better-results-tp35993p35998.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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From matt.mccormick at kitware.com  Thu Aug 13 18:21:44 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 13 Aug 2015 18:21:44 -0400
Subject: [ITK] [ITK-users] general info ICP implementation
In-Reply-To: <50B858FB5F53124F9E32314E5C1B40943511F43B@MBX214.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B40943511F43B@MBX214.d.ethz.ch>
Message-ID: <CALzTN-SbwTKXVs_vw3zORhT_v6-Wanm8Gr_xB9H-HWLx_+A3uQ@mail.gmail.com>

Hello,

ITK uses the Levenberg-Marquardt non-linear least squares optimizer in
the ICP examples.  This has an advantage of the closed formula updates
in that it can work with an arbitrary transform.  But, a different
type of ICP using closed form updates could possibly be created by
utilizing the LandmarkBasedTransformInitializer class [1], which
provides correspondences for a number of transforms.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1LandmarkBasedTransformInitializer.html

On Mon, Aug 10, 2015 at 10:32 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> I am trying to figure out how ICP is implemented in ITK. The general
> approach consists in iterating two steps: first compute the correspondences
> and then find the best transform with the current correspondences by using a
> close formula.
>
>
>
> However in the ITK implementation I can?t see this approach, plus
> LevenbergMarquardt alrgorithm is used instead of close formula to determine
> the transform. I know a special version of LevenbergMarquardt-ICP algorithm
> has been proposed in the following paper, however I can?t see how the ITK
> implementation follows this proposed method (the ITK implementation seems to
> me very generic like any other optimization problem). Where should I look
> for?
>
>
>
> Paper: ?Robust registration of 2D and 3D point sets? Fitzgibbon 2003.
>
>
>
> Thank you very much.
>
> Fabio
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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From blowekamp at mail.nih.gov  Thu Aug 13 20:18:04 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 13 Aug 2015 20:18:04 -0400
Subject: [ITK] [ITK-users] Binary Erosion failed
In-Reply-To: <1613398309.4524159.1439510405840.JavaMail.yahoo@mail.yahoo.com>
References: <1613398309.4524159.1439510405840.JavaMail.yahoo@mail.yahoo.com>
Message-ID: <A0BC57F3-4A24-459C-80D7-BBDE1D928E67@mail.nih.gov>

Hello,

The problem likely relates to defining the "white" box  on a "back" background in terms of a binary image.

You should set the "BackgroundValue"[1] and the "ForegroundValue"[2] in the filter to you "white" pixel intensity value, and "black" pixel intensity value. Those methods a little tricky to find since they are in the parent class. Be careful to note if there are pixels of other values in the image.

HTH,
Brad

[1] SetBackgroundValue
[2] SetForegroundValue


On Aug 13, 2015, at 8:00 PM, Emma Ryan via Insight-users <insight-users at itk.org> wrote:

> Hi,
> 
>  I am attempting a simple erosion on a binary input image which is pretty much a white box on a black background.
> 
>  The following is my code snippet. Not sure why it fails to erode the image. Am I missing something ? 
> 
> typedef itk::FlatStructuringElement<2 >    StructuralElementType;
> StructuralElementType::RadiusType radius;
> radius.Fill(7 );
> StructuralElementType structural_element =   StructuralElementType::Box( radius );
>     
> 
>     typedef itk::BinaryErodeImageFilter <UCharImageType, UCharImageType, StrelType>    BinaryErodeImageFilterType;
>     BinaryErodeImageFilterType::Pointer erodeFilter    = BinaryErodeImageFilterType::New();
>     erodeFilter->SetInput(my_binary_image);
>     erodeFilter->SetKernel(structural_element);
>     try
>     {
>         erodeFilter->Update();
>     }
> catch(...)
> {
>     cout<<"Failure";
> }
> 
> UCharImageType::Pointer new_image = erodeFilter->GetOutput();
> 
> thanks,
> Emma
> 
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
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> 
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From arnaudgelas at gmail.com  Fri Aug 14 02:21:19 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 14 Aug 2015 08:21:19 +0200
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
Message-ID: <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>

Hi Matt,

It happened while directly building ITK with OpenCV 2.4.9, without any
superbuild...
Thanks for the patch, but that does not solve it...

I wonder if it could have something to do with the new linking system (note
it uses COMPILE_DEPENDS) ?

Thanks,
Arnaud

On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Arnaud,
>
> Is this with building the examples with the superbuild?  I think I was
> getting this error, too.  Here is a patch that should address it:
>
>   http://review.source.kitware.com/#/c/20077/
>
> Thanks,
> Matt
>
> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
> > Hi all,
> >
> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I
> get
> > the following link error
> >
> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1
> >
> > [...]
> >
> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> > 'itk::VideoIOBase::VideoIOBase()'
> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> > 'itk::VideoIOBase::~VideoIOBase()'
> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const'
> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> > 'typeinfo for itk::VideoIOBase'
> > collect2: error: ld returned 1 exit status
> >
> > I have checked these methods are implemented in itkVideoIOBase.cxx...
> >
> > Any idea?
> >
> > Thanks
> > Arnaud
> >
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-developers
> >
>
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From arnaudgelas at gmail.com  Fri Aug 14 02:54:20 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 14 Aug 2015 08:54:20 +0200
Subject: [ITK] [ITK-users] Do any of the mesh file formats store
	CellData?
In-Reply-To: <1439488504178-7587666.post@n2.nabble.com>
References: <1439488504178-7587666.post@n2.nabble.com>
Message-ID: <CAK3qF+92n4BnU9D41GpRPe27p-A04Sa=+SXQVMbBwwkkz8c2Nw@mail.gmail.com>

Hi Davis,

First of all, you do not need to call ReadPointData, especially if you want
to read cell data... Anyway, even if you make the change, it is not
required...

Then, if you look carefully at your code, it is normal that it segfault:

  float value2;
  auto mesh2 = reader->GetOutput();
  mesh2->SetCellData(0, value2);
  mesh2->GetCellData()->ElementAt(0);
  std::cout << value2 << std::endl; // Segfault or uninitialized

Right after reading the file, you set the data of the cell 0 to an
uninitialized value, then you get that value back but you do not store in
any variable. Finally, you print the uninitialzed value...

Best,
Arnaud


On Thu, Aug 13, 2015 at 7:55 PM, DVigneault <davis.vigneault at gmail.com>
wrote:

> All--
>
> Do any of the mesh file formats supported by ITK store CellData
> information?
> I've done a test where I've (a) created a mesh, (b) associated a value with
> each cell, (c) written it to file, (d) read it back in, and (e) attempted
> to
> read the associated value.  I did this for each file format.  When I ask
> for
> the cell's data, .vtk and .gii formats return uninitialized data, whereas
> .obj, .byu, .fcv, .fsa, .fsb, and .off segfault.
>
> I looked through itk::MeshFileWriter to see whether there were an option
> (such as WriteCellDataOn()), and there is a method WriteCellData() [1], but
> it is protected.  Looking at the header files of some of the individual
> writer objects (itkVTKPolyDataMeshIO, itkOBJMeshIO, etc), it looks like the
> WriteCellData(void *buffer) method is abstract.
>
> [1]
>
> http://www.itk.org/Doxygen/html/classitk_1_1MeshFileWriter.html#a1819df60ed20493f64a84c1728ddf26b
>
> I've pasted below the test program, in case the problem is due to a mistake
> I've made there.
>
> Best, and thanks!
>
> --Davis
>
> #include "itkMesh.h"
> #include "itkMeshFileReader.h"
> #include "itkMeshFileWriter.h"
> #include "itkRegularSphereMeshSource.h"
>
> const unsigned int Dimension = 3;
> typedef float      TCoordinate;
>
> typedef itk::Mesh< TCoordinate, Dimension >   TMesh;
> typedef itk::RegularSphereMeshSource< TMesh > TSphere;
> typedef itk::MeshFileReader< TMesh >          TMeshReader;
> typedef itk::MeshFileWriter< TMesh >          TMeshWriter;
>
> int main( int argc, char* argv[] )
> {
>
>   auto sphere = TSphere::New();
>   sphere->Update();
>
>   auto mesh = sphere->GetOutput();
>   double value = 10;
>   for (unsigned int i = 0; i < mesh->GetNumberOfCells(); ++i)
>     mesh->SetCellData( i, value);
>   std::cout << mesh->GetCellData()->ElementAt(0) << std::endl; // 10
>
>   auto meshWriter = TMeshWriter::New();
>   meshWriter->SetFileName( argv[1] );
>   meshWriter->SetInput( mesh );
>   meshWriter->Update();
>
>   auto reader = TMeshReader::New();
>   reader->SetFileName( argv[1] );
>   reader->ReadPointData();
>   reader->Update();
>
>   float value2;
>   auto mesh2 = reader->GetOutput();
>   mesh2->SetCellData(0, value2);
>   mesh2->GetCellData()->ElementAt(0);
>   std::cout << value2 << std::endl; // Segfault or uninitialized
>
>   return EXIT_SUCCESS;
>
> }
>
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/Do-any-of-the-mesh-file-formats-store-CellData-tp7587666.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From arnaudgelas at gmail.com  Fri Aug 14 03:48:22 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 14 Aug 2015 09:48:22 +0200
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
Message-ID: <CAK3qF+-2iExu1DMtXNwMgSPXdtBM_pHtFwy0WzzJC1+bTWMeCw@mail.gmail.com>

I have restarted from scratch...

So instead of using gold linker, it is using the default linker, the header
test is now ok, but I still have linking errors:

$ ninja ITKVideoBridgeOpenCV-all
[1/1] Linking CXX executable bin/ITKVideoBridgeOpenCVTestDriver
FAILED: : && /usr/lib/ccache/c++ -Wall -Wcast-align -Wdisabled-optimization
-Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith
-Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow
-Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual
-Wstrict-null-sentinel  -Wno-array-bounds -msse2 -g
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/ITKVideoBridgeOpenCVTestDriver.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeGrayScaleTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeRGBTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOFactoryTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVBasicTypeBridgeTest.cxx.o
-o bin/ITKVideoBridgeOpenCVTestDriver  -rdynamic
lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1
lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1
lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1
lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1
lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1
lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1
lib/libITKVideoBridgeOpenCV-4.9.so.1
/home/arnaud/install/lib/libopencv_videostab.so.2.4.9
/home/arnaud/install/lib/libopencv_video.so.2.4.9
/home/arnaud/install/lib/libopencv_ts.a
/home/arnaud/install/lib/libopencv_superres.so.2.4.9
/home/arnaud/install/lib/libopencv_stitching.so.2.4.9
/home/arnaud/install/lib/libopencv_photo.so.2.4.9
/home/arnaud/install/lib/libopencv_ocl.so.2.4.9
/home/arnaud/install/lib/libopencv_objdetect.so.2.4.9
/home/arnaud/install/lib/libopencv_nonfree.so.2.4.9
/home/arnaud/install/lib/libopencv_ml.so.2.4.9
/home/arnaud/install/lib/libopencv_legacy.so.2.4.9
/home/arnaud/install/lib/libopencv_imgproc.so.2.4.9
/home/arnaud/install/lib/libopencv_highgui.so.2.4.9
/home/arnaud/install/lib/libopencv_gpu.so.2.4.9
/home/arnaud/install/lib/libopencv_flann.so.2.4.9
/home/arnaud/install/lib/libopencv_features2d.so.2.4.9
/home/arnaud/install/lib/libopencv_core.so.2.4.9
/home/arnaud/install/lib/libopencv_contrib.so.2.4.9
/home/arnaud/install/lib/libopencv_calib3d.so.2.4.9
lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1
lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1
lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1
lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1
lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1
lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1
-lm -lpthread -lrt -ltbb
/home/arnaud/install/lib/libopencv_nonfree.so.2.4.9
/home/arnaud/install/lib/libopencv_ocl.so.2.4.9
/home/arnaud/install/lib/libopencv_gpu.so.2.4.9
/home/arnaud/install/lib/libopencv_photo.so.2.4.9
/home/arnaud/install/lib/libopencv_objdetect.so.2.4.9
/home/arnaud/install/lib/libopencv_legacy.so.2.4.9
/home/arnaud/install/lib/libopencv_video.so.2.4.9
/home/arnaud/install/lib/libopencv_ml.so.2.4.9
/home/arnaud/install/lib/libopencv_calib3d.so.2.4.9
/home/arnaud/install/lib/libopencv_features2d.so.2.4.9
/home/arnaud/install/lib/libopencv_highgui.so.2.4.9
/home/arnaud/install/lib/libopencv_imgproc.so.2.4.9
/home/arnaud/install/lib/libopencv_flann.so.2.4.9
/home/arnaud/install/lib/libopencv_core.so.2.4.9 lib/libITKVideoIO-4.9.so.1
lib/libITKIOImageBase-4.9.so.1 lib/libITKVideoCore-4.9.so.1
lib/libITKCommon-4.9.so.1 lib/libitkdouble-conversion-4.9.so.1
lib/libitksys-4.9.so.1 lib/libITKVNLInstantiation-4.9.so.1 -lvnl_algo -lvnl
-lv3p_netlib -lnetlib -lvcl -lpthread -lm -ldl
-Wl,-rpath,/home/arnaud/source/build-itk/lib:/home/arnaud/install/lib
-Wl,-rpath-link,/home/arnaud/source/build-itk/lib && :
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o:
In function `itk::OpenCVVideoIOFactory::New()':
/home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIOFactory.h:46:
undefined reference to `itk::OpenCVVideoIOFactory::OpenCVVideoIOFactory()'
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o:
In function `itk::OpenCVVideoIO::New()':
/home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIO.h:48:
undefined reference to `itk::OpenCVVideoIO::OpenCVVideoIO()'
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o:
In function `itk::ObjectFactory<itk::OpenCVVideoIO>::Create()':
/home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:60:
undefined reference to `typeinfo for itk::OpenCVVideoIO'
/home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:62:
undefined reference to `typeinfo for itk::OpenCVVideoIO'
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.



On Fri, Aug 14, 2015 at 8:21 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi Matt,
>
> It happened while directly building ITK with OpenCV 2.4.9, without any
> superbuild...
> Thanks for the patch, but that does not solve it...
>
> I wonder if it could have something to do with the new linking system
> (note it uses COMPILE_DEPENDS) ?
>
> Thanks,
> Arnaud
>
> On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> Hi Arnaud,
>>
>> Is this with building the examples with the superbuild?  I think I was
>> getting this error, too.  Here is a patch that should address it:
>>
>>   http://review.source.kitware.com/#/c/20077/
>>
>> Thanks,
>> Matt
>>
>> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>> wrote:
>> > Hi all,
>> >
>> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I
>> get
>> > the following link error
>> >
>> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1
>> >
>> > [...]
>> >
>> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> > 'itk::VideoIOBase::VideoIOBase()'
>> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> > 'itk::VideoIOBase::~VideoIOBase()'
>> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const'
>> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> > 'typeinfo for itk::VideoIOBase'
>> > collect2: error: ld returned 1 exit status
>> >
>> > I have checked these methods are implemented in itkVideoIOBase.cxx...
>> >
>> > Any idea?
>> >
>> > Thanks
>> > Arnaud
>> >
>> > _______________________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-developers
>> >
>>
>
>
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From keansum at gmail.com  Fri Aug 14 03:54:08 2015
From: keansum at gmail.com (Kean Sum Ooi)
Date: Fri, 14 Aug 2015 15:54:08 +0800
Subject: [ITK] VTK 4.2 build failed VolumeRayCastMapper_CastRays not
	declared
In-Reply-To: <CADZJ4hPZyKPDaSLGPxegnXLtHEz3CcNW25uRp+GX5+A9mPhmeg@mail.gmail.com>
References: <CAM0-uyXx6Jah0OSEJVfscsCs8N4w=ReFpZEUFJQEHD+2GUTiqw@mail.gmail.com>
 <CADZJ4hPZyKPDaSLGPxegnXLtHEz3CcNW25uRp+GX5+A9mPhmeg@mail.gmail.com>
Message-ID: <CAM0-uyW2DTArSWi5USkXoKk0-ShcdzVgwagSCMyVTXNq-rh9hg@mail.gmail.com>

Hi BIll,
Thank you very much for the pointer. I am now able to successfully build
ITKApps using those instructions!
Have a great day!
Best regards,
Sum

On Sat, Aug 8, 2015 at 8:32 PM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:

> Those are old instructions. They will have to be updated. VTK4.2 is
> really old. Try building the apps with VTK5.10.
>
> Follow these instructions:
> http://www.itk.org/ITK/resources/applications.html
>
>
> On Fri, Aug 7, 2015 at 11:05 PM, Kean Sum Ooi <keansum at gmail.com> wrote:
> > I am trying to install ITKApps with VTK 4.2 as instructed from following
> the
> > instructions at: http://www.itk.org/Wiki/ITK/Insight_Applications
> >
> > However when I try to build VTK 4.2, it fails at the make stage:
> > $ make -j2
> > /home/guest/installScripts/VTK/Rendering/vtkVolumeRayCastMapper.cxx: In
> > member function ?virtual void
> vtkVolumeRayCastMapper::Render(vtkRenderer*,
> > vtkVolume*)?:
> >
> /home/guest/installScripts/VTK/Rendering/vtkVolumeRayCastMapper.cxx:523:38:
> > error: ?VolumeRayCastMapper_CastRays? was not declared in this scope
> >      this->Threader->SetSingleMethod( VolumeRayCastMapper_CastRays,
> >
> > So may I please ask is there something we have to do before we can
> > successfully compile VTK 4.2?
> >
> > I have building from both the VTK-4.2-LatestRelease.tar.gz and by
> checking
> > out v4.2.0 from git with the same results.
> >
> > Thank you,
> > Best regards,
> > Sum
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
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From arnaudgelas at gmail.com  Fri Aug 14 05:30:07 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 14 Aug 2015 11:30:07 +0200
Subject: [ITK] [ITK-dev] use ThreadedIteratorRangePartitioner with itk
	Container ?
Message-ID: <CAK3qF+9xQ3WD3fM2Xwcb87kcVKeV98t1OcrYVdkGt9nAqNwbPg@mail.gmail.com>

Hi Matt,

I would like to use itk::ThreadedIteratorRangePartitioner with
itk::Mesh::PointsContainer or itk::Mesh::CellsContainer (i.e.
itk::VectorContainer or itk::MapContainer).

At first, I am trying to add one test which basically duplicates
itkThreadedIteratorRangePartitionerTest for the case of
itk::VectorContainer, you can find a patch here:

     http://review.source.kitware.com/#/c/20079/

I have compilation errors, due to the fact that internally
itk::ThreadedIteratorRangePartitioner uses std::distance and std::advance
which requires some typedefs which are not available for
itk::VectorContainer iterators...

Should I keep on working in that direction? I mean to try to fix these
classes for itk container's iterator (adapt it for these cases)? Make
specialization?

Thanks,
Arnaud
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From ond at semanchuk.com  Fri Aug 14 08:03:12 2015
From: ond at semanchuk.com (Philip Semanchuk)
Date: Fri, 14 Aug 2015 08:03:12 -0400
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
	(command line too long)
In-Reply-To: <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
 <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
 <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
Message-ID: <E8472563-D485-4D83-B8CB-F951489CFB69@semanchuk.com>


> On Aug 13, 2015, at 12:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> 
> OK,
> 
> Your Visual Studio should be based on VS 2008 then.
> 
> You could try commenting out this line:
> https://github.com/SimpleITK/SimpleITK/blob/1b1745da326bbb67e1752b3edbde344d15712032/SuperBuild/SuperBuild.cmake#L359
> 
> The will remove passing all the language variables on the command line to the SimpleITK sub-project. But they will still be in the initial CMakeCache. This will remove the ability to update the variables in the sub project from the super build. 

That worked! Thanks very much for your help.

Cheers
Philip




> 
> I'll investigate further, to determine if there is a better long-term solution.
> 
> HTH,
> Brad
> 
> On Aug 13, 2015, at 12:19 PM, Philip Semanchuk <ond at semanchuk.com> wrote:
> 
>> 
>>> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>> 
>>> Hello,
>>> 
>>> What version of CMake and Visual Studio are you using?
>> 
>> CMake 3.3.0. I?m using Microsoft Visual C++ for Python 2.7. That's not Visual Studio ? it?s not an IDE. It?s just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008. 
>> 
>> 
>>> What is your build and source path?
>> 
>> Build path is c:\Users\me\sitkb
>> Source path is C:\Users\me\SimpleITK-0.9.0
>> 
>> 
>>> Also know which Super build target that's causing the problem would be helpful too.
>> 
>> The U1095 error comes here:
>> [ 84%] Performing configure step for 'SimpleITK'
>> 
>> 
>>> 
>>> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld?.
>> 
>> Thanks for the suggestion. I?m aware that long paths can contribute to overly-long command lines (I?ve run into that problem earlier in this build process). I don?t think they're the culprits here, though. 
>> 
>> The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don?t control (e.g. lots of references to "C:/Program Files (x86)?). 
>> 
>> If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command. 
>> 
>> Thanks for your willingness to help. I appreciate it!
>> 
>> Philip
>> 
>> 
>>> 
>>> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
>>> 
>>>> Hi, 
>>>> I?m new to CMake and SimpleITK, and I?m trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I?m using the ?SuperBuild? instructions from here:
>>>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>>>> 
>>>> I?m running into a problem where a build.make file creates a shell command that?s almost 5400 characters long. This leads to:
>>>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>>>> 
>>>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>>>> 
>>>> Since I?m new to CMake and SimpleITK, I?m a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I?m in the wrong place, would someone be kind enough to guide me elsewhere?
>>>> 
>>>> I can post my build config and steps if that would help. 
>>>> 
>>>> Thanks
>>>> Philip
>>>> _______________________________________________
>>>> Community mailing list
>>>> Community at itk.org
>>>> http://public.kitware.com/mailman/listinfo/community
>>> 
>> 
> 


From davis.vigneault at gmail.com  Fri Aug 14 08:53:11 2015
From: davis.vigneault at gmail.com (DVigneault)
Date: Fri, 14 Aug 2015 05:53:11 -0700 (MST)
Subject: [ITK] [ITK-users] Do any of the mesh file formats store
	CellData?
In-Reply-To: <CAK3qF+92n4BnU9D41GpRPe27p-A04Sa=+SXQVMbBwwkkz8c2Nw@mail.gmail.com>
References: <1439488504178-7587666.post@n2.nabble.com>
 <CAK3qF+92n4BnU9D41GpRPe27p-A04Sa=+SXQVMbBwwkkz8c2Nw@mail.gmail.com>
Message-ID: <1439556791786-7587675.post@n2.nabble.com>

Thanks very much for the help, Arnaud--sometimes I think I shouldn't be
allowed to post after 5pm.  :-)

However, unless I'm making another silly mistake, that doesn't appear to be
the only problem.  If I open the mesh.vtk file, I don't see where any
CellData has been written.  Moreover, if I std::cout the size of CellData
*before* writing to disk I get 128, whereas immediately after I get 0.

I tried stepping through the itk::MeshFileWriter::Write() method in gdb
(itkMeshFileWriter.hxx:80), and found that p input->GetCellData()->Size()
returns 128 until nonConstInput->Update() is called (b
itkMeshFileWriter.hxx:148), after which p input->GetCellData()->Size()
returns 0.  As a result, the condition if (input->GetCells() &&
input->GetNumberOfCells() ) fails, and the CellData appears not to be
written.  Unfortunately I built ITK in release mode so I can't step into
Update() at the minute, but I'll rebuild and see if I can get more
information.

Thanks again Arnaud et al for your help (and your patience)!

--Davis

////
//// Here's what I'm seeing in GDB:
////

$ gdb ./dv-mesh-test
(gdb) b itkMeshFileWriter.hxx:148
(gdb) b itkMeshFileWriter.hxx:207 // Never triggered
(gdb) b itkMeshFileWriter.hxx:240 // Never triggered
(gdb) r
(gdb) p input->GetCellData() // 0x91b3a0
(gdb) p input->GetCellData()->Size() // 128
(gdb) n
(gdb) p input->GetCellData() // 0x91b3f0 (different pointer)
(gdb) p input->GetCellData()->Size() // 0
(gdb) c // Exits normally, but the size of the mesh's CellData container is
now 0

////
//// And here's the new test file:
////

#include "itkMesh.h"
#include "itkRegularSphereMeshSource.h"
#include "itkMeshFileWriter.h"

const unsigned int Dimension = 3;
typedef float      TCoordinate;

typedef itk::Mesh< TCoordinate, Dimension >   TMesh;
typedef itk::RegularSphereMeshSource< TMesh > TSphere;
typedef itk::MeshFileWriter< TMesh >          TMeshWriter;

int main()
{

  auto sphere = TSphere::New();
  sphere->Update();

  auto mesh = sphere->GetOutput();
  double value = 10;
//  mesh->GetCellData()->Reserve(mesh->GetNumberOfCells()); // No change
//  mesh->SetRequestedRegionToLargestPossibleRegion(); // No change
  for (unsigned int i = 0; i < mesh->GetNumberOfCells(); ++i)
    mesh->SetCellData( i, value);

  std::cout << mesh->GetNumberOfCells() << std::endl; // 128
  std::cout << mesh->GetCellData() << std::endl; // 0x1be13a0
  std::cout << mesh->GetCellData()->Size() << std::endl << std::endl; // 128

  auto meshWriter = TMeshWriter::New();
  meshWriter->SetFileName( "mesh.vtk" );
  meshWriter->SetInput( mesh );
  meshWriter->Update();

  std::cout << mesh->GetNumberOfCells() << std::endl; // 128
  std::cout << mesh->GetCellData() << std::endl; // 0x1be13a0
  std::cout << mesh->GetCellData()->Size() << std::endl << std::endl; // 0

  return EXIT_SUCCESS;

}




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Do-any-of-the-mesh-file-formats-store-CellData-tp7587666p7587675.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
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From blowekamp at mail.nih.gov  Fri Aug 14 09:21:05 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 14 Aug 2015 09:21:05 -0400
Subject: [ITK] [ITK-dev] use ThreadedIteratorRangePartitioner with itk
 Container ?
In-Reply-To: <CAK3qF+9xQ3WD3fM2Xwcb87kcVKeV98t1OcrYVdkGt9nAqNwbPg@mail.gmail.com>
References: <CAK3qF+9xQ3WD3fM2Xwcb87kcVKeV98t1OcrYVdkGt9nAqNwbPg@mail.gmail.com>
Message-ID: <7407F7E9-F13B-4AA4-9116-625F5DD09FDF@mail.nih.gov>

Arnaund,

I would recommend using an index based partitioner as opposed to the iterator based algorithm due to on big O performance of the partitioning algorithms.

Brad

On Aug 14, 2015, at 5:30 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi Matt,
> 
> I would like to use itk::ThreadedIteratorRangePartitioner with itk::Mesh::PointsContainer or itk::Mesh::CellsContainer (i.e. itk::VectorContainer or itk::MapContainer).
> 
> At first, I am trying to add one test which basically duplicates itkThreadedIteratorRangePartitionerTest for the case of itk::VectorContainer, you can find a patch here:
> 
>      http://review.source.kitware.com/#/c/20079/
> 
> I have compilation errors, due to the fact that internally itk::ThreadedIteratorRangePartitioner uses std::distance and std::advance which requires some typedefs which are not available for itk::VectorContainer iterators...
> 
> Should I keep on working in that direction? I mean to try to fix these classes for itk container's iterator (adapt it for these cases)? Make specialization?
> 
> Thanks,
> Arnaud
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

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_______________________________________________
Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From lasso at queensu.ca  Fri Aug 14 09:42:32 2015
From: lasso at queensu.ca (Andras Lasso)
Date: Fri, 14 Aug 2015 13:42:32 +0000
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error
	U1095	(command line too long)
In-Reply-To: <E8472563-D485-4D83-B8CB-F951489CFB69@semanchuk.com>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
 <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
 <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
 <E8472563-D485-4D83-B8CB-F951489CFB69@semanchuk.com>
Message-ID: <CY1PR0701MB16136A1894DEA948309C7E83D87C0@CY1PR0701MB1613.namprd07.prod.outlook.com>

Instead of commenting out the variable value passing, use CMAKE_CACHE_ARGS instead of CMAKE_ARGS.

CMAKE_ARGS can be used for passing any command-line arguments, but it uses the command line, so length limitations apply.

In contrast, CMAKE_CACHE_ARGS uses a file to pass variable values, so there is no limitation on the number or length of variables.

Andras


-----Original Message-----
From: Community [mailto:community-bounces at itk.org] On Behalf Of Philip Semanchuk
Sent: August 14, 2015 8:03 AM
To: Bradley Lowekamp <blowekamp at mail.nih.gov>
Cc: community at itk.org
Subject: Re: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095 (command line too long)

	
> On Aug 13, 2015, at 12:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> 
> OK,
> 
> Your Visual Studio should be based on VS 2008 then.
> 
> You could try commenting out this line:
> https://github.com/SimpleITK/SimpleITK/blob/1b1745da326bbb67e1752b3edbde344d15712032/SuperBuild/SuperBuild.cmake#L359
> 
> The will remove passing all the language variables on the command line to the SimpleITK sub-project. But they will still be in the initial CMakeCache. This will remove the ability to update the variables in the sub project from the super build. 

That worked! Thanks very much for your help.

Cheers
Philip




> 
> I'll investigate further, to determine if there is a better long-term solution.
> 
> HTH,
> Brad
> 
> On Aug 13, 2015, at 12:19 PM, Philip Semanchuk <ond at semanchuk.com> wrote:
> 
>> 
>>> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>> 
>>> Hello,
>>> 
>>> What version of CMake and Visual Studio are you using?
>> 
>> CMake 3.3.0. I'm using Microsoft Visual C++ for Python 2.7. That's not Visual Studio - it's not an IDE. It's just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008. 
>> 
>> 
>>> What is your build and source path?
>> 
>> Build path is c:\Users\me\sitkb
>> Source path is C:\Users\me\SimpleITK-0.9.0
>> 
>> 
>>> Also know which Super build target that's causing the problem would be helpful too.
>> 
>> The U1095 error comes here:
>> [ 84%] Performing configure step for 'SimpleITK'
>> 
>> 
>>> 
>>> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld".
>> 
>> Thanks for the suggestion. I'm aware that long paths can contribute to overly-long command lines (I've run into that problem earlier in this build process). I don't think they're the culprits here, though. 
>> 
>> The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don't control (e.g. lots of references to "C:/Program Files (x86)"). 
>> 
>> If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command. 
>> 
>> Thanks for your willingness to help. I appreciate it!
>> 
>> Philip
>> 
>> 
>>> 
>>> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
>>> 
>>>> Hi, 
>>>> I'm new to CMake and SimpleITK, and I'm trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I'm using the "SuperBuild" instructions from here:
>>>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>>>> 
>>>> I'm running into a problem where a build.make file creates a shell command that's almost 5400 characters long. This leads to:
>>>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>>>> 
>>>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>>>> 
>>>> Since I'm new to CMake and SimpleITK, I'm a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I'm in the wrong place, would someone be kind enough to guide me elsewhere?
>>>> 
>>>> I can post my build config and steps if that would help. 
>>>> 
>>>> Thanks
>>>> Philip
>>>> _______________________________________________
>>>> Community mailing list
>>>> Community at itk.org
>>>> http://public.kitware.com/mailman/listinfo/community
>>> 
>> 
> 

_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community

From ond at semanchuk.com  Fri Aug 14 10:30:48 2015
From: ond at semanchuk.com (Philip Semanchuk)
Date: Fri, 14 Aug 2015 10:30:48 -0400
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
	(command line too long)
In-Reply-To: <CY1PR0701MB16136A1894DEA948309C7E83D87C0@CY1PR0701MB1613.namprd07.prod.outlook.com>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
 <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
 <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
 <E8472563-D485-4D83-B8CB-F951489CFB69@semanchuk.com>
 <CY1PR0701MB16136A1894DEA948309C7E83D87C0@CY1PR0701MB1613.namprd07.prod.outlook.com>
Message-ID: <DDA83E9F-7E63-4E52-9480-52F15A5B109D@semanchuk.com>

Thanks Andras for the tip about CMAKE_CACHE_ARGS and to Brad for the tip about Ninja. I doubt that this is the last time I?ll run into problems with overly-long command lines on Windows so it?s nice to have a variety of techniques to deal with the problem in the future.

Cheers
Philip

> On Aug 14, 2015, at 9:42 AM, Andras Lasso <lasso at queensu.ca> wrote:
> 
> Instead of commenting out the variable value passing, use CMAKE_CACHE_ARGS instead of CMAKE_ARGS.
> 
> CMAKE_ARGS can be used for passing any command-line arguments, but it uses the command line, so length limitations apply.
> 
> In contrast, CMAKE_CACHE_ARGS uses a file to pass variable values, so there is no limitation on the number or length of variables.
> 
> Andras
> 
> 
> -----Original Message-----
> From: Community [mailto:community-bounces at itk.org] On Behalf Of Philip Semanchuk
> Sent: August 14, 2015 8:03 AM
> To: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Cc: community at itk.org
> Subject: Re: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095 (command line too long)
> 
> 	
>> On Aug 13, 2015, at 12:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> 
>> OK,
>> 
>> Your Visual Studio should be based on VS 2008 then.
>> 
>> You could try commenting out this line:
>> https://github.com/SimpleITK/SimpleITK/blob/1b1745da326bbb67e1752b3edbde344d15712032/SuperBuild/SuperBuild.cmake#L359
>> 
>> The will remove passing all the language variables on the command line to the SimpleITK sub-project. But they will still be in the initial CMakeCache. This will remove the ability to update the variables in the sub project from the super build. 
> 
> That worked! Thanks very much for your help.
> 
> Cheers
> Philip
> 
> 
> 
> 
>> 
>> I'll investigate further, to determine if there is a better long-term solution.
>> 
>> HTH,
>> Brad
>> 
>> On Aug 13, 2015, at 12:19 PM, Philip Semanchuk <ond at semanchuk.com> wrote:
>> 
>>> 
>>>> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> What version of CMake and Visual Studio are you using?
>>> 
>>> CMake 3.3.0. I'm using Microsoft Visual C++ for Python 2.7. That's not Visual Studio - it's not an IDE. It's just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008. 
>>> 
>>> 
>>>> What is your build and source path?
>>> 
>>> Build path is c:\Users\me\sitkb
>>> Source path is C:\Users\me\SimpleITK-0.9.0
>>> 
>>> 
>>>> Also know which Super build target that's causing the problem would be helpful too.
>>> 
>>> The U1095 error comes here:
>>> [ 84%] Performing configure step for 'SimpleITK'
>>> 
>>> 
>>>> 
>>>> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld".
>>> 
>>> Thanks for the suggestion. I'm aware that long paths can contribute to overly-long command lines (I've run into that problem earlier in this build process). I don't think they're the culprits here, though. 
>>> 
>>> The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don't control (e.g. lots of references to "C:/Program Files (x86)"). 
>>> 
>>> If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command. 
>>> 
>>> Thanks for your willingness to help. I appreciate it!
>>> 
>>> Philip
>>> 
>>> 
>>>> 
>>>> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
>>>> 
>>>>> Hi, 
>>>>> I'm new to CMake and SimpleITK, and I'm trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I'm using the "SuperBuild" instructions from here:
>>>>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>>>>> 
>>>>> I'm running into a problem where a build.make file creates a shell command that's almost 5400 characters long. This leads to:
>>>>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>>>>> 
>>>>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>>>>> 
>>>>> Since I'm new to CMake and SimpleITK, I'm a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I'm in the wrong place, would someone be kind enough to guide me elsewhere?
>>>>> 
>>>>> I can post my build config and steps if that would help. 
>>>>> 
>>>>> Thanks
>>>>> Philip
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/mailman/listinfo/community
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From blowekamp at mail.nih.gov  Fri Aug 14 09:37:27 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 14 Aug 2015 09:37:27 -0400
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
 (command line too long)
In-Reply-To: <E8472563-D485-4D83-B8CB-F951489CFB69@semanchuk.com>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
 <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
 <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
 <E8472563-D485-4D83-B8CB-F951489CFB69@semanchuk.com>
Message-ID: <12C0144B-5CB8-44B4-928A-FF91DFCB4998@mail.nih.gov>

Hello,

Glad it worked for you.

You also may want to look into the "ninja" build tool [1] as a replacement for nmake. It offers improved parallelization on windows, and may get around some of this command line limit issue. I have not used it on windows by self, but it comes highly recommend.

Brad

[1] https://martine.github.io/ninja/

On Aug 14, 2015, at 8:03 AM, Philip Semanchuk <ond at semanchuk.com> wrote:

> 
>> On Aug 13, 2015, at 12:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> 
>> OK,
>> 
>> Your Visual Studio should be based on VS 2008 then.
>> 
>> You could try commenting out this line:
>> https://github.com/SimpleITK/SimpleITK/blob/1b1745da326bbb67e1752b3edbde344d15712032/SuperBuild/SuperBuild.cmake#L359
>> 
>> The will remove passing all the language variables on the command line to the SimpleITK sub-project. But they will still be in the initial CMakeCache. This will remove the ability to update the variables in the sub project from the super build. 
> 
> That worked! Thanks very much for your help.
> 
> Cheers
> Philip
> 
> 
> 
> 
>> 
>> I'll investigate further, to determine if there is a better long-term solution.
>> 
>> HTH,
>> Brad
>> 
>> On Aug 13, 2015, at 12:19 PM, Philip Semanchuk <ond at semanchuk.com> wrote:
>> 
>>> 
>>>> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> What version of CMake and Visual Studio are you using?
>>> 
>>> CMake 3.3.0. I?m using Microsoft Visual C++ for Python 2.7. That's not Visual Studio ? it?s not an IDE. It?s just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008. 
>>> 
>>> 
>>>> What is your build and source path?
>>> 
>>> Build path is c:\Users\me\sitkb
>>> Source path is C:\Users\me\SimpleITK-0.9.0
>>> 
>>> 
>>>> Also know which Super build target that's causing the problem would be helpful too.
>>> 
>>> The U1095 error comes here:
>>> [ 84%] Performing configure step for 'SimpleITK'
>>> 
>>> 
>>>> 
>>>> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld?.
>>> 
>>> Thanks for the suggestion. I?m aware that long paths can contribute to overly-long command lines (I?ve run into that problem earlier in this build process). I don?t think they're the culprits here, though. 
>>> 
>>> The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don?t control (e.g. lots of references to "C:/Program Files (x86)?). 
>>> 
>>> If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command. 
>>> 
>>> Thanks for your willingness to help. I appreciate it!
>>> 
>>> Philip
>>> 
>>> 
>>>> 
>>>> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
>>>> 
>>>>> Hi, 
>>>>> I?m new to CMake and SimpleITK, and I?m trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I?m using the ?SuperBuild? instructions from here:
>>>>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>>>>> 
>>>>> I?m running into a problem where a build.make file creates a shell command that?s almost 5400 characters long. This leads to:
>>>>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>>>>> 
>>>>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>>>>> 
>>>>> Since I?m new to CMake and SimpleITK, I?m a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I?m in the wrong place, would someone be kind enough to guide me elsewhere?
>>>>> 
>>>>> I can post my build config and steps if that would help. 
>>>>> 
>>>>> Thanks
>>>>> Philip
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/mailman/listinfo/community
>>>> 
>>> 
>> 
> 


From blowekamp at mail.nih.gov  Fri Aug 14 10:32:10 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 14 Aug 2015 10:32:10 -0400
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
 (command line too long)
In-Reply-To: <CY1PR0701MB16136A1894DEA948309C7E83D87C0@CY1PR0701MB1613.namprd07.prod.outlook.com>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
 <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
 <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
 <E8472563-D485-4D83-B8CB-F951489CFB69@semanchuk.com>
 <CY1PR0701MB16136A1894DEA948309C7E83D87C0@CY1PR0701MB1613.namprd07.prod.outlook.com>
Message-ID: <B1746B21-4F8E-4B1F-B03F-A8B3FAFCB85A@mail.nih.gov>

Hello Andas,

The comment out was a quick suggestion to get it working for his case.

Here is a commit in next to reduce the arguments passed [1].

The problem with the "Cache" file is that it's only used for the initial configuration of the sub-project (still correct? It's been a while since I tested). If there is a change to the top level configuration after the initial build then the sub-projects don't get the update values. And I don't like having to rebuild SimpleITK from scratch.

Currently we render the desired cmake variables to both the cache file and to the command line arguments [2].

SimpleITK's cache generator is better than the CMAKE_CACHE_ARGS because I only need to pass the CMake variable names, and then the function uses introspection to get the variable type AND the help string. With the number of language variables passed, it's critical to get the help information into the sub-project to give information on what the variable is suppose to be.

I would hate to give up the feature of being able to update the sub-projects' variable for a rebuild. But relaying sole on the Cache would do this. And the suggested patch just does that.

Thanks for the suggestions. If there is a better way to do this I certainly like to know.

Thanks,
Brad


[1] https://github.com/SimpleITK/SimpleITK/commit/dd3c4353773944194574473569da588d535d80f6
[2] https://github.com/SimpleITK/SimpleITK/blob/master/SuperBuild/SuperBuild.cmake#L333-L338


On Aug 14, 2015, at 9:42 AM, Andras Lasso <lasso at queensu.ca> wrote:

> Instead of commenting out the variable value passing, use CMAKE_CACHE_ARGS instead of CMAKE_ARGS.
> 
> CMAKE_ARGS can be used for passing any command-line arguments, but it uses the command line, so length limitations apply.
> 
> In contrast, CMAKE_CACHE_ARGS uses a file to pass variable values, so there is no limitation on the number or length of variables.
> 
> Andras
> 
> 
> -----Original Message-----
> From: Community [mailto:community-bounces at itk.org] On Behalf Of Philip Semanchuk
> Sent: August 14, 2015 8:03 AM
> To: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Cc: community at itk.org
> Subject: Re: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095 (command line too long)
> 
> 	
>> On Aug 13, 2015, at 12:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> 
>> OK,
>> 
>> Your Visual Studio should be based on VS 2008 then.
>> 
>> You could try commenting out this line:
>> https://github.com/SimpleITK/SimpleITK/blob/1b1745da326bbb67e1752b3edbde344d15712032/SuperBuild/SuperBuild.cmake#L359
>> 
>> The will remove passing all the language variables on the command line to the SimpleITK sub-project. But they will still be in the initial CMakeCache. This will remove the ability to update the variables in the sub project from the super build. 
> 
> That worked! Thanks very much for your help.
> 
> Cheers
> Philip
> 
> 
> 
> 
>> 
>> I'll investigate further, to determine if there is a better long-term solution.
>> 
>> HTH,
>> Brad
>> 
>> On Aug 13, 2015, at 12:19 PM, Philip Semanchuk <ond at semanchuk.com> wrote:
>> 
>>> 
>>>> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> What version of CMake and Visual Studio are you using?
>>> 
>>> CMake 3.3.0. I'm using Microsoft Visual C++ for Python 2.7. That's not Visual Studio - it's not an IDE. It's just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008. 
>>> 
>>> 
>>>> What is your build and source path?
>>> 
>>> Build path is c:\Users\me\sitkb
>>> Source path is C:\Users\me\SimpleITK-0.9.0
>>> 
>>> 
>>>> Also know which Super build target that's causing the problem would be helpful too.
>>> 
>>> The U1095 error comes here:
>>> [ 84%] Performing configure step for 'SimpleITK'
>>> 
>>> 
>>>> 
>>>> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld".
>>> 
>>> Thanks for the suggestion. I'm aware that long paths can contribute to overly-long command lines (I've run into that problem earlier in this build process). I don't think they're the culprits here, though. 
>>> 
>>> The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don't control (e.g. lots of references to "C:/Program Files (x86)"). 
>>> 
>>> If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command. 
>>> 
>>> Thanks for your willingness to help. I appreciate it!
>>> 
>>> Philip
>>> 
>>> 
>>>> 
>>>> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
>>>> 
>>>>> Hi, 
>>>>> I'm new to CMake and SimpleITK, and I'm trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I'm using the "SuperBuild" instructions from here:
>>>>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>>>>> 
>>>>> I'm running into a problem where a build.make file creates a shell command that's almost 5400 characters long. This leads to:
>>>>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>>>>> 
>>>>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>>>>> 
>>>>> Since I'm new to CMake and SimpleITK, I'm a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I'm in the wrong place, would someone be kind enough to guide me elsewhere?
>>>>> 
>>>>> I can post my build config and steps if that would help. 
>>>>> 
>>>>> Thanks
>>>>> Philip
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/mailman/listinfo/community
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From lasso at queensu.ca  Fri Aug 14 11:05:10 2015
From: lasso at queensu.ca (Andras Lasso)
Date: Fri, 14 Aug 2015 15:05:10 +0000
Subject: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095
 (command line too long)
In-Reply-To: <B1746B21-4F8E-4B1F-B03F-A8B3FAFCB85A@mail.nih.gov>
References: <6DD2E18E-1CD9-460E-8ECA-540260FB971F@semanchuk.com>
 <FF776EFB-2E10-455F-8A17-9C8AA463F82F@mail.nih.gov>
 <B198C7D5-04FC-4714-A876-E05F6B942738@semanchuk.com>
 <44C7401D-7AEB-4E09-9ECE-9BE070B6D9D0@mail.nih.gov>
 <E8472563-D485-4D83-B8CB-F951489CFB69@semanchuk.com>
 <CY1PR0701MB16136A1894DEA948309C7E83D87C0@CY1PR0701MB1613.namprd07.prod.outlook.com>,
 <B1746B21-4F8E-4B1F-B03F-A8B3FAFCB85A@mail.nih.gov>
Message-ID: <CY1PR0701MB16135A6626CD19EA85CAF5C8D87C0@CY1PR0701MB1613.namprd07.prod.outlook.com>

Thanks for the explanation. I didn't know that -C is for initial configuration only.

Command line length is limited on all operating systems (although on Windows it's shorter than most *nix, so problems appear first there). A possible solution to keep the current SimpleITK configuration mechanism would be to use response files (pass command-line arguments through file) when running CMake. For this we would need to request this feature in CMake and then update ExternalProject_Add macro to use response file.

Andras
________________________________
From: Bradley Lowekamp<mailto:blowekamp at mail.nih.gov>
Sent: ?2015-?08-?14 10:33
To: Andras Lasso<mailto:lasso at queensu.ca>; Jean-Christophe Fillion-Robin<mailto:jchris.fillionr at kitware.com>
Cc: Philip Semanchuk<mailto:ond at semanchuk.com>; community at itk.org<mailto:community at itk.org>
Subject: Re: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095 (command line too long)

Hello Andas,

The comment out was a quick suggestion to get it working for his case.

Here is a commit in next to reduce the arguments passed [1].

The problem with the "Cache" file is that it's only used for the initial configuration of the sub-project (still correct? It's been a while since I tested). If there is a change to the top level configuration after the initial build then the sub-projects don't get the update values. And I don't like having to rebuild SimpleITK from scratch.

Currently we render the desired cmake variables to both the cache file and to the command line arguments [2].

SimpleITK's cache generator is better than the CMAKE_CACHE_ARGS because I only need to pass the CMake variable names, and then the function uses introspection to get the variable type AND the help string. With the number of language variables passed, it's critical to get the help information into the sub-project to give information on what the variable is suppose to be.

I would hate to give up the feature of being able to update the sub-projects' variable for a rebuild. But relaying sole on the Cache would do this. And the suggested patch just does that.

Thanks for the suggestions. If there is a better way to do this I certainly like to know.

Thanks,
Brad


[1] https://github.com/SimpleITK/SimpleITK/commit/dd3c4353773944194574473569da588d535d80f6
[2] https://github.com/SimpleITK/SimpleITK/blob/master/SuperBuild/SuperBuild.cmake#L333-L338


On Aug 14, 2015, at 9:42 AM, Andras Lasso <lasso at queensu.ca> wrote:

> Instead of commenting out the variable value passing, use CMAKE_CACHE_ARGS instead of CMAKE_ARGS.
>
> CMAKE_ARGS can be used for passing any command-line arguments, but it uses the command line, so length limitations apply.
>
> In contrast, CMAKE_CACHE_ARGS uses a file to pass variable values, so there is no limitation on the number or length of variables.
>
> Andras
>
>
> -----Original Message-----
> From: Community [mailto:community-bounces at itk.org] On Behalf Of Philip Semanchuk
> Sent: August 14, 2015 8:03 AM
> To: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Cc: community at itk.org
> Subject: Re: [ITK] Win64 SimpleITK build error: NMAKE : fatal error U1095 (command line too long)
>
>
>> On Aug 13, 2015, at 12:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>
>> OK,
>>
>> Your Visual Studio should be based on VS 2008 then.
>>
>> You could try commenting out this line:
>> https://github.com/SimpleITK/SimpleITK/blob/1b1745da326bbb67e1752b3edbde344d15712032/SuperBuild/SuperBuild.cmake#L359
>>
>> The will remove passing all the language variables on the command line to the SimpleITK sub-project. But they will still be in the initial CMakeCache. This will remove the ability to update the variables in the sub project from the super build.
>
> That worked! Thanks very much for your help.
>
> Cheers
> Philip
>
>
>
>
>>
>> I'll investigate further, to determine if there is a better long-term solution.
>>
>> HTH,
>> Brad
>>
>> On Aug 13, 2015, at 12:19 PM, Philip Semanchuk <ond at semanchuk.com> wrote:
>>
>>>
>>>> On Aug 13, 2015, at 11:53 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>>
>>>> Hello,
>>>>
>>>> What version of CMake and Visual Studio are you using?
>>>
>>> CMake 3.3.0. I'm using Microsoft Visual C++ for Python 2.7. That's not Visual Studio - it's not an IDE. It's just a compiler, specifically a repackaged version of the compiler that came with Visual C++ 2008.
>>>
>>>
>>>> What is your build and source path?
>>>
>>> Build path is c:\Users\me\sitkb
>>> Source path is C:\Users\me\SimpleITK-0.9.0
>>>
>>>
>>>> Also know which Super build target that's causing the problem would be helpful too.
>>>
>>> The U1095 error comes here:
>>> [ 84%] Performing configure step for 'SimpleITK'
>>>
>>>
>>>>
>>>> Try have having your build and your source in a really short paths like "C:/b/SimpleITK" and "C:/b/bld".
>>>
>>> Thanks for the suggestion. I'm aware that long paths can contribute to overly-long command lines (I've run into that problem earlier in this build process). I don't think they're the culprits here, though.
>>>
>>> The problem IMHO is that there are 105 variables being passed on the command line via -D (e.g. MAKE COMMAND, CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO, Java_JAVAC_EXECUTABLE, CSHARP_COMPILER, etc.), a lot of them containing paths that I don't control (e.g. lots of references to "C:/Program Files (x86)").
>>>
>>> If I paste the offending command into a text editor and search/replace my build and source paths with the shortest possible versions I can use, the command is still 5179 characters long. I think whatever buffer is getting blown out by a 5400 character command is still going to get blown out by a 5179 character command.
>>>
>>> Thanks for your willingness to help. I appreciate it!
>>>
>>> Philip
>>>
>>>
>>>>
>>>> On Aug 13, 2015, at 11:22 AM, Philip Semanchuk <ond at semanchuk.com> wrote:
>>>>
>>>>> Hi,
>>>>> I'm new to CMake and SimpleITK, and I'm trying to use the former to build a 64-bit version of the latter on Windows 7 with Microsoft Visual C++ for Python 2.7. I'm using the "SuperBuild" instructions from here:
>>>>> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
>>>>>
>>>>> I'm running into a problem where a build.make file creates a shell command that's almost 5400 characters long. This leads to:
>>>>> NMAKE : fatal error U1095: expanded command line [blah blah blah x 5400] too long
>>>>>
>>>>> The root cause of the problem is that all of the CMake config variables are being passed on the command line (e.g,. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DCMAKE_MAKE_PROGRAM:STRING=nmake etc.).
>>>>>
>>>>> Since I'm new to CMake and SimpleITK, I'm a little lost as to where I should look to resolve this problem, but my hunch is that I should start with SimpleITK. If I'm in the wrong place, would someone be kind enough to guide me elsewhere?
>>>>>
>>>>> I can post my build config and steps if that would help.
>>>>>
>>>>> Thanks
>>>>> Philip
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/mailman/listinfo/community
>>>>
>>>
>>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

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From fotosentido at gmail.com  Fri Aug 14 11:57:45 2015
From: fotosentido at gmail.com (Marcos)
Date: Fri, 14 Aug 2015 17:57:45 +0200
Subject: [ITK] [ITK-users] Brand new project with itk sentence with
	QtCreator, Qt5 and Cmake crashes
Message-ID: <CAA24WvH3crVTsadBNf8m6HpU3pixoChTKtycfqLE-5rpDsL2zA@mail.gmail.com>

Hi,

I'm just trying to make a Cmake project compile and debug. Nothing else.
I've spent hours trying different things.

It's just a first try to start coding, but it doesn't work. I explain
everything in detail, that's why this post is so long, but I just want to
remark I'm just trying to setup ITK. Nothing else.


I've tried with the .pro configuration. It compiles, until I use some itk
object, then it returns:
unresolved external symbol...: itksys-4.8.lib (it's included in the .pro
file)


So I'm trying with Cmake. Everbody recommends it, but I didn't see a
straight tutorial to set up a simple project with QtCreator and Qt5. So I'm
trying it myself.

I'm using Windows 7, compiling and installing with Visual Studio 2013.
I've compiled and installed successfully VTK first and then ITK (checking
ITVVTKGlue).

I have built them in:
C:\VTK-6.2.0-build
C:\ITK-4.8.0-build

I have them installed in:

C:\VTK-6.2.0-installed
C:\ITK-4.8.0-installed
(Each one has the subdirectories \bin, \include, \lib and \share)

So, I created a QT5 Widgets project from QtCreator, then I added a
CMakeLists.txt containing:

CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
>
>
> PROJECT (UtilityDICOM)
>
>
> SET(CMAKE_INCLUDE_CURRENT_DIR ON)
>
> SET(CMAKE_AUTOMOC ON)
>
>
> FIND_PACKAGE(Qt5Widgets REQUIRED)
>
>
> # VTK
>
> #SET(VTK_DIR "C:\\VTK-6.2.0-build\\")
>
>
> # ITK
>
> #SET(ITK_DIR "C:\\ITK-4.8.0-build\\")
>
> FIND_PACKAGE(ITK REQUIRED)
>
> INCLUDE(${ITK_USE_FILE})
>
>
> IF (ItkVtkGlue_LOADED)
>
>     FIND_PACKAGE(VTK REQUIRED)
>
>     INCLUDE(${VTK_USE_FILE})
>
> ENDIF()
>
>
>
> ADD_EXECUTABLE(UtilityDICOM WIN32 main.cpp mainwindow.cpp)
>
>
> TARGET_LINK_LIBRARIES(UtilityDICOM Qt5::Widgets ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES})
>
>


It returns the error:

CMake Error at CMakeLists.txt:15 (FIND_PACKAGE):

By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has

asked CMake to find a package configuration file provided by "ITK", but

CMake did not find one.


Could not find a package configuration file provided by "ITK" with any of

the following names:


ITKConfig.cmake

itk-config.cmake


Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set "ITK_DIR"

to a directory containing one of the above files. If "ITK" provides a

separate development package or SDK, be sure it has been installed.




Ok, so I uncommented the lines you see. Why do I added the build folders
and not the installed folders? Because I got the same error with the
installed dirs.

After doing that, it compiled, but I got another error when launching:

C:\Users\M\Documents\REPOSITORIO\trunk\UtilidadDICOM\mainwindow.cpp:2:
error: C1083: Cannot open include file: 'ui_mainwindow.h': No such file or
directory

Searching for an answer, I found something here:
https://chan20kaur.wordpress.com/tag/qt-and-cmake/

I changed my CMakeLists.txt to:

CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
>
>
> PROJECT (UtilityDICOM)
>
>
> FIND_PACKAGE(Qt5Widgets REQUIRED)
>
>
> SET(CMAKE_INCLUDE_CURRENT_DIR ON)
>
> SET(CMAKE_AUTOMOC ON)
>
>
> QT5_WRAP_UI(Cmake_form_hdr mainwindow.ui)
>
> add_library(mainwindow mainwindow.cpp ${Cmake_form_hdr})
>
> qt5_use_modules(mainwindow Widgets)
>
>
> # VTK
>
> SET(VTK_DIR "C:\\VTK-6.2.0-build\\")
>
>
> # ITK
>
> SET(ITK_DIR "C:\\ITK-4.8.0-build\\")
>
> FIND_PACKAGE(ITK REQUIRED)
>
> INCLUDE(${ITK_USE_FILE})
>
>
> IF (ItkVtkGlue_LOADED)
>
>     FIND_PACKAGE(VTK REQUIRED)
>
>     INCLUDE(${VTK_USE_FILE})
>
> ENDIF()
>
>
>
> ADD_EXECUTABLE(UtilityDICOM WIN32 main.cpp)
>
> TARGET_LINK_LIBRARIES(UtilityDICOM mainwindow ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES})
>
> QT5_USE_MODULES(UtilityDICOM Core Gui Widgets)
>
>

With this, I compile. And I can launch the executable.


So I added a ITK line. In main.cpp, I added in main method:

itk::Object::GlobalWarningDisplayOff();
>

including

#include <itkObject.h>
>

Just that. By the way, the editor autocompletes this include. And I got:

Starting
> C:\Users\M\Documents\REPOSITORIO\trunk\UtilidadDICOM-build\UtilityDICOM.exe...

The program has unexpectedly finished.


Ok, what now? I just added ONE LINE.

I don't have any clues.

I tought maybe it could be that method.

So I changed my modification to:



typedef itk::Image< double, 2 > ImageType;

typedef itk::ImageFileReader<ImageType> ReaderType;


ReaderType::Pointer reader = ReaderType::New();

with
#include <itkImageFileReader.h>


Same result.
I don't know what to do, really. I read
blogs, wiki entries,... I spent days trying to use this, what am I doing
 wrong? Am I missing something?

I will keep trying, but it's so frustating not being able to even start coding.
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From matt.mccormick at kitware.com  Fri Aug 14 12:04:40 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 14 Aug 2015 12:04:40 -0400
Subject: [ITK] [ITK-users] Brand new project with itk sentence with
 QtCreator, Qt5 and Cmake crashes
In-Reply-To: <CAA24WvH3crVTsadBNf8m6HpU3pixoChTKtycfqLE-5rpDsL2zA@mail.gmail.com>
References: <CAA24WvH3crVTsadBNf8m6HpU3pixoChTKtycfqLE-5rpDsL2zA@mail.gmail.com>
Message-ID: <CALzTN-SUo5LPJdS273Lo-34CSYXW0dmQNg594GtgH=UwDrGsOQ@mail.gmail.com>

Hi Marcos,

On Fri, Aug 14, 2015 at 11:57 AM, Marcos <fotosentido at gmail.com> wrote:
> Hi,
>
> I'm just trying to make a Cmake project compile and debug.

>
> I have them installed in:
>
> C:\VTK-6.2.0-installed
> C:\ITK-4.8.0-installed
> (Each one has the subdirectories \bin, \include, \lib and \share)
>
> So, I created a QT5 Widgets project from QtCreator, then I added a
> CMakeLists.txt containing:
>
>> CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
>>
>>
>> PROJECT (UtilityDICOM)
>>
>>
>> SET(CMAKE_INCLUDE_CURRENT_DIR ON)
>>
>> SET(CMAKE_AUTOMOC ON)
>>
>>
>> FIND_PACKAGE(Qt5Widgets REQUIRED)
>>
>>
>> # VTK
>>
>> #SET(VTK_DIR "C:\\VTK-6.2.0-build\\")
>>
>>
>> # ITK
>>
>> #SET(ITK_DIR "C:\\ITK-4.8.0-build\\")
>>
>> FIND_PACKAGE(ITK REQUIRED)
>>
>> INCLUDE(${ITK_USE_FILE})
>>
>>
>> IF (ItkVtkGlue_LOADED)
>>
>>     FIND_PACKAGE(VTK REQUIRED)
>>
>>     INCLUDE(${VTK_USE_FILE})
>>
>> ENDIF()
>>
>>
>>
>> ADD_EXECUTABLE(UtilityDICOM WIN32 main.cpp mainwindow.cpp)
>>
>>
>> TARGET_LINK_LIBRARIES(UtilityDICOM Qt5::Widgets ${Glue} ${VTK_LIBRARIES}
>> ${ITK_LIBRARIES})
>
>
>
>
> It returns the error:
>
>> CMake Error at CMakeLists.txt:15 (FIND_PACKAGE):
>
> By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has
>
> asked CMake to find a package configuration file provided by "ITK", but
>
> CMake did not find one.
>
>
> Could not find a package configuration file provided by "ITK" with any of
>
> the following names:
>
>
> ITKConfig.cmake
>
> itk-config.cmake
>
>
> Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set "ITK_DIR"
>
> to a directory containing one of the above files. If "ITK" provides a
>
> separate development package or SDK, be sure it has been installed.


This means that in your CMake configuration, set ITK_DIR to
C:\ITK-4.8.0-installed.


For more details, see the Configuring and Building ITK section of the
ITK Software Guide:

http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html

"Both the terminal-based and GUI versions of CMake will require you to
specify the directory where ITK was built in the CMake variable
ITK_DIR. The ITK binary directory will contain a file named
ITKConfig.cmake generated during ITK configuration process with CMake.
>From this file, CMake will recover all information required to
configure your new ITK project."


Hope this helps,
Matt
_____________________________________
Powered by www.kitware.com

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http://www.kitware.com/opensource/opensource.html

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From matt.mccormick at kitware.com  Fri Aug 14 12:11:48 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 14 Aug 2015 12:11:48 -0400
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
Message-ID: <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>

Hi Arnaud,

Yes, you are probably right.  The suggestion by Zach in this patch (to
use DEPENDS) is promising:

  http://review.source.kitware.com/#/c/20078/

Thanks,
Matt

On Fri, Aug 14, 2015 at 2:21 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Hi Matt,
>
> It happened while directly building ITK with OpenCV 2.4.9, without any
> superbuild...
> Thanks for the patch, but that does not solve it...
>
> I wonder if it could have something to do with the new linking system (note
> it uses COMPILE_DEPENDS) ?
>
> Thanks,
> Arnaud
>
> On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi Arnaud,
>>
>> Is this with building the examples with the superbuild?  I think I was
>> getting this error, too.  Here is a patch that should address it:
>>
>>   http://review.source.kitware.com/#/c/20077/
>>
>> Thanks,
>> Matt
>>
>> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>> wrote:
>> > Hi all,
>> >
>> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I
>> > get
>> > the following link error
>> >
>> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1
>> >
>> > [...]
>> >
>> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> > 'itk::VideoIOBase::VideoIOBase()'
>> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> > 'itk::VideoIOBase::~VideoIOBase()'
>> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const'
>> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> > 'typeinfo for itk::VideoIOBase'
>> > collect2: error: ld returned 1 exit status
>> >
>> > I have checked these methods are implemented in itkVideoIOBase.cxx...
>> >
>> > Any idea?
>> >
>> > Thanks
>> > Arnaud
>> >
>> > _______________________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-developers
>> >
>
>
_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From fotosentido at gmail.com  Fri Aug 14 12:20:06 2015
From: fotosentido at gmail.com (Marcos)
Date: Fri, 14 Aug 2015 18:20:06 +0200
Subject: [ITK] [ITK-users] Brand new project with itk sentence with
 QtCreator, Qt5 and Cmake crashes
In-Reply-To: <CALzTN-SUo5LPJdS273Lo-34CSYXW0dmQNg594GtgH=UwDrGsOQ@mail.gmail.com>
References: <CAA24WvH3crVTsadBNf8m6HpU3pixoChTKtycfqLE-5rpDsL2zA@mail.gmail.com>
 <CALzTN-SUo5LPJdS273Lo-34CSYXW0dmQNg594GtgH=UwDrGsOQ@mail.gmail.com>
Message-ID: <CAA24WvEkFuMegmKe9_NshTOJJpaKOn7Fz3OY51F0Gv+YsLZsAw@mail.gmail.com>

As I said, I did that, I set the ITK_DIR to the directory where I installed.

In fact, there is a ITKConfig.cmake in
C:\ITK-4.8.0-installed\lib\cmake\ITK-4.8

and my CMakeLists.txt has a line like this:
SET(ITK_DIR "C:\\ITK-4.8.0-installed\\")

but that way it doesn't find it.


I didn't have problems building ITK, the problem is trying to use it.

Maybe it's not installed correctly, but Visual Studio did it without
problems.

Thank you.



2015-08-14 18:04 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Marcos,
>
> On Fri, Aug 14, 2015 at 11:57 AM, Marcos <fotosentido at gmail.com> wrote:
> > Hi,
> >
> > I'm just trying to make a Cmake project compile and debug.
>
> >
> > I have them installed in:
> >
> > C:\VTK-6.2.0-installed
> > C:\ITK-4.8.0-installed
> > (Each one has the subdirectories \bin, \include, \lib and \share)
> >
> > So, I created a QT5 Widgets project from QtCreator, then I added a
> > CMakeLists.txt containing:
> >
> >> CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
> >>
> >>
> >> PROJECT (UtilityDICOM)
> >>
> >>
> >> SET(CMAKE_INCLUDE_CURRENT_DIR ON)
> >>
> >> SET(CMAKE_AUTOMOC ON)
> >>
> >>
> >> FIND_PACKAGE(Qt5Widgets REQUIRED)
> >>
> >>
> >> # VTK
> >>
> >> #SET(VTK_DIR "C:\\VTK-6.2.0-build\\")
> >>
> >>
> >> # ITK
> >>
> >> #SET(ITK_DIR "C:\\ITK-4.8.0-build\\")
> >>
> >> FIND_PACKAGE(ITK REQUIRED)
> >>
> >> INCLUDE(${ITK_USE_FILE})
> >>
> >>
> >> IF (ItkVtkGlue_LOADED)
> >>
> >>     FIND_PACKAGE(VTK REQUIRED)
> >>
> >>     INCLUDE(${VTK_USE_FILE})
> >>
> >> ENDIF()
> >>
> >>
> >>
> >> ADD_EXECUTABLE(UtilityDICOM WIN32 main.cpp mainwindow.cpp)
> >>
> >>
> >> TARGET_LINK_LIBRARIES(UtilityDICOM Qt5::Widgets ${Glue} ${VTK_LIBRARIES}
> >> ${ITK_LIBRARIES})
> >
> >
> >
> >
> > It returns the error:
> >
> >> CMake Error at CMakeLists.txt:15 (FIND_PACKAGE):
> >
> > By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has
> >
> > asked CMake to find a package configuration file provided by "ITK", but
> >
> > CMake did not find one.
> >
> >
> > Could not find a package configuration file provided by "ITK" with any of
> >
> > the following names:
> >
> >
> > ITKConfig.cmake
> >
> > itk-config.cmake
> >
> >
> > Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set
> "ITK_DIR"
> >
> > to a directory containing one of the above files. If "ITK" provides a
> >
> > separate development package or SDK, be sure it has been installed.
>
>
> This means that in your CMake configuration, set ITK_DIR to
> C:\ITK-4.8.0-installed.
>
>
> For more details, see the Configuring and Building ITK section of the
> ITK Software Guide:
>
> http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html
>
> "Both the terminal-based and GUI versions of CMake will require you to
> specify the directory where ITK was built in the CMake variable
> ITK_DIR. The ITK binary directory will contain a file named
> ITKConfig.cmake generated during ITK configuration process with CMake.
> From this file, CMake will recover all information required to
> configure your new ITK project."
>
>
> Hope this helps,
> Matt
>
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_____________________________________
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Visit other Kitware open-source projects at
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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

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From arnaudgelas at gmail.com  Fri Aug 14 12:24:59 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 14 Aug 2015 18:24:59 +0200
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
 <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
Message-ID: <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>

I have already tried it, does not solve it... I will retry it with a fresh
build once again...

On Fri, Aug 14, 2015 at 6:11 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Arnaud,
>
> Yes, you are probably right.  The suggestion by Zach in this patch (to
> use DEPENDS) is promising:
>
>   http://review.source.kitware.com/#/c/20078/
>
> Thanks,
> Matt
>
> On Fri, Aug 14, 2015 at 2:21 AM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
> > Hi Matt,
> >
> > It happened while directly building ITK with OpenCV 2.4.9, without any
> > superbuild...
> > Thanks for the patch, but that does not solve it...
> >
> > I wonder if it could have something to do with the new linking system
> (note
> > it uses COMPILE_DEPENDS) ?
> >
> > Thanks,
> > Arnaud
> >
> > On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick <
> matt.mccormick at kitware.com>
> > wrote:
> >>
> >> Hi Arnaud,
> >>
> >> Is this with building the examples with the superbuild?  I think I was
> >> getting this error, too.  Here is a patch that should address it:
> >>
> >>   http://review.source.kitware.com/#/c/20077/
> >>
> >> Thanks,
> >> Matt
> >>
> >> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas <arnaudgelas at gmail.com>
> >> wrote:
> >> > Hi all,
> >> >
> >> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I
> >> > get
> >> > the following link error
> >> >
> >> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1
> >> >
> >> > [...]
> >> >
> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> >> > 'itk::VideoIOBase::VideoIOBase()'
> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> >> > 'itk::VideoIOBase::~VideoIOBase()'
> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> >> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const'
> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
> >> > 'typeinfo for itk::VideoIOBase'
> >> > collect2: error: ld returned 1 exit status
> >> >
> >> > I have checked these methods are implemented in itkVideoIOBase.cxx...
> >> >
> >> > Any idea?
> >> >
> >> > Thanks
> >> > Arnaud
> >> >
> >> > _______________________________________________
> >> > Powered by www.kitware.com
> >> >
> >> > Visit other Kitware open-source projects at
> >> > http://www.kitware.com/opensource/opensource.html
> >> >
> >> > Kitware offers ITK Training Courses, for more information visit:
> >> > http://kitware.com/products/protraining.php
> >> >
> >> > Please keep messages on-topic and check the ITK FAQ at:
> >> > http://www.itk.org/Wiki/ITK_FAQ
> >> >
> >> > Follow this link to subscribe/unsubscribe:
> >> > http://public.kitware.com/mailman/listinfo/insight-developers
> >> >
> >
> >
>
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_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From arnaudgelas at gmail.com  Fri Aug 14 12:34:46 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 14 Aug 2015 18:34:46 +0200
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
 <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
 <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>
Message-ID: <CAK3qF+888dOBB_QvhzbixSbgWMkqZRXAEKaM6d47SYxnmE61Rw@mail.gmail.com>

Here is the resulting link error:

[1563/1563] Linking CXX executable bin/ITKVideoBridgeOpenCVTestDriver
FAILED: : && /usr/lib/ccache/c++   -Wall -Wextra  -Wall -Wcast-align
-Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch
-Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
-funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof
-Woverloaded-virtual -Wstrict-null-sentinel  -Wno-array-bounds -msse2 -g
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/ITKVideoBridgeOpenCVTestDriver.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeGrayScaleTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeRGBTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOFactoryTest.cxx.o
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVBasicTypeBridgeTest.cxx.o
-o bin/ITKVideoBridgeOpenCVTestDriver  -rdynamic
lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1
lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1
lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1
lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1
lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1
lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1
lib/libITKVideoBridgeOpenCV-4.9.so.1
/home/arnaud/install/lib/libopencv_videostab.so.2.4.9
/home/arnaud/install/lib/libopencv_video.so.2.4.9
/home/arnaud/install/lib/libopencv_ts.a
/home/arnaud/install/lib/libopencv_superres.so.2.4.9
/home/arnaud/install/lib/libopencv_stitching.so.2.4.9
/home/arnaud/install/lib/libopencv_photo.so.2.4.9
/home/arnaud/install/lib/libopencv_ocl.so.2.4.9
/home/arnaud/install/lib/libopencv_objdetect.so.2.4.9
/home/arnaud/install/lib/libopencv_nonfree.so.2.4.9
/home/arnaud/install/lib/libopencv_ml.so.2.4.9
/home/arnaud/install/lib/libopencv_legacy.so.2.4.9
/home/arnaud/install/lib/libopencv_imgproc.so.2.4.9
/home/arnaud/install/lib/libopencv_highgui.so.2.4.9
/home/arnaud/install/lib/libopencv_gpu.so.2.4.9
/home/arnaud/install/lib/libopencv_flann.so.2.4.9
/home/arnaud/install/lib/libopencv_features2d.so.2.4.9
/home/arnaud/install/lib/libopencv_core.so.2.4.9
/home/arnaud/install/lib/libopencv_contrib.so.2.4.9
/home/arnaud/install/lib/libopencv_calib3d.so.2.4.9
lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1
lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1
lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1
lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1
lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1
lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1
-lpthread -lrt -ltbb /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9
/home/arnaud/install/lib/libopencv_ocl.so.2.4.9
/home/arnaud/install/lib/libopencv_gpu.so.2.4.9
/home/arnaud/install/lib/libopencv_photo.so.2.4.9
/home/arnaud/install/lib/libopencv_objdetect.so.2.4.9
/home/arnaud/install/lib/libopencv_legacy.so.2.4.9
/home/arnaud/install/lib/libopencv_video.so.2.4.9
/home/arnaud/install/lib/libopencv_ml.so.2.4.9
/home/arnaud/install/lib/libopencv_calib3d.so.2.4.9
/home/arnaud/install/lib/libopencv_features2d.so.2.4.9
/home/arnaud/install/lib/libopencv_highgui.so.2.4.9
/home/arnaud/install/lib/libopencv_imgproc.so.2.4.9
/home/arnaud/install/lib/libopencv_flann.so.2.4.9
/home/arnaud/install/lib/libopencv_core.so.2.4.9 lib/libITKVideoIO-4.9.so.1
lib/libITKIOImageBase-4.9.so.1 lib/libITKVideoCore-4.9.so.1
lib/libITKCommon-4.9.so.1 lib/libitkdouble-conversion-4.9.so.1
lib/libitksys-4.9.so.1 lib/libITKVNLInstantiation-4.9.so.1
lib/libitkvnl_algo-4.9.so.1 lib/libitkv3p_lsqr-4.9.so.1
lib/libitkvnl-4.9.so.1 lib/libitkvcl-4.9.so.1 lib/libitkv3p_netlib-4.9.so.1
-lm -lpthread -lm -ldl
-Wl,-rpath,/home/arnaud/source/build-itk/lib:/home/arnaud/install/lib
-Wl,-rpath-link,/home/arnaud/source/build-itk/lib && :
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o:
In function `itk::OpenCVVideoIOFactory::New()':
/home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIOFactory.h:46:
undefined reference to `itk::OpenCVVideoIOFactory::OpenCVVideoIOFactory()'
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o:
In function `itk::OpenCVVideoIO::New()':
/home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIO.h:48:
undefined reference to `itk::OpenCVVideoIO::OpenCVVideoIO()'
Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o:
In function `itk::ObjectFactory<itk::OpenCVVideoIO>::Create()':
/home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:60:
undefined reference to `typeinfo for itk::OpenCVVideoIO'
/home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:62:
undefined reference to `typeinfo for itk::OpenCVVideoIO'
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.


On Fri, Aug 14, 2015 at 6:24 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> I have already tried it, does not solve it... I will retry it with a fresh
> build once again...
>
> On Fri, Aug 14, 2015 at 6:11 PM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> Hi Arnaud,
>>
>> Yes, you are probably right.  The suggestion by Zach in this patch (to
>> use DEPENDS) is promising:
>>
>>   http://review.source.kitware.com/#/c/20078/
>>
>> Thanks,
>> Matt
>>
>> On Fri, Aug 14, 2015 at 2:21 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>> wrote:
>> > Hi Matt,
>> >
>> > It happened while directly building ITK with OpenCV 2.4.9, without any
>> > superbuild...
>> > Thanks for the patch, but that does not solve it...
>> >
>> > I wonder if it could have something to do with the new linking system
>> (note
>> > it uses COMPILE_DEPENDS) ?
>> >
>> > Thanks,
>> > Arnaud
>> >
>> > On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick <
>> matt.mccormick at kitware.com>
>> > wrote:
>> >>
>> >> Hi Arnaud,
>> >>
>> >> Is this with building the examples with the superbuild?  I think I was
>> >> getting this error, too.  Here is a patch that should address it:
>> >>
>> >>   http://review.source.kitware.com/#/c/20077/
>> >>
>> >> Thanks,
>> >> Matt
>> >>
>> >> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>> >> wrote:
>> >> > Hi all,
>> >> >
>> >> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and
>> I
>> >> > get
>> >> > the following link error
>> >> >
>> >> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1
>> >> >
>> >> > [...]
>> >> >
>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> >> > 'itk::VideoIOBase::VideoIOBase()'
>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> >> > 'itk::VideoIOBase::~VideoIOBase()'
>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> >> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const'
>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>> >> > 'typeinfo for itk::VideoIOBase'
>> >> > collect2: error: ld returned 1 exit status
>> >> >
>> >> > I have checked these methods are implemented in itkVideoIOBase.cxx...
>> >> >
>> >> > Any idea?
>> >> >
>> >> > Thanks
>> >> > Arnaud
>> >> >
>> >> > _______________________________________________
>> >> > Powered by www.kitware.com
>> >> >
>> >> > Visit other Kitware open-source projects at
>> >> > http://www.kitware.com/opensource/opensource.html
>> >> >
>> >> > Kitware offers ITK Training Courses, for more information visit:
>> >> > http://kitware.com/products/protraining.php
>> >> >
>> >> > Please keep messages on-topic and check the ITK FAQ at:
>> >> > http://www.itk.org/Wiki/ITK_FAQ
>> >> >
>> >> > Follow this link to subscribe/unsubscribe:
>> >> > http://public.kitware.com/mailman/listinfo/insight-developers
>> >> >
>> >
>> >
>>
>
>
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From arnaudgelas at gmail.com  Fri Aug 14 13:31:39 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 14 Aug 2015 19:31:39 +0200
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <BLUPR04MB676A303299B420A41A98EBA9B7C0@BLUPR04MB676.namprd04.prod.outlook.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
 <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
 <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>
 <CAK3qF+888dOBB_QvhzbixSbgWMkqZRXAEKaM6d47SYxnmE61Rw@mail.gmail.com>
 <BLUPR04MB676A303299B420A41A98EBA9B7C0@BLUPR04MB676.namprd04.prod.outlook.com>
Message-ID: <CAK3qF+_8i6t-5mVLqXU_uaA6WFnaMt+fbPAuGQumdtm+1218=g@mail.gmail.com>

I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not make
much sense to me?), same link error...

If it helps, I can prepare a docker build file to track this error (for
anyone willing to help)?

Thanks

On Fri, Aug 14, 2015 at 6:59 PM, Williamson, Zachary E <
zachary-williamson at uiowa.edu> wrote:

> It's the test driver that is failing here, make sure that all of the
> modules needed for the tests are included under TEST_DEPENDS.
>
>
> ------------------------------
> *From:* Arnaud Gelas <arnaudgelas at gmail.com>
> *Sent:* Friday, August 14, 2015 11:34 AM
> *To:* Matt McCormick
> *Cc:* insight-developers at itk.org; Williamson, Zachary E
> *Subject:* Re: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on
> Ubuntu 14.04
>
> Here is the resulting link error:
>
> [1563/1563] Linking CXX executable bin/ITKVideoBridgeOpenCVTestDriver
> FAILED: : && /usr/lib/ccache/c++   -Wall -Wextra  -Wall -Wcast-align
> -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch
> -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
> -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof
> -Woverloaded-virtual -Wstrict-null-sentinel  -Wno-array-bounds -msse2 -g
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/ITKVideoBridgeOpenCVTestDriver.cxx.o
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeGrayScaleTest.cxx.o
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeRGBTest.cxx.o
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOFactoryTest.cxx.o
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVBasicTypeBridgeTest.cxx.o
> -o bin/ITKVideoBridgeOpenCVTestDriver  -rdynamic
> lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1
> lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1
> lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1
> lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1
> lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1
> lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1
> lib/libITKVideoBridgeOpenCV-4.9.so.1
> /home/arnaud/install/lib/libopencv_videostab.so.2.4.9
> /home/arnaud/install/lib/libopencv_video.so.2.4.9
> /home/arnaud/install/lib/libopencv_ts.a
> /home/arnaud/install/lib/libopencv_superres.so.2.4.9
> /home/arnaud/install/lib/libopencv_stitching.so.2.4.9
> /home/arnaud/install/lib/libopencv_photo.so.2.4.9
> /home/arnaud/install/lib/libopencv_ocl.so.2.4.9
> /home/arnaud/install/lib/libopencv_objdetect.so.2.4.9
> /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9
> /home/arnaud/install/lib/libopencv_ml.so.2.4.9
> /home/arnaud/install/lib/libopencv_legacy.so.2.4.9
> /home/arnaud/install/lib/libopencv_imgproc.so.2.4.9
> /home/arnaud/install/lib/libopencv_highgui.so.2.4.9
> /home/arnaud/install/lib/libopencv_gpu.so.2.4.9
> /home/arnaud/install/lib/libopencv_flann.so.2.4.9
> /home/arnaud/install/lib/libopencv_features2d.so.2.4.9
> /home/arnaud/install/lib/libopencv_core.so.2.4.9
> /home/arnaud/install/lib/libopencv_contrib.so.2.4.9
> /home/arnaud/install/lib/libopencv_calib3d.so.2.4.9
> lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1
> lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1
> lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1
> lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1
> lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1
> lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1
> -lpthread -lrt -ltbb /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9
> /home/arnaud/install/lib/libopencv_ocl.so.2.4.9
> /home/arnaud/install/lib/libopencv_gpu.so.2.4.9
> /home/arnaud/install/lib/libopencv_photo.so.2.4.9
> /home/arnaud/install/lib/libopencv_objdetect.so.2.4.9
> /home/arnaud/install/lib/libopencv_legacy.so.2.4.9
> /home/arnaud/install/lib/libopencv_video.so.2.4.9
> /home/arnaud/install/lib/libopencv_ml.so.2.4.9
> /home/arnaud/install/lib/libopencv_calib3d.so.2.4.9
> /home/arnaud/install/lib/libopencv_features2d.so.2.4.9
> /home/arnaud/install/lib/libopencv_highgui.so.2.4.9
> /home/arnaud/install/lib/libopencv_imgproc.so.2.4.9
> /home/arnaud/install/lib/libopencv_flann.so.2.4.9
> /home/arnaud/install/lib/libopencv_core.so.2.4.9 lib/libITKVideoIO-4.9.so.1
> lib/libITKIOImageBase-4.9.so.1 lib/libITKVideoCore-4.9.so.1
> lib/libITKCommon-4.9.so.1 lib/libitkdouble-conversion-4.9.so.1
> lib/libitksys-4.9.so.1 lib/libITKVNLInstantiation-4.9.so.1
> lib/libitkvnl_algo-4.9.so.1 lib/libitkv3p_lsqr-4.9.so.1
> lib/libitkvnl-4.9.so.1 lib/libitkvcl-4.9.so.1 lib/libitkv3p_netlib-4.9.so.1
> -lm -lpthread -lm -ldl
> -Wl,-rpath,/home/arnaud/source/build-itk/lib:/home/arnaud/install/lib
> -Wl,-rpath-link,/home/arnaud/source/build-itk/lib && :
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o:
> In function `itk::OpenCVVideoIOFactory::New()':
> /home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIOFactory.h:46:
> undefined reference to `itk::OpenCVVideoIOFactory::OpenCVVideoIOFactory()'
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o:
> In function `itk::OpenCVVideoIO::New()':
> /home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIO.h:48:
> undefined reference to `itk::OpenCVVideoIO::OpenCVVideoIO()'
> Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o:
> In function `itk::ObjectFactory<itk::OpenCVVideoIO>::Create()':
> /home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:60:
> undefined reference to `typeinfo for itk::OpenCVVideoIO'
> /home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:62:
> undefined reference to `typeinfo for itk::OpenCVVideoIO'
> collect2: error: ld returned 1 exit status
> ninja: build stopped: subcommand failed.
>
>
> On Fri, Aug 14, 2015 at 6:24 PM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
>
>> I have already tried it, does not solve it... I will retry it with a
>> fresh build once again...
>>
>> On Fri, Aug 14, 2015 at 6:11 PM, Matt McCormick <
>> matt.mccormick at kitware.com> wrote:
>>
>>> Hi Arnaud,
>>>
>>> Yes, you are probably right.  The suggestion by Zach in this patch (to
>>> use DEPENDS) is promising:
>>>
>>>   http://review.source.kitware.com/#/c/20078/
>>>
>>> Thanks,
>>> Matt
>>>
>>> On Fri, Aug 14, 2015 at 2:21 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>>> wrote:
>>> > Hi Matt,
>>> >
>>> > It happened while directly building ITK with OpenCV 2.4.9, without any
>>> > superbuild...
>>> > Thanks for the patch, but that does not solve it...
>>> >
>>> > I wonder if it could have something to do with the new linking system
>>> (note
>>> > it uses COMPILE_DEPENDS) ?
>>> >
>>> > Thanks,
>>> > Arnaud
>>> >
>>> > On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick <
>>> matt.mccormick at kitware.com>
>>> > wrote:
>>> >>
>>> >> Hi Arnaud,
>>> >>
>>> >> Is this with building the examples with the superbuild?  I think I was
>>> >> getting this error, too.  Here is a patch that should address it:
>>> >>
>>> >>   http://review.source.kitware.com/#/c/20077/
>>> >>
>>> >> Thanks,
>>> >> Matt
>>> >>
>>> >> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas <arnaudgelas at gmail.com
>>> >
>>> >> wrote:
>>> >> > Hi all,
>>> >> >
>>> >> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04
>>> and I
>>> >> > get
>>> >> > the following link error
>>> >> >
>>> >> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1
>>> >> >
>>> >> > [...]
>>> >> >
>>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>>> >> > 'itk::VideoIOBase::VideoIOBase()'
>>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>>> >> > 'itk::VideoIOBase::~VideoIOBase()'
>>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>>> >> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const'
>>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to
>>> >> > 'typeinfo for itk::VideoIOBase'
>>> >> > collect2: error: ld returned 1 exit status
>>> >> >
>>> >> > I have checked these methods are implemented in
>>> itkVideoIOBase.cxx...
>>> >> >
>>> >> > Any idea?
>>> >> >
>>> >> > Thanks
>>> >> > Arnaud
>>> >> >
>>> >> > _______________________________________________
>>> >> > Powered by www.kitware.com
>>> >> >
>>> >> > Visit other Kitware open-source projects at
>>> >> > http://www.kitware.com/opensource/opensource.html
>>> >> >
>>> >> > Kitware offers ITK Training Courses, for more information visit:
>>> >> > http://kitware.com/products/protraining.php
>>> >> >
>>> >> > Please keep messages on-topic and check the ITK FAQ at:
>>> >> > http://www.itk.org/Wiki/ITK_FAQ
>>> >> >
>>> >> > Follow this link to subscribe/unsubscribe:
>>> >> > http://public.kitware.com/mailman/listinfo/insight-developers
>>> >> >
>>> >
>>> >
>>>
>>
>>
>
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_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
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Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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Follow this link to subscribe/unsubscribe:
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From fotosentido at gmail.com  Fri Aug 14 14:12:02 2015
From: fotosentido at gmail.com (Marcos)
Date: Fri, 14 Aug 2015 20:12:02 +0200
Subject: [ITK] [ITK-users] Brand new project with itk sentence with
 QtCreator, Qt5 and Cmake crashes
In-Reply-To: <CAA24WvEkFuMegmKe9_NshTOJJpaKOn7Fz3OY51F0Gv+YsLZsAw@mail.gmail.com>
References: <CAA24WvH3crVTsadBNf8m6HpU3pixoChTKtycfqLE-5rpDsL2zA@mail.gmail.com>
 <CALzTN-SUo5LPJdS273Lo-34CSYXW0dmQNg594GtgH=UwDrGsOQ@mail.gmail.com>
 <CAA24WvEkFuMegmKe9_NshTOJJpaKOn7Fz3OY51F0Gv+YsLZsAw@mail.gmail.com>
Message-ID: <CAA24WvH2EcVTxUNhnTgLz_2-_hoURThFibiZgZ1HWsyzPBvSUQ@mail.gmail.com>

Well,

I got something.

Reading the example
http://itk.org/Wiki/ITK/Examples/IO/ImageFileReader

I saw "If ITK is not installed but compiled on your system, you will need
to specify *the path to your ITK build*: "

Well, I installed (or Visual Studio put it in a directory after I clicked
on the INSTALL project).

So it compiled. But the .exe crashed, and QtCreator didn't explain why. So
I clicked the executable and I got messages about QT dlls missing.

So I copied the missing dlls one by one, after finally I saw the window.

I still don't know why it thinks it wasn't installed. And maybe I'll never
know, it's annoying all this quest just to get a simple working .exe.


2015-08-14 18:20 GMT+02:00 Marcos <fotosentido at gmail.com>:

> As I said, I did that, I set the ITK_DIR to the directory where I
> installed.
>
> In fact, there is a ITKConfig.cmake in
> C:\ITK-4.8.0-installed\lib\cmake\ITK-4.8
>
> and my CMakeLists.txt has a line like this:
> SET(ITK_DIR "C:\\ITK-4.8.0-installed\\")
>
> but that way it doesn't find it.
>
>
> I didn't have problems building ITK, the problem is trying to use it.
>
> Maybe it's not installed correctly, but Visual Studio did it without
> problems.
>
> Thank you.
>
>
>
> 2015-08-14 18:04 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:
>
>> Hi Marcos,
>>
>> On Fri, Aug 14, 2015 at 11:57 AM, Marcos <fotosentido at gmail.com> wrote:
>> > Hi,
>> >
>> > I'm just trying to make a Cmake project compile and debug.
>>
>> >
>> > I have them installed in:
>> >
>> > C:\VTK-6.2.0-installed
>> > C:\ITK-4.8.0-installed
>> > (Each one has the subdirectories \bin, \include, \lib and \share)
>> >
>> > So, I created a QT5 Widgets project from QtCreator, then I added a
>> > CMakeLists.txt containing:
>> >
>> >> CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
>> >>
>> >>
>> >> PROJECT (UtilityDICOM)
>> >>
>> >>
>> >> SET(CMAKE_INCLUDE_CURRENT_DIR ON)
>> >>
>> >> SET(CMAKE_AUTOMOC ON)
>> >>
>> >>
>> >> FIND_PACKAGE(Qt5Widgets REQUIRED)
>> >>
>> >>
>> >> # VTK
>> >>
>> >> #SET(VTK_DIR "C:\\VTK-6.2.0-build\\")
>> >>
>> >>
>> >> # ITK
>> >>
>> >> #SET(ITK_DIR "C:\\ITK-4.8.0-build\\")
>> >>
>> >> FIND_PACKAGE(ITK REQUIRED)
>> >>
>> >> INCLUDE(${ITK_USE_FILE})
>> >>
>> >>
>> >> IF (ItkVtkGlue_LOADED)
>> >>
>> >>     FIND_PACKAGE(VTK REQUIRED)
>> >>
>> >>     INCLUDE(${VTK_USE_FILE})
>> >>
>> >> ENDIF()
>> >>
>> >>
>> >>
>> >> ADD_EXECUTABLE(UtilityDICOM WIN32 main.cpp mainwindow.cpp)
>> >>
>> >>
>> >> TARGET_LINK_LIBRARIES(UtilityDICOM Qt5::Widgets ${Glue}
>> ${VTK_LIBRARIES}
>> >> ${ITK_LIBRARIES})
>> >
>> >
>> >
>> >
>> > It returns the error:
>> >
>> >> CMake Error at CMakeLists.txt:15 (FIND_PACKAGE):
>> >
>> > By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has
>> >
>> > asked CMake to find a package configuration file provided by "ITK", but
>> >
>> > CMake did not find one.
>> >
>> >
>> > Could not find a package configuration file provided by "ITK" with any
>> of
>> >
>> > the following names:
>> >
>> >
>> > ITKConfig.cmake
>> >
>> > itk-config.cmake
>> >
>> >
>> > Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set
>> "ITK_DIR"
>> >
>> > to a directory containing one of the above files. If "ITK" provides a
>> >
>> > separate development package or SDK, be sure it has been installed.
>>
>>
>> This means that in your CMake configuration, set ITK_DIR to
>> C:\ITK-4.8.0-installed.
>>
>>
>> For more details, see the Configuring and Building ITK section of the
>> ITK Software Guide:
>>
>> http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html
>>
>> "Both the terminal-based and GUI versions of CMake will require you to
>> specify the directory where ITK was built in the CMake variable
>> ITK_DIR. The ITK binary directory will contain a file named
>> ITKConfig.cmake generated during ITK configuration process with CMake.
>> From this file, CMake will recover all information required to
>> configure your new ITK project."
>>
>>
>> Hope this helps,
>> Matt
>>
>
>
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From siavashk at ece.ubc.ca  Fri Aug 14 14:08:23 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Fri, 14 Aug 2015 11:08:23 -0700 (MST)
Subject: [ITK] [ITK-users] Brand new project with itk sentence with
 QtCreator, Qt5 and Cmake crashes
In-Reply-To: <CAA24WvH2EcVTxUNhnTgLz_2-_hoURThFibiZgZ1HWsyzPBvSUQ@mail.gmail.com>
References: <CAA24WvH3crVTsadBNf8m6HpU3pixoChTKtycfqLE-5rpDsL2zA@mail.gmail.com>
 <CALzTN-SUo5LPJdS273Lo-34CSYXW0dmQNg594GtgH=UwDrGsOQ@mail.gmail.com>
 <CAA24WvEkFuMegmKe9_NshTOJJpaKOn7Fz3OY51F0Gv+YsLZsAw@mail.gmail.com>
 <CAA24WvH2EcVTxUNhnTgLz_2-_hoURThFibiZgZ1HWsyzPBvSUQ@mail.gmail.com>
Message-ID: <1439575703025-36009.post@n7.nabble.com>

Marcos, if you  add
<http://typecastexception.com/post/2014/12/07/Adding-and-Editing-PATH-Environment-Variables-in-Windows.aspx>  
the location of your dlls to the PATH environment variable, QtCreator will
automatically find them for you. Installing ITK /should/ take care of that
for you though. Did you try rebooting your PC before running Qt?

Siavash



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Brand-new-project-with-itk-sentence-with-QtCreator-Qt5-and-Cmake-crashes-tp36005p36009.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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From alex.judisch at gmail.com  Fri Aug 14 15:04:28 2015
From: alex.judisch at gmail.com (Alex Judisch)
Date: Fri, 14 Aug 2015 15:04:28 -0400
Subject: [ITK] [ITK-users] Job Opportunity
Message-ID: <CAA3Vzqi66nfXDzRHyNctTtc=ewe8xhUu95+HfLHcd_-Bd_nAnA@mail.gmail.com>

Our lab is looking for a programmer with experience in image processing. We
use Fiji, ITK, and a variety of other methods.

The link for the job flyer is:
*http://www.ocularbiomechanics.com/PostDocAdImaging
<http://www.ocularbiomechanics.com/PostDocAdImaging>*.

Also, please check out the rest of website (http://ocularbiomechanics.com).
We have several interesting projects in progress using such imaging
modalities as Optical Coherence Tomography and MRI.
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From fotosentido at gmail.com  Fri Aug 14 15:29:08 2015
From: fotosentido at gmail.com (Marcos)
Date: Fri, 14 Aug 2015 21:29:08 +0200
Subject: [ITK] [ITK-users] Brand new project with itk sentence with
 QtCreator, Qt5 and Cmake crashes
In-Reply-To: <1439575703025-36009.post@n7.nabble.com>
References: <CAA24WvH3crVTsadBNf8m6HpU3pixoChTKtycfqLE-5rpDsL2zA@mail.gmail.com>
 <CALzTN-SUo5LPJdS273Lo-34CSYXW0dmQNg594GtgH=UwDrGsOQ@mail.gmail.com>
 <CAA24WvEkFuMegmKe9_NshTOJJpaKOn7Fz3OY51F0Gv+YsLZsAw@mail.gmail.com>
 <CAA24WvH2EcVTxUNhnTgLz_2-_hoURThFibiZgZ1HWsyzPBvSUQ@mail.gmail.com>
 <1439575703025-36009.post@n7.nabble.com>
Message-ID: <CAA24WvF60QNPS23eVbxKS7xaK8O9jGtHfgB1FRA84Qa_8_0XTA@mail.gmail.com>

I tried so many things, and now I think it works...
without setting ITK_DIR in CMakeLists...
I added the ITK and VTK dlls to the PATH... I think I didn't reboot after
that.

I compared the ImageFileReader CMakeLists.txt example, and restored some
lines (about VTKITKGlue) I deleted.

If it helps to someone, my working CMakeLists.txt is now:

CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)


PROJECT (UtilityDICOM)


FIND_PACKAGE(Qt5Widgets REQUIRED)


SET(CMAKE_INCLUDE_CURRENT_DIR ON)

SET(CMAKE_AUTOMOC ON)


QT5_WRAP_UI(Cmake_form_hdr mainwindow.ui)

add_library(mainwindow mainwindow.cpp ${Cmake_form_hdr})

qt5_use_modules(mainwindow Widgets)



# ITK

FIND_PACKAGE(ITK REQUIRED)

INCLUDE(${ITK_USE_FILE})

if (ITKVtkGlue_LOADED)

  find_package(VTK REQUIRED)

  include(${VTK_USE_FILE})

else()

  find_package(ItkVtkGlue REQUIRED)

  include(${ItkVtkGlue_USE_FILE})

  set(Glue ItkVtkGlue)

endif()



ADD_EXECUTABLE(UtilityDICOM WIN32 main.cpp)

TARGET_LINK_LIBRARIES(UtilityDICOM mainwindow ${Glue} ${VTK_LIBRARIES}
${ITK_LIBRARIES})

QT5_USE_MODULES(UtilityDICOM Core Gui Widgets)


Now I can access even to VTK libraries... Finally I can start to develop
something.
I'm not sure what was happening, maybe the dlls in PATH and not rebooting
after adding them.

Thanks for your time. I appreciate it.



2015-08-14 20:08 GMT+02:00 Siavash Khallaghi <siavashk at ece.ubc.ca>:

> Marcos, if you  add
> <
> http://typecastexception.com/post/2014/12/07/Adding-and-Editing-PATH-Environment-Variables-in-Windows.aspx
> >
> the location of your dlls to the PATH environment variable, QtCreator will
> automatically find them for you. Installing ITK /should/ take care of that
> for you though. Did you try rebooting your PC before running Qt?
>
> Siavash
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/ITK-users-Brand-new-project-with-itk-sentence-with-QtCreator-Qt5-and-Cmake-crashes-tp36005p36009.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
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From matt.mccormick at kitware.com  Fri Aug 14 15:54:14 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 14 Aug 2015 15:54:14 -0400
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CAK3qF+_8i6t-5mVLqXU_uaA6WFnaMt+fbPAuGQumdtm+1218=g@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
 <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
 <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>
 <CAK3qF+888dOBB_QvhzbixSbgWMkqZRXAEKaM6d47SYxnmE61Rw@mail.gmail.com>
 <BLUPR04MB676A303299B420A41A98EBA9B7C0@BLUPR04MB676.namprd04.prod.outlook.com>
 <CAK3qF+_8i6t-5mVLqXU_uaA6WFnaMt+fbPAuGQumdtm+1218=g@mail.gmail.com>
Message-ID: <CALzTN-RXZaZW7tmcJrjctPjO8HzZyY+0HZc-UcKC87+rwY1J1w@mail.gmail.com>

On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not make
> much sense to me?), same link error...
>
> If it helps, I can prepare a docker build file to track this error (for
> anyone willing to help)?

That would be awesome :-)

Thanks,
Matt
_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

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From matt.mccormick at kitware.com  Sat Aug 15 14:20:16 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 15 Aug 2015 14:20:16 -0400
Subject: [ITK] [ITK-users] Brand new project with itk sentence with
 QtCreator, Qt5 and Cmake crashes
In-Reply-To: <CAA24WvEkFuMegmKe9_NshTOJJpaKOn7Fz3OY51F0Gv+YsLZsAw@mail.gmail.com>
References: <CAA24WvH3crVTsadBNf8m6HpU3pixoChTKtycfqLE-5rpDsL2zA@mail.gmail.com>
 <CALzTN-SUo5LPJdS273Lo-34CSYXW0dmQNg594GtgH=UwDrGsOQ@mail.gmail.com>
 <CAA24WvEkFuMegmKe9_NshTOJJpaKOn7Fz3OY51F0Gv+YsLZsAw@mail.gmail.com>
Message-ID: <CALzTN-SewWgaAM6N164f77=MLWgrY9P8vvMP962NUQXTADv2LA@mail.gmail.com>

Hi,

On Fri, Aug 14, 2015 at 12:20 PM, Marcos <fotosentido at gmail.com> wrote:
> As I said, I did that, I set the ITK_DIR to the directory where I installed.
>
> In fact, there is a ITKConfig.cmake in
> C:\ITK-4.8.0-installed\lib\cmake\ITK-4.8

In this case, set ITK_DIR to C:\ITK-4.8.0-installed\lib\cmake\ITK-4.8.


> and my CMakeLists.txt has a line like this:
> SET(ITK_DIR "C:\\ITK-4.8.0-installed\\")
>
> but that way it doesn't find it.

Usually, the ITK_DIR is not hard coded in a CMakeLists.txt.  It is set
by the user when they do the CMake configuration so it adjusts to the
situation on any given build machine.

HTH,
Matt




>
>
> I didn't have problems building ITK, the problem is trying to use it.
>
> Maybe it's not installed correctly, but Visual Studio did it without
> problems.
>
> Thank you.
>
>
>
> 2015-08-14 18:04 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>> Hi Marcos,
>>
>> On Fri, Aug 14, 2015 at 11:57 AM, Marcos <fotosentido at gmail.com> wrote:
>> > Hi,
>> >
>> > I'm just trying to make a Cmake project compile and debug.
>>
>> >
>> > I have them installed in:
>> >
>> > C:\VTK-6.2.0-installed
>> > C:\ITK-4.8.0-installed
>> > (Each one has the subdirectories \bin, \include, \lib and \share)
>> >
>> > So, I created a QT5 Widgets project from QtCreator, then I added a
>> > CMakeLists.txt containing:
>> >
>> >> CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
>> >>
>> >>
>> >> PROJECT (UtilityDICOM)
>> >>
>> >>
>> >> SET(CMAKE_INCLUDE_CURRENT_DIR ON)
>> >>
>> >> SET(CMAKE_AUTOMOC ON)
>> >>
>> >>
>> >> FIND_PACKAGE(Qt5Widgets REQUIRED)
>> >>
>> >>
>> >> # VTK
>> >>
>> >> #SET(VTK_DIR "C:\\VTK-6.2.0-build\\")
>> >>
>> >>
>> >> # ITK
>> >>
>> >> #SET(ITK_DIR "C:\\ITK-4.8.0-build\\")
>> >>
>> >> FIND_PACKAGE(ITK REQUIRED)
>> >>
>> >> INCLUDE(${ITK_USE_FILE})
>> >>
>> >>
>> >> IF (ItkVtkGlue_LOADED)
>> >>
>> >>     FIND_PACKAGE(VTK REQUIRED)
>> >>
>> >>     INCLUDE(${VTK_USE_FILE})
>> >>
>> >> ENDIF()
>> >>
>> >>
>> >>
>> >> ADD_EXECUTABLE(UtilityDICOM WIN32 main.cpp mainwindow.cpp)
>> >>
>> >>
>> >> TARGET_LINK_LIBRARIES(UtilityDICOM Qt5::Widgets ${Glue}
>> >> ${VTK_LIBRARIES}
>> >> ${ITK_LIBRARIES})
>> >
>> >
>> >
>> >
>> > It returns the error:
>> >
>> >> CMake Error at CMakeLists.txt:15 (FIND_PACKAGE):
>> >
>> > By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has
>> >
>> > asked CMake to find a package configuration file provided by "ITK", but
>> >
>> > CMake did not find one.
>> >
>> >
>> > Could not find a package configuration file provided by "ITK" with any
>> > of
>> >
>> > the following names:
>> >
>> >
>> > ITKConfig.cmake
>> >
>> > itk-config.cmake
>> >
>> >
>> > Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set
>> > "ITK_DIR"
>> >
>> > to a directory containing one of the above files. If "ITK" provides a
>> >
>> > separate development package or SDK, be sure it has been installed.
>>
>>
>> This means that in your CMake configuration, set ITK_DIR to
>> C:\ITK-4.8.0-installed.
>>
>>
>> For more details, see the Configuring and Building ITK section of the
>> ITK Software Guide:
>>
>> http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html
>>
>> "Both the terminal-based and GUI versions of CMake will require you to
>> specify the directory where ITK was built in the CMake variable
>> ITK_DIR. The ITK binary directory will contain a file named
>> ITKConfig.cmake generated during ITK configuration process with CMake.
>> From this file, CMake will recover all information required to
>> configure your new ITK project."
>>
>>
>> Hope this helps,
>> Matt
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From matt.mccormick at kitware.com  Sat Aug 15 14:24:01 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 15 Aug 2015 14:24:01 -0400
Subject: [ITK] [ITK-users] IterativeClosestPoint2 example: how to get
	better	results
In-Reply-To: <50B858FB5F53124F9E32314E5C1B40943512CAEF@MBX214.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435126779@MBX114.d.ethz.ch>
 <CALzTN-T6MeG=j6dZzgUTni6PgSX+U4W3t1mVUmJG__6VeWh_kA@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B40943512CAEF@MBX214.d.ethz.ch>
Message-ID: <CALzTN-Sm8_rEqUwY++7bGDFv8xEtafdp1L6iL=j2GjZXKSiEwA@mail.gmail.com>

Hi Fabio,

That is great to hear!


Please review this patch:

  http://review.source.kitware.com/#/c/20082/

This adds more status information that can lend insight into the
registration convergence.


Thanks,
Matt

On Fri, Aug 14, 2015 at 1:44 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Hello Matt,
>
> I went through the source code of 3DEuler transform in itk, and I realized that the default Euler sequence ZXY. If I generate my data according to this sequence I get perfect results, as it should be!
>
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Freitag, 14. August 2015 00:09
> To: D'Isidoro Fabio
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] IterativeClosestPoint2 example: how to get better results
>
> Hello,
>
> On Thu, Aug 13, 2015 at 4:06 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
>> I am trying to use the IterativeClosestPoint2 example on the fixed and
>> moving point sets in attachment (called ?src? and ?dest? point sets).
>>
>>
>>
>> The ground truth is ?properly ordered dest = Transform(src)?, where:
>>
>>
>>
>> Euler angles:  (0.349065850398866, 0.349065850398866,
>> 0.349065850398866)
>>
>> Translations: (4.1335200571234, 5.90820985238168, 7.04748773837622)
>>
>>
>>
>> (the dest_point set in attachment is randomly reshuffled)
>>
>>
>>
>>>>> If I use srx = fixed, dest = moving, the registration results is:
>>
>>
>>
>> Euler angles:  (-0.327201, -0.36953, -0.47291)
>>
>> Translations: (-6.28471, -2.64212, -1.50835)
>>
>>
>>
>>>>> If I use dest = fixed, src = moving, the registration results is:
>>
>>
>>
>> Euler angles:  (0.44595, 0.20655, 0.36423)
>>
>> Translations: (6.28471, 2.64212, 1.50835)
>>
>>
>>
>>
>>
>>
>>
>> Question 1):
>>
>>
>>
>> Given that ?properly ordered dest = Transform(src)?, according to the
>> guide src should be the fixed point set. Am I wrong?
>>
>
> This is a bit confusing because it is different from transforms with images, but the src should be the moving point set.  See:
>
>   http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkEuclideanDistancePointMetric.hxx;h=af1b04e91ed9126777134db3dfca6ef05810fc60;hb=HEAD#l87
>
>
>> Question 2):
>>
>>
>>
>> I am not happy with the results, given that there is no additional
>> noise (the underlined values refer to error angles of up to 8 degrees
>> and 3 mm errors). I am surprised because there is no additional noise
>> to the data, so I would expect an accurate registration. Are my
>> results normal? How could I improve the results? Should I change the optimizer, or the transform?
>
> Could the code be shared that generated the inputs?
>
> Thanks,
> Matt
_____________________________________
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From bill.lorensen at gmail.com  Sat Aug 15 15:09:46 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Sat, 15 Aug 2015 15:09:46 -0400
Subject: [ITK] [ITK-dev] Link error after recent commit
Message-ID: <CADZJ4hNDHQFJBtkecBkYxWPodL+zeojo8vJtiBPz1x96Bcxhsw@mail.gmail.com>

I get link errors resembling this:
Linking CXX executable ../../../../bin/ITKLevelSetsv4VisualizationTestDriver
/usr/bin/ld: CMakeFiles/ITKLevelSetsv4VisualizationTestDriver.dir/itkVTKVisualizeLevelSetsInteractivePauseTest.cxx.o:
undefined reference to symbol
'_ZNK3itk18VTKImageExportBase32GetPropagateUpdateExtentCallbackEv'
/usr/bin/ld: note:
'_ZNK3itk18VTKImageExportBase32GetPropagateUpdateExtentCallbackEv' is
defined in DSO /home/lorensen/ProjectsGIT/ITKGerrit-linux/lib/libITKVTK-4.9.so.1
so try adding it to the linker command line
/home/lorensen/ProjectsGIT/ITKGerrit-linux/lib/libITKVTK-4.9.so.1:
could not read symbols: Invalid operation
collect2: error: ld returned 1 exit status
make[2]: *** [bin/ITKLevelSetsv4VisualizationTestDriver] Error 1
make[1]: *** [Modules/Segmentation/LevelSetsv4Visualization/test/CMakeFiles/ITKLevelSetsv4VisualizationTestDriver.dir/all]
Error 2

----------------------------------
git bisect commit identified this commit:

Author: Zach Williamson <zachary-williamson at uiowa.edu>
Date:   Wed Jul 15 10:39:04 2015 -0500

    ENH: Use new linking system macros

    This is a work-in-progress to demonstrate using the new linking system
    (DEPENDS, COMPILE_DEPENDS, PRIVATE_DEPENDS etc.)

    Most changes so far are using private_depends where applicable to reduce the
    total number of links being created (since public dependencies are linked
    recursively while private dependencies are not)

    Change-Id: I41bed74b8d6ed508f2014163854799ed0ef17919

This build has:
Module_ITKLevelSetsv4Visualization:BOOL=ON
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From Olivier.Commowick at inria.fr  Mon Aug 17 04:10:34 2015
From: Olivier.Commowick at inria.fr (Olivier Commowick)
Date: Mon, 17 Aug 2015 10:10:34 +0200
Subject: [ITK] [ITK-users] Symmetric eigen analysis discrepancy
In-Reply-To: <CALzTN-Stue7A1WrwjYP-gPj=6GgnSUNRhb2u0oYddBO8CQmyzg@mail.gmail.com>
References: <F80D6ED3-0AD2-466C-85BA-38C9DE1AC316@inria.fr>
 <CALzTN-Stue7A1WrwjYP-gPj=6GgnSUNRhb2u0oYddBO8CQmyzg@mail.gmail.com>
Message-ID: <87AF4E28-B7B4-49E5-9BFD-73F1B966BA3B@inria.fr>

Hi Matt,

Yes, those are very small numbers indeed :) After digging in the code, I found two discrepancies with respect to the vnl symmetric eigensystem, so I took the vnl code as the reference and did the corrections. I am submitting the two patches on gerrit (I didn?t know they would be separated for review, I can merge them if necessary): 

- http://review.source.kitware.com/#/c/20092/ <http://review.source.kitware.com/#/c/20092/>
- http://review.source.kitware.com/#/c/20093/ <http://review.source.kitware.com/#/c/20093/>

That being said, when digging in the code, it is not clear to me why SymmetricEigenAnalysis is not just a wrapper on vnl_symmetric_eigensystem. This would avoid duplicated code, and I do not see any place in the eigensystem code that wouldn?t be thread safe. But again, I am not an expert of that code and so I may be wrong. In any case, may be something to think of for future work :)

Thanks for the help,
Olivier

> On 13 Aug 2015, at 22:59, Matt McCormick <matt.mccormick at kitware.com> wrote:
> 
> Hi Olivier,
> 
> Those are some pretty small numbers ;-).  Thanks for sharing your experiences.
> 
> It may be necessary to build both ITK and vnl/netlib instances with
> debugging symbols and walk through them in a debugger to see where the
> deviation occurs.
> 
> As always, patches are welcome :-)
> 
> Thanks,
> Matt
> 
> On Thu, Aug 13, 2015 at 9:35 AM, Olivier Commowick
> <Olivier.Commowick at inria.fr> wrote:
>> Hello all,
>> 
>> I have been experiencing a problem when using the itk SymmetricEigenAnalysis class in ITK. When using this class, it sometimes produces NaN eigenvalues/vectors. On the contrary, the vnl_symmetric_eigensystem doesn?t seem to have a problem (and neither does matlab). Looking at the documentation, it seems both use QL decomposition but not implemented in the same place. In addition, the vnl one is said to be not thread safe, although it?s the one working for me.
>> 
>> In fact, I have isolated one 3x3 matrix for which I always have the problem.
>> 
>> A =
>> [7.503107128706855667859804009212206062302e-53 1.870107888834986371214720644344813262375e-52 -8.662047753682068190087788895125120421821e-27;
>> 1.870107888834986371214720644344813262375e-52 4.661140319458029838073740773908360767728e-52 -2.15896741973055935210319454393408888029e-26;
>> -8.662047753682068190087788895125120421821e-27 -2.15896741973055935210319454393408888029e-26 1]
>> 
>> It?s a weird one I know, but again vnl (and matlab) works great on it. Would there be anyone who knows the QL decomposition code enough to help me understand and possibly correct the ITK class so that it does the same as the VNL one ?
>> 
>> Thanks a lot in advance.
>> 
>> ---
>> 
>> Olivier Commowick, Ph.D.
>> Research Scientist
>> INRIA Rennes - Bretagne Atlantique, VISAGES Team
>> Campus de Beaulieu
>> 35042 Rennes
>> FRANCE
>> 
>> Phone: +33 2 99 84 25 92
>> Email: Olivier.Commowick at inria.fr
>> Web: http://olivier.commowick.org/
>> 
>> 
>> 
>> 
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users


---

Olivier Commowick, Ph.D.
Research Scientist
INRIA Rennes - Bretagne Atlantique, VISAGES Team
Campus de Beaulieu
35042 Rennes
FRANCE

Phone: +33 2 99 84 25 92
Email: Olivier.Commowick at inria.fr
Web: http://olivier.commowick.org/





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From Charles.GARRAUD at b-com.com  Mon Aug 17 04:18:16 2015
From: Charles.GARRAUD at b-com.com (Charles GARRAUD)
Date: Mon, 17 Aug 2015 08:18:16 +0000
Subject: [ITK] [ITK-users] 3D/2D registration with
 itkRayCastInterpolateImageFunction
In-Reply-To: <1438725226436-35973.post@n7.nabble.com>
References: <b0b244228f0c4cc9a2d55169deff2cd3@vprd-opci0018.b-com.local>
 <1438725226436-35973.post@n7.nabble.com>
Message-ID: <0e2998cae63c4786a150d6cfb6599dec@vprd-opci0018.b-com.local>

Thanks for your answer. Metric is increasing (is it normal behavior as in the example setMaximized is on?).

And we are using same sample data as used in ITKApp example... As we generate DRR data with itkRayCastInterpolateImageFunction and then try to register data with 
same method, it should be a perfect match?

Thanks for your help and sorry for the late answer (summer break).

Regards,

Charles

-----Message d'origine-----
De?: Insight-users [mailto:insight-users-bounces at itk.org] De la part de Siavash Khallaghi
Envoy??: mardi 4 ao?t 2015 23:54
??: insight-users at itk.org
Objet?: Re: [ITK-users] 3D/2D registration with itkRayCastInterpolateImageFunction

Is the metric decreasing? (i.e. similarity value) It could be that everything is correct, it is just that you have an ill-posed problem. If the metric is decreasing, it could be that you are converging to a local minimum.

Siavash



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From c.spanakis83 at gmail.com  Mon Aug 17 05:17:13 2015
From: c.spanakis83 at gmail.com (Constantinus Spanakis)
Date: Mon, 17 Aug 2015 12:17:13 +0300
Subject: [ITK] Virtual image and TMetricTraits in Joint histogram mutual
	information
Message-ID: <CAOZihbcj3xL+ONjon=ZPhk1jwrpogUqtNdwHnW_EoL0O1pcZZg@mail.gmail.com>

Hello. In the ITK PDFs tutorials, the basic components of the ITKv4
framework, in addition to the components that existed in the previous
framework, there is a new component, the Virtual image, which provides
more flexibility in our efforts to registrate two images. I tried to
use the Joint histrogram mutual information metric and its template is
the following one:

itk::JointHistogramMutualInformationImageToImageMetricv4< TFixedImage,
TMovingImage, TVirtualImage, TInternalComputationValueType,
TMetricTraits > Class Template Reference

In the case where the virtual image is the same as the fixed image, we
can define our metric:

itk::JointHistogramMutualInformationImageToImageMetricv4< TFixedImage,
TMovingImage, TFixedImage, TInternalComputationValueType,
TMetricTraits > Class Template Reference

But what happens when they aren't the same? How can we define our
different-from-fixed-image virtual image? And last but not least, what
are the TMetricTraits and how are they defined?

Thank you

From davis.vigneault at gmail.com  Mon Aug 17 06:57:13 2015
From: davis.vigneault at gmail.com (DVigneault)
Date: Mon, 17 Aug 2015 03:57:13 -0700 (MST)
Subject: [ITK] [ITK-users] Do any of the mesh file formats store
	CellData?
In-Reply-To: <1439488504178-7587666.post@n2.nabble.com>
References: <1439488504178-7587666.post@n2.nabble.com>
Message-ID: <1439809033823-7587689.post@n2.nabble.com>

All--

I've rebuilt in debug mode and stepped through with gdb.  It looks like the
CellData is being deallocated at the following line in itkProcessObject.cxx. 
The comment suggests that this result is expected?

1684	  /**
1685	   * Prepare all the outputs. This may deallocate previous bulk data.
1686	   */
1687	  this->PrepareOutputs();

By putting a breakpoint at itkProcessObject.cxx:1687, we can see where the
pointer is being reset:

$ gdb ./dv-mesh-test 
(gdb) b itkProcessObject.cxx:1687
(gdb) r
(gdb) c # First time is due to sphere source
(gdb) select-frame 3 # Brings us back into itk::MeshFileWriter::Write
(gdb) p input->GetCellData() # A valid pointer
(gdb) n # Step over this 
(gdb) p input->GetCellData() # A null pointer

Here's the backtrace at that point:

#0  itk::ProcessObject::UpdateOutputData (this=0x936a30) at
/local/pemb3433/Developer/ITK/src/Modules/Core/Common/src/itkProcessObject.cxx:1695
#1  0x000000000052f9fd in itk::DataObject::UpdateOutputData (this=0x93b290)
at
/local/pemb3433/Developer/ITK/src/Modules/Core/Common/src/itkDataObject.cxx:416
#2  0x000000000052f6af in itk::DataObject::Update (this=0x93b290) at
/local/pemb3433/Developer/ITK/src/Modules/Core/Common/src/itkDataObject.cxx:341
#3  0x00000000004fb544 in itk::MeshFileWriter<itk::Mesh&lt;float, 3u,
itk::DefaultStaticMeshTraits&lt;float, 3u, 3u, float, float, float> >
>::Write (this=0x93ca40)
    at
/local/pemb3433/Developer/ITK/src/Modules/IO/Mesh/include/itkMeshFileWriter.hxx:148
#4  0x00000000004f9bf1 in itk::MeshFileWriter<itk::Mesh&lt;float, 3u,
itk::DefaultStaticMeshTraits&lt;float, 3u, 3u, float, float, float> >
>::Update (this=0x93ca40)
    at
/local/pemb3433/Developer/ITK/src/Modules/IO/Mesh/include/itkMeshFileWriter.h:145
#5  0x00000000004f8185 in main () at
/local/pemb3433/Developer/Bitbucket/oxford/Stebbing_Method/MeshTest/src/dv-mesh-test.cxx:32

I'm stretching my knowledge both of ITK and gdb here, so please do let me
know if I'm misinterpreting the output--but it seems to me that the CellData
is being deallocated when itkProcessObject.cxx:1687 is called, and therefore
it (a) isn't being written to file and (b) isn't available after the mesh is
written.

Is this a bug in my code?  A bug in ITK?  A feature I don't understand? 
Thanks very much in advance for your help!

Best,

--Davis



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From arnaudgelas at gmail.com  Mon Aug 17 08:49:47 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Mon, 17 Aug 2015 14:49:47 +0200
Subject: [ITK] [ITK-users] Do any of the mesh file formats store
	CellData?
In-Reply-To: <1439809033823-7587689.post@n2.nabble.com>
References: <1439488504178-7587666.post@n2.nabble.com>
 <1439809033823-7587689.post@n2.nabble.com>
Message-ID: <CAK3qF+920TYF-3cq0LWjJ4z66eLx2es+oqzOg6uPUaxrh1mbaA@mail.gmail.com>

Davis,

Can you write a c++ example (please not a c++-11 one) along with
corresponding cmakelists.txt either on itk wiki examples [1], either on
ITKExamples [2] (see [3] for contributing), please?

Thanks,
Arnaud

[1] http://itk.org/Wiki/ITK/Examples
[2] http://itk.org/ITKExamples/index.html
[3] http://itk.org/ITKExamples/Documentation/Contribute/index.html

On Mon, Aug 17, 2015 at 12:57 PM, DVigneault <davis.vigneault at gmail.com>
wrote:

> All--
>
> I've rebuilt in debug mode and stepped through with gdb.  It looks like the
> CellData is being deallocated at the following line in
> itkProcessObject.cxx.
> The comment suggests that this result is expected?
>
> 1684      /**
> 1685       * Prepare all the outputs. This may deallocate previous bulk
> data.
> 1686       */
> 1687      this->PrepareOutputs();
>
> By putting a breakpoint at itkProcessObject.cxx:1687, we can see where the
> pointer is being reset:
>
> $ gdb ./dv-mesh-test
> (gdb) b itkProcessObject.cxx:1687
> (gdb) r
> (gdb) c # First time is due to sphere source
> (gdb) select-frame 3 # Brings us back into itk::MeshFileWriter::Write
> (gdb) p input->GetCellData() # A valid pointer
> (gdb) n # Step over this
> (gdb) p input->GetCellData() # A null pointer
>
> Here's the backtrace at that point:
>
> #0  itk::ProcessObject::UpdateOutputData (this=0x936a30) at
>
> /local/pemb3433/Developer/ITK/src/Modules/Core/Common/src/itkProcessObject.cxx:1695
> #1  0x000000000052f9fd in itk::DataObject::UpdateOutputData (this=0x93b290)
> at
>
> /local/pemb3433/Developer/ITK/src/Modules/Core/Common/src/itkDataObject.cxx:416
> #2  0x000000000052f6af in itk::DataObject::Update (this=0x93b290) at
>
> /local/pemb3433/Developer/ITK/src/Modules/Core/Common/src/itkDataObject.cxx:341
> #3  0x00000000004fb544 in itk::MeshFileWriter<itk::Mesh&lt;float, 3u,
> itk::DefaultStaticMeshTraits&lt;float, 3u, 3u, float, float, float> >
> >::Write (this=0x93ca40)
>     at
>
> /local/pemb3433/Developer/ITK/src/Modules/IO/Mesh/include/itkMeshFileWriter.hxx:148
> #4  0x00000000004f9bf1 in itk::MeshFileWriter<itk::Mesh&lt;float, 3u,
> itk::DefaultStaticMeshTraits&lt;float, 3u, 3u, float, float, float> >
> >::Update (this=0x93ca40)
>     at
>
> /local/pemb3433/Developer/ITK/src/Modules/IO/Mesh/include/itkMeshFileWriter.h:145
> #5  0x00000000004f8185 in main () at
>
> /local/pemb3433/Developer/Bitbucket/oxford/Stebbing_Method/MeshTest/src/dv-mesh-test.cxx:32
>
> I'm stretching my knowledge both of ITK and gdb here, so please do let me
> know if I'm misinterpreting the output--but it seems to me that the
> CellData
> is being deallocated when itkProcessObject.cxx:1687 is called, and
> therefore
> it (a) isn't being written to file and (b) isn't available after the mesh
> is
> written.
>
> Is this a bug in my code?  A bug in ITK?  A feature I don't understand?
> Thanks very much in advance for your help!
>
> Best,
>
> --Davis
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/Do-any-of-the-mesh-file-formats-store-CellData-tp7587666p7587689.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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From rphellan2210 at gmail.com  Mon Aug 17 09:02:23 2015
From: rphellan2210 at gmail.com (Renzo Ph)
Date: Mon, 17 Aug 2015 10:02:23 -0300
Subject: [ITK] Vessel enhancement
Message-ID: <CAOvLtO66t_kiVtW7poM=fK578Yjf0PHZCSZfuBtfTka5sWxyvA@mail.gmail.com>

Hi everybody,

I found this class for vessel enhancement: HessianSmoothed3DToVesselnessM
easureImageFilter. Nevertheless, it requires the
HessianSmoothedRecursiveGaussianImageFilter. I wasn't able to found that
filter in ITK, so do you know where can I get it or if its a patented code?

Renzo
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From davis.vigneault at gmail.com  Mon Aug 17 09:22:44 2015
From: davis.vigneault at gmail.com (DVigneault)
Date: Mon, 17 Aug 2015 06:22:44 -0700 (MST)
Subject: [ITK] [ITK-users] Do any of the mesh file formats store
	CellData?
In-Reply-To: <1439488504178-7587666.post@n2.nabble.com>
References: <1439488504178-7587666.post@n2.nabble.com>
Message-ID: <1439817764524-7587691.post@n2.nabble.com>

Thanks very much for the reply, Arnaud!

I've put up the example on the Wiki [1].  I removed auto, but I should state
that I'm still compiling with c++11--I don't have a non-c++11 build of ITK
to test against at the moment.  And, in case it's helpful, I'm on Ubuntu
14.04, compiling with g++ 4.8.4.

Best, and thanks,

--Davis

[1] http://itk.org/Wiki/ITK/Examples/Meshes/PointAndCellData



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From arnaudgelas at gmail.com  Mon Aug 17 10:03:26 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Mon, 17 Aug 2015 16:03:26 +0200
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CALzTN-RXZaZW7tmcJrjctPjO8HzZyY+0HZc-UcKC87+rwY1J1w@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
 <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
 <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>
 <CAK3qF+888dOBB_QvhzbixSbgWMkqZRXAEKaM6d47SYxnmE61Rw@mail.gmail.com>
 <BLUPR04MB676A303299B420A41A98EBA9B7C0@BLUPR04MB676.namprd04.prod.outlook.com>
 <CAK3qF+_8i6t-5mVLqXU_uaA6WFnaMt+fbPAuGQumdtm+1218=g@mail.gmail.com>
 <CALzTN-RXZaZW7tmcJrjctPjO8HzZyY+0HZc-UcKC87+rwY1J1w@mail.gmail.com>
Message-ID: <CAK3qF+8mNo8RJyjgjTa-JxWQAh0+qPmp0cnX-BK7bb=wikf2Qg@mail.gmail.com>

Matt,

Here you go

Thanks,
Arnaud

On Fri, Aug 14, 2015 at 9:54 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
> > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not make
> > much sense to me?), same link error...
> >
> > If it helps, I can prepare a docker build file to track this error (for
> > anyone willing to help)?
>
> That would be awesome :-)
>
> Thanks,
> Matt
>
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From marco.dev.open at gmail.com  Mon Aug 17 10:14:56 2015
From: marco.dev.open at gmail.com (Marco Dev)
Date: Mon, 17 Aug 2015 07:14:56 -0700
Subject: [ITK] [ITK-dev] vtk transform filter on .RAW
Message-ID: <CAKcUdn4LpHTnVYTsGQiji9swKZ_kWN+8VP=+h_AHJR-xBV=YBw@mail.gmail.com>

Hi,
why does not work vtk transform filter correctly on .RAW file
I read the .raw file through ifstream then create a image type from this
buffer as follow bellow:

ifstream fin(filePath[0], ios::in | ios::binary);

signed short iSample;

cout << "Samples Output" << endl;
while (fin.read((char *)&iSample, sizeof(signed short)))
{

m_Short.push_back(iSample);

}

cout << " size of short vector " << m_Short.size();


m_Aloc = (signed short*)malloc(m_Short.size() * 2);
int counter = 0;
for (std::vector<signed short>::iterator it = m_Short.begin(); it !=
m_Short.end(); ++it, counter++){

m_Aloc[counter] = (*it);


}

.
. // set nidex size orientation spacing  ,,,,, to itk filter
.
.
importFilter->SetImportPointer(m_Aloc,sizeX*sizeY*sizeZ, true);

try
{
importFilter->Update();
pVol = importFilter->GetOutput();
}
catch (itk::ExceptionObject & err)
{
return false;
}
pVol->Register();


typedef itk::ImageToVTKImageFilter<ImageType> itkVtkConverter;
itkVtkConverter::Pointer conv = itkVtkConverter::New();

conv->SetInput(pVol);
conv->Update();

vtkSmartPointer<vtkImageData> vtkImage =
vtkSmartPointer<vtkImageData>::New();
vtkImage->ShallowCopy(conv->GetOutput());
//shallow copy is vtk's equivalent of disconnect pipeline

volumeRayCatMapper =
vtkSmartPointer<vtkFixedPointVolumeRayCastMapper>::New();


volumeRayCatMapper->SetInputData(vtkImage);
.
.
.
.
//Skin
color->AddRGBPoint(-3024, 0, 0, 0, 0.5, 0.0);
color->AddRGBPoint(-1000, .62, .36, .18, 0.5, 0.0);
color->AddRGBPoint(-500, .88, .60, .29, 0.33, 0.45);
color->AddRGBPoint(3071, .83, .66, 1, 0.5, 0.0);

compositeOpacity->AddPoint(-3024, 0, 0.5, 0.0);
compositeOpacity->AddPoint(-1000, 0, 0.5, 0.0);
compositeOpacity->AddPoint(-500, 1.0, 0.33, 0.45);
compositeOpacity->AddPoint(3071, 1.0, 0.5, 0.0);

volumeRayCatMapper->SetBlendModeToComposite();
volumeProperty->ShadeOn();
volumeProperty->SetAmbient(0.1);
volumeProperty->SetDiffuse(0.9);
volumeProperty->SetSpecular(0.2);
volumeProperty->SetSpecularPower(10.0);
volumeProperty->SetScalarOpacityUnitDistance(0.8919);

why does not work correctly on volume ?
if I read the dicom series from itk reader it does work correctly

Thanks
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From siavashk at ece.ubc.ca  Mon Aug 17 15:51:12 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Mon, 17 Aug 2015 12:51:12 -0700 (MST)
Subject: [ITK] [ITK-users] 3D/2D registration with
 itkRayCastInterpolateImageFunction
In-Reply-To: <0e2998cae63c4786a150d6cfb6599dec@vprd-opci0018.b-com.local>
References: <b0b244228f0c4cc9a2d55169deff2cd3@vprd-opci0018.b-com.local>
 <1438725226436-35973.post@n7.nabble.com>
 <0e2998cae63c4786a150d6cfb6599dec@vprd-opci0018.b-com.local>
Message-ID: <1439841072404-36020.post@n7.nabble.com>

Hi Charles,

For the record, I do not think that you have a software bug per say. I think
your problem is a bit more fundamental, i.e. the combination of
optimizer/metric might not have sufficient capture range to guide the
registration to the true solution.

In order to investigate this, I would suggest trying the following:

1. If you generate your projection from identity (which I assume is the true
solution), and start your registration from identity, would the registration
converge to identity as well? This tells you how stable your metric is.

2. At this point, I would definitely start plotting the metric value against
transformation parameters. See /Section 3.10.1 Mean Squares Metric:
Exploring a Metric/ of the  Software Guide
<http://se.csie.dyu.edu.tw/canseco/PDF/InsightSoftwareGuide-Book2-4.6.0.pdf> 
. Since your registration does not converge to the correct solution for
rotations, I suspect that it is getting stuck in a local minima for these
parameters.

Siavash



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-3D-2D-registration-with-itkRayCastInterpolateImageFunction-tp35970p36020.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From christophe.vandijck at kuleuven.be  Tue Aug 18 02:14:25 2015
From: christophe.vandijck at kuleuven.be (christophevd)
Date: Mon, 17 Aug 2015 23:14:25 -0700 (MST)
Subject: [ITK] [ITK-users] Multi-threading in pointsettopointsetmetric
In-Reply-To: <9103909A-6192-4F07-8C35-DB2354408742@gmail.com>
References: <1439386054435-35985.post@n7.nabble.com>
 <38C7F2DA-EBE7-4A10-9C0F-5F0F5E75450F@gmail.com>
 <001101d0d50d$2e317a30$8a946e90$@kuleuven.be>
 <9103909A-6192-4F07-8C35-DB2354408742@gmail.com>
Message-ID: <1439878465576-36021.post@n7.nabble.com>

Thanks, 

I've looked at it, but when I try to set-up the pipeline for pointset to
pointset registrations, I have errors concerning an unset virtual domain.
When I try a dummy image to image registration, this does not seem to occur.

Are there any examples available, eg ICP registration, that use the new
imageregistrationmethodv4 framework? 

Regards,
Christophe



--
View this message in context: http://itk-users.7.n7.nabble.com/Multi-threading-in-pointsettopointsetmetric-tp35985p36021.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From ribaluigi at gmail.com  Tue Aug 18 06:05:44 2015
From: ribaluigi at gmail.com (Luigi Riba)
Date: Tue, 18 Aug 2015 12:05:44 +0200
Subject: [ITK] FEM registration algorithm
Message-ID: <CAJaJUhNGAchUwpbRhR9RChCABqkByECOReepL-MhScZ9XsD_TQ@mail.gmail.com>

Dear ITK community,

I have read the manual and checked online for a detailed description of the
algorithm implemented in ITK regarding FEM registration. In particular, I
have come across a good ppt here
<https://www.google.fr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=6&cad=rja&uact=8&ved=0CFUQFjAFahUKEwi3xuqQr7LHAhWDtBQKHSzNCTY&url=http%3A%2F%2Fwww.na-mic.org%2FWiki%2Fimages%2Fc%2Fc1%2FInsight-DeformableRegistration-FEM.ppt&ei=hwHTVffmMYPpUqyap7AD&usg=AFQjCNGUO8MaoJE_Gj6ChBJ1Oa5gxgOTJg>
.

For the moment, I have understood how to use the registration process and
how to use FEM library in ITK. By the way, I need some elucidation and
further details on the actual FEM registration implementation in ITK.

Could you please indicate me where I could find this piece of information?
Is there a paper I could look for?

Best,

Luigi
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From bill.lorensen at gmail.com  Tue Aug 18 09:00:29 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 18 Aug 2015 09:00:29 -0400
Subject: [ITK] [ITK-dev] Sphinx and ITK WIki example regression
Message-ID: <CADZJ4hNFnyxwC55ogaTKMq=3yd169aFRaByiO_BEhBEFz0pvZA@mail.gmail.com>

Folks,

The addition of the new math equality checks caused Sphinx and Wiki
examples using itkCustomColormapFunction to segfault.

I submitted a patch to fix this.

However, this brings up an issue. I'm sorry now that I did not review
the math equality check changes.

I see the need for fuzzy math comparison for real types, but why for
integral types?

What is the justification for replacing
int i;
int j;

if (i == j) ?

with
if (Math::AlmostEquals(i,j)) ?
of
if(Math::AlmostEquals(i,j))...

-- 
Unpaid intern in BillsBasement at noware dot com
_______________________________________________
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From c.spanakis83 at gmail.com  Tue Aug 18 10:08:05 2015
From: c.spanakis83 at gmail.com (Constantinus Spanakis)
Date: Tue, 18 Aug 2015 17:08:05 +0300
Subject: [ITK] Problem with Mattes' mutual information
Message-ID: <CAOZihbfrDhivyxcrc5nBJ6-G1VetLzL6LM6Po_W0aHtgX=Vzrg@mail.gmail.com>

Hello, i tried to modify the example  DeformableRegistration15.cxx by
replacing the Regular step gradient Descent optimizer with One plus
One optimizer. At first i had problem with having too many samples
outside moving image buffer. I corrected that problem by reducing the
number of spatial samples. Then i got this problem:

itk::ExceptionObject (00000000002FE348)
Location: "double __cdecl itk::MattesMutualInformationImageToImageMetric<class i
tk::Image<short,3>,class itk::Image<short,3> >::GetValue(const class itk::Optimi
zerParameters<double> &) const"
File: c:\itk\modules\registration\common\include\itkMattesMutualInformationImage
ToImageMetric.hxx
Line: 571
Description: itk::ERROR: MattesMutualInformationImageToImageMetric(00000000027FA
FF0): Joint PDF summed to zero
Image (0000000002815040)
  RTTI typeinfo:   class itk::Image<double,2>
  Reference Count: 2
  Modified Time: 462
  Debug: Off
  Object Name:
  Observers:
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 0
  RealTimeStamp: 0 seconds
  LargestPossibleRegion:
    Dimension: 2
    Index: [0, 0]
    Size: [50, 50]
  BufferedRegion:
    Dimension: 2
    Index: [0, 0]
    Size: [50, 50]
  RequestedRegion:
    Dimension: 2
    Index: [0, 0]
    Size: [50, 50]
  Spacing: [83.0652, 46.913]
  Origin: [2, 2]
  Direction:
1 0
0 1

  IndexToPointMatrix:
83.0652 0
0 46.913

  PointToIndexMatrix:
0.0120387 0
0 0.021316

  Inverse Direction:
1 0
0 1

  PixelContainer:
    ImportImageContainer (0000000002777D40)
      RTTI typeinfo:   class itk::ImportImageContainer<unsigned long,double>
      Reference Count: 1
      Modified Time: 463
      Debug: Off
      Object Name:
      Observers:
        none
      Pointer: 0000000002911380
      Container manages memory: true
      Size: 2500
      Capacity: 2500

Could someone please explain the problem more analytically and help me solve it?

Thank you

From arnaudgelas at gmail.com  Tue Aug 18 11:36:30 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Tue, 18 Aug 2015 17:36:30 +0200
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CAK3qF+8mNo8RJyjgjTa-JxWQAh0+qPmp0cnX-BK7bb=wikf2Qg@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
 <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
 <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>
 <CAK3qF+888dOBB_QvhzbixSbgWMkqZRXAEKaM6d47SYxnmE61Rw@mail.gmail.com>
 <BLUPR04MB676A303299B420A41A98EBA9B7C0@BLUPR04MB676.namprd04.prod.outlook.com>
 <CAK3qF+_8i6t-5mVLqXU_uaA6WFnaMt+fbPAuGQumdtm+1218=g@mail.gmail.com>
 <CALzTN-RXZaZW7tmcJrjctPjO8HzZyY+0HZc-UcKC87+rwY1J1w@mail.gmail.com>
 <CAK3qF+8mNo8RJyjgjTa-JxWQAh0+qPmp0cnX-BK7bb=wikf2Qg@mail.gmail.com>
Message-ID: <CAK3qF+_QRKWBP7GDeKfUhNRf9mMxDcV2vHU8h2m45oWhK6Ef9g@mail.gmail.com>

Matt,

Do you have any idea on that matter?

Thanks
Arnaud

On Mon, Aug 17, 2015 at 4:03 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Matt,
>
> Here you go
>
> Thanks,
> Arnaud
>
> On Fri, Aug 14, 2015 at 9:54 PM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas <arnaudgelas at gmail.com>
>> wrote:
>> > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not make
>> > much sense to me?), same link error...
>> >
>> > If it helps, I can prepare a docker build file to track this error (for
>> > anyone willing to help)?
>>
>> That would be awesome :-)
>>
>> Thanks,
>> Matt
>>
>
>
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From bill.lorensen at gmail.com  Tue Aug 18 11:42:46 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 18 Aug 2015 11:42:46 -0400
Subject: [ITK] [ITK-dev] New math comparison methods
Message-ID: <CADZJ4hPpjwg7jmxw8ggou3YUsOm7gwxmJEY+WN1mKaby+qSLpg@mail.gmail.com>

Folks,

It is hard for me see see why the new math comparison operators are
used for statements like this one in Core/Common/test/
itkDerivativeOperatorTest

    if( itk::Math::NotAlmostEquals( expected.size(), coefficients.size() ) )
instead of the original:
    if( expected.size() != coefficients.size() )

Can we revisit this topic?

Bill
_______________________________________________
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From matt.mccormick at kitware.com  Tue Aug 18 11:43:50 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 18 Aug 2015 11:43:50 -0400
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CAK3qF+_QRKWBP7GDeKfUhNRf9mMxDcV2vHU8h2m45oWhK6Ef9g@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
 <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
 <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>
 <CAK3qF+888dOBB_QvhzbixSbgWMkqZRXAEKaM6d47SYxnmE61Rw@mail.gmail.com>
 <BLUPR04MB676A303299B420A41A98EBA9B7C0@BLUPR04MB676.namprd04.prod.outlook.com>
 <CAK3qF+_8i6t-5mVLqXU_uaA6WFnaMt+fbPAuGQumdtm+1218=g@mail.gmail.com>
 <CALzTN-RXZaZW7tmcJrjctPjO8HzZyY+0HZc-UcKC87+rwY1J1w@mail.gmail.com>
 <CAK3qF+8mNo8RJyjgjTa-JxWQAh0+qPmp0cnX-BK7bb=wikf2Qg@mail.gmail.com>
 <CAK3qF+_QRKWBP7GDeKfUhNRf9mMxDcV2vHU8h2m45oWhK6Ef9g@mail.gmail.com>
Message-ID: <CALzTN-TnV+w7LJnj0eGn=hvMhzqNB5wCTAad-srzhay5z+qawA@mail.gmail.com>

Hi Arnaud,

With the excellent Dockerfile, I have been able to reproduce the error
:-), but I have not had a chance to dive in further.  I will do soon.

Thanks,
Matt

On Tue, Aug 18, 2015 at 11:36 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Matt,
>
> Do you have any idea on that matter?
>
> Thanks
> Arnaud
>
> On Mon, Aug 17, 2015 at 4:03 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>
>> Matt,
>>
>> Here you go
>>
>> Thanks,
>> Arnaud
>>
>> On Fri, Aug 14, 2015 at 9:54 PM, Matt McCormick
>> <matt.mccormick at kitware.com> wrote:
>>>
>>> On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas <arnaudgelas at gmail.com>
>>> wrote:
>>> > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not
>>> > make
>>> > much sense to me?), same link error...
>>> >
>>> > If it helps, I can prepare a docker build file to track this error (for
>>> > anyone willing to help)?
>>>
>>> That would be awesome :-)
>>>
>>> Thanks,
>>> Matt
>>
>>
>
_______________________________________________
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From bill.lorensen at gmail.com  Tue Aug 18 12:07:21 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 18 Aug 2015 12:07:21 -0400
Subject: [ITK] [ITK-dev] New math comparison methods
In-Reply-To: <CADZJ4hPpjwg7jmxw8ggou3YUsOm7gwxmJEY+WN1mKaby+qSLpg@mail.gmail.com>
References: <CADZJ4hPpjwg7jmxw8ggou3YUsOm7gwxmJEY+WN1mKaby+qSLpg@mail.gmail.com>
Message-ID: <CADZJ4hMbqZJG+3BnWh0nTv_u_si01qGRVm92XfuU_KiBY=9aRg@mail.gmail.com>

If there are no objections, I'll take a pass on changing new math
comparison operators back to vanilla comparisons for cases where

two integral types of the same type are compared
for example in
Modules/Segmentation/Classifiers/include/itkImageGaussianModelEstimator.hxx:
  if ( Math::NotAlmostEquals( ( m_NumberOfSamples[classIndex][0] - 1 ), 0.0 ) )

I think there may be other cases that can be reverted but I won't know
until I do a line by line inspection./




On Tue, Aug 18, 2015 at 11:42 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> Folks,
>
> It is hard for me see see why the new math comparison operators are
> used for statements like this one in Core/Common/test/
> itkDerivativeOperatorTest
>
>     if( itk::Math::NotAlmostEquals( expected.size(), coefficients.size() ) )
> instead of the original:
>     if( expected.size() != coefficients.size() )
>
> Can we revisit this topic?
>
> Bill



-- 
Unpaid intern in BillsBasement at noware dot com
_______________________________________________
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From matt.mccormick at kitware.com  Tue Aug 18 12:12:34 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 18 Aug 2015 12:12:34 -0400
Subject: [ITK] [ITK-dev]   New math comparison methods
In-Reply-To: <CADZJ4hMbqZJG+3BnWh0nTv_u_si01qGRVm92XfuU_KiBY=9aRg@mail.gmail.com>
References: <CADZJ4hPpjwg7jmxw8ggou3YUsOm7gwxmJEY+WN1mKaby+qSLpg@mail.gmail.com>
 <CADZJ4hMbqZJG+3BnWh0nTv_u_si01qGRVm92XfuU_KiBY=9aRg@mail.gmail.com>
Message-ID: <CALzTN-RL8wz=bdxHJXB4TFz1xE=+Rk-fpEVcr94XkuEBSk0-4A@mail.gmail.com>

Hi Bill,

Thanks for taking a look at this, and trying to improve the result.

Yes, we should probably only use the operator in situations where
templates generate comparisons in a hybrid of floating point and
integer situations -- integer only could use operator==.

Thanks,
Matt

On Tue, Aug 18, 2015 at 12:07 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> If there are no objections, I'll take a pass on changing new math
> comparison operators back to vanilla comparisons for cases where
>
> two integral types of the same type are compared
> for example in
> Modules/Segmentation/Classifiers/include/itkImageGaussianModelEstimator.hxx:
>   if ( Math::NotAlmostEquals( ( m_NumberOfSamples[classIndex][0] - 1 ), 0.0 ) )
>
> I think there may be other cases that can be reverted but I won't know
> until I do a line by line inspection./
>
>
>
>
> On Tue, Aug 18, 2015 at 11:42 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>> Folks,
>>
>> It is hard for me see see why the new math comparison operators are
>> used for statements like this one in Core/Common/test/
>> itkDerivativeOperatorTest
>>
>>     if( itk::Math::NotAlmostEquals( expected.size(), coefficients.size() ) )
>> instead of the original:
>>     if( expected.size() != coefficients.size() )
>>
>> Can we revisit this topic?
>>
>> Bill
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
_______________________________________________
Powered by www.kitware.com

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From mohammedrashadkm at gmail.com  Tue Aug 18 14:26:15 2015
From: mohammedrashadkm at gmail.com (Rashad M)
Date: Tue, 18 Aug 2015 20:26:15 +0200
Subject: [ITK] [ITK-dev] regarding
	ImageFileReader::GenerateOutputInformation()
In-Reply-To: <3284837D-9DD6-48A1-A65D-5ED81EC1A95B@mail.nih.gov>
References: <CANNqv9fxcUOACxh2EcXkQAE6hpcn=uJuYgtxcMwp3wRkYF8s1g@mail.gmail.com>
 <3284837D-9DD6-48A1-A65D-5ED81EC1A95B@mail.nih.gov>
Message-ID: <CANNqv9cgQXvvfkbHSufyK=q2sb63pfncBp4zZYhgA54RPd-QQQ@mail.gmail.com>

Hello Brad,

Thanks for your reply. I had check the UpdateOutputInformation() with a
seperate test code and there was no problem. I found that there are
multiple instances of Reader created in every execution of the my code
which was the cause of the error/behaviour I was having.

On Thu, Aug 13, 2015 at 9:11 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello Rashad,
>
> If you call ImageFileReader::UpdateOutputInformation() 2 times is "should"
> only call GenerateOutputInformation once.
>
> The key to this behavior is the management of the timestamps in the
> process object classes done here [1].
>
> What is required for this to work correctly is that the only the correct
> object get modified in these pipeline methods. When an object is modified
> the timestamp should be updated, and downstream processes get marked as out
> of date.
>
> The best way to make sure your ImageSource does not get call twice is to
> write a test, that makes sure the process object's MTime does not change in
> GenerateOutputInformation call.
>
> HTH,
> Brad
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/9f88e4e3b388ee2f1c1c006ae36de0613d305284/Modules/Core/Common/src/itkProcessObject.cxx#L1431-L1542
>
> On Aug 13, 2015, at 2:55 PM, Rashad M <mohammedrashadkm at gmail.com> wrote:
>
> Hello all,
>
> The documentation of   itk::ProcessObject::GenerateOutputInformation( )
>  says
> Generate the information describing the output data. [1]. The GenerateOutputInformation()
> in itkImageFileReader first create all instances of ImageIO and setup
> direction, spacing, etc..
>
> If I understand correctly, the GenerateOutputInformation in the image file
> reader is  called by UpdateOutputInformation( )
>
> To my question,
> If I call reader->UpdateOutputInformation() for first time it calls
> reader->GenerateOutputInformation() as described in docs[2].
>
> Now If I have a second call to reader->UpdateOutputInformation( ) ?
>
> Will it again go to GenerateOutputInformation() and createAllInstances of
> imageio , do the same thing again!
>
> In itkProcessObject.cxx, there is the below documentation
>
>    * Call GenerateOutputInformation for subclass specific information.
>    * Since UpdateOutputInformation propagates all the way up the pipeline,
>    * we need to be careful here to call GenerateOutputInformation only if
>    * necessary. Otherwise, we may cause this source to be modified which
>    * will cause it to execute again on the next update.
>
> How can I prevent it from calling it again in class sub class of
> itk::ImageSource?
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#abe61fb6b7de8c443e7af1561bd722736
>
>
> --
> Regards,
>    Rashad
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
>
>


-- 
Regards,
   Rashad
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From dzenanz at gmail.com  Tue Aug 18 15:57:22 2015
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 18 Aug 2015 15:57:22 -0400
Subject: [ITK] Problem with Mattes' mutual information
In-Reply-To: <CAOZihbfrDhivyxcrc5nBJ6-G1VetLzL6LM6Po_W0aHtgX=Vzrg@mail.gmail.com>
References: <CAOZihbfrDhivyxcrc5nBJ6-G1VetLzL6LM6Po_W0aHtgX=Vzrg@mail.gmail.com>
Message-ID: <CAPf2UMTaO=PgWfH27PS3guyorbVFQ4=TNRdOp+OXWHzbb6tv8w@mail.gmail.com>

Joint PDF summed to zero is usually triggered when the images you are
trying to register do not overlap. I guess the first issue is caused by
this too. You should have better initialization. At least translate the
images enough so the partly overlap.

HTH

On Tue, Aug 18, 2015 at 10:08 AM, Constantinus Spanakis <
c.spanakis83 at gmail.com> wrote:

> Hello, i tried to modify the example  DeformableRegistration15.cxx by
> replacing the Regular step gradient Descent optimizer with One plus
> One optimizer. At first i had problem with having too many samples
> outside moving image buffer. I corrected that problem by reducing the
> number of spatial samples. Then i got this problem:
>
> itk::ExceptionObject (00000000002FE348)
> Location: "double __cdecl
> itk::MattesMutualInformationImageToImageMetric<class i
> tk::Image<short,3>,class itk::Image<short,3> >::GetValue(const class
> itk::Optimi
> zerParameters<double> &) const"
> File:
> c:\itk\modules\registration\common\include\itkMattesMutualInformationImage
> ToImageMetric.hxx
> Line: 571
> Description: itk::ERROR:
> MattesMutualInformationImageToImageMetric(00000000027FA
> FF0): Joint PDF summed to zero
> Image (0000000002815040)
>   RTTI typeinfo:   class itk::Image<double,2>
>   Reference Count: 2
>   Modified Time: 462
>   Debug: Off
>   Object Name:
>   Observers:
>     none
>   Source: (none)
>   Source output name: (none)
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 0
>   UpdateMTime: 0
>   RealTimeStamp: 0 seconds
>   LargestPossibleRegion:
>     Dimension: 2
>     Index: [0, 0]
>     Size: [50, 50]
>   BufferedRegion:
>     Dimension: 2
>     Index: [0, 0]
>     Size: [50, 50]
>   RequestedRegion:
>     Dimension: 2
>     Index: [0, 0]
>     Size: [50, 50]
>   Spacing: [83.0652, 46.913]
>   Origin: [2, 2]
>   Direction:
> 1 0
> 0 1
>
>   IndexToPointMatrix:
> 83.0652 0
> 0 46.913
>
>   PointToIndexMatrix:
> 0.0120387 0
> 0 0.021316
>
>   Inverse Direction:
> 1 0
> 0 1
>
>   PixelContainer:
>     ImportImageContainer (0000000002777D40)
>       RTTI typeinfo:   class itk::ImportImageContainer<unsigned
> long,double>
>       Reference Count: 1
>       Modified Time: 463
>       Debug: Off
>       Object Name:
>       Observers:
>         none
>       Pointer: 0000000002911380
>       Container manages memory: true
>       Size: 2500
>       Capacity: 2500
>
> Could someone please explain the problem more analytically and help me
> solve it?
>
> Thank you
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From matt.mccormick at kitware.com  Tue Aug 18 15:57:49 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 18 Aug 2015 15:57:49 -0400
Subject: [ITK] Virtual image and TMetricTraits in Joint histogram mutual
	information
In-Reply-To: <CAOZihbcj3xL+ONjon=ZPhk1jwrpogUqtNdwHnW_EoL0O1pcZZg@mail.gmail.com>
References: <CAOZihbcj3xL+ONjon=ZPhk1jwrpogUqtNdwHnW_EoL0O1pcZZg@mail.gmail.com>
Message-ID: <CALzTN-TSvVqAqNDdTpXbTb55UDfBU6csK0TGkxA4-+AqLB20EQ@mail.gmail.com>

Hello Constantinus,

On Mon, Aug 17, 2015 at 5:17 AM, Constantinus Spanakis
<c.spanakis83 at gmail.com> wrote:
> Hello. In the ITK PDFs tutorials, the basic components of the ITKv4
> framework, in addition to the components that existed in the previous
> framework, there is a new component, the Virtual image, which provides
> more flexibility in our efforts to registrate two images. I tried to
> use the Joint histrogram mutual information metric and its template is
> the following one:
>
> itk::JointHistogramMutualInformationImageToImageMetricv4< TFixedImage,
> TMovingImage, TVirtualImage, TInternalComputationValueType,
> TMetricTraits > Class Template Reference
>
> In the case where the virtual image is the same as the fixed image, we
> can define our metric:
>
> itk::JointHistogramMutualInformationImageToImageMetricv4< TFixedImage,
> TMovingImage, TFixedImage, TInternalComputationValueType,
> TMetricTraits > Class Template Reference
>
> But what happens when they aren't the same? How can we define our
> different-from-fixed-image virtual image?

This is defined when you create the typedef for the metric.

> And last but not least, what
> are the TMetricTraits and how are they defined?

There are currently two MetricTraits classes,
DefaultImageToImageMetricTraitsv4 [1] and
VectorImageToImageMetricTraitsv4 [2].

Hope this helps,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1DefaultImageToImageMetricTraitsv4.html

[2] http://www.itk.org/Doxygen/html/classitk_1_1VectorImageToImageMetricTraitsv4.html

From matt.mccormick at kitware.com  Tue Aug 18 16:05:24 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 18 Aug 2015 16:05:24 -0400
Subject: [ITK] Vessel enhancement
In-Reply-To: <CAOvLtO66t_kiVtW7poM=fK578Yjf0PHZCSZfuBtfTka5sWxyvA@mail.gmail.com>
References: <CAOvLtO66t_kiVtW7poM=fK578Yjf0PHZCSZfuBtfTka5sWxyvA@mail.gmail.com>
Message-ID: <CALzTN-SG9TiJKnFGMOVjPjbYL8QMPbM9USXv8-V+PqQ7XCyWJA@mail.gmail.com>

Hi Renzo,

Why / where does it require HessianSmoothedRecursiveGaussianImageFilter?

Thanks,
Matt

On Mon, Aug 17, 2015 at 9:02 AM, Renzo Ph <rphellan2210 at gmail.com> wrote:
> Hi everybody,
>
> I found this class for vessel enhancement:
> HessianSmoothed3DToVesselnessMeasureImageFilter. Nevertheless, it requires
> the HessianSmoothedRecursiveGaussianImageFilter. I wasn't able to found that
> filter in ITK, so do you know where can I get it or if its a patented code?
>
> Renzo
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From rphellan2210 at gmail.com  Tue Aug 18 16:09:27 2015
From: rphellan2210 at gmail.com (Renzo Ph)
Date: Tue, 18 Aug 2015 17:09:27 -0300
Subject: [ITK] Vessel enhancement
In-Reply-To: <CALzTN-SG9TiJKnFGMOVjPjbYL8QMPbM9USXv8-V+PqQ7XCyWJA@mail.gmail.com>
References: <CAOvLtO66t_kiVtW7poM=fK578Yjf0PHZCSZfuBtfTka5sWxyvA@mail.gmail.com>
 <CALzTN-SG9TiJKnFGMOVjPjbYL8QMPbM9USXv8-V+PqQ7XCyWJA@mail.gmail.com>
Message-ID: <CAOvLtO7pDFnEYEeVWoLb_Ss1o5KggWJZv_AbvsVTTu+e+oKqLw@mail.gmail.com>

Hi Matt,

Thanks for your answer. If you go to this page:
https://github.com/vmtk/vmtk/blob/master/vtkVmtk/Segmentation/itkHessianSmoothed3DToVesselnessMeasureImageFilter.h
 , starting at line 28 it says:

 * The vesselness measure is based on the analysis of the the Hessian
 * eigen system. The vesseleness function is a smoothed (continuous)
 * version of the Frang's vesselness function. The filter takes an
 * image of a Hessian pixels ( SymmetricSecondRankTensor pixels ) and
 * produces an enhanced image. The Hessian input image can be produced
using
 * itkHessianSmoothedRecursiveGaussianImageFilter.

I think I could use the HessianRecursiveGaussianImageFilter, but I would
like to try the HessianSmoothedRecursiveGaussianImageFilter. It may give
better results.

Renzo

2015-08-18 17:05 GMT-03:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Renzo,
>
> Why / where does it require HessianSmoothedRecursiveGaussianImageFilter?
>
> Thanks,
> Matt
>
> On Mon, Aug 17, 2015 at 9:02 AM, Renzo Ph <rphellan2210 at gmail.com> wrote:
> > Hi everybody,
> >
> > I found this class for vessel enhancement:
> > HessianSmoothed3DToVesselnessMeasureImageFilter. Nevertheless, it
> requires
> > the HessianSmoothedRecursiveGaussianImageFilter. I wasn't able to found
> that
> > filter in ITK, so do you know where can I get it or if its a patented
> code?
> >
> > Renzo
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
>
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From matt.mccormick at kitware.com  Tue Aug 18 22:33:19 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 18 Aug 2015 22:33:19 -0400
Subject: [ITK] [ITK-users] Symmetric eigen analysis discrepancy
In-Reply-To: <87AF4E28-B7B4-49E5-9BFD-73F1B966BA3B@inria.fr>
References: <F80D6ED3-0AD2-466C-85BA-38C9DE1AC316@inria.fr>
 <CALzTN-Stue7A1WrwjYP-gPj=6GgnSUNRhb2u0oYddBO8CQmyzg@mail.gmail.com>
 <87AF4E28-B7B4-49E5-9BFD-73F1B966BA3B@inria.fr>
Message-ID: <CALzTN-RKiX4JBsTZPKYvGSh7vm=FDggeWHKwtEx=s2aFv9B5-w@mail.gmail.com>

Hi Olivier,

Thanks for digging down and submitting the patches! The split is fine
-- it is nice to have one topic per commit.  I have rebased them on
the release branch before merging to help get them into the next
bugfix release.

Yes, we should re-use code as much as possible!  I am not sure about
source of the thread-safe warning, be it can be attacked another time
:-).

Thank you for your contribution,
Matt

On Mon, Aug 17, 2015 at 4:10 AM, Olivier Commowick
<Olivier.Commowick at inria.fr> wrote:
> Hi Matt,
>
> Yes, those are very small numbers indeed :) After digging in the code, I
> found two discrepancies with respect to the vnl symmetric eigensystem, so I
> took the vnl code as the reference and did the corrections. I am submitting
> the two patches on gerrit (I didn?t know they would be separated for review,
> I can merge them if necessary):
>
> - http://review.source.kitware.com/#/c/20092/
> - http://review.source.kitware.com/#/c/20093/
>
> That being said, when digging in the code, it is not clear to me why
> SymmetricEigenAnalysis is not just a wrapper on vnl_symmetric_eigensystem.
> This would avoid duplicated code, and I do not see any place in the
> eigensystem code that wouldn?t be thread safe. But again, I am not an expert
> of that code and so I may be wrong. In any case, may be something to think
> of for future work :)
>
> Thanks for the help,
> Olivier
>
> On 13 Aug 2015, at 22:59, Matt McCormick <matt.mccormick at kitware.com> wrote:
>
> Hi Olivier,
>
> Those are some pretty small numbers ;-).  Thanks for sharing your
> experiences.
>
> It may be necessary to build both ITK and vnl/netlib instances with
> debugging symbols and walk through them in a debugger to see where the
> deviation occurs.
>
> As always, patches are welcome :-)
>
> Thanks,
> Matt
>
> On Thu, Aug 13, 2015 at 9:35 AM, Olivier Commowick
> <Olivier.Commowick at inria.fr> wrote:
>
> Hello all,
>
> I have been experiencing a problem when using the itk SymmetricEigenAnalysis
> class in ITK. When using this class, it sometimes produces NaN
> eigenvalues/vectors. On the contrary, the vnl_symmetric_eigensystem doesn?t
> seem to have a problem (and neither does matlab). Looking at the
> documentation, it seems both use QL decomposition but not implemented in the
> same place. In addition, the vnl one is said to be not thread safe, although
> it?s the one working for me.
>
> In fact, I have isolated one 3x3 matrix for which I always have the problem.
>
> A =
> [7.503107128706855667859804009212206062302e-53
> 1.870107888834986371214720644344813262375e-52
> -8.662047753682068190087788895125120421821e-27;
> 1.870107888834986371214720644344813262375e-52
> 4.661140319458029838073740773908360767728e-52
> -2.15896741973055935210319454393408888029e-26;
> -8.662047753682068190087788895125120421821e-27
> -2.15896741973055935210319454393408888029e-26 1]
>
> It?s a weird one I know, but again vnl (and matlab) works great on it. Would
> there be anyone who knows the QL decomposition code enough to help me
> understand and possibly correct the ITK class so that it does the same as
> the VNL one ?
>
> Thanks a lot in advance.
>
> ---
>
> Olivier Commowick, Ph.D.
> Research Scientist
> INRIA Rennes - Bretagne Atlantique, VISAGES Team
> Campus de Beaulieu
> 35042 Rennes
> FRANCE
>
> Phone: +33 2 99 84 25 92
> Email: Olivier.Commowick at inria.fr
> Web: http://olivier.commowick.org/
>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
> ---
>
> Olivier Commowick, Ph.D.
> Research Scientist
> INRIA Rennes - Bretagne Atlantique, VISAGES Team
> Campus de Beaulieu
> 35042 Rennes
> FRANCE
>
> Phone: +33 2 99 84 25 92
> Email: Olivier.Commowick at inria.fr
> Web: http://olivier.commowick.org/
>
>
>
>
>
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From matt.mccormick at kitware.com  Tue Aug 18 22:36:05 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 18 Aug 2015 22:36:05 -0400
Subject: [ITK] [ITK-users] Multi-threading in pointsettopointsetmetric
In-Reply-To: <1439878465576-36021.post@n7.nabble.com>
References: <1439386054435-35985.post@n7.nabble.com>
 <38C7F2DA-EBE7-4A10-9C0F-5F0F5E75450F@gmail.com>
 <001101d0d50d$2e317a30$8a946e90$@kuleuven.be>
 <9103909A-6192-4F07-8C35-DB2354408742@gmail.com>
 <1439878465576-36021.post@n7.nabble.com>
Message-ID: <CALzTN-Rqq9LdmaD4pPeFx53_fKzyAmdgtLQwEWWH=c1Eoa2VYg@mail.gmail.com>

Hello Christophe,

Currently, the unit tests can be used as a reference.  New example
code is welcome.  I will also be contributing some point set v4
registration examples.

Thanks,
Matt

On Tue, Aug 18, 2015 at 2:14 AM, christophevd
<christophe.vandijck at kuleuven.be> wrote:
> Thanks,
>
> I've looked at it, but when I try to set-up the pipeline for pointset to
> pointset registrations, I have errors concerning an unset virtual domain.
> When I try a dummy image to image registration, this does not seem to occur.
>
> Are there any examples available, eg ICP registration, that use the new
> imageregistrationmethodv4 framework?
>
> Regards,
> Christophe
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Multi-threading-in-pointsettopointsetmetric-tp35985p36021.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
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From matt.mccormick at kitware.com  Wed Aug 19 00:20:27 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Aug 2015 00:20:27 -0400
Subject: [ITK] [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1
	on	Ubuntu 14.04
In-Reply-To: <CALzTN-TnV+w7LJnj0eGn=hvMhzqNB5wCTAad-srzhay5z+qawA@mail.gmail.com>
References: <CAK3qF+9v+OGh=hAjK3Dh1oo=rbtLa59ZK=3QT4pjyYsR3=TG1g@mail.gmail.com>
 <CALzTN-T7rtwADbpo=DvuhLrPc5fwU-YkWv94uiks1FpdDQxQVg@mail.gmail.com>
 <CAK3qF+-c3oeEGzpUHjR79NWMBngzY6qz83V8R8bXoWgXoDhT=Q@mail.gmail.com>
 <CALzTN-TUfqGe+TfKBjy=+JZmC=um2XV5sLKGHpC6oU+aYhDO_w@mail.gmail.com>
 <CAK3qF+8s_VPcPLkNLW_bBKUCtKTiTm7FUVj7feQUzRJuze3Jcg@mail.gmail.com>
 <CAK3qF+888dOBB_QvhzbixSbgWMkqZRXAEKaM6d47SYxnmE61Rw@mail.gmail.com>
 <BLUPR04MB676A303299B420A41A98EBA9B7C0@BLUPR04MB676.namprd04.prod.outlook.com>
 <CAK3qF+_8i6t-5mVLqXU_uaA6WFnaMt+fbPAuGQumdtm+1218=g@mail.gmail.com>
 <CALzTN-RXZaZW7tmcJrjctPjO8HzZyY+0HZc-UcKC87+rwY1J1w@mail.gmail.com>
 <CAK3qF+8mNo8RJyjgjTa-JxWQAh0+qPmp0cnX-BK7bb=wikf2Qg@mail.gmail.com>
 <CAK3qF+_QRKWBP7GDeKfUhNRf9mMxDcV2vHU8h2m45oWhK6Ef9g@mail.gmail.com>
 <CALzTN-TnV+w7LJnj0eGn=hvMhzqNB5wCTAad-srzhay5z+qawA@mail.gmail.com>
Message-ID: <CALzTN-Q5Cgb+pzcrZOoorfdovmh4CO0QAJwxf733oCjg76f1eA@mail.gmail.com>

Hi Arnaud,

It looks like there are some missing export macros -- I uploaded a new
patch set to your change.

Thanks,
Matt

On Tue, Aug 18, 2015 at 11:43 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Hi Arnaud,
>
> With the excellent Dockerfile, I have been able to reproduce the error
> :-), but I have not had a chance to dive in further.  I will do soon.
>
> Thanks,
> Matt
>
> On Tue, Aug 18, 2015 at 11:36 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> Matt,
>>
>> Do you have any idea on that matter?
>>
>> Thanks
>> Arnaud
>>
>> On Mon, Aug 17, 2015 at 4:03 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>>
>>> Matt,
>>>
>>> Here you go
>>>
>>> Thanks,
>>> Arnaud
>>>
>>> On Fri, Aug 14, 2015 at 9:54 PM, Matt McCormick
>>> <matt.mccormick at kitware.com> wrote:
>>>>
>>>> On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas <arnaudgelas at gmail.com>
>>>> wrote:
>>>> > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not
>>>> > make
>>>> > much sense to me?), same link error...
>>>> >
>>>> > If it helps, I can prepare a docker build file to track this error (for
>>>> > anyone willing to help)?
>>>>
>>>> That would be awesome :-)
>>>>
>>>> Thanks,
>>>> Matt
>>>
>>>
>>
_______________________________________________
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From bill.lorensen at gmail.com  Wed Aug 19 10:45:47 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Wed, 19 Aug 2015 10:45:47 -0400
Subject: [ITK] [ITK-dev] Recent changes have introduced valgrind defects
Message-ID: <CADZJ4hNFgM_FP_mzLWn+hpb61UU-MzdbkaX=k_3_rj81xZg8gw@mail.gmail.com>

Folks,

Recent changes have caused valgrid defects:
https://open.cdash.org/viewDynamicAnalysis.php?buildid=3962722

Bill

-- 
Unpaid intern in BillsBasement at noware dot com
_______________________________________________
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From matt.mccormick at kitware.com  Wed Aug 19 11:41:14 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Aug 2015 11:41:14 -0400
Subject: [ITK] [ITK-dev] Recent changes have introduced valgrind defects
In-Reply-To: <CADZJ4hNFgM_FP_mzLWn+hpb61UU-MzdbkaX=k_3_rj81xZg8gw@mail.gmail.com>
References: <CADZJ4hNFgM_FP_mzLWn+hpb61UU-MzdbkaX=k_3_rj81xZg8gw@mail.gmail.com>
Message-ID: <CALzTN-R5Qhvee9FQO85pNN5u0J=Ds7Re-ez0kh=8TzQvo4QRqw@mail.gmail.com>

Hi Luc,

These are probably related to this change:

  http://review.source.kitware.com/#/c/19962/

Could you please take a look?

Thanks,
Matt

On Wed, Aug 19, 2015 at 10:45 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> Folks,
>
> Recent changes have caused valgrid defects:
> https://open.cdash.org/viewDynamicAnalysis.php?buildid=3962722
>
> Bill
>
> --
> Unpaid intern in BillsBasement at noware dot com
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
_______________________________________________
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From davis.vigneault at gmail.com  Wed Aug 19 12:33:45 2015
From: davis.vigneault at gmail.com (DVigneault)
Date: Wed, 19 Aug 2015 09:33:45 -0700 (MST)
Subject: [ITK] [ITK-users] Do any of the mesh file formats store
	CellData?
In-Reply-To: <1439817764524-7587691.post@n2.nabble.com>
References: <1439488504178-7587666.post@n2.nabble.com>
 <1439817764524-7587691.post@n2.nabble.com>
Message-ID: <1440002025391-7587696.post@n2.nabble.com>

All--

After a few more iterations, I realized that I only had the problem when I
used itk::RegularSphereMeshSource, and not when I created the mesh
procedurally.  A bit more googling lead to an old ITK thread [1] which
mentioned DisconnectPipeline().  Calling this method on the mesh before
writing to file prevented the point and cell data from being deallocated,
and solved the problem.  I've updated the ITK Wiki example [2] to be a
generic (hopefully useful) example demonstrating how to use point and cell
data containers and write to file.

Thanks again, and apologies for any trouble,

--Davis

[1]
http://public.kitware.com/pipermail/insight-users/2002-October/001368.html
[2] http://itk.org/Wiki/ITK/Examples/Meshes/PointAndCellData



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Do-any-of-the-mesh-file-formats-store-CellData-tp7587666p7587696.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
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From matt.mccormick at kitware.com  Wed Aug 19 12:55:38 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Aug 2015 12:55:38 -0400
Subject: [ITK] [ITK-dev] Recent changes have introduced valgrind defects
In-Reply-To: <55D4A74C.2020506@c-s.fr>
References: <CADZJ4hNFgM_FP_mzLWn+hpb61UU-MzdbkaX=k_3_rj81xZg8gw@mail.gmail.com>
 <CALzTN-R5Qhvee9FQO85pNN5u0J=Ds7Re-ez0kh=8TzQvo4QRqw@mail.gmail.com>
 <55D4A74C.2020506@c-s.fr>
Message-ID: <CALzTN-Q2auurEqnxz-s8FK5AiE8NY9mTSc5YiTV48k3q7TVddA@mail.gmail.com>

On Wed, Aug 19, 2015 at 11:57 AM, Luc Hermitte <luc.hermitte at c-s.fr> wrote:
>>> Recent changes have caused valgrid defects:
>>> https://open.cdash.org/viewDynamicAnalysis.php?buildid=3962722
>> These are probably related to this change:
>>
>>   http://review.source.kitware.com/#/c/19962/
>>

> The tests on lines 160, 166, and 172 are incorrect. After the SetSize,
> the value x[0] is left uninitialized on purpose. It could be equal to
> ref[0].
> Instead, we should test that x[0] is uninitialized. But I don't know any
> way to do it.

In that case, please remove them.


> I'll comment these lines for my next commit (on C++ rvalue references)
> if it's OK with you.

Please keep the patches divided by subject if possible.


Is there a different issue causing the defect in
itkImageToVectorImageFilterTest?

Thanks,
Matt
_______________________________________________
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From jhlegarreta at vicomtech.org  Wed Aug 19 13:45:34 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 19 Aug 2015 19:45:34 +0200
Subject: [ITK] [EXAMPLES] Problems creating a new example through the Python
	script
Message-ID: <CAAKhGh9FxAwOzTRH_HEHu7YHONBW-wds_YVGsByZjYtLmt4g3A@mail.gmail.com>

Hi there,
I'm trying to contribute with an example to ITK, but the CreateNewExample
Python script is yielding an error related to the location of the ITK
source directory.

According to the ITK example contribution documentation [1] and the command
help, to contribute with an example of a given class (say
itk::ParametricSpaceToImageSpaceMeshFilter), I should run

cd /path/to/ITKExamples-build/Utilities
./CreateNewExample.py --class-name ParametricSpaceToImageSpaceMeshFilter
/path/to/source/ITK

It looks like I'm failing to correctly specify the path to my ITK source:
I've tried with the root of my ITK sources (located in a different folder
from the example):
/path/to/source/ITK

Then the Python script fails on line 18:
Traceback (most recen call last):
File "./CreateNewExample.py", line 239, in module
write_all_itk_headers(itk_dir)
File "./CreateNewExample.py", line 18, in write_all_itk_headers
output = file('listofITKheader','w')


I've also tried with the folders where the mentioned filter's files lie
/path/to/source/ITK/Modules/Core/Mesh
and
/path/to/source/ITK/Modules/Core/Mesh/include
and
/path/to/source/ITK/Modules/Core/Mesh/src

In these cases git says
Error: wrong path for itk source tree

Any thoughts?

Thank you,
JON HAITZ


[1]
http://itk.org/ITKExamples/Documentation/Contribute/ContributeWithGit.html#createnewexample
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From matt.mccormick at kitware.com  Wed Aug 19 15:35:05 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Aug 2015 15:35:05 -0400
Subject: [ITK] [EXAMPLES] Problems creating a new example through the
 Python script
In-Reply-To: <CAAKhGh9FxAwOzTRH_HEHu7YHONBW-wds_YVGsByZjYtLmt4g3A@mail.gmail.com>
References: <CAAKhGh9FxAwOzTRH_HEHu7YHONBW-wds_YVGsByZjYtLmt4g3A@mail.gmail.com>
Message-ID: <CALzTN-R7EXmvkAQxG9PXDXSgocDJJtCy2B=19cSSP+WXJCQ+7g@mail.gmail.com>

Hi Jon,

Thanks for working on a new example :-)

What is the actual path to the source tree in your case?

Thanks,
Matt

On Wed, Aug 19, 2015 at 1:45 PM, Jon Haitz Legarreta
<jhlegarreta at vicomtech.org> wrote:
> Hi there,
> I'm trying to contribute with an example to ITK, but the CreateNewExample
> Python script is yielding an error related to the location of the ITK source
> directory.
>
> According to the ITK example contribution documentation [1] and the command
> help, to contribute with an example of a given class (say
> itk::ParametricSpaceToImageSpaceMeshFilter), I should run
>
> cd /path/to/ITKExamples-build/Utilities
> ./CreateNewExample.py --class-name ParametricSpaceToImageSpaceMeshFilter
> /path/to/source/ITK
>
> It looks like I'm failing to correctly specify the path to my ITK source:
> I've tried with the root of my ITK sources (located in a different folder
> from the example):
> /path/to/source/ITK
>
> Then the Python script fails on line 18:
> Traceback (most recen call last):
> File "./CreateNewExample.py", line 239, in module
> write_all_itk_headers(itk_dir)
> File "./CreateNewExample.py", line 18, in write_all_itk_headers
> output = file('listofITKheader','w')
>
>
> I've also tried with the folders where the mentioned filter's files lie
> /path/to/source/ITK/Modules/Core/Mesh
> and
> /path/to/source/ITK/Modules/Core/Mesh/include
> and
> /path/to/source/ITK/Modules/Core/Mesh/src
>
> In these cases git says
> Error: wrong path for itk source tree
>
> Any thoughts?
>
> Thank you,
> JON HAITZ
>
>
> [1]
> http://itk.org/ITKExamples/Documentation/Contribute/ContributeWithGit.html#createnewexample
>
>
>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From jhlegarreta at vicomtech.org  Wed Aug 19 18:04:59 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Thu, 20 Aug 2015 00:04:59 +0200
Subject: [ITK] [EXAMPLES] Problems creating a new example through the
 Python script
In-Reply-To: <CALzTN-R7EXmvkAQxG9PXDXSgocDJJtCy2B=19cSSP+WXJCQ+7g@mail.gmail.com>
References: <CAAKhGh9FxAwOzTRH_HEHu7YHONBW-wds_YVGsByZjYtLmt4g3A@mail.gmail.com>
 <CALzTN-R7EXmvkAQxG9PXDXSgocDJJtCy2B=19cSSP+WXJCQ+7g@mail.gmail.com>
Message-ID: <CAAKhGh-q3JvjPj1Z=oofgm=bxNAWx=midKLCqB8eSJZZG73i6A@mail.gmail.com>

Hi Matt,
thanks for the follow-up.

My /path/to/source/ITK is:
C:/SDKs/ITK/itk-head/ITK

When it comes to submitting patches to the ITK source this path is not a
problem, though.

Any guess?

JON HAITZ





On 19 August 2015 at 21:35, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Jon,
>
> Thanks for working on a new example :-)
>
> What is the actual path to the source tree in your case?
>
> Thanks,
> Matt
>
> On Wed, Aug 19, 2015 at 1:45 PM, Jon Haitz Legarreta
> <jhlegarreta at vicomtech.org> wrote: follow-up.
> > Hi there,
> > I'm trying to contribute with an example to ITK, but the CreateNewExample
> > Python script is yielding an error related to the location of the ITK
> source
> > directory.
> >
> > According to the ITK example contribution documentation [1] and the
> command
> > help, to contribute with an example of a given class (say
> > itk::ParametricSpaceToImageSpaceMeshFilter), I should run
> >
> > cd /path/to/ITKExamples-build/Utilities
> > ./CreateNewExample.py --class-name ParametricSpaceToImageSpaceMeshFilter
> > /path/to/source/ITK
> >
> > It looks like I'm failing to correctly specify the path to my ITK source:
> > I've tried with the root of my ITK sources (located in a different folder
> > from the example):
> > /path/to/source/ITK
> >
> > Then the Python script fails on line 18:
> > Traceback (most recen call last):
> > File "./CreateNewExample.py", line 239, in module
> > write_all_itk_headers(itk_dir)
> > File "./CreateNewExample.py", line 18, in write_all_itk_headers
> > output = file('listofITKheader','w')
> >
> >
> > I've also tried with the folders where the mentioned filter's files lie
> > /path/to/source/ITK/Modules/Core/Mesh
> > and
> > /path/to/source/ITK/Modules/Core/Mesh/include
> > and
> > /path/to/source/ITK/Modules/Core/Mesh/src
> >
> > In these cases git says
> > Error: wrong path for itk source tree
> >
> > Any thoughts?
> >
> > Thank you,
> > JON HAITZ
> >
> >
> > [1]
> >
> http://itk.org/ITKExamples/Documentation/Contribute/ContributeWithGit.html#createnewexample
> >
> >
> >
> >
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
>
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From matt.mccormick at kitware.com  Thu Aug 20 15:01:02 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 20 Aug 2015 15:01:02 -0400
Subject: [ITK] [ITK-dev] CDash Downtime Wednesday 8/26
Message-ID: <CALzTN-TrZNQ2EbK2tio6z4uLWP-HON9ZJg24V1nx4DGMDvyXJA@mail.gmail.com>

Hello,

There is planned CDash downtime effecting ITK / SimpleITK:

Wednesday 8/26, 4:30 - 6:30 PM Eastern US Time


Matt
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From matt.mccormick at kitware.com  Thu Aug 20 22:37:43 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 20 Aug 2015 22:37:43 -0400
Subject: [ITK] [ITK-dev] Failing tests related to eigen analysis change
Message-ID: <CALzTN-Q-r=FUMRJHKEm0AaWk8n58hBzYna-iCv_=txTSwZN9MQ@mail.gmail.com>

Hi Olivier,

Since it requires Module_ITKReview to be ON, we missed some failing
tests that result from the eigen analysis update:

  https://open.cdash.org/viewTest.php?onlyfailed&buildid=3965258


Git bisect confirms they follow from this patch:

  http://review.source.kitware.com/#/c/20092/


If the result is more correct, we should just update the baseline
images, agreed?

Thanks,
Matt
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From Charles.GARRAUD at b-com.com  Fri Aug 21 12:01:32 2015
From: Charles.GARRAUD at b-com.com (Charles GARRAUD)
Date: Fri, 21 Aug 2015 16:01:32 +0000
Subject: [ITK] [ITK-users] 3D/2D registration with
 itkRayCastInterpolateImageFunction
Message-ID: <a950ee36138b42e4a8e704c1c98d61f6@vprd-opci0018.b-com.local>

Hi,

Thanks for your answer. My coworker tried a few experiments and here are the results.

1- Identity test

We first generated a DRR with no motion (./GenerateProjection  -t -0 0 0 /data/BrainWeb/brainweb165a10f17.mha  projection.mhd).
Then we tested the registration script against the generated projection (./IntensityBased2D3DRegistration  -t 0 0 0 /data/BrainWeb/brainweb165a10f17.mha  projection.mhd).
Final transform is not Identity...

Iteration: 0
Similarity: 131072
Position: [2.153758987711231, -2.2185832563517227, 0.13470062489014054, -0.66118
02734569167, -2.4462025457148213, -0.0002246616408056843]
Iteration: 1
Similarity: 122450
Position: [2.4187300917467964, -3.773162111555794, -0.9755229703094714, -2.07458
8877483574, -0.537315819701732, -2.5768321309606987]
Iteration: 2
Similarity: 119478
Position: [2.470584982717309, -5.832612304775175, -2.348307788159638, -4.0557547
39210535, 1.4910774048756184, -1.2233031986406182]
Iteration: 3
Similarity: 89670.6
Position: [0.5294851105555496, -7.488726388306614, -4.4764177747675395, -5.03037
4241557845, 3.3801762897017995, -0.5584817620767086]
Iteration: 4
Similarity: 117654
Position: [0.8070122506477464, -6.806625924939558, -4.184289615511856, -5.001986
557143484, 3.568233605537047, 1.2680470135769937]
Iteration: 5
Similarity: 120137
Position: [0.8986014091035406, -7.370639324747829, -4.600946472732313, -4.991937
760754552, 4.252209504897678, 1.4468579892082352]
Iteration: 6
Similarity: 121092
Position: [1.0389929549096333, -7.269481426616463, -4.5893416922553545, -4.80836
5473207177, 4.620462234241913, 2.341628219578606]
Result =
Translation X = 1.03899
Translation Y = -7.26948
Translation Z = -4.58934
Rotation X = -4.80837
Rotation Y = 4.62046
Rotation Z = 2.34163
Iterations    = 8
Metric value  = 122604

2- Metric test

Since the registration pipeline involved an Euler3DTransform transformation but our results were not converging even for translations only, I made a simple test case :

First of all, I have generated a DRR projection with a (-100, -100, -100) translation with this command line :

./GenerateProjection  -t -100 -100 -100 brainweb165a10f17.mha projection.mhd 

After that, I have generated translated DRR projections, from 5 to 20 with a step of 5 along the X axis and the Y axis one at a time. 
The aim was to check if, by plotting the metric value for a range of displacements all around the translated projection, the best similarity value would be obtained for the exact displacement we used to generate this translated projection.

For instance, for the translated projection obtained by this command line : 

./GenerateProjection  -t -105 -100 -100 brainweb165a10f17.mha projectionx5.mhd 

The best similarity value between projection.mhd and projectionx5.mhd would be obtained for a (5, 0) displacement.

The result of this experiment can be observed on the following table :

	x0 y0	x5 y0	x10 y0	x15 y0	x20 y0	x0 y5	x0 y10	x0 y15	x0 y20
Best (x, y)	(0, 0)	(9, 0)	(18, 0)	(26, 0)	(34, 0)	(0, 9)	(0, 17)	(0, 26)	(0, 34)
Similarity	131072	112939	100953	94482	90848	113021	101068	95829	92632

We can observe that, even for translations only, our results do not converge to the right value, which can lead us to imagine that the metric is not appropriate for the purpose of registrating the example data...

Is this test case relevant ? It seems to indicate that, even for simple cases, the registration is not reliable and could be the source of the wrong results I have.

Thanks for your help!
	
Charles
Garraud

{P}
Software Engineer
E-health
{T}
+33?(0)?2 56 35 88 25
{W}
www.b-com.com


-----Message d'origine-----
De?: Insight-users [mailto:insight-users-bounces at itk.org] De la part de Siavash Khallaghi
Envoy??: lundi 17 ao?t 2015 21:51
??: insight-users at itk.org
Objet?: Re: [ITK-users] 3D/2D registration with itkRayCastInterpolateImageFunction

Hi Charles,

For the record, I do not think that you have a software bug per say. I think your problem is a bit more fundamental, i.e. the combination of optimizer/metric might not have sufficient capture range to guide the registration to the true solution.

In order to investigate this, I would suggest trying the following:

1. If you generate your projection from identity (which I assume is the true solution), and start your registration from identity, would the registration converge to identity as well? This tells you how stable your metric is.

2. At this point, I would definitely start plotting the metric value against transformation parameters. See /Section 3.10.1 Mean Squares Metric:
Exploring a Metric/ of the  Software Guide <http://se.csie.dyu.edu.tw/canseco/PDF/InsightSoftwareGuide-Book2-4.6.0.pdf>
. Since your registration does not converge to the correct solution for rotations, I suspect that it is getting stuck in a local minima for these parameters.

Siavash



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From marco.dev.open at gmail.com  Fri Aug 21 12:16:00 2015
From: marco.dev.open at gmail.com (Marco Dev)
Date: Fri, 21 Aug 2015 20:46:00 +0430
Subject: [ITK] [ITK-dev] gdcm2.x dicom parse
Message-ID: <CAKcUdn5a0X-LOZ=Ph7sftOP6a0eTi4FD4QiPaq_H29YBeKKuPQ@mail.gmail.com>

Hi ,
As you know gdcm used by ITK for parsing dicom images how many kind of
dicom images can read with the GDCM 2.X I also read some feature about
reding Compress dicom images .....
 It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE ......
for all of kind of DICOM images ?
Thanks
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From siavashk at ece.ubc.ca  Fri Aug 21 14:04:27 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Fri, 21 Aug 2015 11:04:27 -0700 (MST)
Subject: [ITK] [ITK-users] 3D/2D registration with
 itkRayCastInterpolateImageFunction
In-Reply-To: <a950ee36138b42e4a8e704c1c98d61f6@vprd-opci0018.b-com.local>
References: <b0b244228f0c4cc9a2d55169deff2cd3@vprd-opci0018.b-com.local>
 <a950ee36138b42e4a8e704c1c98d61f6@vprd-opci0018.b-com.local>
Message-ID: <1440180267538-36026.post@n7.nabble.com>

Hi Charles,

Your results /suggest/ that the optimizer does not converge to the solution.
Based on your results, I cannot conclusively say why this happens. This is
why I asked you to plot the metric.

The identity test and metric test basically tell you this: "If you start the
registration from these initial parameters, you will converge to some final
parameters." The final parameters being /Best (x, y)/ in your notation.
However, this experiment does not tell you /why/ you converge to these
parameters.

To make it more clear, I will make you an analogy. Think of the registration
as a sledge that takes you from one point on the mountain (A) to the lowest
point in the valley (B). The goal is to arrive at the lowest valley. During
your trip from A to B, you only see glimpses of your position through your
goggles (observer values). After some iterations you arrive at B (final
parameters). If you did not have a map of what the curvature of the mountain
looks like, you have no idea why you ended up at B. You also have no idea if
you are indeed at the lowest valley (global minima). This is your problem.

What I would like to ask you to do, is to plot the metric for a range of
values around the true solution. For example, if the solution is at
x-translation = 0.0 mm an you start at x = 6.0 mm, you should plot the
metric between [-10.0, +10.0] mm (+4 mm for padding). Do this for other
transformation parameters as well. Keep the projection constant during this
experiment.

For example, if your metric looks like the attached image, we can safely say
that the registration gets stuck at a local minima around 8.0 mm. If that is
the case, you have to: 1) make your metric more convex; 
and/or 2) start closer to the solution. There are solutions to both of these
problems.

<http://itk-users.7.n7.nabble.com/file/n36026/metric_pm10.png> 

Siavash





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From prashanth.dumpuri at gmail.com  Fri Aug 21 17:22:23 2015
From: prashanth.dumpuri at gmail.com (Prashanth)
Date: Fri, 21 Aug 2015 21:22:23 +0000
Subject: [ITK] [ITK-users] speed function for itkSpeedToPathFilter
Message-ID: <CAP+vBKQN7E2vRR5YxZrqKYioCN5jwW+3FbQ4fDV55n2WVwBv5A@mail.gmail.com>

All,

I'm working on finding the shortest path between two points in a vessel
tree. itkSpeedToPathFilter seems to be working well for me as long as I
select the right speed function. Digging through Insight Journal, I found a
link to Deschamp's Ph.D. thesis (
https://tel.archives-ouvertes.fr/file/index/docid/45537/filename/index.html)
which outlines one method to select a speed function:

1. Approximate centerline based on the input image
2. Segmentation using the approximate centerline
3. Use the segmented image and approximate centerline to create an image
with signed distances to the approximate centerline
4. Use the above image as the  input speed function for itkSpeedToPathFilter

The above steps seem to work (I say 'seem to work' because I tested it just
three 2D images so far), but are there other methods to select the speed
function? My input images are contrast enhanced CT images and the vessels
are easy to identify and segment. Any help on how to select the correct
speed function will be appreciated.

Thanks
Prashanth
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From matt.mccormick at kitware.com  Fri Aug 21 17:28:05 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 21 Aug 2015 17:28:05 -0400
Subject: [ITK] [ITK-dev] gdcm2.x dicom parse
In-Reply-To: <CAKcUdn5a0X-LOZ=Ph7sftOP6a0eTi4FD4QiPaq_H29YBeKKuPQ@mail.gmail.com>
References: <CAKcUdn5a0X-LOZ=Ph7sftOP6a0eTi4FD4QiPaq_H29YBeKKuPQ@mail.gmail.com>
Message-ID: <CALzTN-R98=9LdoLZSJNKCARtARvrUx0VFWXkULgXhZck7uHW-g@mail.gmail.com>

Hi Marco,

A list of supported formats can be found here:

  http://gdcm.sourceforge.net/wiki/index.php/Main_Page

ITK does build with JPEG 2000 support.

HTH,
Matt

On Fri, Aug 21, 2015 at 12:16 PM, Marco Dev <marco.dev.open at gmail.com> wrote:
> Hi ,
> As you know gdcm used by ITK for parsing dicom images how many kind of dicom
> images can read with the GDCM 2.X I also read some feature about reding
> Compress dicom images .....
>  It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE ......
> for all of kind of DICOM images ?
> Thanks
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
_______________________________________________
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From fisidoro at ethz.ch  Sat Aug 22 03:02:28 2015
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Sat, 22 Aug 2015 07:02:28 +0000
Subject: [ITK] [ITK-users] ITK Python wrapping
Message-ID: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>

I am a newbie, trying to use ITK with Python wrapping on Windows 7. Using the short ITKSoftwareGuide, but could not find a comprehensive guide to use Python wrappers for dummies.

My problem is: I can't make the Python wrapping work. I can import itk with no errors when running Python in the new virtual environment configured inside my ITK build directory. But:


-        As in this example (http://www.vtk.org/Wiki/ITK/Release_4/Wrapping/Examples) , I get no error for "PixelType = itk.UC" but when trying "ImageType = itk.Image[ImageType, 2]" I get the error1 in attachment (no module named _ITKPyBasePython ... something related to SWIG, that I don't have). Do I need to install Swig? (In a similar question in the iTK Wiki page the answer was: you will need the ITKv4 wrapping to use this example ... ?)


-        Seemingly, in the new virtual env I try to run "python ImageRegistration3.py BrainProtonDensitySliceBorder20.png BrainProtonDensitySliceShifted13x17y.png output_image" in attachment (modified from the Examples folder with proper inputs), which starts with "import itk ; fixedImageReader  = itkImageFileReaderF2_New()" I get the error "name itkImageFileReaderF2_New is not defined".


Lacking of a guide, I actually have no clue about how to use Python wrappers in general. Is there any guide that I could follow?

Useful info:

I have successfully built ITK with Cmake with the ITK-WRAP-PYTHON option. The build had some failures related to the CastXML tool... could this be a problem?

I configured a new Python virtual environment within my ITK build directory.

I copied/pasted the file /path/to/myITK_wrapped/Wrapping/Generators/Python/Debug/WrapITK.pth into wrap_itk_venv/Lib/site-packages. Is that correct to generate a symbolic link in Windows?

I also added path/to/myITK_wrapped,  path/to/myITK_wrapped/bin and path/to/myITK_wrapped/bin/Debug in my user env variable PATH

Thank you for your help.

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From dan.muel at gmail.com  Sun Aug 23 05:49:18 2015
From: dan.muel at gmail.com (Dan Mueller)
Date: Sun, 23 Aug 2015 19:19:18 +0930
Subject: [ITK] [ITK-users] speed function for itkSpeedToPathFilter
In-Reply-To: <CAP+vBKQN7E2vRR5YxZrqKYioCN5jwW+3FbQ4fDV55n2WVwBv5A@mail.gmail.com>
References: <CAP+vBKQN7E2vRR5YxZrqKYioCN5jwW+3FbQ4fDV55n2WVwBv5A@mail.gmail.com>
Message-ID: <CAPNvZ5bVU1nUCRb_A1QBAMU0bHhea-Q+TTxbwKKE8pQasu-i4w@mail.gmail.com>

Hi Prashanth,

Essentially you want your speed function to be white (1.0) in the
vessels and black (0.0) outside of the vessels ? any way you can
achieve this is fine. The method you have outline is very general, and
the issue is step (1) i.e. finding an approximate centreline. Some
have suggested achieving this by applying multiscale Hessian line
filtering (aka vessel enhancement filtering) such as Sato/Frangi
method ? while this can achieve good results, personally I find this
method very slow. In my own work, I have found morphological top-hat
by opening (aka white top-hat or WTH) produces good results at a
fraction of the computation expense, especially using the box
structuring element with acceleration (e.g. see [1]).

Good luck.

Cheers, Dan

[1] ?Direct volume illustration for cardiac applications,? chapter 4,
page 83?109, http://eprints.qut.edu.au/17028/1/Daniel_Mueller_Thesis.pdf

On 22 August 2015 at 06:52, Prashanth <prashanth.dumpuri at gmail.com> wrote:
> All,
>
> I'm working on finding the shortest path between two points in a vessel
> tree. itkSpeedToPathFilter seems to be working well for me as long as I
> select the right speed function. Digging through Insight Journal, I found a
> link to Deschamp's Ph.D. thesis
> (https://tel.archives-ouvertes.fr/file/index/docid/45537/filename/index.html)
> which outlines one method to select a speed function:
>
> 1. Approximate centerline based on the input image
> 2. Segmentation using the approximate centerline
> 3. Use the segmented image and approximate centerline to create an image
> with signed distances to the approximate centerline
> 4. Use the above image as the  input speed function for itkSpeedToPathFilter
>
> The above steps seem to work (I say 'seem to work' because I tested it just
> three 2D images so far), but are there other methods to select the speed
> function? My input images are contrast enhanced CT images and the vessels
> are easy to identify and segment. Any help on how to select the correct
> speed function will be appreciated.
>
> Thanks
> Prashanth
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From matt.mccormick at kitware.com  Sun Aug 23 10:42:45 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 23 Aug 2015 10:42:45 -0400
Subject: [ITK] [EXAMPLES] Problems creating a new example through the
 Python script
In-Reply-To: <CAAKhGh-q3JvjPj1Z=oofgm=bxNAWx=midKLCqB8eSJZZG73i6A@mail.gmail.com>
References: <CAAKhGh9FxAwOzTRH_HEHu7YHONBW-wds_YVGsByZjYtLmt4g3A@mail.gmail.com>
 <CALzTN-R7EXmvkAQxG9PXDXSgocDJJtCy2B=19cSSP+WXJCQ+7g@mail.gmail.com>
 <CAAKhGh-q3JvjPj1Z=oofgm=bxNAWx=midKLCqB8eSJZZG73i6A@mail.gmail.com>
Message-ID: <CALzTN-TCU4pGHcqT4mq_GLbmhQFcXJS_Ax4sbtNX3YiP+d1H4g@mail.gmail.com>

Hi Jon,

I am not sure why there was difficulty writing to the file, but this
patch avoids writing to a file altogether:

  http://review.source.kitware.com/#/c/20117/

Also, this patch handles paths better on Windows:

  http://review.source.kitware.com/#/c/20116/

Thanks,
Matt

On Wed, Aug 19, 2015 at 6:04 PM, Jon Haitz Legarreta
<jhlegarreta at vicomtech.org> wrote:
> Hi Matt,
> thanks for the follow-up.
>
> My /path/to/source/ITK is:
> C:/SDKs/ITK/itk-head/ITK
>
> When it comes to submitting patches to the ITK source this path is not a
> problem, though.
>
> Any guess?
>
> JON HAITZ
>
>
>
>
>
> On 19 August 2015 at 21:35, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi Jon,
>>
>> Thanks for working on a new example :-)
>>
>> What is the actual path to the source tree in your case?
>>
>> Thanks,
>> Matt
>>
>> On Wed, Aug 19, 2015 at 1:45 PM, Jon Haitz Legarreta
>> <jhlegarreta at vicomtech.org> wrote: follow-up.
>>
>> > Hi there,
>> > I'm trying to contribute with an example to ITK, but the
>> > CreateNewExample
>> > Python script is yielding an error related to the location of the ITK
>> > source
>> > directory.
>> >
>> > According to the ITK example contribution documentation [1] and the
>> > command
>> > help, to contribute with an example of a given class (say
>> > itk::ParametricSpaceToImageSpaceMeshFilter), I should run
>> >
>> > cd /path/to/ITKExamples-build/Utilities
>> > ./CreateNewExample.py --class-name ParametricSpaceToImageSpaceMeshFilter
>> > /path/to/source/ITK
>> >
>> > It looks like I'm failing to correctly specify the path to my ITK
>> > source:
>> > I've tried with the root of my ITK sources (located in a different
>> > folder
>> > from the example):
>> > /path/to/source/ITK
>> >
>> > Then the Python script fails on line 18:
>> > Traceback (most recen call last):
>> > File "./CreateNewExample.py", line 239, in module
>> > write_all_itk_headers(itk_dir)
>> > File "./CreateNewExample.py", line 18, in write_all_itk_headers
>> > output = file('listofITKheader','w')
>> >
>> >
>> > I've also tried with the folders where the mentioned filter's files lie
>> > /path/to/source/ITK/Modules/Core/Mesh
>> > and
>> > /path/to/source/ITK/Modules/Core/Mesh/include
>> > and
>> > /path/to/source/ITK/Modules/Core/Mesh/src
>> >
>> > In these cases git says
>> > Error: wrong path for itk source tree
>> >
>> > Any thoughts?
>> >
>> > Thank you,
>> > JON HAITZ
>> >
>> >
>> > [1]
>> >
>> > http://itk.org/ITKExamples/Documentation/Contribute/ContributeWithGit.html#createnewexample
>> >
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Community mailing list
>> > Community at itk.org
>> > http://public.kitware.com/mailman/listinfo/community
>> >
>
>

From matt.mccormick at kitware.com  Sun Aug 23 16:53:27 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 23 Aug 2015 16:53:27 -0400
Subject: [ITK] [ITK-users] ITK Python wrapping
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>
Message-ID: <CALzTN-R2_viV6Y0-AkNpmicZTOaaA98E99ReZSoWkU6tb_xuYQ@mail.gmail.com>

Hi Fabio,

There is information in The ITK Software Guide, but we could improve
it based on your experiences.


In the ITK "lib" directory, or one of its subdirectories, there should
be a _ITKPyBasePython.pyd.  This is the file that the error message
indicates it cannot find. First, check that it exists.  Next, check
that the folder it lives in is listed in the WrapITK.pth file and that
the WrapITK.pth file was added to the Libs/site-packages directory of
your virtualenv.


Some more information regarding the other questions:

- Swig is automatically downloaded when building ITK Python wrapping,
but it is no longer needed after the wrappers are built.

- There should not be CastXML errors, and if there were, that may be a
problem.  What are the errors?

- Windows cannot create symbolic links -- files must be copied
instead.  We can simplify the documentation to state that the
WrapITK.pth file should be copied on all platforms.  Where was the
instruction to create a symbolic link?


Please let us know how it goes,
Matt



On Sat, Aug 22, 2015 at 3:02 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> I am a newbie, trying to use ITK with Python wrapping on Windows 7. Using
> the short ITKSoftwareGuide, but could not find a comprehensive guide to use
> Python wrappers for dummies.
>
>
>
> My problem is: I can?t make the Python wrapping work. I can import itk with
> no errors when running Python in the new virtual environment configured
> inside my ITK build directory. But:
>
>
>
> -        As in this example
> (http://www.vtk.org/Wiki/ITK/Release_4/Wrapping/Examples) , I get no error
> for ?PixelType = itk.UC? but when trying ?ImageType = itk.Image[ImageType,
> 2]? I get the error1 in attachment (no module named _ITKPyBasePython ?
> something related to SWIG, that I don?t have). Do I need to install Swig?
> (In a similar question in the iTK Wiki page the answer was: you will need
> the ITKv4 wrapping to use this example ? ?)
>
>
>
> -        Seemingly, in the new virtual env I try to run ?python
> ImageRegistration3.py BrainProtonDensitySliceBorder20.png
> BrainProtonDensitySliceShifted13x17y.png output_image? in attachment
> (modified from the Examples folder with proper inputs), which starts with
> ?import itk ; fixedImageReader  = itkImageFileReaderF2_New()? I get the
> error ?name itkImageFileReaderF2_New is not defined?.
>
>
>
> Lacking of a guide, I actually have no clue about how to use Python wrappers
> in general. Is there any guide that I could follow?
>
>
>
> Useful info:
>
>
>
> I have successfully built ITK with Cmake with the ITK-WRAP-PYTHON option.
> The build had some failures related to the CastXML tool? could this be a
> problem?
>
>
>
> I configured a new Python virtual environment within my ITK build directory.
>
>
>
> I copied/pasted the file
> /path/to/myITK_wrapped/Wrapping/Generators/Python/Debug/WrapITK.pth into
> wrap_itk_venv/Lib/site-packages. Is that correct to generate a symbolic link
> in Windows?
>
>
>
> I also added path/to/myITK_wrapped,  path/to/myITK_wrapped/bin and
> path/to/myITK_wrapped/bin/Debug in my user env variable PATH
>
>
>
> Thank you for your help.
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
_____________________________________
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From matt.mccormick at kitware.com  Mon Aug 24 11:08:22 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 24 Aug 2015 11:08:22 -0400
Subject: [ITK] [ITK-users] ITK Python wrapping
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409435ACEB17@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>
 <CALzTN-R2_viV6Y0-AkNpmicZTOaaA98E99ReZSoWkU6tb_xuYQ@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACEB17@MBX212.d.ethz.ch>
Message-ID: <CALzTN-R3f+fi5pRze+a68d14YgLcYJPCnwwjPnz5Fm9W4hBV8A@mail.gmail.com>

Hi Fabio,

> - Well, I have a ITKPyBasePython.pyc file in the ITK lib (and the things you told me to check are allright). So the difference is that the name has no underscore _ITKPyBasePython (as reported in the error) and the extension is pyc rather than pyd (although I have read it should not make the difference). Are those things relevant? If yes, how to correct for them? Maybe the dlls were not properly compiled so the underscore is missing?

Both the .pyc and the .pyd files are required.


> Depending on your reply to this email, I will then try to build ITK with Python wrapping again so that I can report the compilation failures I got regarding CastXML.

Great, thank you.  A Release build instead of a Debug build is
recommended -- build size and runtime performance are greatly
improved.  There is on going work to substantially decrease the
wrapping build time in ITK Git master, but it is currently unstable.
The 4.8.0 release is recommended until that is resolved.


> About the symbolic link, I just read on the guide "ln -s /path/to/ITK-Wrapped/Wrapping/Generators/Python/WrapITK.pth" and went to find out what ln -s was ... but you are right, the guide says to copy the file, so I guess you don't have improve this part. Maybe just specifiy that there is no need to download Swig.

Thanks for the feedback.  We will improve the wrapping process description.


> Thank you, I have spent 5 long days already with no success on this issue (which seems to me a very common issue for users willing to use the Python wrapping, from my extensive google search).

Yes, wrapping has been difficult in the past, but things are changing.
With your help, it will improve even quicker :-).


Thanks,
Matt
_____________________________________
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From marina.bendersky at gmail.com  Mon Aug 24 15:37:05 2015
From: marina.bendersky at gmail.com (Marina Bendersky)
Date: Mon, 24 Aug 2015 12:37:05 -0700
Subject: [ITK] [ITK-users] How can I convert a versor into the three
	rotation	angles?
Message-ID: <CABy89onmiLg4sY+BAz=a_X=gqxTTxFrCP_-xb1XsQfBNPXGd4Q@mail.gmail.com>

 New to image registration and ITK, I?m following the ITK software guide
and trying to understand the different outputs. I?m focusing on the example
ImageRegistration8.cxx: a rigid transform in 3D, and the example is
detailed in the Software guide Book2, section 3.6.4.

The manual explains that the versor (page 211)

? Versor=(?6.03744e?05,5.91487e?06,?0.0871932)

is equivalent to a rotation of 9.98 degrees around the Z axis.

I understand a versor is a unit quarterion, and have been trying to convert
this versor to the ~10 degrees angle (in the z direction) using the
equations in wikipedia. I read the slides on Quarterions found at
http://www.itk.org/CourseWare/Training/QuaternionsI.pdf, among other
sources, but I still cannot resolve my question.

I appreciate any help and advice.

Thank you!
Marina
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From siavashk at ece.ubc.ca  Mon Aug 24 15:15:15 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Mon, 24 Aug 2015 12:15:15 -0700 (MST)
Subject: [ITK] [ITK-users] How can I convert a versor into the three
 rotation angles?
In-Reply-To: <CABy89onmiLg4sY+BAz=a_X=gqxTTxFrCP_-xb1XsQfBNPXGd4Q@mail.gmail.com>
References: <CABy89onmiLg4sY+BAz=a_X=gqxTTxFrCP_-xb1XsQfBNPXGd4Q@mail.gmail.com>
Message-ID: <1440443715241-36033.post@n7.nabble.com>

Hi Marina,

https://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles

should be helpful for you.

Siavash



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-How-can-I-convert-a-versor-into-the-three-rotation-angles-tp36032p36033.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From pablo.hernandez.cerdan at outlook.com  Mon Aug 24 22:52:59 2015
From: pablo.hernandez.cerdan at outlook.com (=?iso-8859-1?B?UGFibG8gSGVybuFuZGV6?=)
Date: Tue, 25 Aug 2015 04:52:59 +0200
Subject: [ITK] [ITK-users] Contour detector: Pb algorithm in itk?
Message-ID: <DUB125-W94D9509D7ED5C599C66ACED6610@phx.gbl>

Hello, is there any external module using ITK, that has implemented the Pb family of algorithms?

http://www.eecs.berkeley.edu/Research/Projects/CS/vision/grouping/resources.html

Thanks,
Pablo
 		 	   		  
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From lassi.paavolainen at jyu.fi  Tue Aug 25 08:54:47 2015
From: lassi.paavolainen at jyu.fi (Paavolainen, Lassi)
Date: Tue, 25 Aug 2015 12:54:47 +0000
Subject: [ITK] [ITK-users] Building ITK 4.8.0 with Python wrapping in
	Visual	Studio 2015
Message-ID: <BB43A6B0CAEAFC439640CD9D13607DC24E6D30A2@mbs1.ad.jyu.fi>

I'm trying to build ITK 4.8.0 with Python wrapping using Visual Studio 2015. Have anyone been successful in this? I know that with CastXML the Python wrapping issues were solved in ITK 4.8.0 so the issues might be related to Visual Studio 2015 instead of Python wrapping.

Here are some error messages I get. First in CMake I get
Debug Assertion Failed!
...\src\itkhdf5\CMake\CMakeFiles\CMakeTmp\Debug\cmTC_07479.exe
File: minkernel\crts\ucrt\inc\corecrt_internal_stdio_output.h
Expression: ("Invalid integer length modifier",0)
and
Checking for appropriate format for 64 bit long:
CMake: Width with l64 failed with result: FAILED_TO_RUN

same happens with a few other types as well. Maybe this already indicate coming issues. Anyway I went to build the solution which fails with
Error	C2664	'void llvm::BitstreamWriter::EmitRecordWithBlob<uint64_t>(unsigned int,llvm::SmallVectorImpl<uint64_t> &,llvm::StringRef)': cannot convert argument 3 from 'unsigned int *' to 'llvm::StringRef' [C:\ITK-4.8.0\Wrapping\Generators\CastXML\clang-prefix\src\clang-build\lib\Serialization\clangSerialization.vcxproj]	clang	C:\ITK-4.8.0\Wrapping\Generators\CastXML\cfe-3.6.0\lib\Serialization\ASTWriter.cpp	1517
and with similar errors.

Any ideas how to fix it? I haven't yet tried building ITK without Python wrapping but could do it now.

Lassi
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From matt.mccormick at kitware.com  Tue Aug 25 10:31:06 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 25 Aug 2015 10:31:06 -0400
Subject: [ITK] [ITK-users] FW:  ITK Python wrapping
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409435ACECAC@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>
 <CALzTN-R2_viV6Y0-AkNpmicZTOaaA98E99ReZSoWkU6tb_xuYQ@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACEB17@MBX212.d.ethz.ch>
 <CALzTN-R3f+fi5pRze+a68d14YgLcYJPCnwwjPnz5Fm9W4hBV8A@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACECAC@MBX212.d.ethz.ch>
Message-ID: <CALzTN-SX9vduwxUSTi-XFVStWLCTYCdGccjEPy6a+XiEtH1Ryg@mail.gmail.com>

Hi Fabio,

Thanks for the updates.

The apparent errors are not actual errors.  These result when CMake
configuration runs (indicated by the preceding "--"), and CMake tests
the availability of compiler features with try_compiles [1].  If an
error occurs, then that feature is not used in the build.

It is good to see that the *.pyd files are there and your Python path.
There should still be *.dll files whose folder needs to be added to
the PATH system environmental variable.  These are usually in the
"bin" instead of "lib" directory. Search for a file
"ITKCommon-4.8.dll" if you built ITK 4.8.

Hope this helps,
Matt

PS. Please reply-to-all so conversations remain on the mailing lists.

[1] http://www.cmake.org/cmake/help/v3.3/command/try_compile.html

On Tue, Aug 25, 2015 at 3:02 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Sorry forgot the attachments
>
> -----Original Message-----
> From: D'Isidoro Fabio
> Sent: Dienstag, 25. August 2015 09:01
> To: 'Matt McCormick'
> Subject: RE: [ITK-users] ITK Python wrapping
>
> One more thing: in the guide it's written to add to the PATH the directories containing the .dll files, suggesting ITKbuild, ITKbuild/bin and ITKbuild/bin/Release.
>
> However as you can see from the attachments the suggested directory has only executables, while the .lib files (I don't have .dll files) are in the ITKbuild/lib/Release (second attachment)...
>
> Anyway I tried to add the the ITKbuild/lib/Release directory to the PATH but it did not work either.
>
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 24. August 2015 17:08
> To: D'Isidoro Fabio
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] ITK Python wrapping
>
> Hi Fabio,
>
>> - Well, I have a ITKPyBasePython.pyc file in the ITK lib (and the things you told me to check are allright). So the difference is that the name has no underscore _ITKPyBasePython (as reported in the error) and the extension is pyc rather than pyd (although I have read it should not make the difference). Are those things relevant? If yes, how to correct for them? Maybe the dlls were not properly compiled so the underscore is missing?
>
> Both the .pyc and the .pyd files are required.
>
>
>> Depending on your reply to this email, I will then try to build ITK with Python wrapping again so that I can report the compilation failures I got regarding CastXML.
>
> Great, thank you.  A Release build instead of a Debug build is recommended -- build size and runtime performance are greatly improved.  There is on going work to substantially decrease the wrapping build time in ITK Git master, but it is currently unstable.
> The 4.8.0 release is recommended until that is resolved.
>
>
>> About the symbolic link, I just read on the guide "ln -s /path/to/ITK-Wrapped/Wrapping/Generators/Python/WrapITK.pth" and went to find out what ln -s was ... but you are right, the guide says to copy the file, so I guess you don't have improve this part. Maybe just specifiy that there is no need to download Swig.
>
> Thanks for the feedback.  We will improve the wrapping process description.
>
>
>> Thank you, I have spent 5 long days already with no success on this issue (which seems to me a very common issue for users willing to use the Python wrapping, from my extensive google search).
>
> Yes, wrapping has been difficult in the past, but things are changing.
> With your help, it will improve even quicker :-).
>
>
> Thanks,
> Matt
_____________________________________
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From marco.dev.open at gmail.com  Tue Aug 25 10:41:32 2015
From: marco.dev.open at gmail.com (Marco Dev)
Date: Tue, 25 Aug 2015 19:11:32 +0430
Subject: [ITK] [ITK-dev] Fusion in action
Message-ID: <CAKcUdn5fRnVzWiwMJiWE4F9oVCPNsXhWU2LCRq7LhDGwCE5OsQ@mail.gmail.com>

Hi,
As you knew  there some Examples in itk for registration RIGID -
DEFORMABLE  .... in other hand
We have Fusion issue in registration which algorithm should be used for
doing the FUSION can you give me a guide line whole this subject
Thanks
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From fisidoro at ethz.ch  Tue Aug 25 11:25:48 2015
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Tue, 25 Aug 2015 15:25:48 +0000
Subject: [ITK] [ITK-users] FW:  ITK Python wrapping
In-Reply-To: <CALzTN-SX9vduwxUSTi-XFVStWLCTYCdGccjEPy6a+XiEtH1Ryg@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>
 <CALzTN-R2_viV6Y0-AkNpmicZTOaaA98E99ReZSoWkU6tb_xuYQ@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACEB17@MBX212.d.ethz.ch>
 <CALzTN-R3f+fi5pRze+a68d14YgLcYJPCnwwjPnz5Fm9W4hBV8A@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACECAC@MBX212.d.ethz.ch>
 <CALzTN-SX9vduwxUSTi-XFVStWLCTYCdGccjEPy6a+XiEtH1Ryg@mail.gmail.com>
Message-ID: <50B858FB5F53124F9E32314E5C1B409435ACED36@MBX212.d.ethz.ch>

Hi Matt,

Thank you. Actually I have the .dll in the bin/release. 

Shortly, I (redundantly) added then ITKbuild/bin, ITKbuild/bin/release, ITKbuild/lib, ITKbuild/lib/release to BOTH my PATH environmental variable and the WrapITK.pth. Still not working, however I have a new error (see attachment 'error').

Therefore I went to check the ITKTransformPython module but it's not there in lib/Release where all other .lib files relative to the other modules are. I went in the directory shown in attachment 'directory' (it's in the Wrapping/Module/.. directory) and found a  log file (attachment): the build of this module failed (I check other modules and there build there did not fail). Could you please read the log? Why did just this module fail?

Thank you again!

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com] 
Sent: Dienstag, 25. August 2015 16:31
To: D'Isidoro Fabio; insight-users at itk.org
Subject: Re: FW: [ITK-users] ITK Python wrapping

Hi Fabio,

Thanks for the updates.

The apparent errors are not actual errors.  These result when CMake configuration runs (indicated by the preceding "--"), and CMake tests the availability of compiler features with try_compiles [1].  If an error occurs, then that feature is not used in the build.

It is good to see that the *.pyd files are there and your Python path.
There should still be *.dll files whose folder needs to be added to the PATH system environmental variable.  These are usually in the "bin" instead of "lib" directory. Search for a file "ITKCommon-4.8.dll" if you built ITK 4.8.

Hope this helps,
Matt

PS. Please reply-to-all so conversations remain on the mailing lists.

[1] http://www.cmake.org/cmake/help/v3.3/command/try_compile.html

On Tue, Aug 25, 2015 at 3:02 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Sorry forgot the attachments
>
> -----Original Message-----
> From: D'Isidoro Fabio
> Sent: Dienstag, 25. August 2015 09:01
> To: 'Matt McCormick'
> Subject: RE: [ITK-users] ITK Python wrapping
>
> One more thing: in the guide it's written to add to the PATH the directories containing the .dll files, suggesting ITKbuild, ITKbuild/bin and ITKbuild/bin/Release.
>
> However as you can see from the attachments the suggested directory has only executables, while the .lib files (I don't have .dll files) are in the ITKbuild/lib/Release (second attachment)...
>
> Anyway I tried to add the the ITKbuild/lib/Release directory to the PATH but it did not work either.
>
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 24. August 2015 17:08
> To: D'Isidoro Fabio
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] ITK Python wrapping
>
> Hi Fabio,
>
>> - Well, I have a ITKPyBasePython.pyc file in the ITK lib (and the things you told me to check are allright). So the difference is that the name has no underscore _ITKPyBasePython (as reported in the error) and the extension is pyc rather than pyd (although I have read it should not make the difference). Are those things relevant? If yes, how to correct for them? Maybe the dlls were not properly compiled so the underscore is missing?
>
> Both the .pyc and the .pyd files are required.
>
>
>> Depending on your reply to this email, I will then try to build ITK with Python wrapping again so that I can report the compilation failures I got regarding CastXML.
>
> Great, thank you.  A Release build instead of a Debug build is recommended -- build size and runtime performance are greatly improved.  There is on going work to substantially decrease the wrapping build time in ITK Git master, but it is currently unstable.
> The 4.8.0 release is recommended until that is resolved.
>
>
>> About the symbolic link, I just read on the guide "ln -s /path/to/ITK-Wrapped/Wrapping/Generators/Python/WrapITK.pth" and went to find out what ln -s was ... but you are right, the guide says to copy the file, so I guess you don't have improve this part. Maybe just specifiy that there is no need to download Swig.
>
> Thanks for the feedback.  We will improve the wrapping process description.
>
>
>> Thank you, I have spent 5 long days already with no success on this issue (which seems to me a very common issue for users willing to use the Python wrapping, from my extensive google search).
>
> Yes, wrapping has been difficult in the past, but things are changing.
> With your help, it will improve even quicker :-).
>
>
> Thanks,
> Matt
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From matt.mccormick at kitware.com  Tue Aug 25 12:37:59 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 25 Aug 2015 12:37:59 -0400
Subject: [ITK] [ITK-users] FW:  ITK Python wrapping
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409435ACED36@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>
 <CALzTN-R2_viV6Y0-AkNpmicZTOaaA98E99ReZSoWkU6tb_xuYQ@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACEB17@MBX212.d.ethz.ch>
 <CALzTN-R3f+fi5pRze+a68d14YgLcYJPCnwwjPnz5Fm9W4hBV8A@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACECAC@MBX212.d.ethz.ch>
 <CALzTN-SX9vduwxUSTi-XFVStWLCTYCdGccjEPy6a+XiEtH1Ryg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACED36@MBX212.d.ethz.ch>
Message-ID: <CALzTN-SH7qnfGH_qHoXib6iVOf_W0kHnDDtVsC3oHhp7j5YEcg@mail.gmail.com>

Hi Fabio,

We are making good progress :-).

The build log indicates that the build did not complete correctly:

           Traceback (most recent call last):
           File
"C:/Users/difabio/ITK/InsightToolkit-4.8.0/Wrapping/Generators/SwigInterface/igenerator.py",
line 923, in <module>
             with open(options.typedef_output, "w") as f:
         IOError: [Errno 13] Permission denied:
'E:/ITK/ITK_bin_Win64_Python_Wrap/Wrapping/Typedefs/itkAffineTransformSwigInterface.h'
     1>C:\Program Files
(x86)\MSBuild\Microsoft.Cpp\v4.0\V110\Microsoft.CppCommon.targets(172,5):
error MSB6006: "cmd.exe" exited with code 1.
     1>Done Building Project
"E:\ITK\ITK_bin_Win64_Python_Wrap\Wrapping\Modules\ITKTransform\ITKTransformPython.vcxproj"
(Build target(s)) -- FAILED.

Please make sure the directory is writable, and run the build again.
Sometimes, for example, anti-virus software can interfere with a
build, and it should be disabled on a build directory.

Hope this helps,
Matt

On Tue, Aug 25, 2015 at 11:25 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Hi Matt,
>
> Thank you. Actually I have the .dll in the bin/release.
>
> Shortly, I (redundantly) added then ITKbuild/bin, ITKbuild/bin/release, ITKbuild/lib, ITKbuild/lib/release to BOTH my PATH environmental variable and the WrapITK.pth. Still not working, however I have a new error (see attachment 'error').
>
> Therefore I went to check the ITKTransformPython module but it's not there in lib/Release where all other .lib files relative to the other modules are. I went in the directory shown in attachment 'directory' (it's in the Wrapping/Module/.. directory) and found a  log file (attachment): the build of this module failed (I check other modules and there build there did not fail). Could you please read the log? Why did just this module fail?
>
> Thank you again!
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Dienstag, 25. August 2015 16:31
> To: D'Isidoro Fabio; insight-users at itk.org
> Subject: Re: FW: [ITK-users] ITK Python wrapping
>
> Hi Fabio,
>
> Thanks for the updates.
>
> The apparent errors are not actual errors.  These result when CMake configuration runs (indicated by the preceding "--"), and CMake tests the availability of compiler features with try_compiles [1].  If an error occurs, then that feature is not used in the build.
>
> It is good to see that the *.pyd files are there and your Python path.
> There should still be *.dll files whose folder needs to be added to the PATH system environmental variable.  These are usually in the "bin" instead of "lib" directory. Search for a file "ITKCommon-4.8.dll" if you built ITK 4.8.
>
> Hope this helps,
> Matt
>
> PS. Please reply-to-all so conversations remain on the mailing lists.
>
> [1] http://www.cmake.org/cmake/help/v3.3/command/try_compile.html
>
> On Tue, Aug 25, 2015 at 3:02 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
>> Sorry forgot the attachments
>>
>> -----Original Message-----
>> From: D'Isidoro Fabio
>> Sent: Dienstag, 25. August 2015 09:01
>> To: 'Matt McCormick'
>> Subject: RE: [ITK-users] ITK Python wrapping
>>
>> One more thing: in the guide it's written to add to the PATH the directories containing the .dll files, suggesting ITKbuild, ITKbuild/bin and ITKbuild/bin/Release.
>>
>> However as you can see from the attachments the suggested directory has only executables, while the .lib files (I don't have .dll files) are in the ITKbuild/lib/Release (second attachment)...
>>
>> Anyway I tried to add the the ITKbuild/lib/Release directory to the PATH but it did not work either.
>>
>>
>> -----Original Message-----
>> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
>> Sent: Montag, 24. August 2015 17:08
>> To: D'Isidoro Fabio
>> Cc: insight-users at itk.org
>> Subject: Re: [ITK-users] ITK Python wrapping
>>
>> Hi Fabio,
>>
>>> - Well, I have a ITKPyBasePython.pyc file in the ITK lib (and the things you told me to check are allright). So the difference is that the name has no underscore _ITKPyBasePython (as reported in the error) and the extension is pyc rather than pyd (although I have read it should not make the difference). Are those things relevant? If yes, how to correct for them? Maybe the dlls were not properly compiled so the underscore is missing?
>>
>> Both the .pyc and the .pyd files are required.
>>
>>
>>> Depending on your reply to this email, I will then try to build ITK with Python wrapping again so that I can report the compilation failures I got regarding CastXML.
>>
>> Great, thank you.  A Release build instead of a Debug build is recommended -- build size and runtime performance are greatly improved.  There is on going work to substantially decrease the wrapping build time in ITK Git master, but it is currently unstable.
>> The 4.8.0 release is recommended until that is resolved.
>>
>>
>>> About the symbolic link, I just read on the guide "ln -s /path/to/ITK-Wrapped/Wrapping/Generators/Python/WrapITK.pth" and went to find out what ln -s was ... but you are right, the guide says to copy the file, so I guess you don't have improve this part. Maybe just specifiy that there is no need to download Swig.
>>
>> Thanks for the feedback.  We will improve the wrapping process description.
>>
>>
>>> Thank you, I have spent 5 long days already with no success on this issue (which seems to me a very common issue for users willing to use the Python wrapping, from my extensive google search).
>>
>> Yes, wrapping has been difficult in the past, but things are changing.
>> With your help, it will improve even quicker :-).
>>
>>
>> Thanks,
>> Matt
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From matt.mccormick at kitware.com  Tue Aug 25 13:52:43 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 25 Aug 2015 13:52:43 -0400
Subject: [ITK] [ITK-users] speed function for itkSpeedToPathFilter
In-Reply-To: <CAPNvZ5bVU1nUCRb_A1QBAMU0bHhea-Q+TTxbwKKE8pQasu-i4w@mail.gmail.com>
References: <CAP+vBKQN7E2vRR5YxZrqKYioCN5jwW+3FbQ4fDV55n2WVwBv5A@mail.gmail.com>
 <CAPNvZ5bVU1nUCRb_A1QBAMU0bHhea-Q+TTxbwKKE8pQasu-i4w@mail.gmail.com>
Message-ID: <CALzTN-QPjWoRVYAr1pBAYEDRPXYtO_STdQKTTM5DK_7cHB4HqQ@mail.gmail.com>

Hi Prashanth,

Classes within TubeTK [1] specialize in creating input images that
would work well as an input to the itk::SpeedToPathFilter.

Hope this helps,
Matt

[1] https://github.com/KitwareMedical/TubeTK

On Sun, Aug 23, 2015 at 5:49 AM, Dan Mueller <dan.muel at gmail.com> wrote:
> Hi Prashanth,
>
> Essentially you want your speed function to be white (1.0) in the
> vessels and black (0.0) outside of the vessels ? any way you can
> achieve this is fine. The method you have outline is very general, and
> the issue is step (1) i.e. finding an approximate centreline. Some
> have suggested achieving this by applying multiscale Hessian line
> filtering (aka vessel enhancement filtering) such as Sato/Frangi
> method ? while this can achieve good results, personally I find this
> method very slow. In my own work, I have found morphological top-hat
> by opening (aka white top-hat or WTH) produces good results at a
> fraction of the computation expense, especially using the box
> structuring element with acceleration (e.g. see [1]).
>
> Good luck.
>
> Cheers, Dan
>
> [1] ?Direct volume illustration for cardiac applications,? chapter 4,
> page 83?109, http://eprints.qut.edu.au/17028/1/Daniel_Mueller_Thesis.pdf
>
> On 22 August 2015 at 06:52, Prashanth <prashanth.dumpuri at gmail.com> wrote:
>> All,
>>
>> I'm working on finding the shortest path between two points in a vessel
>> tree. itkSpeedToPathFilter seems to be working well for me as long as I
>> select the right speed function. Digging through Insight Journal, I found a
>> link to Deschamp's Ph.D. thesis
>> (https://tel.archives-ouvertes.fr/file/index/docid/45537/filename/index.html)
>> which outlines one method to select a speed function:
>>
>> 1. Approximate centerline based on the input image
>> 2. Segmentation using the approximate centerline
>> 3. Use the segmented image and approximate centerline to create an image
>> with signed distances to the approximate centerline
>> 4. Use the above image as the  input speed function for itkSpeedToPathFilter
>>
>> The above steps seem to work (I say 'seem to work' because I tested it just
>> three 2D images so far), but are there other methods to select the speed
>> function? My input images are contrast enhanced CT images and the vessels
>> are easy to identify and segment. Any help on how to select the correct
>> speed function will be appreciated.
>>
>> Thanks
>> Prashanth
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From matt.mccormick at kitware.com  Tue Aug 25 13:59:49 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 25 Aug 2015 13:59:49 -0400
Subject: [ITK] [ITK-users] Building ITK 4.8.0 with Python wrapping in
 Visual Studio 2015
In-Reply-To: <BB43A6B0CAEAFC439640CD9D13607DC24E6D30A2@mbs1.ad.jyu.fi>
References: <BB43A6B0CAEAFC439640CD9D13607DC24E6D30A2@mbs1.ad.jyu.fi>
Message-ID: <CALzTN-QXULGQa4MkomJBMdOC2dk1SRzORguC+LQ-7=4rxSGF4g@mail.gmail.com>

Hi Lassi,

ITK 4.8.0 was released with CastXML based on LLVM 3.6, which likely
does not support Visual Studio 2015.  However, support for this will
be added soon.

Thanks,
Matt

On Tue, Aug 25, 2015 at 8:54 AM, Paavolainen, Lassi
<lassi.paavolainen at jyu.fi> wrote:
> I'm trying to build ITK 4.8.0 with Python wrapping using Visual Studio 2015. Have anyone been successful in this? I know that with CastXML the Python wrapping issues were solved in ITK 4.8.0 so the issues might be related to Visual Studio 2015 instead of Python wrapping.
>
> Here are some error messages I get. First in CMake I get
> Debug Assertion Failed!
> ...\src\itkhdf5\CMake\CMakeFiles\CMakeTmp\Debug\cmTC_07479.exe
> File: minkernel\crts\ucrt\inc\corecrt_internal_stdio_output.h
> Expression: ("Invalid integer length modifier",0)
> and
> Checking for appropriate format for 64 bit long:
> CMake: Width with l64 failed with result: FAILED_TO_RUN
>
> same happens with a few other types as well. Maybe this already indicate coming issues. Anyway I went to build the solution which fails with
> Error   C2664   'void llvm::BitstreamWriter::EmitRecordWithBlob<uint64_t>(unsigned int,llvm::SmallVectorImpl<uint64_t> &,llvm::StringRef)': cannot convert argument 3 from 'unsigned int *' to 'llvm::StringRef' [C:\ITK-4.8.0\Wrapping\Generators\CastXML\clang-prefix\src\clang-build\lib\Serialization\clangSerialization.vcxproj]   clang   C:\ITK-4.8.0\Wrapping\Generators\CastXML\cfe-3.6.0\lib\Serialization\ASTWriter.cpp      1517
> and with similar errors.
>
> Any ideas how to fix it? I haven't yet tried building ITK without Python wrapping but could do it now.
>
> Lassi
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From prashanth.dumpuri at gmail.com  Tue Aug 25 14:15:49 2015
From: prashanth.dumpuri at gmail.com (Prashanth)
Date: Tue, 25 Aug 2015 18:15:49 +0000
Subject: [ITK] [ITK-users] speed function for itkSpeedToPathFilter
In-Reply-To: <CALzTN-QPjWoRVYAr1pBAYEDRPXYtO_STdQKTTM5DK_7cHB4HqQ@mail.gmail.com>
References: <CAP+vBKQN7E2vRR5YxZrqKYioCN5jwW+3FbQ4fDV55n2WVwBv5A@mail.gmail.com>
 <CAPNvZ5bVU1nUCRb_A1QBAMU0bHhea-Q+TTxbwKKE8pQasu-i4w@mail.gmail.com>
 <CALzTN-QPjWoRVYAr1pBAYEDRPXYtO_STdQKTTM5DK_7cHB4HqQ@mail.gmail.com>
Message-ID: <CAP+vBKSkV6783FxNR527=dkm+CvpowkDLOMfg2agF4xDQAG8bw@mail.gmail.com>

Matt and Dan - Thank you so much for getting back to me.

Dan - If I understood your email correctly then a binary image (with 1
inside the vessels and 0 outside) should work as a speed function. And if
that is the case then a binary mask did not work for me. I get no points in
the output of SpeedToPath filter if I use a binary mask. I'm looking into
White top hat filtering and vesselness currently. Like you pointed out (and
as mentioned in your thesis), vesselness is slower but so far it seems to
be working better than white top hat.

Matt - I will look into TubeTk as well and post an update to the mailing
list.

Thanks again
Prashanth

On Tue, Aug 25, 2015 at 10:52 AM Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Prashanth,
>
> Classes within TubeTK [1] specialize in creating input images that
> would work well as an input to the itk::SpeedToPathFilter.
>
> Hope this helps,
> Matt
>
> [1] https://github.com/KitwareMedical/TubeTK
>
> On Sun, Aug 23, 2015 at 5:49 AM, Dan Mueller <dan.muel at gmail.com> wrote:
> > Hi Prashanth,
> >
> > Essentially you want your speed function to be white (1.0) in the
> > vessels and black (0.0) outside of the vessels ? any way you can
> > achieve this is fine. The method you have outline is very general, and
> > the issue is step (1) i.e. finding an approximate centreline. Some
> > have suggested achieving this by applying multiscale Hessian line
> > filtering (aka vessel enhancement filtering) such as Sato/Frangi
> > method ? while this can achieve good results, personally I find this
> > method very slow. In my own work, I have found morphological top-hat
> > by opening (aka white top-hat or WTH) produces good results at a
> > fraction of the computation expense, especially using the box
> > structuring element with acceleration (e.g. see [1]).
> >
> > Good luck.
> >
> > Cheers, Dan
> >
> > [1] ?Direct volume illustration for cardiac applications,? chapter 4,
> > page 83?109, http://eprints.qut.edu.au/17028/1/Daniel_Mueller_Thesis.pdf
> >
> > On 22 August 2015 at 06:52, Prashanth <prashanth.dumpuri at gmail.com>
> wrote:
> >> All,
> >>
> >> I'm working on finding the shortest path between two points in a vessel
> >> tree. itkSpeedToPathFilter seems to be working well for me as long as I
> >> select the right speed function. Digging through Insight Journal, I
> found a
> >> link to Deschamp's Ph.D. thesis
> >> (
> https://tel.archives-ouvertes.fr/file/index/docid/45537/filename/index.html
> )
> >> which outlines one method to select a speed function:
> >>
> >> 1. Approximate centerline based on the input image
> >> 2. Segmentation using the approximate centerline
> >> 3. Use the segmented image and approximate centerline to create an image
> >> with signed distances to the approximate centerline
> >> 4. Use the above image as the  input speed function for
> itkSpeedToPathFilter
> >>
> >> The above steps seem to work (I say 'seem to work' because I tested it
> just
> >> three 2D images so far), but are there other methods to select the speed
> >> function? My input images are contrast enhanced CT images and the
> vessels
> >> are easy to identify and segment. Any help on how to select the correct
> >> speed function will be appreciated.
> >>
> >> Thanks
> >> Prashanth
> >>
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://public.kitware.com/mailman/listinfo/insight-users
> >>
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
>
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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
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Kitware offers ITK Training Courses, for more information visit:
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From chadrothenberg at gmail.com  Tue Aug 25 20:46:06 2015
From: chadrothenberg at gmail.com (Chadwick Rothenberg)
Date: Tue, 25 Aug 2015 20:46:06 -0400
Subject: [ITK] b-spline registration performance
Message-ID: <CAGvK_pFMLk_qGXP=55WtyU4YrdQGsDPaAUUspOaHcWy2sbPiaQ@mail.gmail.com>

Hello,

I'm new to non-rigid image registration and ITK, and I've been using
SimpleITK to perform b-spline registrations.

I am working with relatively large images (pixels, x: 3000, y: 2500, z:
100) with dense information (microscopy images), and I'm quite frustrated
with the speed / computation time.

I'm following (
https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistrationMethodBSpline2.py)
except that I'm using (25, 25, 10) mesh (ideally higher numbers if
feasible), correlation for metrics (I'm working with unimodal), and using
down-sampled images with multi-resolution registration (12x smaller, 6x
smaller). With two E5 2687w processors, the Python process (the SimpleITK)
takes about 70~80% CPU. Ideally I'd like to use at least (40, 40, 20) mesh.

1. Will I gain any performance by using ITK instead of SimpleITK?

2. What advice could you give me to improve the b-spline registration speed
(both in general and specifically in SimpleITK)?

Thanks in advance, and I'd greatly appreciate your reply.

Regards,
Chad
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From matt.mccormick at kitware.com  Tue Aug 25 22:51:39 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 25 Aug 2015 22:51:39 -0400
Subject: [ITK] b-spline registration performance
In-Reply-To: <CAGvK_pFMLk_qGXP=55WtyU4YrdQGsDPaAUUspOaHcWy2sbPiaQ@mail.gmail.com>
References: <CAGvK_pFMLk_qGXP=55WtyU4YrdQGsDPaAUUspOaHcWy2sbPiaQ@mail.gmail.com>
Message-ID: <CALzTN-SUTEitJh2+e9VRSpgo3_Nh2iEaPtRVvLuYvRQKD0biJQ@mail.gmail.com>

Hi Chad,

> I'm new to non-rigid image registration and ITK, and I've been using
> SimpleITK to perform b-spline registrations.

Welcome to ITK!


> I am working with relatively large images (pixels, x: 3000, y: 2500, z: 100)
> with dense information (microscopy images), and I'm quite frustrated with
> the speed / computation time.
>
> I'm following
> (https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistrationMethodBSpline2.py)
> except that I'm using (25, 25, 10) mesh (ideally higher numbers if
> feasible), correlation for metrics (I'm working with unimodal), and using
> down-sampled images with multi-resolution registration (12x smaller, 6x
> smaller). With two E5 2687w processors, the Python process (the SimpleITK)
> takes about 70~80% CPU. Ideally I'd like to use at least (40, 40, 20) mesh.
>
> 1. Will I gain any performance by using ITK instead of SimpleITK?

If you are using the same approach, there will effectively be no
performance difference.


> 2. What advice could you give me to improve the b-spline registration speed
> (both in general and specifically in SimpleITK)?

Get the registration working well with the large image when densely
sampling the images for metric computation.  Then, progressively
decimate the metric sampling [1] until registration performance
declines.  Increase the sampling percentage again with an additional
safety factor.

Hope this helps,
Matt


[1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html#adca6e03c04216fca8ba0d90d84cb9600

From blowekamp at mail.nih.gov  Wed Aug 26 08:36:39 2015
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 26 Aug 2015 12:36:39 +0000
Subject: [ITK] NLM RFP: ITK Algorithms, Extensibility, Integration,
 & Outreach for SimpleITK 2015
Message-ID: <DA2915A530468E47B3C4845298E6EB0355AE93E8@msgb06.nih.gov>

The National Institutes of Health (NIH), National Library of Medicine (NLM) is solicitation proposals for improvements to SimpleITK/ITK.

The FedBizOpps has complete information:
          https://www.fbo.gov/spg/HHS/NIH/OAM/RFP_NIHLM2015597KB/listing.html

The response date is Sep 08, 2015 12:00pm Eastern.

Bradley Lowekamp
MSC Contractor
NIH/NLM/LHC/OHPCC

From fisidoro at ethz.ch  Wed Aug 26 10:41:59 2015
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Wed, 26 Aug 2015 14:41:59 +0000
Subject: [ITK] [ITK-users] FW:  ITK Python wrapping
In-Reply-To: <CALzTN-SH7qnfGH_qHoXib6iVOf_W0kHnDDtVsC3oHhp7j5YEcg@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>
 <CALzTN-R2_viV6Y0-AkNpmicZTOaaA98E99ReZSoWkU6tb_xuYQ@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACEB17@MBX212.d.ethz.ch>
 <CALzTN-R3f+fi5pRze+a68d14YgLcYJPCnwwjPnz5Fm9W4hBV8A@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACECAC@MBX212.d.ethz.ch>
 <CALzTN-SX9vduwxUSTi-XFVStWLCTYCdGccjEPy6a+XiEtH1Ryg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACED36@MBX212.d.ethz.ch>
 <CALzTN-SH7qnfGH_qHoXib6iVOf_W0kHnDDtVsC3oHhp7j5YEcg@mail.gmail.com>
Message-ID: <50B858FB5F53124F9E32314E5C1B409435ACEE97@MBX212.d.ethz.ch>

Hi Matt,

I did the build again and this time everything is working properly :)

As a summary of my issue: the key factor is that building ITK with Python Wrapping on Visual Studio on DEBUG mode did not produced the required *.pyd files. So in the guide you may want to remind an unexperienced Windows user that the build should be performed on RELEADE mode. My second problem was that the build did not work the first time for one of the modules.

Just to figure out how to write in python with itk: I was trying to be lucky and to run an example similar to the example ImageRegistration3.py in the Examples folder of InsightToolkit-4.8.0 (in attachment). I start the code with 'import itk'. However fixedImageReader  = itk.ImageFileReaderF2.New()' returns an error. Is this an old version and should I just write ' fixedImageReader  = itk.ImageFileReader[ImageType].New()' instead? 

Which guide should I look for figuring these things out?

Thank you for your valuable support.

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com] 
Sent: Dienstag, 25. August 2015 18:38
To: D'Isidoro Fabio
Cc: insight-users at itk.org
Subject: Re: FW: [ITK-users] ITK Python wrapping

Hi Fabio,

We are making good progress :-).

The build log indicates that the build did not complete correctly:

           Traceback (most recent call last):
           File
"C:/Users/difabio/ITK/InsightToolkit-4.8.0/Wrapping/Generators/SwigInterface/igenerator.py",
line 923, in <module>
             with open(options.typedef_output, "w") as f:
         IOError: [Errno 13] Permission denied:
'E:/ITK/ITK_bin_Win64_Python_Wrap/Wrapping/Typedefs/itkAffineTransformSwigInterface.h'
     1>C:\Program Files
(x86)\MSBuild\Microsoft.Cpp\v4.0\V110\Microsoft.CppCommon.targets(172,5):
error MSB6006: "cmd.exe" exited with code 1.
     1>Done Building Project
"E:\ITK\ITK_bin_Win64_Python_Wrap\Wrapping\Modules\ITKTransform\ITKTransformPython.vcxproj"
(Build target(s)) -- FAILED.

Please make sure the directory is writable, and run the build again.
Sometimes, for example, anti-virus software can interfere with a build, and it should be disabled on a build directory.

Hope this helps,
Matt

On Tue, Aug 25, 2015 at 11:25 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Hi Matt,
>
> Thank you. Actually I have the .dll in the bin/release.
>
> Shortly, I (redundantly) added then ITKbuild/bin, ITKbuild/bin/release, ITKbuild/lib, ITKbuild/lib/release to BOTH my PATH environmental variable and the WrapITK.pth. Still not working, however I have a new error (see attachment 'error').
>
> Therefore I went to check the ITKTransformPython module but it's not there in lib/Release where all other .lib files relative to the other modules are. I went in the directory shown in attachment 'directory' (it's in the Wrapping/Module/.. directory) and found a  log file (attachment): the build of this module failed (I check other modules and there build there did not fail). Could you please read the log? Why did just this module fail?
>
> Thank you again!
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Dienstag, 25. August 2015 16:31
> To: D'Isidoro Fabio; insight-users at itk.org
> Subject: Re: FW: [ITK-users] ITK Python wrapping
>
> Hi Fabio,
>
> Thanks for the updates.
>
> The apparent errors are not actual errors.  These result when CMake configuration runs (indicated by the preceding "--"), and CMake tests the availability of compiler features with try_compiles [1].  If an error occurs, then that feature is not used in the build.
>
> It is good to see that the *.pyd files are there and your Python path.
> There should still be *.dll files whose folder needs to be added to the PATH system environmental variable.  These are usually in the "bin" instead of "lib" directory. Search for a file "ITKCommon-4.8.dll" if you built ITK 4.8.
>
> Hope this helps,
> Matt
>
> PS. Please reply-to-all so conversations remain on the mailing lists.
>
> [1] http://www.cmake.org/cmake/help/v3.3/command/try_compile.html
>
> On Tue, Aug 25, 2015 at 3:02 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
>> Sorry forgot the attachments
>>
>> -----Original Message-----
>> From: D'Isidoro Fabio
>> Sent: Dienstag, 25. August 2015 09:01
>> To: 'Matt McCormick'
>> Subject: RE: [ITK-users] ITK Python wrapping
>>
>> One more thing: in the guide it's written to add to the PATH the directories containing the .dll files, suggesting ITKbuild, ITKbuild/bin and ITKbuild/bin/Release.
>>
>> However as you can see from the attachments the suggested directory has only executables, while the .lib files (I don't have .dll files) are in the ITKbuild/lib/Release (second attachment)...
>>
>> Anyway I tried to add the the ITKbuild/lib/Release directory to the PATH but it did not work either.
>>
>>
>> -----Original Message-----
>> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
>> Sent: Montag, 24. August 2015 17:08
>> To: D'Isidoro Fabio
>> Cc: insight-users at itk.org
>> Subject: Re: [ITK-users] ITK Python wrapping
>>
>> Hi Fabio,
>>
>>> - Well, I have a ITKPyBasePython.pyc file in the ITK lib (and the things you told me to check are allright). So the difference is that the name has no underscore _ITKPyBasePython (as reported in the error) and the extension is pyc rather than pyd (although I have read it should not make the difference). Are those things relevant? If yes, how to correct for them? Maybe the dlls were not properly compiled so the underscore is missing?
>>
>> Both the .pyc and the .pyd files are required.
>>
>>
>>> Depending on your reply to this email, I will then try to build ITK with Python wrapping again so that I can report the compilation failures I got regarding CastXML.
>>
>> Great, thank you.  A Release build instead of a Debug build is recommended -- build size and runtime performance are greatly improved.  There is on going work to substantially decrease the wrapping build time in ITK Git master, but it is currently unstable.
>> The 4.8.0 release is recommended until that is resolved.
>>
>>
>>> About the symbolic link, I just read on the guide "ln -s /path/to/ITK-Wrapped/Wrapping/Generators/Python/WrapITK.pth" and went to find out what ln -s was ... but you are right, the guide says to copy the file, so I guess you don't have improve this part. Maybe just specifiy that there is no need to download Swig.
>>
>> Thanks for the feedback.  We will improve the wrapping process description.
>>
>>
>>> Thank you, I have spent 5 long days already with no success on this issue (which seems to me a very common issue for users willing to use the Python wrapping, from my extensive google search).
>>
>> Yes, wrapping has been difficult in the past, but things are changing.
>> With your help, it will improve even quicker :-).
>>
>>
>> Thanks,
>> Matt
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From blowekamp at mail.nih.gov  Wed Aug 26 09:52:44 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 26 Aug 2015 09:52:44 -0400
Subject: [ITK] b-spline registration performance
In-Reply-To: <CALzTN-SUTEitJh2+e9VRSpgo3_Nh2iEaPtRVvLuYvRQKD0biJQ@mail.gmail.com>
References: <CAGvK_pFMLk_qGXP=55WtyU4YrdQGsDPaAUUspOaHcWy2sbPiaQ@mail.gmail.com>
 <CALzTN-SUTEitJh2+e9VRSpgo3_Nh2iEaPtRVvLuYvRQKD0biJQ@mail.gmail.com>
Message-ID: <D5FD420C-E13C-4C0A-89B3-91398EF84FCC@mail.nih.gov>

Hello,

The obvious thing to do is try to compute less. Use less pixels, and less samples ( as Matt already suggested ).

What the size of you image (3000x2500x100) and an initial BSpline mesh size of (25x25x10) you may want to run the BinShrink filter with 10x10x2 to reduce the resolution of the image for the first pass with the low resolution mesh. Still use multi-scale and only a percentage of the pixels for the metric. Also note how long it take the registration to start, before the iterations start.

Then you can run another registration with a higher resolution mesh and image. You likely still don't need to full resolution image.

What metric are you using? It may be worth profiling the effect of the number of threads for the metric you are using.

HTH,
Brad


On Aug 25, 2015, at 10:51 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> Hi Chad,
> 
>> I'm new to non-rigid image registration and ITK, and I've been using
>> SimpleITK to perform b-spline registrations.
> 
> Welcome to ITK!
> 
> 
>> I am working with relatively large images (pixels, x: 3000, y: 2500, z: 100)
>> with dense information (microscopy images), and I'm quite frustrated with
>> the speed / computation time.
>> 
>> I'm following
>> (https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistrationMethodBSpline2.py)
>> except that I'm using (25, 25, 10) mesh (ideally higher numbers if
>> feasible), correlation for metrics (I'm working with unimodal), and using
>> down-sampled images with multi-resolution registration (12x smaller, 6x
>> smaller). With two E5 2687w processors, the Python process (the SimpleITK)
>> takes about 70~80% CPU. Ideally I'd like to use at least (40, 40, 20) mesh.
>> 
>> 1. Will I gain any performance by using ITK instead of SimpleITK?
> 
> If you are using the same approach, there will effectively be no
> performance difference.
> 
> 
>> 2. What advice could you give me to improve the b-spline registration speed
>> (both in general and specifically in SimpleITK)?
> 
> Get the registration working well with the large image when densely
> sampling the images for metric computation.  Then, progressively
> decimate the metric sampling [1] until registration performance
> declines.  Increase the sampling percentage again with an additional
> safety factor.
> 
> Hope this helps,
> Matt
> 
> 
> [1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html#adca6e03c04216fca8ba0d90d84cb9600
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From chadrothenberg at gmail.com  Wed Aug 26 11:16:12 2015
From: chadrothenberg at gmail.com (Chadwick Rothenberg)
Date: Wed, 26 Aug 2015 11:16:12 -0400
Subject: [ITK] b-spline registration performance
In-Reply-To: <D5FD420C-E13C-4C0A-89B3-91398EF84FCC@mail.nih.gov>
References: <CAGvK_pFMLk_qGXP=55WtyU4YrdQGsDPaAUUspOaHcWy2sbPiaQ@mail.gmail.com>
 <CALzTN-SUTEitJh2+e9VRSpgo3_Nh2iEaPtRVvLuYvRQKD0biJQ@mail.gmail.com>
 <D5FD420C-E13C-4C0A-89B3-91398EF84FCC@mail.nih.gov>
Message-ID: <CAGvK_pHidwPJ0E6N6_MVaZ9cZs-zxvuPhWS1Q9evW-8h1YJ-DQ@mail.gmail.com>

Hello,

Thank you for the helpful replies.

For the metric, I am using correlation since it's unimodal registration,
and I have 32 threads (16 physical cores total with 2 CPUs, 8 cores on
each).

Also, I've heard that the interpolator can affect the registration
performance, and I'm currently trying out different ones (using linear for
default).

For the registration initiation, the Python (SimpleITK) process's CPU %
goes up all the way for couple minutes, and then it drops?I only see 1~3%
activity (virtually no activity) and no change in memory. And this period
seems to be correlated with the image size and also the mesh size for
b-spline transformation?if I use a large number of nodes for the mesh, it
can even take up to couple hours.

Is this a known issue? or Am I doing something wrong?

Thanks!

Regards,
Chad

On Wed, Aug 26, 2015 at 9:52 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> The obvious thing to do is try to compute less. Use less pixels, and less
> samples ( as Matt already suggested ).
>
> What the size of you image (3000x2500x100) and an initial BSpline mesh
> size of (25x25x10) you may want to run the BinShrink filter with 10x10x2 to
> reduce the resolution of the image for the first pass with the low
> resolution mesh. Still use multi-scale and only a percentage of the pixels
> for the metric. Also note how long it take the registration to start,
> before the iterations start.
>
> Then you can run another registration with a higher resolution mesh and
> image. You likely still don't need to full resolution image.
>
> What metric are you using? It may be worth profiling the effect of the
> number of threads for the metric you are using.
>
> HTH,
> Brad
>
>
> On Aug 25, 2015, at 10:51 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>
> > Hi Chad,
> >
> >> I'm new to non-rigid image registration and ITK, and I've been using
> >> SimpleITK to perform b-spline registrations.
> >
> > Welcome to ITK!
> >
> >
> >> I am working with relatively large images (pixels, x: 3000, y: 2500, z:
> 100)
> >> with dense information (microscopy images), and I'm quite frustrated
> with
> >> the speed / computation time.
> >>
> >> I'm following
> >> (
> https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistrationMethodBSpline2.py
> )
> >> except that I'm using (25, 25, 10) mesh (ideally higher numbers if
> >> feasible), correlation for metrics (I'm working with unimodal), and
> using
> >> down-sampled images with multi-resolution registration (12x smaller, 6x
> >> smaller). With two E5 2687w processors, the Python process (the
> SimpleITK)
> >> takes about 70~80% CPU. Ideally I'd like to use at least (40, 40, 20)
> mesh.
> >>
> >> 1. Will I gain any performance by using ITK instead of SimpleITK?
> >
> > If you are using the same approach, there will effectively be no
> > performance difference.
> >
> >
> >> 2. What advice could you give me to improve the b-spline registration
> speed
> >> (both in general and specifically in SimpleITK)?
> >
> > Get the registration working well with the large image when densely
> > sampling the images for metric computation.  Then, progressively
> > decimate the metric sampling [1] until registration performance
> > declines.  Increase the sampling percentage again with an additional
> > safety factor.
> >
> > Hope this helps,
> > Matt
> >
> >
> > [1]
> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html#adca6e03c04216fca8ba0d90d84cb9600
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
>
>
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From alii.ghayoor at gmail.com  Wed Aug 26 12:47:01 2015
From: alii.ghayoor at gmail.com (Ali Ghayoor)
Date: Wed, 26 Aug 2015 11:47:01 -0500
Subject: [ITK] [ITK-users] Iterating through images in SimpleITK
In-Reply-To: <D20351AC.251A7%ali-ghayoor@uiowa.edu>
References: <D12B8872-0C0F-49F6-96CC-B7B34E4620E8@uiowa.edu>
 <8E996EF4-D71D-4832-BA01-99D76AB7E667@mail.nih.gov>
 <D201F790.250A4%ali-ghayoor@uiowa.edu>
 <C9519966-288D-46ED-9F6C-4C71C4A4B6B9@mail.nih.gov>
 <D20351AC.251A7%ali-ghayoor@uiowa.edu>
Message-ID: <D2035743.251C7%ali-ghayoor@uiowa.edu>

Hello ITK users,

Here is my conversation with 'Bradley Lowekamp' about the ways to iterate
through an image in SimpleITK, since ITK image iterators are not included in
SimpleITK interface.
We were thinking that the question and answers may be helpful to entire
community of ITK users.

Regards,
Ali

From: Bradley Lowekamp <blowekamp at mail.nih.gov>
Date: Tuesday, August 25, 2015 at 12:02 PM
To: Ali Ghayoor <ali-ghayoor at uiowa.edu>
Subject: Re: Iterating through images in SimpleITK

This is numpy boadcasting:

http://docs.scipy.org/doc/numpy/user/basics.broadcasting.html

Very similar to how to use matlab efficiently.

>From this notebook [1], look at this:

def marschner_lobb(size=40, alpha=0.25, f_M=6.0):
    img = sitk.PhysicalPointSource( sitk.sitkVectorFloat32, [size]*3,
[-1]*3, [2.0/size]*3)
    imgx = sitk.VectorIndexSelectionCast(img, 0)
    imgy = sitk.VectorIndexSelectionCast(img, 1)
    imgz = sitk.VectorIndexSelectionCast(img, 2)
    del img
    r = sitk.Sqrt(imgx**2 + imgy**2)
    del imgx, imgy
    pr = sitk.Cos((2.0*math.pi*f_M)*sitk.Cos((math.pi/2.0)*r))
    return (1.0 - sitk.Sin((math.pi/2.0)*imgz) +
alpha*(1.0+pr))/(2.0*(1.0+alpha))

This simple computation of a function, could be implemented as a function of
XYX. But it's implemented using operations on the whole images. Many
algorithms can be structured this way where you might first thing you need
the index.

I don't know what you are trying to do so I can't be more specific.

Brad

[1] 
http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/20_Expand_Wit
h_Interpolators.html


On Aug 25, 2015, at 12:36 PM, Ghayoor, Ali <ali-ghayoor at uiowa.edu> wrote:

> Brad,
> 
> Thank you for your response. I think iterating using the python interface
> is the easiest way if you do not need to check the index that you are
> operating on at each iteration. In my case, I need to know the index
> information at each iteration.
> 
> Also, I am curious about your suggested fastest way, but I did not quite
> understand that. Could you please explain that with a little more details?
> 
> Thank you,
> Ali
> 
> 
> On 8/24/15, 10:09 PM, "Bradley Lowekamp" <blowekamp at mail.nih.gov> wrote:
> 
>> Hello Ali,
>> 
>> As for iterating on SimpleITK image, there is the totally Python
>> interface to make the Image class iterable [1]. This is as slow as the 3
>> nested for loop, which is about as slow as iterating on a numpy array.
>> This is the easiest and most Pythonic way.
>> 
>> The fastest way is to reconsider your algorithm to operating on the whole
>> image/array by using broadcasts and multiplying by 0s and 1s for
>> conditionals.
>> 
>> HTH,
>> Brad
>> 
>> p.s. This kind of question should be directed to the ITK mailing list so
>> that the entire community can benefit.
>> 
>> 
>> [1] 
>> https://github.com/SimpleITK/SimpleITK/blob/6acfc05c01c946316cac9bd8803d62
>> a4e0cda5b9/Wrapping/Python.i#L289-L310
>> 
>> On Aug 24, 2015, at 10:45 PM, Ghayoor, Ali <ali-ghayoor at uiowa.edu> wrote:
>> 
>>> Hello Brad,
>>> 
>>> I noticed that image iterators are not included in SimpleITK interface, so I
>>> needed your
>>> suggestion about the best way to iterate through an image while using
>>> SimpleITK in Ipython notebook. I'm not sure that using three nested
>>> 'for' loops is the most efficient way to do that and was thinking maybe
>>> there is a better method.
>>> 
>>> Thank you for your help,
>>> Ali
>> 
> 



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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

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From alii.ghayoor at gmail.com  Wed Aug 26 13:51:49 2015
From: alii.ghayoor at gmail.com (Ali Ghayoor)
Date: Wed, 26 Aug 2015 12:51:49 -0500
Subject: [ITK] [ITK-users] Evaluate an image at a continues index or at a
 physical point in SimpleITK
Message-ID: <D20366E5.251E9%alii.ghayoor@gmail.com>

Hello,

I need to evaluate an image at a continues index or at a physical point in
SimpleITK.
However, as I noticed in SimpleITK, interpolators are created as
non-callable binary objects to be passed to other filters like
ResampleImageFilter() or ImageRegistrationMethod().
It would be great if interpolators were provided as filters as well, so we
could easily pass them an input image and evaluate that image in continues
indices.
Now, based on the current infrastructure, is there any way to get the value
of an image at non-integer indices in SimpleITK?

Thank you,
Ali


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From zivrafael.yaniv at nih.gov  Wed Aug 26 17:09:13 2015
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Wed, 26 Aug 2015 21:09:13 +0000
Subject: [ITK] b-spline registration performance
In-Reply-To: <CAGvK_pHidwPJ0E6N6_MVaZ9cZs-zxvuPhWS1Q9evW-8h1YJ-DQ@mail.gmail.com>
References: <CAGvK_pFMLk_qGXP=55WtyU4YrdQGsDPaAUUspOaHcWy2sbPiaQ@mail.gmail.com>
 <CALzTN-SUTEitJh2+e9VRSpgo3_Nh2iEaPtRVvLuYvRQKD0biJQ@mail.gmail.com>
 <D5FD420C-E13C-4C0A-89B3-91398EF84FCC@mail.nih.gov>
 <CAGvK_pHidwPJ0E6N6_MVaZ9cZs-zxvuPhWS1Q9evW-8h1YJ-DQ@mail.gmail.com>
Message-ID: <D203A208.4501%yanivz@mail.nih.gov>

Hello Chad,

One other thing you can try is to use an even simpler similarity metric. For unimodal registration you can try the mean squares metric. It is simpler than correlation, but the assumption on the data becomes stricter (intensities haven?t changed vs. a linear change which is what the correlation is accommodating).

Possibly this will provide some speedup.
             Ziv


From: Chadwick Rothenberg <chadrothenberg at gmail.com<mailto:chadrothenberg at gmail.com>>
Date: Wednesday, August 26, 2015 at 11:16 AM
To: "Lowekamp, Bradley (NIH/NLM/LHC) [C]" <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>>
Cc: "community at itk.org<mailto:community at itk.org>" <community at itk.org<mailto:community at itk.org>>
Subject: Re: [ITK] b-spline registration performance

Hello,

Thank you for the helpful replies.

For the metric, I am using correlation since it's unimodal registration, and I have 32 threads (16 physical cores total with 2 CPUs, 8 cores on each).

Also, I've heard that the interpolator can affect the registration performance, and I'm currently trying out different ones (using linear for default).

For the registration initiation, the Python (SimpleITK) process's CPU % goes up all the way for couple minutes, and then it drops?I only see 1~3% activity (virtually no activity) and no change in memory. And this period seems to be correlated with the image size and also the mesh size for b-spline transformation?if I use a large number of nodes for the mesh, it can even take up to couple hours.

Is this a known issue? or Am I doing something wrong?

Thanks!

Regards,
Chad

On Wed, Aug 26, 2015 at 9:52 AM, Bradley Lowekamp <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
Hello,

The obvious thing to do is try to compute less. Use less pixels, and less samples ( as Matt already suggested ).

What the size of you image (3000x2500x100) and an initial BSpline mesh size of (25x25x10) you may want to run the BinShrink filter with 10x10x2 to reduce the resolution of the image for the first pass with the low resolution mesh. Still use multi-scale and only a percentage of the pixels for the metric. Also note how long it take the registration to start, before the iterations start.

Then you can run another registration with a higher resolution mesh and image. You likely still don't need to full resolution image.

What metric are you using? It may be worth profiling the effect of the number of threads for the metric you are using.

HTH,
Brad


On Aug 25, 2015, at 10:51 PM, Matt McCormick <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>> wrote:

> Hi Chad,
>
>> I'm new to non-rigid image registration and ITK, and I've been using
>> SimpleITK to perform b-spline registrations.
>
> Welcome to ITK!
>
>
>> I am working with relatively large images (pixels, x: 3000, y: 2500, z: 100)
>> with dense information (microscopy images), and I'm quite frustrated with
>> the speed / computation time.
>>
>> I'm following
>> (https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistrationMethodBSpline2.py)
>> except that I'm using (25, 25, 10) mesh (ideally higher numbers if
>> feasible), correlation for metrics (I'm working with unimodal), and using
>> down-sampled images with multi-resolution registration (12x smaller, 6x
>> smaller). With two E5 2687w processors, the Python process (the SimpleITK)
>> takes about 70~80% CPU. Ideally I'd like to use at least (40, 40, 20) mesh.
>>
>> 1. Will I gain any performance by using ITK instead of SimpleITK?
>
> If you are using the same approach, there will effectively be no
> performance difference.
>
>
>> 2. What advice could you give me to improve the b-spline registration speed
>> (both in general and specifically in SimpleITK)?
>
> Get the registration working well with the large image when densely
> sampling the images for metric computation.  Then, progressively
> decimate the metric sampling [1] until registration performance
> declines.  Increase the sampling percentage again with an additional
> safety factor.
>
> Hope this helps,
> Matt
>
>
> [1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html#adca6e03c04216fca8ba0d90d84cb9600
> _______________________________________________
> Community mailing list
> Community at itk.org<mailto:Community at itk.org>
> http://public.kitware.com/mailman/listinfo/community


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From matt.mccormick at kitware.com  Thu Aug 27 00:38:22 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Aug 2015 00:38:22 -0400
Subject: [ITK] b-spline registration performance
In-Reply-To: <CAGvK_pHidwPJ0E6N6_MVaZ9cZs-zxvuPhWS1Q9evW-8h1YJ-DQ@mail.gmail.com>
References: <CAGvK_pFMLk_qGXP=55WtyU4YrdQGsDPaAUUspOaHcWy2sbPiaQ@mail.gmail.com>
 <CALzTN-SUTEitJh2+e9VRSpgo3_Nh2iEaPtRVvLuYvRQKD0biJQ@mail.gmail.com>
 <D5FD420C-E13C-4C0A-89B3-91398EF84FCC@mail.nih.gov>
 <CAGvK_pHidwPJ0E6N6_MVaZ9cZs-zxvuPhWS1Q9evW-8h1YJ-DQ@mail.gmail.com>
Message-ID: <CALzTN-Rf6a5ynaNCuDAzhBMt7FvDLVPEemx8tfeiynMibTexmw@mail.gmail.com>

Hi Chad,

> For the metric, I am using correlation since it's unimodal registration, and
> I have 32 threads (16 physical cores total with 2 CPUs, 8 cores on each).
>
> Also, I've heard that the interpolator can affect the registration
> performance, and I'm currently trying out different ones (using linear for
> default).
>
> For the registration initiation, the Python (SimpleITK) process's CPU % goes
> up all the way for couple minutes, and then it drops?I only see 1~3%
> activity (virtually no activity) and no change in memory. And this period
> seems to be correlated with the image size and also the mesh size for
> b-spline transformation?if I use a large number of nodes for the mesh, it
> can even take up to couple hours.
>
> Is this a known issue? or Am I doing something wrong?

Yes, this is a known issue. There is room for improvement in ITK
related to thread re-use and data starvation in threads.

It may be worth setting the ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
environmental variable to a smaller value, e.g

  export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=6

HTH,
Matt

From matt.mccormick at kitware.com  Thu Aug 27 00:56:40 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Aug 2015 00:56:40 -0400
Subject: [ITK] [ITK-users] FW:  ITK Python wrapping
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409435ACEE97@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435ACEA2D@MBX212.d.ethz.ch>
 <CALzTN-R2_viV6Y0-AkNpmicZTOaaA98E99ReZSoWkU6tb_xuYQ@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACEB17@MBX212.d.ethz.ch>
 <CALzTN-R3f+fi5pRze+a68d14YgLcYJPCnwwjPnz5Fm9W4hBV8A@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACECAC@MBX212.d.ethz.ch>
 <CALzTN-SX9vduwxUSTi-XFVStWLCTYCdGccjEPy6a+XiEtH1Ryg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACED36@MBX212.d.ethz.ch>
 <CALzTN-SH7qnfGH_qHoXib6iVOf_W0kHnDDtVsC3oHhp7j5YEcg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409435ACEE97@MBX212.d.ethz.ch>
Message-ID: <CALzTN-RQdjYvRHnqsYs4k9RKk5FyXVpEeSQNRezoZnbN6keeUQ@mail.gmail.com>

Hi Fabio,

> I did the build again and this time everything is working properly :)

Fantastic!!


> As a summary of my issue: the key factor is that building ITK with Python Wrapping on Visual Studio on DEBUG mode did not produced the required *.pyd files. So in the guide you may want to remind an unexperienced Windows user that the build should be performed on RELEADE mode. My second problem was that the build did not work the first time for one of the modules.

Thanks for the feedback.  Please review this patch, which improves the
documentation correspondingly:

  http://review.source.kitware.com/#/c/20143/


> Just to figure out how to write in python with itk: I was trying to be lucky and to run an example similar to the example ImageRegistration3.py in the Examples folder of InsightToolkit-4.8.0 (in attachment). I start the code with 'import itk'. However fixedImageReader  = itk.ImageFileReaderF2.New()' returns an error. Is this an old version and should I just write ' fixedImageReader  = itk.ImageFileReader[ImageType].New()' instead?
>
> Which guide should I look for figuring these things out?

These examples are in a need of a major update.  I have created an
issue in the tracker to keep track of progress:

  https://issues.itk.org/jira/browse/ITK-3376

You can find some current Python examples in the ITK Sphinx Examples:

  http://itk.org/ITKExamples/src/Filtering/LabelMap/RemoveHolesNotConnectedToImageBoundaries/Documentation.html

There are also some SimpleITK IPython notebooks on image registration here:

  https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks


Thanks,
Matt
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From sami.koho at gmail.com  Thu Aug 27 02:14:20 2015
From: sami.koho at gmail.com (Sami Koho)
Date: Thu, 27 Aug 2015 09:14:20 +0300
Subject: [ITK] [ITK-users] CenteredTransformInitializer Python Wrapping
Message-ID: <CADfpT84Ke1gLp9=Gn7AFJLnnrncxRsaSVvtO7JR6MLmU5RA36Q@mail.gmail.com>

Hello,

I tried to convert a registration method that I have to use the
CenteredSimilarity2DTransform instead of the CenteredRigid2DTransform in
Python. There seems to be a problem however, as the
CenteredTransformInitializer in Python only seems to work with the rigid
transforms now. The wrapping file looks like this:

itk_wrap_include("itkVersorRigid3DTransform.h")
itk_wrap_include("itkCenteredRigid2DTransform.h")
itk_wrap_class("itk::CenteredTransformInitializer" POINTER)
    itk_wrap_filter_dims(d 3)
    if(d)
        foreach(t ${WRAP_ITK_SCALAR})

itk_wrap_template("VR3DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}"
"itk::VersorRigid3DTransform< ${ITKT_D}
>,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
        endforeach()
    endif(d)

    itk_wrap_filter_dims(d 2)
    if(d)
        foreach(t ${WRAP_ITK_SCALAR})

itk_wrap_template("CR2DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}"
"itk::CenteredRigid2DTransform< ${ITKT_D}
>,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
        endforeach()
    endif(d)
itk_end_wrap_class()

How would I go about fixing this? Should I just add a new line, like:

 itk_wrap_template("CS2DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}"
"itk::CenteredSimilarity2DTransform< ${ITKT_D}
>,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")

inside the if(d)...endif(d) for the 2D images? I could of course just try,
but I thought to ask, as compilation always takes a while with the Python
wrapping :-)

Best,

Sami
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From sami.koho at gmail.com  Thu Aug 27 05:38:45 2015
From: sami.koho at gmail.com (Sami Koho)
Date: Thu, 27 Aug 2015 12:38:45 +0300
Subject: [ITK] [ITK-users] CenteredTransformInitializer Python Wrapping
In-Reply-To: <CADfpT84Ke1gLp9=Gn7AFJLnnrncxRsaSVvtO7JR6MLmU5RA36Q@mail.gmail.com>
References: <CADfpT84Ke1gLp9=Gn7AFJLnnrncxRsaSVvtO7JR6MLmU5RA36Q@mail.gmail.com>
Message-ID: <09279851-32AB-4125-8ED9-9E47A8BA9425@gmail.com>

Hello again,

I fixed the wrapping issue. I thought that I might submit a patch to ITK, but I have a question. I am using the ITK version 4.8.0, which I obtained with a checkout from the GIT repository. Is it totally fine that I create the Patch for the 4.8.0 release, or should I switch to the main branch? 

Best,

Sami


> On 27 Aug 2015, at 09:14, Sami Koho <sami.koho at gmail.com> wrote:
> 
> Hello,
> 
> I tried to convert a registration method that I have to use the CenteredSimilarity2DTransform instead of the CenteredRigid2DTransform in Python. There seems to be a problem however, as the CenteredTransformInitializer in Python only seems to work with the rigid transforms now. The wrapping file looks like this:
> 
> itk_wrap_include("itkVersorRigid3DTransform.h")
> itk_wrap_include("itkCenteredRigid2DTransform.h")
> itk_wrap_class("itk::CenteredTransformInitializer" POINTER)
>     itk_wrap_filter_dims(d 3)
>     if(d)
>         foreach(t ${WRAP_ITK_SCALAR})
>           itk_wrap_template("VR3DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::VersorRigid3DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
>         endforeach()
>     endif(d)
> 
>     itk_wrap_filter_dims(d 2)
>     if(d)
>         foreach(t ${WRAP_ITK_SCALAR})
>           itk_wrap_template("CR2DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::CenteredRigid2DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
>         endforeach()
>     endif(d)
> itk_end_wrap_class()
> 
> How would I go about fixing this? Should I just add a new line, like:
> 
>  itk_wrap_template("CS2DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::CenteredSimilarity2DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
> 
> inside the if(d)...endif(d) for the 2D images? I could of course just try, but I thought to ask, as compilation always takes a while with the Python wrapping :-)
> 
> Best,
> 
> Sami

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From blowekamp at mail.nih.gov  Thu Aug 27 08:19:18 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 27 Aug 2015 08:19:18 -0400
Subject: [ITK] [ITK-users] CenteredTransformInitializer Python Wrapping
In-Reply-To: <09279851-32AB-4125-8ED9-9E47A8BA9425@gmail.com>
References: <CADfpT84Ke1gLp9=Gn7AFJLnnrncxRsaSVvtO7JR6MLmU5RA36Q@mail.gmail.com>
 <09279851-32AB-4125-8ED9-9E47A8BA9425@gmail.com>
Message-ID: <A88934F1-939B-40F5-8154-33DE158696CD@mail.nih.gov>

Hello,

I would recommend using the "MatrixOffsetTransformBase" class for the template parameters. This enables the class to be used with any derived type.

This is they way I did it in SimpleITK [1].


Brad

[1] https://github.com/SimpleITK/SimpleITK/blob/master/Code/BasicFilters/src/sitkCenteredTransformInitializerFilter.cxx#L125-L126

On Aug 27, 2015, at 5:38 AM, Sami Koho <sami.koho at gmail.com> wrote:

> Hello again,
> 
> I fixed the wrapping issue. I thought that I might submit a patch to ITK, but I have a question. I am using the ITK version 4.8.0, which I obtained with a checkout from the GIT repository. Is it totally fine that I create the Patch for the 4.8.0 release, or should I switch to the main branch? 
> 
> Best,
> 
> Sami
> 
> 
>> On 27 Aug 2015, at 09:14, Sami Koho <sami.koho at gmail.com> wrote:
>> 
>> Hello,
>> 
>> I tried to convert a registration method that I have to use the CenteredSimilarity2DTransform instead of the CenteredRigid2DTransform in Python. There seems to be a problem however, as the CenteredTransformInitializer in Python only seems to work with the rigid transforms now. The wrapping file looks like this:
>> 
>> itk_wrap_include("itkVersorRigid3DTransform.h")
>> itk_wrap_include("itkCenteredRigid2DTransform.h")
>> itk_wrap_class("itk::CenteredTransformInitializer" POINTER)
>>    itk_wrap_filter_dims(d 3)
>>    if(d)
>>        foreach(t ${WRAP_ITK_SCALAR})
>>          itk_wrap_template("VR3DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::VersorRigid3DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
>>        endforeach()
>>    endif(d)
>> 
>>    itk_wrap_filter_dims(d 2)
>>    if(d)
>>        foreach(t ${WRAP_ITK_SCALAR})
>>          itk_wrap_template("CR2DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::CenteredRigid2DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
>>        endforeach()
>>    endif(d)
>> itk_end_wrap_class()
>> 
>> How would I go about fixing this? Should I just add a new line, like:
>> 
>> itk_wrap_template("CS2DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::CenteredSimilarity2DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
>> 
>> inside the if(d)...endif(d) for the 2D images? I could of course just try, but I thought to ask, as compilation always takes a while with the Python wrapping :-)
>> 
>> Best,
>> 
>> Sami
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
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From blowekamp at mail.nih.gov  Thu Aug 27 11:16:52 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 27 Aug 2015 11:16:52 -0400
Subject: [ITK] [ITK-dev] libpng valgrind issue
Message-ID: <83129BAA-6BB0-4DAF-AA63-77469C4FB818@mail.nih.gov>

Hello,

I narrowed down a couple valgrind [1] defects to a recent change to fix a warning.

I am surprised to see how active the libpng library is. It looks like we are a good bit out of date. I was thinking of working on a ThirdParty update script with the subtree to update the library.

Wondering if there is any prior work or experience with updating libpng?

Thanks,
Brad

[1] https://open.cdash.org/viewDynamicAnalysisFile.php?id=3530475
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From bhathaw1 at nycap.rr.com  Thu Aug 27 11:12:43 2015
From: bhathaw1 at nycap.rr.com (Barry Hathaway)
Date: Thu, 27 Aug 2015 11:12:43 -0400
Subject: [ITK] [ITK-users] Installing ITK into Eclipse/PyDev
Message-ID: <55DF28EB.3030707@nycap.rr.com>

I'm trying to get the ITK Python wrapping to work in my Eclipse/PyDev 
environment which
references a Python virtual environment. I have copied WrapITK.pth into 
the virtual environment's
Lib/site-packages and have verified that I can call various methods. The 
problem is that
within the Eclipse editor all the ITK references appear in red as errors 
because it cannot
find the methods.  Also the method hints/autocompletion does not work.  
Any ideas?
Thanks in advance.

Barry Hathaway

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From matt.mccormick at kitware.com  Thu Aug 27 11:41:12 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Aug 2015 11:41:12 -0400
Subject: [ITK] [ITK-users] CenteredTransformInitializer Python Wrapping
In-Reply-To: <A88934F1-939B-40F5-8154-33DE158696CD@mail.nih.gov>
References: <CADfpT84Ke1gLp9=Gn7AFJLnnrncxRsaSVvtO7JR6MLmU5RA36Q@mail.gmail.com>
 <09279851-32AB-4125-8ED9-9E47A8BA9425@gmail.com>
 <A88934F1-939B-40F5-8154-33DE158696CD@mail.nih.gov>
Message-ID: <CALzTN-SB2Go3kpO8OEGi8jyKiqSFERHrpzoCkZT1vpSNAOD2=A@mail.gmail.com>

Hi Sami,

Any patches are welcome and appreciated!  Please see here [1] for Git
contribution instructions.  The patch can be based off the release
branch.  Including "release" in the topic name will help us know that
is a possible patch to include in the release branch.

Thanks,
Matt

[1] http://www.itk.org/Wiki/ITK/Git/Develop

On Thu, Aug 27, 2015 at 8:19 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Hello,
>
> I would recommend using the "MatrixOffsetTransformBase" class for the template parameters. This enables the class to be used with any derived type.
>
> This is they way I did it in SimpleITK [1].
>
>
> Brad
>
> [1] https://github.com/SimpleITK/SimpleITK/blob/master/Code/BasicFilters/src/sitkCenteredTransformInitializerFilter.cxx#L125-L126
>
> On Aug 27, 2015, at 5:38 AM, Sami Koho <sami.koho at gmail.com> wrote:
>
>> Hello again,
>>
>> I fixed the wrapping issue. I thought that I might submit a patch to ITK, but I have a question. I am using the ITK version 4.8.0, which I obtained with a checkout from the GIT repository. Is it totally fine that I create the Patch for the 4.8.0 release, or should I switch to the main branch?
>>
>> Best,
>>
>> Sami
>>
>>
>>> On 27 Aug 2015, at 09:14, Sami Koho <sami.koho at gmail.com> wrote:
>>>
>>> Hello,
>>>
>>> I tried to convert a registration method that I have to use the CenteredSimilarity2DTransform instead of the CenteredRigid2DTransform in Python. There seems to be a problem however, as the CenteredTransformInitializer in Python only seems to work with the rigid transforms now. The wrapping file looks like this:
>>>
>>> itk_wrap_include("itkVersorRigid3DTransform.h")
>>> itk_wrap_include("itkCenteredRigid2DTransform.h")
>>> itk_wrap_class("itk::CenteredTransformInitializer" POINTER)
>>>    itk_wrap_filter_dims(d 3)
>>>    if(d)
>>>        foreach(t ${WRAP_ITK_SCALAR})
>>>          itk_wrap_template("VR3DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::VersorRigid3DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
>>>        endforeach()
>>>    endif(d)
>>>
>>>    itk_wrap_filter_dims(d 2)
>>>    if(d)
>>>        foreach(t ${WRAP_ITK_SCALAR})
>>>          itk_wrap_template("CR2DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::CenteredRigid2DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
>>>        endforeach()
>>>    endif(d)
>>> itk_end_wrap_class()
>>>
>>> How would I go about fixing this? Should I just add a new line, like:
>>>
>>> itk_wrap_template("CS2DT${ITKM_D}${ITKM_I${t}${d}}${ITKM_I${t}${d}}" "itk::CenteredSimilarity2DTransform< ${ITKT_D} >,${ITKT_I${t}${d}},${ITKT_I${t}${d}}")
>>>
>>> inside the if(d)...endif(d) for the 2D images? I could of course just try, but I thought to ask, as compilation always takes a while with the Python wrapping :-)
>>>
>>> Best,
>>>
>>> Sami
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
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From matt.mccormick at kitware.com  Thu Aug 27 12:05:30 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Aug 2015 12:05:30 -0400
Subject: [ITK] [ITK-dev] libpng valgrind issue
In-Reply-To: <83129BAA-6BB0-4DAF-AA63-77469C4FB818@mail.nih.gov>
References: <83129BAA-6BB0-4DAF-AA63-77469C4FB818@mail.nih.gov>
Message-ID: <CALzTN-RJRgUmPTt2x7mszs-+oevCMHFDmYBnDpZ7QRZFQjd2KQ@mail.gmail.com>

Hi Brad,

Updating libpng with the ThirdParty update script is a great idea!

As a reminder, there are some methods detailed in itk_tiff_mangle.h
[1] that may be helpful for the name mangling process. [1]

HTH,
Matt

[1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/TIFF/src/itktiff/itk_tiff_mangle.h;h=e65dadec55cf9d03d68580a39fa986c1147b3520;hb=HEAD

On Thu, Aug 27, 2015 at 11:16 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Hello,
>
> I narrowed down a couple valgrind [1] defects to a recent change to fix a warning.
>
> I am surprised to see how active the libpng library is. It looks like we are a good bit out of date. I was thinking of working on a ThirdParty update script with the subtree to update the library.
>
> Wondering if there is any prior work or experience with updating libpng?
>
> Thanks,
> Brad
>
> [1] https://open.cdash.org/viewDynamicAnalysisFile.php?id=3530475
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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From prashanth.dumpuri at gmail.com  Thu Aug 27 13:03:54 2015
From: prashanth.dumpuri at gmail.com (Prashanth)
Date: Thu, 27 Aug 2015 17:03:54 +0000
Subject: [ITK] [ITK-users] rescaling output of vesselness filter 0 and 1
Message-ID: <CAP+vBKRRH8ZkJTc0FERjTud=KLfmLgcucJwv8yjf+QZstGvyvQ@mail.gmail.com>

All,

What is the best way/filter to rescale the output of Vesselness filters
(like MultiScaleHessianBasedMeasureImageFilter) to lie between 0 and 1
without losing any of the information from the vesselness image?

I'm using the data type of my input image as the data type for the
vesselness image. So, if my input image is an int, then my vesselness image
is an int image as well. I have tried itk's RescaleIntensityImageFilter and
ShiftScaleImageFilter with no luck.

Thanks
Prashanth
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From matt.mccormick at kitware.com  Thu Aug 27 13:51:52 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Aug 2015 13:51:52 -0400
Subject: [ITK] [ITK-users] Installing ITK into Eclipse/PyDev
In-Reply-To: <55DF28EB.3030707@nycap.rr.com>
References: <55DF28EB.3030707@nycap.rr.com>
Message-ID: <CALzTN-S=oLa5zp5JuB59VU+a7P2DgiMgWou_NyrNwZwRcpg87w@mail.gmail.com>

Hi Barry,

ITK uses lazy loading of its modules so that 'import itk' does not
cause all of the modules to be loaded.  This improves start time, but
it may interfere with Eclipse/PyDev's inspection. Maybe if the IDE's
Python initialization code called something like:

def load_itk():
    try import itk:
        from itk import *
    except ImportError:
        pass

load_itk()

the references it is seeking will be found.

HTH,
Matt


On Thu, Aug 27, 2015 at 11:12 AM, Barry Hathaway <bhathaw1 at nycap.rr.com> wrote:
> I'm trying to get the ITK Python wrapping to work in my Eclipse/PyDev
> environment which
> references a Python virtual environment. I have copied WrapITK.pth into the
> virtual environment's
> Lib/site-packages and have verified that I can call various methods. The
> problem is that
> within the Eclipse editor all the ITK references appear in red as errors
> because it cannot
> find the methods.  Also the method hints/autocompletion does not work.  Any
> ideas?
> Thanks in advance.
>
> Barry Hathaway
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
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From matimontg at gmail.com  Thu Aug 27 15:42:36 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Thu, 27 Aug 2015 19:42:36 +0000
Subject: [ITK] [ITK-users] ActiViz Compile Errors
Message-ID: <CAKKNfu+NHxwWEP61QQqbBOi=j3=jU6s_K-R1GPj+pU+Fo37JQA@mail.gmail.com>

Hi,

I've downloaded Activiz 6.2 and was trying to compile (Using VS2008) and I
get 151 errors.

I was able to compile gccxml and mummy (with some errors) and now ActiViz
throws errors like these (I only list some)

Error 3658 fatal error LNK1104: cannot open file
'vtkRenderingFreeTypeOpenGL.lib' Kitware.VTK.vtkImagingCore.Unmanaged
Error 3675 fatal error C1083: Cannot open source file:
'.\export-layer\vtkGeoAlignedImageRepresentationEL.cxx': No such file or
directory c1xx
Error 3684 fatal error C1083: Cannot open source file:
'.\export-layer\vtkGeoSourceEL.cxx': No such file or directory c1xx


Error 3765 error PRJ0019: A tool returned an error code from "Building C#
library 'Kitware.VTK'..." Kitware.VTK

Error 3761 error PRJ0019: A tool returned an error code from "Generating
bin/Debug/vtkzlib-6.2.dll" Kitware.VTK.CopyDLLs

Error 3323 error: 'vtkViewUpdater' does not name a type
C:/Users/montroul/Downloads/Programacion/ActiViz/activizdotnet_build/xml/vtkViewUpdater_gccxml.cxx:12


Any clues what could be causing these type of errors? May it be related to
Mummy?

Thank you,

Matias.
-- 
Matias
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From tjklein at gmail.com  Thu Aug 27 15:42:58 2015
From: tjklein at gmail.com (Tassilo Klein)
Date: Thu, 27 Aug 2015 15:42:58 -0400
Subject: [ITK] [ITK-users] SimpleITK Anaconda Issue
Message-ID: <CAF3cZLuDHh8pJm2pSB80E7nERxttcJ3cbyt0f9eYZVYKnq+vXA@mail.gmail.com>

Hi,

I have issues getting my SimpleITK running on a Linux machine.

I used to get errors:

http://public.kitware.com/pipermail/community/2015-May/009117.html

ImportError: libpng15.so.15: cannot open shared object file: No such



Then I took an earlier version of libpng as mentioned here:

http://public.kitware.com/pipermail/community/2015-May/009120.html

conda install libpng=1.5.13



But then I get the following error:

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py
in <module>()     32 import matplotlib.artist as martist     33 import
matplotlib.cbook as cbook---> 34 import matplotlib.collections as
collections     35 import matplotlib.colors as colors     36 import
matplotlib.contour as contour
/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/collections.py
in <module>()     25 import matplotlib.artist as artist     26 from
matplotlib.artist import allow_rasterization---> 27 import
matplotlib.backend_bases as backend_bases     28 import
matplotlib.path as mpath     29 from matplotlib import _path
/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py
in <module>()     54      55 import matplotlib.tight_bbox as
tight_bbox---> 56 import matplotlib.textpath as textpath     57 from
matplotlib.path import Path     58 from matplotlib.cbook import
mplDeprecation
/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py
in <module>()     17 from matplotlib.path import Path     18 from
matplotlib import rcParams---> 19 import matplotlib.font_manager as
font_manager     20 from matplotlib.ft2font import FT2Font,
KERNING_DEFAULT, LOAD_NO_HINTING     21 from matplotlib.ft2font import
LOAD_TARGET_LIGHT
/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py
in <module>()     56 import matplotlib     57 from matplotlib import
afm---> 58 from matplotlib import ft2font     59 from matplotlib
import rcParams, get_cachedir     60 from matplotlib.cbook import
is_string_like
ImportError: libpng16.so.16: cannot open shared object file: No such
file or directory



Any idea?

Best,
 Tassilo
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From zivrafael.yaniv at nih.gov  Thu Aug 27 15:55:04 2015
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Thu, 27 Aug 2015 19:55:04 +0000
Subject: [ITK] [ITK-users] SimpleITK Anaconda Issue
In-Reply-To: <CAF3cZLuDHh8pJm2pSB80E7nERxttcJ3cbyt0f9eYZVYKnq+vXA@mail.gmail.com>
References: <CAF3cZLuDHh8pJm2pSB80E7nERxttcJ3cbyt0f9eYZVYKnq+vXA@mail.gmail.com>
Message-ID: <B2DE09A5824F4746A0528DAB608EF52002688213@msgb10.nih.gov>

Hello Tassilo,

Please follow the instructions found in our FAQ 'I am using the binary distribution of SimpleITK for Anaconda, why do I get an error about libpng?' found here: http://www.itk.org/Wiki/SimpleITK/FAQ

We are working on a more permanent solution for our next release.

               regards
                      Ziv

________________________________
From: Tassilo Klein [tjklein at gmail.com]
Sent: Thursday, August 27, 2015 3:42 PM
To: insight-users at itk.org
Subject: [ITK-users] SimpleITK Anaconda Issue

Hi,

I have issues getting my SimpleITK running on a Linux machine.

I used to get errors:

http://public.kitware.com/pipermail/community/2015-May/009117.html


ImportError: libpng15.so.15: cannot open shared object file: No such


Then I took an earlier version of libpng as mentioned here:

http://public.kitware.com/pipermail/community/2015-May/009120.html

conda install libpng=1.5.13


But then I get the following error:


/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py in <module>()
     32 import matplotlib.artist as martist
     33 import matplotlib.cbook as cbook
---> 34 import matplotlib.collections as collections
     35 import matplotlib.colors as colors
     36 import matplotlib.contour as contour

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/collections.py in <module>()
     25 import matplotlib.artist as artist
     26 from matplotlib.artist import allow_rasterization
---> 27 import matplotlib.backend_bases as backend_bases
     28 import matplotlib.path as mpath
     29 from matplotlib import _path

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py in <module>()
     54
     55 import matplotlib.tight_bbox as tight_bbox
---> 56 import matplotlib.textpath as textpath
     57 from matplotlib.path import Path
     58 from matplotlib.cbook import mplDeprecation

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py in <module>()
     17 from matplotlib.path import Path
     18 from matplotlib import rcParams
---> 19 import matplotlib.font_manager as font_manager
     20 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT, LOAD_NO_HINTING
     21 from matplotlib.ft2font import LOAD_TARGET_LIGHT

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()
     56 import matplotlib
     57 from matplotlib import afm
---> 58 from matplotlib import ft2font
     59 from matplotlib import rcParams, get_cachedir
     60 from matplotlib.cbook import is_string_like

ImportError: libpng16.so.16: cannot open shared object file: No such file or directory


Any idea?

Best,
 Tassilo
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From bhathaw1 at nycap.rr.com  Thu Aug 27 14:09:26 2015
From: bhathaw1 at nycap.rr.com (Barry Hathaway)
Date: Thu, 27 Aug 2015 14:09:26 -0400
Subject: [ITK] [ITK-users] Installing ITK into Eclipse/PyDev
In-Reply-To: <CALzTN-S=oLa5zp5JuB59VU+a7P2DgiMgWou_NyrNwZwRcpg87w@mail.gmail.com>
References: <55DF28EB.3030707@nycap.rr.com>
 <CALzTN-S=oLa5zp5JuB59VU+a7P2DgiMgWou_NyrNwZwRcpg87w@mail.gmail.com>
Message-ID: <55DF5256.6040608@nycap.rr.com>

I have also tried setting LazyLoading=False in itkConfig.py, but that 
did not seem to help in PyDev.

On 8/27/2015 1:51 PM, Matt McCormick wrote:
> Hi Barry,
>
> ITK uses lazy loading of its modules so that 'import itk' does not
> cause all of the modules to be loaded.  This improves start time, but
> it may interfere with Eclipse/PyDev's inspection. Maybe if the IDE's
> Python initialization code called something like:
>
> def load_itk():
>      try import itk:
>          from itk import *
>      except ImportError:
>          pass
>
> load_itk()
>
> the references it is seeking will be found.
>
> HTH,
> Matt
>
>
> On Thu, Aug 27, 2015 at 11:12 AM, Barry Hathaway <bhathaw1 at nycap.rr.com> wrote:
>> I'm trying to get the ITK Python wrapping to work in my Eclipse/PyDev
>> environment which
>> references a Python virtual environment. I have copied WrapITK.pth into the
>> virtual environment's
>> Lib/site-packages and have verified that I can call various methods. The
>> problem is that
>> within the Eclipse editor all the ITK references appear in red as errors
>> because it cannot
>> find the methods.  Also the method hints/autocompletion does not work.  Any
>> ideas?
>> Thanks in advance.
>>
>> Barry Hathaway
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>


_____________________________________
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http://www.kitware.com/products/protraining.php

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From tjklein at gmail.com  Thu Aug 27 16:56:26 2015
From: tjklein at gmail.com (Tassilo Klein)
Date: Thu, 27 Aug 2015 16:56:26 -0400
Subject: [ITK] [ITK-users] SimpleITK Anaconda Issue
In-Reply-To: <B2DE09A5824F4746A0528DAB608EF52002688213@msgb10.nih.gov>
References: <CAF3cZLuDHh8pJm2pSB80E7nERxttcJ3cbyt0f9eYZVYKnq+vXA@mail.gmail.com>
 <B2DE09A5824F4746A0528DAB608EF52002688213@msgb10.nih.gov>
Message-ID: <CAF3cZLue_tdmUXLkOsyKaJ=E_AOa+61VN94EpC6x4xVZTC1pkQ@mail.gmail.com>

Hi Ziv,

thanks. yes, that's what I did but then I get these  errors:

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py
in <module>()     56 import matplotlib     57 from matplotlib import
afm---> 58 from matplotlib import ft2font     59 from matplotlib
import rcParams, get_cachedir     60 from matplotlib.cbook import
is_string_like
ImportError: libpng16.so.16: cannot open shared object file: No such
file or directory


On Thu, Aug 27, 2015 at 3:55 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <
zivrafael.yaniv at nih.gov> wrote:

> Hello Tassilo,
>
> Please follow the instructions found in our FAQ 'I am using the binary
> distribution of SimpleITK for Anaconda, why do I get an error about
> libpng?' found here: http://www.itk.org/Wiki/SimpleITK/FAQ
>
> We are working on a more permanent solution for our next release.
>
>                regards
>                       Ziv
>
> ------------------------------
> *From:* Tassilo Klein [tjklein at gmail.com]
> *Sent:* Thursday, August 27, 2015 3:42 PM
> *To:* insight-users at itk.org
> *Subject:* [ITK-users] SimpleITK Anaconda Issue
>
> Hi,
>
> I have issues getting my SimpleITK running on a Linux machine.
>
> I used to get errors:
>
> http://public.kitware.com/pipermail/community/2015-May/009117.html
>
> ImportError: libpng15.so.15: cannot open shared object file: No such
>
>
>
> Then I took an earlier version of libpng as mentioned here:
>
> http://public.kitware.com/pipermail/community/2015-May/009120.html
>
> conda install libpng=1.5.13
>
>
>
> But then I get the following error:
>
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py in <module>()     32 import matplotlib.artist as martist     33 import matplotlib.cbook as cbook---> 34 import matplotlib.collections as collections     35 import matplotlib.colors as colors     36 import matplotlib.contour as contour
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/collections.py in <module>()     25 import matplotlib.artist as artist     26 from matplotlib.artist import allow_rasterization---> 27 import matplotlib.backend_bases as backend_bases     28 import matplotlib.path as mpath     29 from matplotlib import _path
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py in <module>()     54      55 import matplotlib.tight_bbox as tight_bbox---> 56 import matplotlib.textpath as textpath     57 from matplotlib.path import Path     58 from matplotlib.cbook import mplDeprecation
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py in <module>()     17 from matplotlib.path import Path     18 from matplotlib import rcParams---> 19 import matplotlib.font_manager as font_manager     20 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT, LOAD_NO_HINTING     21 from matplotlib.ft2font import LOAD_TARGET_LIGHT
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()     56 import matplotlib     57 from matplotlib import afm---> 58 from matplotlib import ft2font     59 from matplotlib import rcParams, get_cachedir     60 from matplotlib.cbook import is_string_like
> ImportError: libpng16.so.16: cannot open shared object file: No such file or directory
>
>
>
> Any idea?
>
> Best,
>  Tassilo
>
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From zivrafael.yaniv at nih.gov  Thu Aug 27 17:10:43 2015
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Thu, 27 Aug 2015 21:10:43 +0000
Subject: [ITK] [ITK-users] SimpleITK Anaconda Issue
In-Reply-To: <CAF3cZLue_tdmUXLkOsyKaJ=E_AOa+61VN94EpC6x4xVZTC1pkQ@mail.gmail.com>
References: <CAF3cZLuDHh8pJm2pSB80E7nERxttcJ3cbyt0f9eYZVYKnq+vXA@mail.gmail.com>
 <B2DE09A5824F4746A0528DAB608EF52002688213@msgb10.nih.gov>,
 <CAF3cZLue_tdmUXLkOsyKaJ=E_AOa+61VN94EpC6x4xVZTC1pkQ@mail.gmail.com>
Message-ID: <B2DE09A5824F4746A0528DAB608EF5200268823D@msgb10.nih.gov>

Hi Tassilo,

Did you downgrade to libpng1.5 after creating the virtual environment? This is what I suggested in the thread you cited and was the solution at the time.  It no longer works because anaconda upgraded additional packages.

When you create the virtual environment with libpng set to 1.5 (conda create -n sitkpy anaconda libpng=1.5) all of the dependent packages are downgraded to work with this version of libpng and then you will not have this issue. The three steps are given in the FAQ that I pointed you to - I am assuming here you did not follow that solution, it is pasted below for your convenience:

conda create -n sitkpy anaconda libpng=1.5
conda install -c https://conda.binstar.org/simpleitk/channel/main SimpleITK
conda install libpng=1.5

If you followed this set of instructions and it doesn't work, let us know and we will try to recreate the problem and find a solution.

          regards
              Ziv

________________________________
From: Tassilo Klein [tjklein at gmail.com]
Sent: Thursday, August 27, 2015 4:56 PM
To: Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
Cc: insight-users at itk.org
Subject: Re: [ITK-users] SimpleITK Anaconda Issue

Hi Ziv,

thanks. yes, that's what I did but then I get these  errors:


/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()
     56 import matplotlib
     57 from matplotlib import afm
---> 58 from matplotlib import ft2font
     59 from matplotlib import rcParams, get_cachedir
     60 from matplotlib.cbook import is_string_like

ImportError: libpng16.so.16: cannot open shared object file: No such file or directory

On Thu, Aug 27, 2015 at 3:55 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov<mailto:zivrafael.yaniv at nih.gov>> wrote:
Hello Tassilo,

Please follow the instructions found in our FAQ 'I am using the binary distribution of SimpleITK for Anaconda, why do I get an error about libpng?' found here: http://www.itk.org/Wiki/SimpleITK/FAQ

We are working on a more permanent solution for our next release.

               regards
                      Ziv

________________________________
From: Tassilo Klein [tjklein at gmail.com<mailto:tjklein at gmail.com>]
Sent: Thursday, August 27, 2015 3:42 PM
To: insight-users at itk.org<mailto:insight-users at itk.org>
Subject: [ITK-users] SimpleITK Anaconda Issue

Hi,

I have issues getting my SimpleITK running on a Linux machine.

I used to get errors:

http://public.kitware.com/pipermail/community/2015-May/009117.html


ImportError: libpng15.so.15: cannot open shared object file: No such


Then I took an earlier version of libpng as mentioned here:

http://public.kitware.com/pipermail/community/2015-May/009120.html

conda install libpng=1.5.13


But then I get the following error:


/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py in <module>()
     32 import matplotlib.artist as martist
     33 import matplotlib.cbook as cbook
---> 34 import matplotlib.collections as collections
     35 import matplotlib.colors as colors
     36 import matplotlib.contour as contour

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/collections.py in <module>()
     25 import matplotlib.artist as artist
     26 from matplotlib.artist import allow_rasterization
---> 27 import matplotlib.backend_bases as backend_bases
     28 import matplotlib.path as mpath
     29 from matplotlib import _path

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py in <module>()
     54
     55 import matplotlib.tight_bbox as tight_bbox
---> 56 import matplotlib.textpath as textpath
     57 from matplotlib.path import Path
     58 from matplotlib.cbook import mplDeprecation

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py in <module>()
     17 from matplotlib.path import Path
     18 from matplotlib import rcParams
---> 19 import matplotlib.font_manager as font_manager
     20 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT, LOAD_NO_HINTING
     21 from matplotlib.ft2font import LOAD_TARGET_LIGHT

/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()
     56 import matplotlib
     57 from matplotlib import afm
---> 58 from matplotlib import ft2font
     59 from matplotlib import rcParams, get_cachedir
     60 from matplotlib.cbook import is_string_like

ImportError: libpng16.so.16: cannot open shared object file: No such file or directory


Any idea?

Best,
 Tassilo

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From tevain at telecom-paristech.fr  Fri Aug 28 05:26:20 2015
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Fri, 28 Aug 2015 11:26:20 +0200 (CEST)
Subject: [ITK] [ITK-users] rescaling output of vesselness filter 0 and 1
In-Reply-To: <CAP+vBKRRH8ZkJTc0FERjTud=KLfmLgcucJwv8yjf+QZstGvyvQ@mail.gmail.com>
References: <CAP+vBKRRH8ZkJTc0FERjTud=KLfmLgcucJwv8yjf+QZstGvyvQ@mail.gmail.com>
Message-ID: <710919340.97742408.1440753980328.JavaMail.zimbra@enst.fr>

Hello Prashanth,

What's the problem with the RescaleIntensityImageFilter ? 
If you set the output min / max to 0 and 1 with corresponding functions it should works.
Don't forget to switch to float (or double) for the Rescaler filter output also, otherwise it's obvious you will lose information.

Tim

----- Mail original -----
De: "Prashanth" <prashanth.dumpuri at gmail.com>
?: "itk" <insight-users at itk.org>
Envoy?: Jeudi 27 Ao?t 2015 19:03:54
Objet: [ITK] [ITK-users] rescaling output of vesselness filter 0 and 1

All, 

What is the best way/filter to rescale the output of Vesselness filters (like MultiScaleHessianBasedMeasureImageFilter) to lie between 0 and 1 without losing any of the information from the vesselness image? 

I'm using the data type of my input image as the data type for the vesselness image. So, if my input image is an int, then my vesselness image is an int image as well. I have tried itk's RescaleIntensityImageFilter and ShiftScaleImageFilter with no luck. 

Thanks 
Prashanth 

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From bhathaw1 at nycap.rr.com  Fri Aug 28 08:39:20 2015
From: bhathaw1 at nycap.rr.com (Barry Hathaway)
Date: Fri, 28 Aug 2015 08:39:20 -0400
Subject: [ITK] [ITK-users] Building PyBuffer (itk 4.8.0/Win7/VS2012)
In-Reply-To: <CALzTN-S=oLa5zp5JuB59VU+a7P2DgiMgWou_NyrNwZwRcpg87w@mail.gmail.com>
References: <55DF28EB.3030707@nycap.rr.com>
 <CALzTN-S=oLa5zp5JuB59VU+a7P2DgiMgWou_NyrNwZwRcpg87w@mail.gmail.com>
Message-ID: <55E05678.7000702@nycap.rr.com>

I'm having problems building PyBuffer (itk 4.8.0) under Windows 7 64-bit 
using Visual Studio 2012. Numpy is 1.9.2.
I get the following errors when building the BridgeNumPyPython project:

Warning  1    warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION    c:\python27\virtualenv\cmcenv\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h    12    1    BridgeNumPyPython

Error    2    error C2057: expected constant expression    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    61    1    BridgeNumPyPython

Error    3    error C2466: cannot allocate an array of constant size 0    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    61    1    BridgeNumPyPython

Error    4    error C2133: 'dimensions' : unknown size    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    61    1    BridgeNumPyPython

Error    5    error C2057: expected constant expression    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    79    1    BridgeNumPyPython

Error    6    error C2466: cannot allocate an array of constant size 0    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    79    1    BridgeNumPyPython

Error    7    error C2133: 'reverseDimensions' : unknown size    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    79    1    BridgeNumPyPython

Any ideas?
Thanks in advance.

Barry Hathaway

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From blowekamp at mail.nih.gov  Fri Aug 28 09:21:28 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 28 Aug 2015 09:21:28 -0400
Subject: [ITK] [ITK-users] Building PyBuffer (itk 4.8.0/Win7/VS2012)
In-Reply-To: <55E05678.7000702@nycap.rr.com>
References: <55DF28EB.3030707@nycap.rr.com>
 <CALzTN-S=oLa5zp5JuB59VU+a7P2DgiMgWou_NyrNwZwRcpg87w@mail.gmail.com>
 <55E05678.7000702@nycap.rr.com>
Message-ID: <F273F3BB-988F-4BC7-85DB-BF65D7D7B675@mail.nih.gov>

Hello,

There were some recent updates to this module [1] that were remote module merged into the release branch.

Try getting the ITK git repository [2], and checking out the release branch.

HTH,
Brad

[1] http://review.source.kitware.com/#/c/20108/
[2] http://www.itk.org/Wiki/ITK/Git

On Aug 28, 2015, at 8:39 AM, Barry Hathaway <bhathaw1 at nycap.rr.com> wrote:

> I'm having problems building PyBuffer (itk 4.8.0) under Windows 7 64-bit using Visual Studio 2012. Numpy is 1.9.2.
> I get the following errors when building the BridgeNumPyPython project:
> 
> Warning  1    warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION    c:\python27\virtualenv\cmcenv\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h    12    1    BridgeNumPyPython
> 
> Error    2    error C2057: expected constant expression    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    61    1    BridgeNumPyPython
> 
> Error    3    error C2466: cannot allocate an array of constant size 0    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    61    1    BridgeNumPyPython
> 
> Error    4    error C2133: 'dimensions' : unknown size    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    61    1    BridgeNumPyPython
> 
> Error    5    error C2057: expected constant expression    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    79    1    BridgeNumPyPython
> 
> Error    6    error C2466: cannot allocate an array of constant size 0    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    79    1    BridgeNumPyPython
> 
> Error    7    error C2133: 'reverseDimensions' : unknown size    c:\insighttoolkit-4.8.0\modules\remote\bridgenumpy\include\itkPyBuffer.hxx    79    1    BridgeNumPyPython
> 
> Any ideas?
> Thanks in advance.
> 
> Barry Hathaway
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

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From emily-hammond at uiowa.edu  Fri Aug 28 10:22:10 2015
From: emily-hammond at uiowa.edu (Hammond, Emily M)
Date: Fri, 28 Aug 2015 14:22:10 +0000
Subject: [ITK] [ITK-users] import Slicer defined ROI into ITK
Message-ID: <2609C492EC89AB4CAAD3647B8D1A43CC2FB99252@ITSNT437.iowa.uiowa.edu>

Hello,

I have defined regions of interest created with Slicer (the 3D box region not a label mask) and I want to import that as a defined region into ITK so I can use it to crop an image in my pipeline. Does anyone have any insight into how I can do this?

Thanks
Emily H
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From matt.mccormick at kitware.com  Fri Aug 28 11:16:53 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 28 Aug 2015 11:16:53 -0400
Subject: [ITK] =?utf-8?q?=5BITK-dev=5D_Test_failures_on_RogueResearch9_?=
	=?utf-8?q?=EF=BF=BCMac10=2E6-gcc-rel-x86=5F64-static?=
Message-ID: <CALzTN-QWkW4OMwpEJPx5OY=GJ3dOK5OP3r5WjD9oKdgRMT09Uw@mail.gmail.com>

Hi Sean,

In checking up on the dashboard, we recently have acquired 8 failing
tests on RogueResearch9 ?Mac10.6-gcc-rel-x86_64-static:

  https://open.cdash.org/viewTest.php?onlyfailed&buildid=3973444


They started on August 18th, but there were many changes that day:

  https://open.cdash.org/index.php?project=Insight&date=20150818

and it is difficult to know the source of the problem.  Could git
bisect please be run on that box or is there any other information to
help find the source of the issue?

Thanks,
Matt
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From blowekamp at mail.nih.gov  Fri Aug 28 10:37:27 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 28 Aug 2015 10:37:27 -0400
Subject: [ITK] [ITK-users]   import Slicer defined ROI into ITK
In-Reply-To: <2609C492EC89AB4CAAD3647B8D1A43CC2FB99252@ITSNT437.iowa.uiowa.edu>
References: <2609C492EC89AB4CAAD3647B8D1A43CC2FB99252@ITSNT437.iowa.uiowa.edu>
Message-ID: <C8CEDC1C-B9F1-42E6-AEC0-2F60ED4996B7@mail.nih.gov>

Hello Emilly,

You didn't say if this was for a CLI, or python. Here is how I didn't it for a CLI:

https://github.com/blowekamp/Slicer-IASEM/blob/346a71558368117b61c9b2b26e40568597c23423/IASEMImport/IASEMImport.cxx#L73-L125

HTH,
Brad

On Aug 28, 2015, at 10:22 AM, Hammond, Emily M <emily-hammond at uiowa.edu> wrote:

> Hello,
> 
> I have defined regions of interest created with Slicer (the 3D box region not a label mask) and I want to import that as a defined region into ITK so I can use it to crop an image in my pipeline. Does anyone have any insight into how I can do this?
> 
> Thanks
> Emily H
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
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> Community mailing list
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> http://public.kitware.com/mailman/listinfo/community

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From emily-hammond at uiowa.edu  Fri Aug 28 13:13:31 2015
From: emily-hammond at uiowa.edu (Hammond, Emily M)
Date: Fri, 28 Aug 2015 17:13:31 +0000
Subject: [ITK] [ITK-users]   import Slicer defined ROI into ITK
In-Reply-To: <C8CEDC1C-B9F1-42E6-AEC0-2F60ED4996B7@mail.nih.gov>
References: <2609C492EC89AB4CAAD3647B8D1A43CC2FB99252@ITSNT437.iowa.uiowa.edu>, 
 <C8CEDC1C-B9F1-42E6-AEC0-2F60ED4996B7@mail.nih.gov>
Message-ID: <2609C492EC89AB4CAAD3647B8D1A43CC2FB992AB@ITSNT437.iowa.uiowa.edu>

That makes sense! Thanks much!!

________________________________
From: Bradley Lowekamp [blowekamp at mail.nih.gov]
Sent: Friday, August 28, 2015 9:37 AM
To: Hammond, Emily M
Cc: insight users
Subject: Re: [ITK] [ITK-users] import Slicer defined ROI into ITK

Hello Emilly,

You didn't say if this was for a CLI, or python. Here is how I didn't it for a CLI:

https://github.com/blowekamp/Slicer-IASEM/blob/346a71558368117b61c9b2b26e40568597c23423/IASEMImport/IASEMImport.cxx#L73-L125

HTH,
Brad

On Aug 28, 2015, at 10:22 AM, Hammond, Emily M <emily-hammond at uiowa.edu<mailto:emily-hammond at uiowa.edu>> wrote:

Hello,

I have defined regions of interest created with Slicer (the 3D box region not a label mask) and I want to import that as a defined region into ITK so I can use it to crop an image in my pipeline. Does anyone have any insight into how I can do this?

Thanks
Emily H
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From matt.mccormick at kitware.com  Fri Aug 28 14:52:49 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 28 Aug 2015 14:52:49 -0400
Subject: [ITK] [ITK-users] ActiViz Compile Errors
In-Reply-To: <CAKKNfu+NHxwWEP61QQqbBOi=j3=jU6s_K-R1GPj+pU+Fo37JQA@mail.gmail.com>
References: <CAKKNfu+NHxwWEP61QQqbBOi=j3=jU6s_K-R1GPj+pU+Fo37JQA@mail.gmail.com>
Message-ID: <CALzTN-T=gcxwfAQCAcB1BwM1d3nwo6Gh78ejfUTt9N--h3cKwQ@mail.gmail.com>

Hi Matias,

The vtk-users may be more helpful with this.

Matt

On Thu, Aug 27, 2015 at 3:42 PM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I've downloaded Activiz 6.2 and was trying to compile (Using VS2008) and I
> get 151 errors.
>
> I was able to compile gccxml and mummy (with some errors) and now ActiViz
> throws errors like these (I only list some)
>
> Error 3658 fatal error LNK1104: cannot open file
> 'vtkRenderingFreeTypeOpenGL.lib' Kitware.VTK.vtkImagingCore.Unmanaged
> Error 3675 fatal error C1083: Cannot open source file:
> '.\export-layer\vtkGeoAlignedImageRepresentationEL.cxx': No such file or
> directory c1xx
> Error 3684 fatal error C1083: Cannot open source file:
> '.\export-layer\vtkGeoSourceEL.cxx': No such file or directory c1xx
>
>
> Error 3765 error PRJ0019: A tool returned an error code from "Building C#
> library 'Kitware.VTK'..." Kitware.VTK
>
> Error 3761 error PRJ0019: A tool returned an error code from "Generating
> bin/Debug/vtkzlib-6.2.dll" Kitware.VTK.CopyDLLs
>
> Error 3323 error: 'vtkViewUpdater' does not name a type
> C:/Users/montroul/Downloads/Programacion/ActiViz/activizdotnet_build/xml/vtkViewUpdater_gccxml.cxx:12
>
>
> Any clues what could be causing these type of errors? May it be related to
> Mummy?
>
> Thank you,
>
> Matias.
> --
> Matias
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
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>
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From tjklein at gmail.com  Fri Aug 28 18:52:54 2015
From: tjklein at gmail.com (Tassilo Klein)
Date: Fri, 28 Aug 2015 18:52:54 -0400
Subject: [ITK] [ITK-users] SimpleITK Anaconda Issue
In-Reply-To: <B2DE09A5824F4746A0528DAB608EF5200268823D@msgb10.nih.gov>
References: <CAF3cZLuDHh8pJm2pSB80E7nERxttcJ3cbyt0f9eYZVYKnq+vXA@mail.gmail.com>
 <B2DE09A5824F4746A0528DAB608EF52002688213@msgb10.nih.gov>
 <CAF3cZLue_tdmUXLkOsyKaJ=E_AOa+61VN94EpC6x4xVZTC1pkQ@mail.gmail.com>
 <B2DE09A5824F4746A0528DAB608EF5200268823D@msgb10.nih.gov>
Message-ID: <CAF3cZLvvJC-Qo1Xvsv3wRfnauwgBQ2mmvnOCcrt-c-AQLqJT5A@mail.gmail.com>

Thanks Ziv,

I forgot to activate the environment before.

After following the steps, now I get a different error when trying to load
an image, which worked some time before:

/home/tjklein/anaconda/envs/sitkpy3/lib/python2.7/site-packages/SimpleITK/SimpleITK.py
in ReadImage(*args)   7726    7727     """-> 7728     return
_SimpleITK.ReadImage(*args)   7729 class
HashImageFilter(ProcessObject):   7730     """
RuntimeError: Exception thrown in SimpleITK ReadImage:
/home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageSeriesReader.cxx:143:
sitk::ERROR: The file in the series have unsupported 3 dimensions.



On Thu, Aug 27, 2015 at 5:10 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <
zivrafael.yaniv at nih.gov> wrote:

> Hi Tassilo,
>
> Did you downgrade to libpng1.5 after creating the virtual environment?
> This is what I suggested in the thread you cited and was the solution at
> the time.  It no longer works because anaconda upgraded additional packages.
>
> When you create the virtual environment with libpng set to 1.5 (conda
> create -n sitkpy anaconda libpng=1.5) all of the dependent packages are
> downgraded to work with this version of libpng and then you will not have
> this issue. The three steps are given in the FAQ that I pointed you to - I
> am assuming here you did not follow that solution, it is pasted below for
> your convenience:
>
> conda create -n sitkpy anaconda libpng=1.5
> conda install -c https://conda.binstar.org/simpleitk/channel/main
> SimpleITK
> conda install libpng=1.5
>
> If you followed this set of instructions and it doesn't work, let us know
> and we will try to recreate the problem and find a solution.
>
>           regards
>               Ziv
>
> ------------------------------
> *From:* Tassilo Klein [tjklein at gmail.com]
> *Sent:* Thursday, August 27, 2015 4:56 PM
> *To:* Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
> *Cc:* insight-users at itk.org
> *Subject:* Re: [ITK-users] SimpleITK Anaconda Issue
>
> Hi Ziv,
>
> thanks. yes, that's what I did but then I get these  errors:
>
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()     56 import matplotlib     57 from matplotlib import afm---> 58 from matplotlib import ft2font     59 from matplotlib import rcParams, get_cachedir     60 from matplotlib.cbook import is_string_like
> ImportError: libpng16.so.16: cannot open shared object file: No such file or directory
>
>
> On Thu, Aug 27, 2015 at 3:55 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <
> zivrafael.yaniv at nih.gov> wrote:
>
>> Hello Tassilo,
>>
>> Please follow the instructions found in our FAQ 'I am using the binary
>> distribution of SimpleITK for Anaconda, why do I get an error about
>> libpng?' found here: http://www.itk.org/Wiki/SimpleITK/FAQ
>>
>> We are working on a more permanent solution for our next release.
>>
>>                regards
>>                       Ziv
>>
>> ------------------------------
>> *From:* Tassilo Klein [tjklein at gmail.com]
>> *Sent:* Thursday, August 27, 2015 3:42 PM
>> *To:* insight-users at itk.org
>> *Subject:* [ITK-users] SimpleITK Anaconda Issue
>>
>> Hi,
>>
>> I have issues getting my SimpleITK running on a Linux machine.
>>
>> I used to get errors:
>>
>> http://public.kitware.com/pipermail/community/2015-May/009117.html
>>
>> ImportError: libpng15.so.15: cannot open shared object file: No such
>>
>>
>>
>> Then I took an earlier version of libpng as mentioned here:
>>
>> http://public.kitware.com/pipermail/community/2015-May/009120.html
>>
>> conda install libpng=1.5.13
>>
>>
>>
>> But then I get the following error:
>>
>> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py in <module>()     32 import matplotlib.artist as martist     33 import matplotlib.cbook as cbook---> 34 import matplotlib.collections as collections     35 import matplotlib.colors as colors     36 import matplotlib.contour as contour
>> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/collections.py in <module>()     25 import matplotlib.artist as artist     26 from matplotlib.artist import allow_rasterization---> 27 import matplotlib.backend_bases as backend_bases     28 import matplotlib.path as mpath     29 from matplotlib import _path
>> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py in <module>()     54      55 import matplotlib.tight_bbox as tight_bbox---> 56 import matplotlib.textpath as textpath     57 from matplotlib.path import Path     58 from matplotlib.cbook import mplDeprecation
>> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py in <module>()     17 from matplotlib.path import Path     18 from matplotlib import rcParams---> 19 import matplotlib.font_manager as font_manager     20 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT, LOAD_NO_HINTING     21 from matplotlib.ft2font import LOAD_TARGET_LIGHT
>> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()     56 import matplotlib     57 from matplotlib import afm---> 58 from matplotlib import ft2font     59 from matplotlib import rcParams, get_cachedir     60 from matplotlib.cbook import is_string_like
>> ImportError: libpng16.so.16: cannot open shared object file: No such file or directory
>>
>>
>>
>> Any idea?
>>
>> Best,
>>  Tassilo
>>
>
>
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From fotosentido at gmail.com  Fri Aug 28 19:37:02 2015
From: fotosentido at gmail.com (Marcos)
Date: Sat, 29 Aug 2015 01:37:02 +0200
Subject: [ITK] [ITK-users] Connecting multiframe dicom file to VTK
Message-ID: <CAA24WvHvSGcc3v=qEvSaDx77SZz6TVQxNWehB9czHGLvQHg7Mw@mail.gmail.com>

Hi,

I'm using itk::ImageToVTKImageFilter to connect itk::ImageFileReader with
vtkImageViewer2.

I can visualize my image in QVTKWidget.

I don't know if I'm reading correctly with ITK to pass that to VTK:

I'd like to access every frame, but vtkImageViewer2::getMaxSlice() is
returning 0 every time.

I'm connecting the pipeline with:

imageData->DeepCopy(connector->GetOutput());

imageViewer->SetInputData(imageData);



Any ideas?

Thanks.
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From matt.mccormick at kitware.com  Fri Aug 28 19:52:49 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 28 Aug 2015 19:52:49 -0400
Subject: [ITK] [ITK-users] Connecting multiframe dicom file to VTK
In-Reply-To: <CAA24WvHvSGcc3v=qEvSaDx77SZz6TVQxNWehB9czHGLvQHg7Mw@mail.gmail.com>
References: <CAA24WvHvSGcc3v=qEvSaDx77SZz6TVQxNWehB9czHGLvQHg7Mw@mail.gmail.com>
Message-ID: <CALzTN-QT=thgpxJNjFmPWnhkoH892psnusxwHoVxdEBrk+4ibA@mail.gmail.com>

Hi Marcos,

Are you calling ->Update() on connector?

Matt

On Fri, Aug 28, 2015 at 7:37 PM, Marcos <fotosentido at gmail.com> wrote:
> Hi,
>
> I'm using itk::ImageToVTKImageFilter to connect itk::ImageFileReader with
> vtkImageViewer2.
>
> I can visualize my image in QVTKWidget.
>
> I don't know if I'm reading correctly with ITK to pass that to VTK:
>
> I'd like to access every frame, but vtkImageViewer2::getMaxSlice() is
> returning 0 every time.
>
> I'm connecting the pipeline with:
>
> imageData->DeepCopy(connector->GetOutput());
>
> imageViewer->SetInputData(imageData);
>
>
>
> Any ideas?
>
> Thanks.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From fotosentido at gmail.com  Fri Aug 28 20:04:35 2015
From: fotosentido at gmail.com (Marcos)
Date: Sat, 29 Aug 2015 02:04:35 +0200
Subject: [ITK] [ITK-users] Connecting multiframe dicom file to VTK
In-Reply-To: <CALzTN-QT=thgpxJNjFmPWnhkoH892psnusxwHoVxdEBrk+4ibA@mail.gmail.com>
References: <CAA24WvHvSGcc3v=qEvSaDx77SZz6TVQxNWehB9czHGLvQHg7Mw@mail.gmail.com>
 <CALzTN-QT=thgpxJNjFmPWnhkoH892psnusxwHoVxdEBrk+4ibA@mail.gmail.com>
Message-ID: <CAA24WvGYp18aahu1iomxBQLK4TCwOs=AzF1ckxOW7X28YJvnNg@mail.gmail.com>

Hi Matt,

yes, otherwise I guess I couldn't see anything:

con->SetInput(itkImage);

con->Update();


imageData->DeepCopy(con->GetOutput());

imageViewer->SetInputData(imageData);

imageViewer->GetRenderer()->ResetCamera();


// some renderwindow and interactor settings for the widget


widget->update()



I'd like to change frames, but I guess I'm sending just one frame.

Also, I can't find an example from ITK to access each frame. If I
can't set a pipeline so I can do it from VTK, maybe I can read a slice
in ITK when I need it and pass that frame through the connector and
update.


Maybe I shouldn't use an itk::ImageFileReader, I don't know.



2015-08-29 1:52 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Marcos,
>
> Are you calling ->Update() on connector?
>
> Matt
>
> On Fri, Aug 28, 2015 at 7:37 PM, Marcos <fotosentido at gmail.com> wrote:
> > Hi,
> >
> > I'm using itk::ImageToVTKImageFilter to connect itk::ImageFileReader with
> > vtkImageViewer2.
> >
> > I can visualize my image in QVTKWidget.
> >
> > I don't know if I'm reading correctly with ITK to pass that to VTK:
> >
> > I'd like to access every frame, but vtkImageViewer2::getMaxSlice() is
> > returning 0 every time.
> >
> > I'm connecting the pipeline with:
> >
> > imageData->DeepCopy(connector->GetOutput());
> >
> > imageViewer->SetInputData(imageData);
> >
> >
> >
> > Any ideas?
> >
> > Thanks.
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
>
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From siavashk at ece.ubc.ca  Fri Aug 28 19:36:58 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Fri, 28 Aug 2015 16:36:58 -0700 (MST)
Subject: [ITK] [ITK-users] Connecting multiframe dicom file to VTK
In-Reply-To: <CAA24WvGYp18aahu1iomxBQLK4TCwOs=AzF1ckxOW7X28YJvnNg@mail.gmail.com>
References: <CAA24WvHvSGcc3v=qEvSaDx77SZz6TVQxNWehB9czHGLvQHg7Mw@mail.gmail.com>
 <CALzTN-QT=thgpxJNjFmPWnhkoH892psnusxwHoVxdEBrk+4ibA@mail.gmail.com>
 <CAA24WvGYp18aahu1iomxBQLK4TCwOs=AzF1ckxOW7X28YJvnNg@mail.gmail.com>
Message-ID: <1440805018163-36071.post@n7.nabble.com>

Marcos, isn't vtkImageViewer2 only suitable for 2D images? If that is the
case, it most likely ignores data along the z-axis.

Siavash



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Connecting-multiframe-dicom-file-to-VTK-tp36068p36071.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From fotosentido at gmail.com  Fri Aug 28 20:28:25 2015
From: fotosentido at gmail.com (Marcos)
Date: Sat, 29 Aug 2015 02:28:25 +0200
Subject: [ITK] [ITK-users] Connecting multiframe dicom file to VTK
In-Reply-To: <1440805018163-36071.post@n7.nabble.com>
References: <CAA24WvHvSGcc3v=qEvSaDx77SZz6TVQxNWehB9czHGLvQHg7Mw@mail.gmail.com>
 <CALzTN-QT=thgpxJNjFmPWnhkoH892psnusxwHoVxdEBrk+4ibA@mail.gmail.com>
 <CAA24WvGYp18aahu1iomxBQLK4TCwOs=AzF1ckxOW7X28YJvnNg@mail.gmail.com>
 <1440805018163-36071.post@n7.nabble.com>
Message-ID: <CAA24WvFaU8dd0=g4SNGe7AKGrCSLhyCsxtLYjL5O6CYH12OgGw@mail.gmail.com>

Wow, that's the idea!!

When I readed your answer, I tought: "maybe I should try ImageSeriesReader
with my file"

But then I remembered my itk::Image was of 2 dimensions ( I visualize 2D
images ).

So I set it to 3 and voil?: my vtkImageReader object told me my file has 11
frames, and I can iterate from that object.

So vtkImageViewer2 is suitable for multiframe images as long as you specify
your itk Image has 3 dimensions.

Thank you so much.


2015-08-29 1:36 GMT+02:00 Siavash Khallaghi <siavashk at ece.ubc.ca>:

> Marcos, isn't vtkImageViewer2 only suitable for 2D images? If that is the
> case, it most likely ignores data along the z-axis.
>
> Siavash
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/ITK-users-Connecting-multiframe-dicom-file-to-VTK-tp36068p36071.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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From bakkari.abdelkhalek at hotmail.fr  Sat Aug 29 03:53:45 2015
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sat, 29 Aug 2015 08:53:45 +0100
Subject: [ITK] ITK MAC WATERSHED
Message-ID: <DUB129-W57F28B7292C514D161AA50836D0@phx.gbl>

Hello!
Please, How can I build the Watershed algorithm with ITK in MAC ?
Regards, 		 	   		  
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From blowekamp at mail.nih.gov  Sat Aug 29 11:12:35 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Sat, 29 Aug 2015 11:12:35 -0400
Subject: [ITK] [ITK-users] SimpleITK Anaconda Issue
In-Reply-To: <CAF3cZLvvJC-Qo1Xvsv3wRfnauwgBQ2mmvnOCcrt-c-AQLqJT5A@mail.gmail.com>
References: <CAF3cZLuDHh8pJm2pSB80E7nERxttcJ3cbyt0f9eYZVYKnq+vXA@mail.gmail.com>
 <B2DE09A5824F4746A0528DAB608EF52002688213@msgb10.nih.gov>
 <CAF3cZLue_tdmUXLkOsyKaJ=E_AOa+61VN94EpC6x4xVZTC1pkQ@mail.gmail.com>
 <B2DE09A5824F4746A0528DAB608EF5200268823D@msgb10.nih.gov>
 <CAF3cZLvvJC-Qo1Xvsv3wRfnauwgBQ2mmvnOCcrt-c-AQLqJT5A@mail.gmail.com>
Message-ID: <8E140389-E26E-4949-9000-52A3958666E0@mail.nih.gov>

Hello,

That is great you got SimpleITK up and running by following those updated instructions for Anaconda.

Could you describe what you are trying to do and have a snippet of code?

Brad

On Aug 28, 2015, at 6:52 PM, Tassilo Klein <tjklein at gmail.com> wrote:

> Thanks Ziv,
> 
> I forgot to activate the environment before.
> 
> After following the steps, now I get a different error when trying to load an image, which worked some time before:
> 
> /home/tjklein/anaconda/envs/sitkpy3/lib/python2.7/site-packages/SimpleITK/SimpleITK.py in ReadImage(*args)
>    7726 
>    7727     """
> -> 7728     return _SimpleITK.ReadImage(*args)
>    7729 class HashImageFilter(ProcessObject):
>    7730     """
> 
> RuntimeError: Exception thrown in SimpleITK ReadImage: /home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageSeriesReader.cxx:143:
> sitk::ERROR: The file in the series have unsupported 3 dimensions.
> 
> 
> On Thu, Aug 27, 2015 at 5:10 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
> Hi Tassilo,
> 
> Did you downgrade to libpng1.5 after creating the virtual environment? This is what I suggested in the thread you cited and was the solution at the time.  It no longer works because anaconda upgraded additional packages.
> 
> When you create the virtual environment with libpng set to 1.5 (conda create -n sitkpy anaconda libpng=1.5) all of the dependent packages are downgraded to work with this version of libpng and then you will not have this issue. The three steps are given in the FAQ that I pointed you to - I am assuming here you did not follow that solution, it is pasted below for your convenience:
> 
> conda create -n sitkpy anaconda libpng=1.5 
> conda install -c https://conda.binstar.org/simpleitk/channel/main SimpleITK 
> conda install libpng=1.5 
> 
> If you followed this set of instructions and it doesn't work, let us know and we will try to recreate the problem and find a solution.
> 
>           regards
>               Ziv
> 
> From: Tassilo Klein [tjklein at gmail.com]
> Sent: Thursday, August 27, 2015 4:56 PM
> To: Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] SimpleITK Anaconda Issue
> 
> Hi Ziv,
> 
> thanks. yes, that's what I did but then I get these  errors:
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()
>      56 import matplotlib
>      57 from matplotlib import afm
> ---> 58 from matplotlib import ft2font
>      59 from matplotlib import rcParams, get_cachedir
>      60 from matplotlib.cbook import is_string_like
> 
> ImportError: libpng16.so.16: cannot open shared object file: No such file or directory
> 
> On Thu, Aug 27, 2015 at 3:55 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
> Hello Tassilo,
> 
> Please follow the instructions found in our FAQ 'I am using the binary distribution of SimpleITK for Anaconda, why do I get an error about libpng?' found here: http://www.itk.org/Wiki/SimpleITK/FAQ
> 
> We are working on a more permanent solution for our next release.
> 
>                regards
>                       Ziv
> 
> From: Tassilo Klein [tjklein at gmail.com]
> Sent: Thursday, August 27, 2015 3:42 PM
> To: insight-users at itk.org
> Subject: [ITK-users] SimpleITK Anaconda Issue
> 
> Hi,
> 
> I have issues getting my SimpleITK running on a Linux machine.
> 
> I used to get errors:
> 
> http://public.kitware.com/pipermail/community/2015-May/009117.html
> 
> ImportError: libpng15.so.15: cannot open shared object file: No such
> 
> 
> Then I took an earlier version of libpng as mentioned here:
> 
> http://public.kitware.com/pipermail/community/2015-May/009120.html
> conda install libpng=1.5.13
> 
> 
> But then I get the following error:
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py in <module>()
>      32 import matplotlib.artist as martist
>      33 import matplotlib.cbook as cbook
> ---> 34 import matplotlib.collections as collections
>      35 import matplotlib.colors as colors
>      36 import matplotlib.contour as contour
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/collections.py in <module>()
>      25 import matplotlib.artist as artist
>      26 from matplotlib.artist import allow_rasterization
> ---> 27 import matplotlib.backend_bases as backend_bases
>      28 import matplotlib.path as mpath
>      29 from matplotlib import _path
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py in <module>()
>      54 
>      55 import matplotlib.tight_bbox as tight_bbox
> ---> 56 import matplotlib.textpath as textpath
>      57 from matplotlib.path import Path
>      58 from matplotlib.cbook import mplDeprecation
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py in <module>()
>      17 from matplotlib.path import Path
>      18 from matplotlib import rcParams
> ---> 19 import matplotlib.font_manager as font_manager
>      20 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT, LOAD_NO_HINTING
>      21 from matplotlib.ft2font import LOAD_TARGET_LIGHT
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()
>      56 import matplotlib
>      57 from matplotlib import afm
> ---> 58 from matplotlib import ft2font
>      59 from matplotlib import rcParams, get_cachedir
>      60 from matplotlib.cbook import is_string_like
> 
> ImportError: libpng16.so.16: cannot open shared object file: No such file or directory
> 
> 
> Any idea?
> 
> Best,
>  Tassilo
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
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From marco.dev.open at gmail.com  Sat Aug 29 12:18:52 2015
From: marco.dev.open at gmail.com (Marco Dev)
Date: Sat, 29 Aug 2015 20:48:52 +0430
Subject: [ITK] [ITK-dev] compare between MITK.ORG AND 3D SLICER
Message-ID: <CAKcUdn7+zdyfNsuQEdr-7-ok+fgqC5SyH3Y_Z5e6cHjAHdqomg@mail.gmail.com>

Hi,
I want to choice between MITK and 3d slicer for working in medical features
which one is powerful and going to improving in aspect code and example ...
Thanks
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From fotosentido at gmail.com  Sat Aug 29 16:51:37 2015
From: fotosentido at gmail.com (Marcos)
Date: Sat, 29 Aug 2015 22:51:37 +0200
Subject: [ITK] [ITK-users] Can't iterate over MetadataDictionary from
	GDCMImageIO
Message-ID: <CAA24WvHgHXyy0Bo6R4xT31p4HedNFHtOfaBsPY9QqOhRDMHrvw@mail.gmail.com>

Hi,

I'm using this example:
http://www.itk.org/Doxygen/html/Examples_2IO_2DicomSeriesReadPrintTags_8cxx-example.html

to try to get metadata info, but it never gets into the while:

typedef itk::MetaDataDictionary DictionaryType;

itk::GDCMImageIO::Pointer dicomIO = itk::GDCMImageIO::New();

const DictionaryType &dic = dicomIO->GetMetaDataDictionary();


typedef itk::MetaDataObject<std::string> MetadataStringType;

DictionaryType::ConstIterator itr = dic.Begin();

DictionaryType::ConstIterator end = dic.End();


while (itr != end)

{

...

}



It doesn't depend on the file, I'm using it inside that while. But I
never get into. The two iterators are the same? Why?


I'm using ITK 4.8.0.


The code is fine, right?


Thanks.
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From matt.mccormick at kitware.com  Sat Aug 29 17:44:51 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 29 Aug 2015 17:44:51 -0400
Subject: [ITK] [ITK-users] Can't iterate over MetadataDictionary
	from	GDCMImageIO
In-Reply-To: <CAA24WvHgHXyy0Bo6R4xT31p4HedNFHtOfaBsPY9QqOhRDMHrvw@mail.gmail.com>
References: <CAA24WvHgHXyy0Bo6R4xT31p4HedNFHtOfaBsPY9QqOhRDMHrvw@mail.gmail.com>
Message-ID: <CALzTN-Rgb_sYVci30YHjfchafmPWjzPt7bLNbXyKE1quNyGfhA@mail.gmail.com>

Hi Marcos,

If BUILD_EXAMPLES and BUILD_TESTING is turned on in your ITK CMake
configuration, and the ITKData target has been built, the example and
testing data are available in the build tree. Run

  ./bin/DicomSeriesReadPrintTag ./ExternalData/Testing/Data/Input/DicomSeries

and the tags will be printed out.

Hope this helps,
Matt



On Sat, Aug 29, 2015 at 4:51 PM, Marcos <fotosentido at gmail.com> wrote:
> Hi,
>
> I'm using this example:
> http://www.itk.org/Doxygen/html/Examples_2IO_2DicomSeriesReadPrintTags_8cxx-example.html
>
> to try to get metadata info, but it never gets into the while:
>
> typedef itk::MetaDataDictionary DictionaryType;
>
> itk::GDCMImageIO::Pointer dicomIO = itk::GDCMImageIO::New();
>
> const DictionaryType &dic = dicomIO->GetMetaDataDictionary();
>
>
> typedef itk::MetaDataObject<std::string> MetadataStringType;
>
> DictionaryType::ConstIterator itr = dic.Begin();
>
> DictionaryType::ConstIterator end = dic.End();
>
>
> while (itr != end)
>
> {
>
> ...
>
> }
>
>
>
> It doesn't depend on the file, I'm using it inside that while. But I never
> get into. The two iterators are the same? Why?
>
>
> I'm using ITK 4.8.0.
>
>
> The code is fine, right?
>
>
> Thanks.
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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From fotosentido at gmail.com  Sat Aug 29 18:40:46 2015
From: fotosentido at gmail.com (Marcos)
Date: Sun, 30 Aug 2015 00:40:46 +0200
Subject: [ITK] [ITK-users] Can't iterate over MetadataDictionary
	from	GDCMImageIO
In-Reply-To: <CALzTN-Rgb_sYVci30YHjfchafmPWjzPt7bLNbXyKE1quNyGfhA@mail.gmail.com>
References: <CAA24WvHgHXyy0Bo6R4xT31p4HedNFHtOfaBsPY9QqOhRDMHrvw@mail.gmail.com>
 <CALzTN-Rgb_sYVci30YHjfchafmPWjzPt7bLNbXyKE1quNyGfhA@mail.gmail.com>
Message-ID: <CAA24WvHcOBM19e-etviE5FORNEfv7RXM-MMDDWaqceL609OGbw@mail.gmail.com>

Hi,

I did that, but it gives me the error:

itk::ExceptionObject <...>
Location: "void __thiscall itk::ImageSeriesReader<class
itk::Image<short,3>::GenerateOutputInformation(void)"
File ...ImageSeriesReader.hxx: Line 122
At least one filename is required.

Instead of ./ExternalData/Testing/Data/Input/DicomSeries (which is a
directory), I've tried a dcm file, for example. The error is the same.

I'm on Windows, so I did on cmd:


C:\ITK-4.8.0-build> bin\Debug\DicomSeriesReadPrintTags.exe
/ExternalData/Testing/Data/Input/DicomSeries

And also:
C:\ITK-4.8.0-build> bin\Debug\DicomSeriesReadPrintTags.exe C:\myfile.dcm




2015-08-29 23:44 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Marcos,
>
> If BUILD_EXAMPLES and BUILD_TESTING is turned on in your ITK CMake
> configuration, and the ITKData target has been built, the example and
> testing data are available in the build tree. Run
>
>   ./bin/DicomSeriesReadPrintTag
> ./ExternalData/Testing/Data/Input/DicomSeries
>
> and the tags will be printed out.
>
> Hope this helps,
> Matt
>
>
>
> On Sat, Aug 29, 2015 at 4:51 PM, Marcos <fotosentido at gmail.com> wrote:
> > Hi,
> >
> > I'm using this example:
> >
> http://www.itk.org/Doxygen/html/Examples_2IO_2DicomSeriesReadPrintTags_8cxx-example.html
> >
> > to try to get metadata info, but it never gets into the while:
> >
> > typedef itk::MetaDataDictionary DictionaryType;
> >
> > itk::GDCMImageIO::Pointer dicomIO = itk::GDCMImageIO::New();
> >
> > const DictionaryType &dic = dicomIO->GetMetaDataDictionary();
> >
> >
> > typedef itk::MetaDataObject<std::string> MetadataStringType;
> >
> > DictionaryType::ConstIterator itr = dic.Begin();
> >
> > DictionaryType::ConstIterator end = dic.End();
> >
> >
> > while (itr != end)
> >
> > {
> >
> > ...
> >
> > }
> >
> >
> >
> > It doesn't depend on the file, I'm using it inside that while. But I
> never
> > get into. The two iterators are the same? Why?
> >
> >
> > I'm using ITK 4.8.0.
> >
> >
> > The code is fine, right?
> >
> >
> > Thanks.
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
>
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http://www.kitware.com/opensource/opensource.html

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From sean at rogue-research.com  Sat Aug 29 19:56:44 2015
From: sean at rogue-research.com (Sean McBride)
Date: Sat, 29 Aug 2015 19:56:44 -0400
Subject: [ITK] [ITK-dev] Test failures on
	RogueResearch9	?Mac10.6-gcc-rel-x86_64-static
In-Reply-To: <CALzTN-QWkW4OMwpEJPx5OY=GJ3dOK5OP3r5WjD9oKdgRMT09Uw@mail.gmail.com>
References: <CALzTN-QWkW4OMwpEJPx5OY=GJ3dOK5OP3r5WjD9oKdgRMT09Uw@mail.gmail.com>
Message-ID: <20150829235644.614532161@mail.rogue-research.com>

On Fri, 28 Aug 2015 11:16:53 -0400, Matt McCormick said:

>Hi Sean,
>
>In checking up on the dashboard, we recently have acquired 8 failing
>tests on RogueResearch9 ?Mac10.6-gcc-rel-x86_64-static:
>
>  https://open.cdash.org/viewTest.php?onlyfailed&buildid=3973444
>
>
>They started on August 18th, but there were many changes that day:
>
>  https://open.cdash.org/index.php?project=Insight&date=20150818
>
>and it is difficult to know the source of the problem.  Could git
>bisect please be run on that box or is there any other information to
>help find the source of the issue?

Took a while to run, but:

git bisect start
git bisect good 27e871d35c12ff85c798359c87b1828ee6d55d48
git bisect bad 0d769889367c013836d43691d13091326d6a998d

9ea5521e0fd2ed30404a72c53b1bdb15ab51a057 is the first bad commit
commit 9ea5521e0fd2ed30404a72c53b1bdb15ab51a057
Author: Alexander Leinoff <alexander-leinoff at uiowa.edu>
Date:   Fri Aug 14 09:11:46 2015 -0500

    COMP: Removes floating-point equality checks
    
    Equality checks between floating point values and other types are
    sometimes required to be exact and other times need only be approximate.
    Here direct equality checks are replaced with functions calls to either
    an exact or approximate comparison. Using these functions explicitly
    stating which kind of comparison is being requested improves clarity and
    readability of code, and removes compiler warnings ie. Wfloat-equal.
    
    Change-Id: I93241acc40178b50ab04158acfdbce5a93242890

:040000 040000 0875e6abbbbe9ae31f0e5992a25b8f17ef72ea8c 3bb3c0776a4e65c2a5dc35624b67f7a8e836c5fb M	Examples
:040000 040000 d8cbeb4d22f289a1c590b8cb43e4f05826e2c476 4e62bf45576ef2ff5b42326330b5eced60c4e367 M	Modules


Cheers,

-- 
____________________________________________________________
Sean McBride, B. Eng                 sean at rogue-research.com
Rogue Research                        www.rogue-research.com 
Mac Software Developer              Montr?al, Qu?bec, Canada


_______________________________________________
Powered by www.kitware.com

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http://www.kitware.com/opensource/opensource.html

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From matt.mccormick at kitware.com  Sat Aug 29 20:28:02 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 29 Aug 2015 20:28:02 -0400
Subject: [ITK] [ITK-users] Can't iterate over MetadataDictionary
	from	GDCMImageIO
In-Reply-To: <CAA24WvHcOBM19e-etviE5FORNEfv7RXM-MMDDWaqceL609OGbw@mail.gmail.com>
References: <CAA24WvHgHXyy0Bo6R4xT31p4HedNFHtOfaBsPY9QqOhRDMHrvw@mail.gmail.com>
 <CALzTN-Rgb_sYVci30YHjfchafmPWjzPt7bLNbXyKE1quNyGfhA@mail.gmail.com>
 <CAA24WvHcOBM19e-etviE5FORNEfv7RXM-MMDDWaqceL609OGbw@mail.gmail.com>
Message-ID: <CALzTN-SNXiZ6+EJHboxYXraOC_ODJwXEE7ZbJbPbj9iZtALNvA@mail.gmail.com>

On Sat, Aug 29, 2015 at 6:40 PM, Marcos <fotosentido at gmail.com> wrote:
> Hi,
>
> I did that, but it gives me the error:
>
> itk::ExceptionObject <...>
> Location: "void __thiscall itk::ImageSeriesReader<class
> itk::Image<short,3>::GenerateOutputInformation(void)"
> File ...ImageSeriesReader.hxx: Line 122
> At least one filename is required.
>
> Instead of ./ExternalData/Testing/Data/Input/DicomSeries (which is a
> directory), I've tried a dcm file, for example. The error is the same.
>
> I'm on Windows, so I did on cmd:
>
>
> C:\ITK-4.8.0-build> bin\Debug\DicomSeriesReadPrintTags.exe
> /ExternalData/Testing/Data/Input/DicomSeries

It needs to be ./ExternalData instead of /ExternalData.

Check that the files are there with the "dir" command.

HTH,
Matt
_____________________________________
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From fotosentido at gmail.com  Sun Aug 30 05:42:51 2015
From: fotosentido at gmail.com (Marcos)
Date: Sun, 30 Aug 2015 11:42:51 +0200
Subject: [ITK] [ITK-users] Can't iterate over MetadataDictionary
	from	GDCMImageIO
In-Reply-To: <CALzTN-SNXiZ6+EJHboxYXraOC_ODJwXEE7ZbJbPbj9iZtALNvA@mail.gmail.com>
References: <CAA24WvHgHXyy0Bo6R4xT31p4HedNFHtOfaBsPY9QqOhRDMHrvw@mail.gmail.com>
 <CALzTN-Rgb_sYVci30YHjfchafmPWjzPt7bLNbXyKE1quNyGfhA@mail.gmail.com>
 <CAA24WvHcOBM19e-etviE5FORNEfv7RXM-MMDDWaqceL609OGbw@mail.gmail.com>
 <CALzTN-SNXiZ6+EJHboxYXraOC_ODJwXEE7ZbJbPbj9iZtALNvA@mail.gmail.com>
Message-ID: <CAA24WvF+zmFiof0K+aaD0un9d3S3g14gFptMiO_U25TYG5XjgQ@mail.gmail.com>

You're right, these were only .md5 files

I built it again and now I have dcm files.

And yes, I can see tags.

So I don't understand why I can't get into that while loop. It's just a few
lines of code, it compiles... It's not really a big thing.

I guess I'm missing something.

2015-08-30 2:28 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:

> On Sat, Aug 29, 2015 at 6:40 PM, Marcos <fotosentido at gmail.com> wrote:
> > Hi,
> >
> > I did that, but it gives me the error:
> >
> > itk::ExceptionObject <...>
> > Location: "void __thiscall itk::ImageSeriesReader<class
> > itk::Image<short,3>::GenerateOutputInformation(void)"
> > File ...ImageSeriesReader.hxx: Line 122
> > At least one filename is required.
> >
> > Instead of ./ExternalData/Testing/Data/Input/DicomSeries (which is a
> > directory), I've tried a dcm file, for example. The error is the same.
> >
> > I'm on Windows, so I did on cmd:
> >
> >
> > C:\ITK-4.8.0-build> bin\Debug\DicomSeriesReadPrintTags.exe
> > /ExternalData/Testing/Data/Input/DicomSeries
>
> It needs to be ./ExternalData instead of /ExternalData.
>
> Check that the files are there with the "dir" command.
>
> HTH,
> Matt
>
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From fotosentido at gmail.com  Sun Aug 30 06:04:53 2015
From: fotosentido at gmail.com (Marcos)
Date: Sun, 30 Aug 2015 12:04:53 +0200
Subject: [ITK] [ITK-users] Can't iterate over MetadataDictionary
	from	GDCMImageIO
In-Reply-To: <CAA24WvF+zmFiof0K+aaD0un9d3S3g14gFptMiO_U25TYG5XjgQ@mail.gmail.com>
References: <CAA24WvHgHXyy0Bo6R4xT31p4HedNFHtOfaBsPY9QqOhRDMHrvw@mail.gmail.com>
 <CALzTN-Rgb_sYVci30YHjfchafmPWjzPt7bLNbXyKE1quNyGfhA@mail.gmail.com>
 <CAA24WvHcOBM19e-etviE5FORNEfv7RXM-MMDDWaqceL609OGbw@mail.gmail.com>
 <CALzTN-SNXiZ6+EJHboxYXraOC_ODJwXEE7ZbJbPbj9iZtALNvA@mail.gmail.com>
 <CAA24WvF+zmFiof0K+aaD0un9d3S3g14gFptMiO_U25TYG5XjgQ@mail.gmail.com>
Message-ID: <CAA24WvEMZ1kiXcNjYOTooDqrSDHRAZpe-2Q6qcWokmuKAa1Waw@mail.gmail.com>

I got it:

I created a new GDCMImageIO::Pointer (inside another method), instead of
using the one that let me read the file. That was the reason.

Sorry for not seeing it before.

Thanks, as always, for your time.


2015-08-30 11:42 GMT+02:00 Marcos <fotosentido at gmail.com>:

> You're right, these were only .md5 files
>
> I built it again and now I have dcm files.
>
> And yes, I can see tags.
>
> So I don't understand why I can't get into that while loop. It's just a
> few lines of code, it compiles... It's not really a big thing.
>
> I guess I'm missing something.
>
> 2015-08-30 2:28 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:
>
>> On Sat, Aug 29, 2015 at 6:40 PM, Marcos <fotosentido at gmail.com> wrote:
>> > Hi,
>> >
>> > I did that, but it gives me the error:
>> >
>> > itk::ExceptionObject <...>
>> > Location: "void __thiscall itk::ImageSeriesReader<class
>> > itk::Image<short,3>::GenerateOutputInformation(void)"
>> > File ...ImageSeriesReader.hxx: Line 122
>> > At least one filename is required.
>> >
>> > Instead of ./ExternalData/Testing/Data/Input/DicomSeries (which is a
>> > directory), I've tried a dcm file, for example. The error is the same.
>> >
>> > I'm on Windows, so I did on cmd:
>> >
>> >
>> > C:\ITK-4.8.0-build> bin\Debug\DicomSeriesReadPrintTags.exe
>> > /ExternalData/Testing/Data/Input/DicomSeries
>>
>> It needs to be ./ExternalData instead of /ExternalData.
>>
>> Check that the files are there with the "dir" command.
>>
>> HTH,
>> Matt
>>
>
>
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From andras.osztroluczki at gmail.com  Mon Aug 31 07:42:24 2015
From: andras.osztroluczki at gmail.com (=?UTF-8?Q?Andr=C3=A1s=2C_Osztroluczki?=)
Date: Mon, 31 Aug 2015 13:42:24 +0200
Subject: [ITK] Smoothing under a mask
Message-ID: <CAGJ5W5MQNCxLTsnidP1hehh0ztT=u6Rb6MAjgyPy5q0A9sLmjQ@mail.gmail.com>

Dear ITK users,

Is there a way to perform smoothing (for example
with: RecursiveGaussianImageFilter) under a masked region only (e.g.: the
computation only use those pixel values which are marked by the mask).
Smoothing the whole image and crop the masked region from the smoothed
image is not good for me unfortunately.

Thanks,
Andras
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From fotosentido at gmail.com  Mon Aug 31 15:54:58 2015
From: fotosentido at gmail.com (Marcos)
Date: Mon, 31 Aug 2015 21:54:58 +0200
Subject: [ITK] [ITK-users] Export specific frame/slice of multiframe dicom
	file:	ExtractSliceImageFilter?
Message-ID: <CAA24WvHjtG0zFza5Ys-f9aU4xm6n_k=FBfCX=T2Tgd1cRmO70A@mail.gmail.com>

Hi,

I have an itk:Image<unsigned short, 3> so I can see the different
slices/frames on an QVTKWidget.

I can export the frame I'm viewing to an JPG with vtkJPEGWriter() but it
uses the windowrenderer and the output depends on the size of the widget.

So I think it would be better to export the original. I'm using
itk:ImageFileWriter, but I can't find how to specify the frame I want, so
it gives an error saying my image has 3 dimensions and it can't export to
2D dimensions.

I found itk::ExtractSliceImageFilter, but I can't find examples. I don't
understand how to apply it to this case, can't find how to tell it "your
output is the n frame".

Is that the class I need? Any hints using it?
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From prashanth.dumpuri at gmail.com  Mon Aug 31 16:14:17 2015
From: prashanth.dumpuri at gmail.com (Prashanth)
Date: Mon, 31 Aug 2015 20:14:17 +0000
Subject: [ITK] [ITK-users] speed function for itkSpeedToPathFilter
In-Reply-To: <CAP+vBKSkV6783FxNR527=dkm+CvpowkDLOMfg2agF4xDQAG8bw@mail.gmail.com>
References: <CAP+vBKQN7E2vRR5YxZrqKYioCN5jwW+3FbQ4fDV55n2WVwBv5A@mail.gmail.com>
 <CAPNvZ5bVU1nUCRb_A1QBAMU0bHhea-Q+TTxbwKKE8pQasu-i4w@mail.gmail.com>
 <CALzTN-QPjWoRVYAr1pBAYEDRPXYtO_STdQKTTM5DK_7cHB4HqQ@mail.gmail.com>
 <CAP+vBKSkV6783FxNR527=dkm+CvpowkDLOMfg2agF4xDQAG8bw@mail.gmail.com>
Message-ID: <CAP+vBKQPgB2==jd31mY5bKTiKc8XweMfbipM-bRNKkKK43VA3A@mail.gmail.com>

Matt - I did not have success building TubeTk. First I got errors related
to Boost (even though the build instructions said it was optional) and then
I got errors related to KW Widgets. So, I abandoned building TubeTk.

Dan - Thanks again for the link but WhiteHatTopImageFilter did not work for
me. Again, if I read your email correctly then you said that a binary image
(1 inside vessel, 0 outside) should work as input for
itkSpeedFunctionToPathFilter. Binary images did not work for me either - I
ended up with zero points in my shortest path.

In case someone else stumbles across this post here's what worked for me:

(Defining the problem again) My goal is to find the shortest path between
two points that lie on a vessel's centerline.

What worked for me:
(assumes that input image and all other intermediate outputs are double
images. if not, cast your image).

1. Crop the input image (to speed up computations)
2. Select seeds on cropped image and use itkConfidenceConnectedmageFilter
to segment vessel
3. Fill the holes in the segmented binary image
4. Multiply the above image (hole filled binary segmented image) with
cropped image
5. Use image from step 4 as input for
itkMultiScaleHessianBasedMeasureImageFilter.
      I used itkHessianToObjectnessMeasureImageFilter as my hessian measure
filter input. Note that I had to set  SetScaleObjectnessMeasure to TRUE
           for itkHessianToObjectnessMeasureImageFilter  to work.
6. Rescale  itkMultiScaleHessianBasedMeasureImageFilter to lie between 0
and 1
7. Select start and end point and run itkSpeedFunctionToPathFilter

Thanks again to Matt and Dan for responding and helping me out.
Prashanth


On Tue, Aug 25, 2015 at 11:16 AM Prashanth <prashanth.dumpuri at gmail.com>
wrote:

> Matt and Dan - Thank you so much for getting back to me.
>
> Dan - If I understood your email correctly then a binary image (with 1
> inside the vessels and 0 outside) should work as a speed function. And if
> that is the case then a binary mask did not work for me. I get no points in
> the output of SpeedToPath filter if I use a binary mask. I'm looking into
> White top hat filtering and vesselness currently. Like you pointed out (and
> as mentioned in your thesis), vesselness is slower but so far it seems to
> be working better than white top hat.
>
> Matt - I will look into TubeTk as well and post an update to the mailing
> list.
>
> Thanks again
> Prashanth
>
> On Tue, Aug 25, 2015 at 10:52 AM Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> Hi Prashanth,
>>
>> Classes within TubeTK [1] specialize in creating input images that
>> would work well as an input to the itk::SpeedToPathFilter.
>>
>> Hope this helps,
>> Matt
>>
>> [1] https://github.com/KitwareMedical/TubeTK
>>
>> On Sun, Aug 23, 2015 at 5:49 AM, Dan Mueller <dan.muel at gmail.com> wrote:
>> > Hi Prashanth,
>> >
>> > Essentially you want your speed function to be white (1.0) in the
>> > vessels and black (0.0) outside of the vessels ? any way you can
>> > achieve this is fine. The method you have outline is very general, and
>> > the issue is step (1) i.e. finding an approximate centreline. Some
>> > have suggested achieving this by applying multiscale Hessian line
>> > filtering (aka vessel enhancement filtering) such as Sato/Frangi
>> > method ? while this can achieve good results, personally I find this
>> > method very slow. In my own work, I have found morphological top-hat
>> > by opening (aka white top-hat or WTH) produces good results at a
>> > fraction of the computation expense, especially using the box
>> > structuring element with acceleration (e.g. see [1]).
>> >
>> > Good luck.
>> >
>> > Cheers, Dan
>> >
>> > [1] ?Direct volume illustration for cardiac applications,? chapter 4,
>> > page 83?109,
>> http://eprints.qut.edu.au/17028/1/Daniel_Mueller_Thesis.pdf
>> >
>> > On 22 August 2015 at 06:52, Prashanth <prashanth.dumpuri at gmail.com>
>> wrote:
>> >> All,
>> >>
>> >> I'm working on finding the shortest path between two points in a vessel
>> >> tree. itkSpeedToPathFilter seems to be working well for me as long as I
>> >> select the right speed function. Digging through Insight Journal, I
>> found a
>> >> link to Deschamp's Ph.D. thesis
>> >> (
>> https://tel.archives-ouvertes.fr/file/index/docid/45537/filename/index.html
>> )
>> >> which outlines one method to select a speed function:
>> >>
>> >> 1. Approximate centerline based on the input image
>> >> 2. Segmentation using the approximate centerline
>> >> 3. Use the segmented image and approximate centerline to create an
>> image
>> >> with signed distances to the approximate centerline
>> >> 4. Use the above image as the  input speed function for
>> itkSpeedToPathFilter
>> >>
>> >> The above steps seem to work (I say 'seem to work' because I tested it
>> just
>> >> three 2D images so far), but are there other methods to select the
>> speed
>> >> function? My input images are contrast enhanced CT images and the
>> vessels
>> >> are easy to identify and segment. Any help on how to select the correct
>> >> speed function will be appreciated.
>> >>
>> >> Thanks
>> >> Prashanth
>> >>
>> >> _____________________________________
>> >> Powered by www.kitware.com
>> >>
>> >> Visit other Kitware open-source projects at
>> >> http://www.kitware.com/opensource/opensource.html
>> >>
>> >> Kitware offers ITK Training Courses, for more information visit:
>> >> http://www.kitware.com/products/protraining.php
>> >>
>> >> Please keep messages on-topic and check the ITK FAQ at:
>> >> http://www.itk.org/Wiki/ITK_FAQ
>> >>
>> >> Follow this link to subscribe/unsubscribe:
>> >> http://public.kitware.com/mailman/listinfo/insight-users
>> >>
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>>
>
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From bill.hoffman at kitware.com  Mon Aug 31 17:10:32 2015
From: bill.hoffman at kitware.com (Bill Hoffman)
Date: Mon, 31 Aug 2015 17:10:32 -0400
Subject: [ITK] [ITK-dev] Happy Birthday CMake!
Message-ID: <55E4C2C8.1040501@kitware.com>

Today is the 15th birthday of CMake:

http://www.kitware.com/blog/home/post/959

Thanks to everyone that has used and contributed to CMake over the years!

-Bill
_______________________________________________
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From bill.hoffman at kitware.com  Mon Aug 31 17:10:32 2015
From: bill.hoffman at kitware.com (Bill Hoffman)
Date: Mon, 31 Aug 2015 17:10:32 -0400
Subject: [ITK] [ITK-users] Happy Birthday CMake!
Message-ID: <55E4C2C8.1040501@kitware.com>

Today is the 15th birthday of CMake:

http://www.kitware.com/blog/home/post/959

Thanks to everyone that has used and contributed to CMake over the years!

-Bill
_____________________________________
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From siavashk at ece.ubc.ca  Mon Aug 31 19:16:36 2015
From: siavashk at ece.ubc.ca (Siavash Khallaghi)
Date: Mon, 31 Aug 2015 16:16:36 -0700 (MST)
Subject: [ITK] [ITK-users] Export specific frame/slice of multiframe
 dicom file: ExtractSliceImageFilter?
In-Reply-To: <CAA24WvHjtG0zFza5Ys-f9aU4xm6n_k=FBfCX=T2Tgd1cRmO70A@mail.gmail.com>
References: <CAA24WvHjtG0zFza5Ys-f9aU4xm6n_k=FBfCX=T2Tgd1cRmO70A@mail.gmail.com>
Message-ID: <1441062996943-36084.post@n7.nabble.com>

Hi Marcos,

How do you set the input of your vtkJPEGWriter?

Siavash



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Export-specific-frame-slice-of-multiframe-dicom-file-ExtractSliceImageFilter-tp36081p36084.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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