[Insight-users] How to turn Off sorting by size in RelabelComponentFilter
Emma Ryan
eryanvtk at yahoo.com
Mon Aug 9 18:45:19 EDT 2010
Hello All,
By default the itk::RelabelComponentImageFilter seems to be sorting the
labels by size. I would like the label to be number according to their raster
position. Is there a way to turn off the sorting ?
Thank you,
Emma
________________________________
From: "insight-users-request at itk.org" <insight-users-request at itk.org>
To: insight-users at itk.org
Sent: Mon, August 9, 2010 12:42:15 PM
Subject: Insight-users Digest, Vol 76, Issue 24
Send Insight-users mailing list submissions to
insight-users at itk.org
To subscribe or unsubscribe via the World Wide Web, visit
http://www.itk.org/mailman/listinfo/insight-users
or, via email, send a message with subject or body 'help' to
insight-users-request at itk.org
You can reach the person managing the list at
insight-users-owner at itk.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Insight-users digest..."
Today's Topics:
1. Tcon Agenda Posted (Tuesday 1pm EST) (Luis Ibanez)
2. Re: Tcon Agenda Posted (Tuesday 1pm EST) (Bradley Lowekamp)
3. Re: [Insight-developers] Tcon Agenda Posted (Tuesday 1pm EST)
(Arnaud GELAS)
4. itk::BilateralImageFilter extremely slow (Oleksandr Dzyubak)
5. Re: Problem with passing images to functions (habibbaluwala2010)
----------------------------------------------------------------------
Message: 1
Date: Mon, 9 Aug 2010 14:35:09 -0400
From: Luis Ibanez <luis.ibanez at kitware.com>
Subject: [Insight-users] Tcon Agenda Posted (Tuesday 1pm EST)
To: itk <Insight-users at itk.org>, Insight Developers
<Insight-developers at itk.org>
Message-ID:
<AANLkTi=OgJ1OyJRuRDOqY=t70iSYpWT1JAVZcj_5HC5Y at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
The Agenda for tomorrow's tcon has been posted at:
http://www.itk.org/Wiki/Agenda%26Status_081010
As discussed in the last tcon,
we are inverting the order of the agenda,
in order to address some topics for which
we have run out of time in previous calls.
Please feel free to add any topics of your interest.
Luis
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
<http://www.itk.org/pipermail/insight-users/attachments/20100809/286a83b3/attachment-0001.htm>
------------------------------
Message: 2
Date: Mon, 9 Aug 2010 15:06:45 -0400
From: Bradley Lowekamp <blowekamp at mail.nih.gov>
Subject: Re: [Insight-users] Tcon Agenda Posted (Tuesday 1pm EST)
To: Luis Ibanez <luis.ibanez at kitware.com>
Cc: itk <Insight-users at itk.org>, Insight Developers
<Insight-developers at itk.org>
Message-ID: <3640D14E-D614-41AA-BE09-5223002184CB at mail.nih.gov>
Content-Type: text/plain; charset="us-ascii"
Hello Luis,
Looking over the agenda for tomorrow, I can't help but think that the
Microscopy should be a break out t-con (unless I missed it, and this is a
summary). I have had experience with streaming and many related issues to the
large datasets complications, so I would like to participate in such a break
out.
Perhaps the agenda item should just be to schedule such a meeting?
Brad
On Aug 9, 2010, at 2:35 PM, Luis Ibanez wrote:
>
> The Agenda for tomorrow's tcon has been posted at:
>
> http://www.itk.org/Wiki/Agenda%26Status_081010
>
> As discussed in the last tcon,
> we are inverting the order of the agenda,
> in order to address some topics for which
> we have run out of time in previous calls.
>
> Please feel free to add any topics of your interest.
>
>
> Luis
>
>
> <ATT00001..txt>
========================================================
Bradley Lowekamp
Lockheed Martin Contractor for
Office of High Performance Computing and Communications
National Library of Medicine
blowekamp at mail.nih.gov
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
<http://www.itk.org/pipermail/insight-users/attachments/20100809/bd7b55cd/attachment-0001.htm>
------------------------------
Message: 3
Date: Mon, 9 Aug 2010 15:16:54 -0400
From: Arnaud GELAS <arnaud_gelas at hms.harvard.edu>
Subject: Re: [Insight-users] [Insight-developers] Tcon Agenda Posted
(Tuesday 1pm EST)
To: Bradley Lowekamp <blowekamp at mail.nih.gov>
Cc: itk <Insight-users at itk.org>, Insight Developers
<Insight-developers at itk.org>, Luis Ibanez <luis.ibanez at kitware.com>,
"Megason, Sean" <Sean_Megason at hms.harvard.edu>
Message-ID: <4C605426.4080103 at hms.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
Hi Brad,
I think we should do both, first to present problems from the microscopy
community. At least everyone can understand some of the related problems
in terms of design. Then interested people and people that have ideas on
how to address these issues can then meet in another break out t-con.
It seems to be important to discuss at least in the main t-conf:
* how to deal with time?
* how to deal with channels? (Note that for one channel, the pixel
type could be a scalar, vector or tensor)...
Then we could discuss other details in the break out one...
Arnaud
On 08/09/2010 03:06 PM, Bradley Lowekamp wrote:
> Hello Luis,
>
> Looking over the agenda for tomorrow, I can't help but think that the
> Microscopy should be a break out t-con (unless I missed it, and this
> is a summary). I have had experience with streaming and many related
> issues to the large datasets complications, so I would like to
> participate in such a break out.
>
> Perhaps the agenda item should just be to schedule such a meeting?
>
> Brad
>
> On Aug 9, 2010, at 2:35 PM, Luis Ibanez wrote:
>
>>
>> The Agenda for tomorrow's tcon has been posted at:
>>
>> http://www.itk.org/Wiki/Agenda%26Status_081010
>>
>> As discussed in the last tcon,
>> we are inverting the order of the agenda,
>> in order to address some topics for which
>> we have run out of time in previous calls.
>>
>> Please feel free to add any topics of your interest.
>>
>>
>> Luis
>>
>>
>> <ATT00001..txt>
>
> ========================================================
>
> Bradley Lowekamp
>
> Lockheed Martin Contractor for
>
> Office of High Performance Computing and Communications
>
> National Library of Medicine
>
> blowekamp at mail.nih.gov <mailto:blowekamp at mail.nih.gov>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
<http://www.itk.org/pipermail/insight-users/attachments/20100809/424eaff2/attachment-0001.htm>
------------------------------
Message: 4
Date: Mon, 09 Aug 2010 14:35:37 -0500
From: Oleksandr Dzyubak <adzyubak at gmail.com>
Subject: [Insight-users] itk::BilateralImageFilter extremely slow
To: insight-users <Insight-users at itk.org>
Message-ID: <4C605889.6020103 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear ITK users and developers,
A while ago for my experiments I ran into a need of using
a narrow kernel bilateral filter so I decided to give
the itk:: BilateralImageFilter class a try.
After some pre-tests with small test images, I ran a filter on real images.
Well, my first impression is somewhat discouraging.
But it might be that I am doing some terrible mistake which I do not see.
My setup.
1) Hardware: 4x4 core server with 64 bit Debian Linux.
2) ITK-3.18 with p-threads support ON.
3) Image 561x561x478.
I followed the recommendations from the ITK user guide
and below are results.
dzyubak at helium: /H61_Mo_721Views_July_31_2009$ time
./Bilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds05_rs4.hdr 0.5 4.0
With all 16 CPUs 100% busy after 1241m29.741s it was still running.
Thus I should cancel the run not having an output.
real 1241m29.741s
user 19600m14.380s
sys 6m33.993s
After I changed the parameters, I got something but it was not what I
wanted.
dzyubak at helium: /H61_Mo_721Views_July_31_2009$ time
./Bilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds005_rs4.hdr
0.05 4.0
real 63m46.774s
user 764m24.782s
sys 0m18.849s
Since this filter worked extremely slow even with 16 horses under the hood,
I started digging the Insight Journal and found the contribution
"A Fast Approximation to the Bilateral Filter for ITK" by J. Woehr.
I was attracted by the word "Fast" since it quite often means "faster
performance".
Even though I did not like the author's note "it is single threaded",
I decided to eventually try it and, to be fair,
I used exactly the same parameters as for itk:: BilateralImageFilter.
dzyubak at helium: /H61_Mo_721Views_July_31_2009$ time
./FastBilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds05_rs4.hdr
0.5 4.0
ImageFileName: h61_with_psf.img
real 4m49.325s
user 4m35.085s
sys 0m5.804s
In the submission description J. Woehr said that FastBilateral
performs poorer for the narrow kernels thus if someone is
in a need of such cases (it is exactly me!),
then the itk:: BilateralImageFilter should be used instead.
Well, I would like to but FastBilateral performed 200 times
as much vs itk:: BilateralImageFilter.
And in addition to that, for some kernel sizes it never
went out of the loop.
What am I missing here?
Did someone experience the same filter behaver?
Is it wrong conditional causing such a "prolongated" loop?
Is there any recipe I could used to shorten
such unacceptable long run time of itk:: BilateralImageFilter?
I appreciate any suggestions/discussions on this matter.
Regards,
Alex
------------------------------
Message: 5
Date: Mon, 9 Aug 2010 12:42:12 -0700 (PDT)
From: habibbaluwala2010 <habibbaluwala at gmail.com>
Subject: Re: [Insight-users] Problem with passing images to functions
To: insight-users at itk.org
Message-ID: <29391440.post at talk.nabble.com>
Content-Type: text/plain; charset=UTF-8
Hello Sergio,
Can you give me an example of how to use this in context
with the syntax? I am really thankful for the help.
Kind regards,
Habib Baluwala
Sergio Vera wrote:
>
> Following advices from Luis Iba?ez in a previous mail of the list, we now
> use the following rules:
>
> const ITKImgType *ImgIn when images are input to a method and
>
> ITKImgType::Pointer &ImgOut when the image will be created inside the
> function
>
> regards
>
> 2010/8/6 D?enan Zuki? <dzenanz at gmail.com>
>
>> Use ImageType::Pointer. Here is an example:
>>
>> void calc2DJointHistogram(VisualizingImageType::Pointer x,
>> VisualizingImageType::Pointer y, std::string savefilename)
>> {
>> ...
>> }
>>
>> //calling it
>> VisualizingImageType::Pointer lVis, hVis;
>> ...
>> hVis=hReader->GetOutput();
>> calc2DJointHistogram(lVis, hVis, fnNoExt+"_LH.png");
>>
>> D?enan
>>
>> On Fri, Aug 6, 2010 at 15:32, habibbaluwala2010
>> <habibbaluwala at gmail.com>wrote:
>>
>>>
>>> Hi Everyone,
>>> I am a biot confused on how can i pass an image with
>>> smart
>>> pointers to an outside function . I basically need this to avoid
>>> reproducing
>>> the code again and again and also to avoid composite filters. It would
>>> be
>>> very helpful if you can provide an example which does the job!!! Anyways
>>> looking forward to your replies.
>>> --
>>> View this message in context:
>>>http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29356451.html
>>>l
>>> 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.html
>>>
>>> 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://www.itk.org/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.html
>>
>> 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://www.itk.org/mailman/listinfo/insight-users
>>
>>
>
>
> --
> Sergio Vera
>
> Alma IT Systems
> C/ Vilana, 4B, 4? 1?
> 08022 Barcelona
> T. (+34) 932 380 592
> www.alma3d.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.html
>
> 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://www.itk.org/mailman/listinfo/insight-users
>
>
--
View this message in context:
http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29391440.html
Sent from the ITK - Users mailing list archive at Nabble.com.
------------------------------
_______________________________________________
Insight-users mailing list
Insight-users at itk.org
http://www.itk.org/mailman/listinfo/insight-users
End of Insight-users Digest, Vol 76, Issue 24
*********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20100809/1094a088/attachment-0001.htm>
More information about the Insight-users
mailing list