From amarnaths161 at gmail.com  Fri Jan 11 06:45:28 2019
From: amarnaths161 at gmail.com (Amarnath S)
Date: Fri, 11 Jan 2019 17:15:28 +0530
Subject: [Rtk-users] Running the WaterPreCorrection Example
Message-ID: <CAHdw6At+cE4aY0k_MPBNYx7wokd0=yC2FYRSK035Xua26VUajw@mail.gmail.com>

Hi,

     Requesting you to please help me in running the WaterPreCorrection
example found here: http://wiki.openrtk.org/index.php/WaterPreCorrection

     I have built RTK using the WRAP_PYTHON flag set as On in CMake,
However, I am not getting the file setup.py as output within the
folder \SimpleRTK-build\Wrapping\Python\Packaging. It is creating a file
called setupegg.py, which in turn calls setup.py. I followed the
instructions mentioned on top of this page -
http://wiki.openrtk.org/index.php/SimpleRTK. But the file setup.py is not
generated.

    Consequently, I am not able to run this example on my machine.
Requesting you to please help me with this.

Thanks and Regards
- Amarnath
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From amarnaths161 at gmail.com  Mon Jan 14 06:22:41 2019
From: amarnaths161 at gmail.com (Amarnath S)
Date: Mon, 14 Jan 2019 16:52:41 +0530
Subject: [Rtk-users] WaterPreCorrectionImageFilter - C++ Sample available?
Message-ID: <CAHdw6AtQx_R+nSdmNf5O454uTMsRsmtz8XzpL9UMC-MHma01dA@mail.gmail.com>

Hi,

     Is there a C++ example file illustrating the use of
rtk::WaterPreCorrectionImageFilter? If so, can it please be shared across.
Thanks a lot.

Thanks and regards
- Amarnath
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From simon.rit at creatis.insa-lyon.fr  Mon Jan 14 09:05:59 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 14 Jan 2019 15:05:59 +0100
Subject: [Rtk-users] Running the WaterPreCorrection Example
In-Reply-To: <CAHdw6At+cE4aY0k_MPBNYx7wokd0=yC2FYRSK035Xua26VUajw@mail.gmail.com>
References: <CAHdw6At+cE4aY0k_MPBNYx7wokd0=yC2FYRSK035Xua26VUajw@mail.gmail.com>
Message-ID: <CAF0oig1aaLPOoAmutxitNV_CEzKGs3NucaXZgqX5i227v-53Vw@mail.gmail.com>

Hi,
Have you checked that it's not in a subfolder? I remember that it got in a
subfolder for some versions. To be honest, we are not using SimpleRTK
anymore, we are gradually switching to a python package for RTK as an
external module of ITK. I will update the examples when we release it.
Best regards,
Simon

On Fri, Jan 11, 2019 at 12:45 PM Amarnath S <amarnaths161 at gmail.com> wrote:

> Hi,
>
>      Requesting you to please help me in running the WaterPreCorrection
> example found here: http://wiki.openrtk.org/index.php/WaterPreCorrection
>
>      I have built RTK using the WRAP_PYTHON flag set as On in CMake,
> However, I am not getting the file setup.py as output within the
> folder \SimpleRTK-build\Wrapping\Python\Packaging. It is creating a file
> called setupegg.py, which in turn calls setup.py. I followed the
> instructions mentioned on top of this page -
> http://wiki.openrtk.org/index.php/SimpleRTK. But the file setup.py is not
> generated.
>
>     Consequently, I am not able to run this example on my machine.
> Requesting you to please help me with this.
>
> Thanks and Regards
> - Amarnath
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From simon.rit at creatis.insa-lyon.fr  Mon Jan 14 09:08:52 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 14 Jan 2019 15:08:52 +0100
Subject: [Rtk-users] WaterPreCorrectionImageFilter - C++ Sample
 available?
In-Reply-To: <CAHdw6AtQx_R+nSdmNf5O454uTMsRsmtz8XzpL9UMC-MHma01dA@mail.gmail.com>
References: <CAHdw6AtQx_R+nSdmNf5O454uTMsRsmtz8XzpL9UMC-MHma01dA@mail.gmail.com>
Message-ID: <CAF0oig3OYCYAD4xhx4NkaNtym8YiHDg2F_7+06_wOboZ8m=0aw@mail.gmail.com>

Hi,
No, we don't have any C++ code to do the polynomial fit, we found it more
straightforward to do it in Python. When you have the polynomial, you can
apply it using the --wpc option from the reconstruction command line tools,
e.g., rtkfdk.
Best regards,
Simon

On Mon, Jan 14, 2019 at 12:23 PM Amarnath S <amarnaths161 at gmail.com> wrote:

> Hi,
>
>      Is there a C++ example file illustrating the use of
> rtk::WaterPreCorrectionImageFilter? If so, can it please be shared across.
> Thanks a lot.
>
> Thanks and regards
> - Amarnath
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From colddiesun at gmail.com  Wed Jan 16 16:59:40 2019
From: colddiesun at gmail.com (tao sun)
Date: Wed, 16 Jan 2019 16:59:40 -0500
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
Message-ID: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>

Hi,

I have read in some image using  itk::ImportImageFilter.
 ImportFilterType::Pointer projectionReader = ImportFilterType::New();
...
 projectionReader->Update();

The type of the image is itk:::Image<float,3>. I wonder if there is any way
I can cast it to itk::CudaImage<float,3>?
In rtkforwardprojections.cxx the imageReaderType is defined as
CudaImageType so there is no such problem.

Thanks,
Tao
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From andreasga22 at gmail.com  Wed Jan 16 17:06:30 2019
From: andreasga22 at gmail.com (Andreas Andersen)
Date: Wed, 16 Jan 2019 23:06:30 +0100
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
Message-ID: <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>

Hi Tao,

I think you want the CastImageFilter
<https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html> from ITK.

Something like this:
using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
itk::CudaImage<float,3>>;
typename castToImageType::Pointer castfilter = castToImageType::New();
castfilter->SetInput(projectionReader->GetOutput());
castfilter->Update();
auto cuda_image = castfilter->GetOutput();

Best regards Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     agravgaard at protonmail.com

Cell:      +45 3165 8140


On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:

> Hi,
>
> I have read in some image using  itk::ImportImageFilter.
>  ImportFilterType::Pointer projectionReader = ImportFilterType::New();
> ...
>  projectionReader->Update();
>
> The type of the image is itk:::Image<float,3>. I wonder if there is any
> way I can cast it to itk::CudaImage<float,3>?
> In rtkforwardprojections.cxx the imageReaderType is defined as
> CudaImageType so there is no such problem.
>
> Thanks,
> Tao
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From simon.rit at creatis.insa-lyon.fr  Thu Jan 17 00:26:38 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 17 Jan 2019 06:26:38 +0100
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
Message-ID: <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>

Hi,
That's one solution. Two other:
- graft the output to a Cuda image
itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float, 3>::New();
cuImg->Graft(projectionReader->GetOutput())
- use the rtk::ImportImageFilter which is templated over image type to
allow precisely this (I used it in Gate here
<https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
).
Best regards,
Simon

On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <andreasga22 at gmail.com>
wrote:

> Hi Tao,
>
> I think you want the CastImageFilter
> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html> from ITK.
>
> Something like this:
> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
> itk::CudaImage<float,3>>;
> typename castToImageType::Pointer castfilter = castToImageType::New();
> castfilter->SetInput(projectionReader->GetOutput());
> castfilter->Update();
> auto cuda_image = castfilter->GetOutput();
>
> Best regards Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     agravgaard at protonmail.com
>
> Cell:      +45 3165 8140
>
>
> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:
>
>> Hi,
>>
>> I have read in some image using  itk::ImportImageFilter.
>>  ImportFilterType::Pointer projectionReader = ImportFilterType::New();
>> ...
>>  projectionReader->Update();
>>
>> The type of the image is itk:::Image<float,3>. I wonder if there is any
>> way I can cast it to itk::CudaImage<float,3>?
>> In rtkforwardprojections.cxx the imageReaderType is defined as
>> CudaImageType so there is no such problem.
>>
>> Thanks,
>> Tao
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From amarnaths161 at gmail.com  Thu Jan 17 07:57:18 2019
From: amarnaths161 at gmail.com (Amarnath S)
Date: Thu, 17 Jan 2019 18:27:18 +0530
Subject: [Rtk-users] Running the WaterPreCorrection Example
In-Reply-To: <CAF0oig1aaLPOoAmutxitNV_CEzKGs3NucaXZgqX5i227v-53Vw@mail.gmail.com>
References: <CAHdw6At+cE4aY0k_MPBNYx7wokd0=yC2FYRSK035Xua26VUajw@mail.gmail.com>
 <CAF0oig1aaLPOoAmutxitNV_CEzKGs3NucaXZgqX5i227v-53Vw@mail.gmail.com>
Message-ID: <CAHdw6AvjCK2LTNSk7S7iWtaz__m7uFvQGs252mHvORFPrx++4Q@mail.gmail.com>

Hi Simon,

    Thanks for your reply. I am in the process of converting the Python
program to C++, and have done more than half the file. Since I am new to
RTK, there is some amount of trial/ experimentation in coding. I am now in
the place where the Update() method of the FDKConeBeamReconstructionFilter
object is first called. This line is throwing an exception, which is:

itk::ERROR: FDKBackProjectionImageFilter(00000263E25240A0): Mismatch
between the number of projections and the geometry entries. Geometry has 5
entries, which is less than the last index of the projections stack, i.e.,
6.

Now, I know for sure that there are 5 entries in the Geometry file, which I
downloaded from the site mentioned. earlier. What I am not seeing is where
is it getting the last index of the projections stack, which is shown as 6.

Any help in this regard would be highly appreciated.

Thanks and regards
- Amarnath

On Mon, Jan 14, 2019 at 7:36 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Have you checked that it's not in a subfolder? I remember that it got in a
> subfolder for some versions. To be honest, we are not using SimpleRTK
> anymore, we are gradually switching to a python package for RTK as an
> external module of ITK. I will update the examples when we release it.
> Best regards,
> Simon
>
> On Fri, Jan 11, 2019 at 12:45 PM Amarnath S <amarnaths161 at gmail.com>
> wrote:
>
>> Hi,
>>
>>      Requesting you to please help me in running the WaterPreCorrection
>> example found here: http://wiki.openrtk.org/index.php/WaterPreCorrection
>>
>>      I have built RTK using the WRAP_PYTHON flag set as On in CMake,
>> However, I am not getting the file setup.py as output within the
>> folder \SimpleRTK-build\Wrapping\Python\Packaging. It is creating a file
>> called setupegg.py, which in turn calls setup.py. I followed the
>> instructions mentioned on top of this page -
>> http://wiki.openrtk.org/index.php/SimpleRTK. But the file setup.py is
>> not generated.
>>
>>     Consequently, I am not able to run this example on my machine.
>> Requesting you to please help me with this.
>>
>> Thanks and Regards
>> - Amarnath
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Jan 17 08:06:37 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 17 Jan 2019 14:06:37 +0100
Subject: [Rtk-users] Running the WaterPreCorrection Example
In-Reply-To: <CAHdw6AvjCK2LTNSk7S7iWtaz__m7uFvQGs252mHvORFPrx++4Q@mail.gmail.com>
References: <CAHdw6At+cE4aY0k_MPBNYx7wokd0=yC2FYRSK035Xua26VUajw@mail.gmail.com>
 <CAF0oig1aaLPOoAmutxitNV_CEzKGs3NucaXZgqX5i227v-53Vw@mail.gmail.com>
 <CAHdw6AvjCK2LTNSk7S7iWtaz__m7uFvQGs252mHvORFPrx++4Q@mail.gmail.com>
Message-ID: <CAF0oig2YCz4HLcx83HP9sPAMLEuCg6tQRSFtbVPQ4ESaQE9Unw@mail.gmail.com>

Hi,
The second input of FDK is the projection stack. This stack is a 3D image
and the last dimension must equal the number of projections in the geometry
file. So maybe you are reading 6 projections?
I hope this helps,
Simon

On Thu, Jan 17, 2019 at 1:57 PM Amarnath S <amarnaths161 at gmail.com> wrote:

> Hi Simon,
>
>     Thanks for your reply. I am in the process of converting the Python
> program to C++, and have done more than half the file. Since I am new to
> RTK, there is some amount of trial/ experimentation in coding. I am now in
> the place where the Update() method of the FDKConeBeamReconstructionFilter
> object is first called. This line is throwing an exception, which is:
>
> itk::ERROR: FDKBackProjectionImageFilter(00000263E25240A0): Mismatch
> between the number of projections and the geometry entries. Geometry has 5
> entries, which is less than the last index of the projections stack, i.e.,
> 6.
>
> Now, I know for sure that there are 5 entries in the Geometry file, which
> I downloaded from the site mentioned. earlier. What I am not seeing is
> where is it getting the last index of the projections stack, which is shown
> as 6.
>
> Any help in this regard would be highly appreciated.
>
> Thanks and regards
> - Amarnath
>
> On Mon, Jan 14, 2019 at 7:36 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Hi,
>> Have you checked that it's not in a subfolder? I remember that it got in
>> a subfolder for some versions. To be honest, we are not using SimpleRTK
>> anymore, we are gradually switching to a python package for RTK as an
>> external module of ITK. I will update the examples when we release it.
>> Best regards,
>> Simon
>>
>> On Fri, Jan 11, 2019 at 12:45 PM Amarnath S <amarnaths161 at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>>      Requesting you to please help me in running the WaterPreCorrection
>>> example found here: http://wiki.openrtk.org/index.php/WaterPreCorrection
>>>
>>>      I have built RTK using the WRAP_PYTHON flag set as On in CMake,
>>> However, I am not getting the file setup.py as output within the
>>> folder \SimpleRTK-build\Wrapping\Python\Packaging. It is creating a file
>>> called setupegg.py, which in turn calls setup.py. I followed the
>>> instructions mentioned on top of this page -
>>> http://wiki.openrtk.org/index.php/SimpleRTK. But the file setup.py is
>>> not generated.
>>>
>>>     Consequently, I am not able to run this example on my machine.
>>> Requesting you to please help me with this.
>>>
>>> Thanks and Regards
>>> - Amarnath
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>
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From fredrik.hellman at gmail.com  Thu Jan 17 11:20:19 2019
From: fredrik.hellman at gmail.com (Fredrik Hellman)
Date: Thu, 17 Jan 2019 17:20:19 +0100
Subject: [Rtk-users] RTK going to become an ITK external module?
Message-ID: <CACMrisy9ey76_AVxdOSn-E7JVPM=p4NC0=EexdpHwfivXgZ8kw@mail.gmail.com>

Hi all,

I have noticed that there is work going on in the master branch in the RTK
repo towards some kind of tighter integration with ITK. External Module?

I am interested in following this development and in particular how it will
affect the builds in the future. Is there any discussion thread that I can
subscribe to somewhere to get updates on this topic?

Best regards,
Fredrik Hellman
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From simon.rit at creatis.insa-lyon.fr  Thu Jan 17 11:29:13 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 17 Jan 2019 17:29:13 +0100
Subject: [Rtk-users] RTK going to become an ITK external module?
In-Reply-To: <CACMrisy9ey76_AVxdOSn-E7JVPM=p4NC0=EexdpHwfivXgZ8kw@mail.gmail.com>
References: <CACMrisy9ey76_AVxdOSn-E7JVPM=p4NC0=EexdpHwfivXgZ8kw@mail.gmail.com>
Message-ID: <CAF0oig1p-c0hyoXGQU_EbDKCRq9k+O_nU230rgTtpoBfjK1Mxg@mail.gmail.com>

Hi Fredrik,
Yes, we have been working on that in the past year. I'm correcting a few
last things before releasing a new RTK version. When this is done, I'll
submit the Modules/Remote
<https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Remote>/RTK.remote.cmake
file to the itk repository. You can give it a try already with the enclosed
file (which will download master).
Impact:
- you can either turn on RTK compilation from the ITK compilation or
provide the ITK build path in a separate RTK build (as before except the
ITK dir cannot be an installed ITK),
- check the evolution of the examples/FirstReconstruction/CMakeLists
compared to the last release to see how the CMakeLists.txt has changed,
- we'll provide pre-compiled python packages compatible with the
pre-compiled ITK python packages.
There is no specific thread, just follow the mailing list and I'll post a
message for (1) the RTK release and (2) when the RTK remote module file has
been integrated to ITK.
Best regards,
Simon

On Thu, Jan 17, 2019 at 5:20 PM Fredrik Hellman <fredrik.hellman at gmail.com>
wrote:

> Hi all,
>
> I have noticed that there is work going on in the master branch in the RTK
> repo towards some kind of tighter integration with ITK. External Module?
>
> I am interested in following this development and in particular how it
> will affect the builds in the future. Is there any discussion thread that I
> can subscribe to somewhere to get updates on this topic?
>
> Best regards,
> Fredrik Hellman
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From colddiesun at gmail.com  Sat Jan 19 20:51:05 2019
From: colddiesun at gmail.com (tao sun)
Date: Sat, 19 Jan 2019 20:51:05 -0500
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
Message-ID: <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>

Thank you all! I will give a try using your solutions.
Tao

Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ?? ??12:26???

> Hi,
> That's one solution. Two other:
> - graft the output to a Cuda image
> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float, 3>::New();
> cuImg->Graft(projectionReader->GetOutput())
> - use the rtk::ImportImageFilter which is templated over image type to
> allow precisely this (I used it in Gate here
> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
> ).
> Best regards,
> Simon
>
> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <andreasga22 at gmail.com>
> wrote:
>
>> Hi Tao,
>>
>> I think you want the CastImageFilter
>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html> from ITK.
>>
>> Something like this:
>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
>> itk::CudaImage<float,3>>;
>> typename castToImageType::Pointer castfilter = castToImageType::New();
>> castfilter->SetInput(projectionReader->GetOutput());
>> castfilter->Update();
>> auto cuda_image = castfilter->GetOutput();
>>
>> Best regards Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     agravgaard at protonmail.com
>>
>> Cell:      +45 3165 8140
>>
>>
>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I have read in some image using  itk::ImportImageFilter.
>>>  ImportFilterType::Pointer projectionReader = ImportFilterType::New();
>>> ...
>>>  projectionReader->Update();
>>>
>>> The type of the image is itk:::Image<float,3>. I wonder if there is any
>>> way I can cast it to itk::CudaImage<float,3>?
>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>> CudaImageType so there is no such problem.
>>>
>>> Thanks,
>>> Tao
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
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From amarnaths161 at gmail.com  Mon Jan 28 05:45:40 2019
From: amarnaths161 at gmail.com (Amarnath S)
Date: Mon, 28 Jan 2019 16:15:40 +0530
Subject: [Rtk-users] Regarding rtk::ProjectionsReader
Message-ID: <CAHdw6AtePftg=faAzRMgMFSpwB0VmM_yLOz8VrqxiaYeUyE04Q@mail.gmail.com>

Hi,

     I am using a rtk::ProjectionsReader as follows:

typedef float OutputPixelType;
const unsigned int Dimension = 3;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;

rtk::ProjectionsReader<OutputImageType>::Pointer projReader;
projReader = rtk::ProjectionsReader<OutputImageType>::New();
projReader->SetFileNames(fileNames); // filenames is defined and set earlier

Now, according to this page
http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html,
this class has a GenerateData() method, which does the real work. In the
GitHub rtk-master downloaded last week, this method does not seem to be
present. There is only one method name beginning with Generate..., and it
is GenerateOutputInformation(). What is the new method name for
GenerateData(). If it cannot be called directly, how else is it to be
invoked? Will calling of Update() internally call GenerateData()?

Thanks and regards
- Amarnath
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From andreasga22 at gmail.com  Mon Jan 28 06:39:23 2019
From: andreasga22 at gmail.com (Andreas Andersen)
Date: Mon, 28 Jan 2019 12:39:23 +0100
Subject: [Rtk-users] Regarding rtk::ProjectionsReader
In-Reply-To: <CAHdw6AtePftg=faAzRMgMFSpwB0VmM_yLOz8VrqxiaYeUyE04Q@mail.gmail.com>
References: <CAHdw6AtePftg=faAzRMgMFSpwB0VmM_yLOz8VrqxiaYeUyE04Q@mail.gmail.com>
Message-ID: <CAE0aawH_WivsqUVJzs4WF5-Doy9AyS9144PUqVxzx487VQ3xgw@mail.gmail.com>

Yes, as far as I remember:
Update calls Generate on all filters (a reader is also a filter) in the
pipeline.
UpdateOutputInformation calls GenerateOutputInformation, which might be
useful if you need properties of an image without reading the actual data,
yet.

Best regards
Andreas

On Mon, 28 Jan 2019, 11:45 Amarnath S <amarnaths161 at gmail.com wrote:

> Hi,
>
>      I am using a rtk::ProjectionsReader as follows:
>
> typedef float OutputPixelType;
> const unsigned int Dimension = 3;
> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>
> rtk::ProjectionsReader<OutputImageType>::Pointer projReader;
> projReader = rtk::ProjectionsReader<OutputImageType>::New();
> projReader->SetFileNames(fileNames); // filenames is defined and set
> earlier
>
> Now, according to this page
> http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html,
> this class has a GenerateData() method, which does the real work. In the
> GitHub rtk-master downloaded last week, this method does not seem to be
> present. There is only one method name beginning with Generate..., and it
> is GenerateOutputInformation(). What is the new method name for
> GenerateData(). If it cannot be called directly, how else is it to be
> invoked? Will calling of Update() internally call GenerateData()?
>
> Thanks and regards
> - Amarnath
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From simon.rit at creatis.insa-lyon.fr  Tue Jan 29 04:04:43 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 29 Jan 2019 10:04:43 +0100
Subject: [Rtk-users] Regarding rtk::ProjectionsReader
In-Reply-To: <CAE0aawH_WivsqUVJzs4WF5-Doy9AyS9144PUqVxzx487VQ3xgw@mail.gmail.com>
References: <CAHdw6AtePftg=faAzRMgMFSpwB0VmM_yLOz8VrqxiaYeUyE04Q@mail.gmail.com>
 <CAE0aawH_WivsqUVJzs4WF5-Doy9AyS9144PUqVxzx487VQ3xgw@mail.gmail.com>
Message-ID: <CAF0oig3YKFgkkuiazh+c0ROetQ=VXRB8HauVn4h4fAc3b4jVtA@mail.gmail.com>

Dear Amarnath,
GenerateData exists, see
http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader-members.html
This is ITK's internal machinery. When you call Update, it will call
itk::DataObject::Update(). This will call UpdateOutputInformation,
PropagateRequestedRegion and UpdateOutputData. The latter will call
UpdateOutputData in ImageSource which will eventually call GenerateData.
See ITK doc for more info.
Cheers,
Simon

On Mon, Jan 28, 2019 at 12:39 PM Andreas Andersen <andreasga22 at gmail.com>
wrote:

> Yes, as far as I remember:
> Update calls Generate on all filters (a reader is also a filter) in the
> pipeline.
> UpdateOutputInformation calls GenerateOutputInformation, which might be
> useful if you need properties of an image without reading the actual data,
> yet.
>
> Best regards
> Andreas
>
> On Mon, 28 Jan 2019, 11:45 Amarnath S <amarnaths161 at gmail.com wrote:
>
>> Hi,
>>
>>      I am using a rtk::ProjectionsReader as follows:
>>
>> typedef float OutputPixelType;
>> const unsigned int Dimension = 3;
>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>
>> rtk::ProjectionsReader<OutputImageType>::Pointer projReader;
>> projReader = rtk::ProjectionsReader<OutputImageType>::New();
>> projReader->SetFileNames(fileNames); // filenames is defined and set
>> earlier
>>
>> Now, according to this page
>> http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html,
>> this class has a GenerateData() method, which does the real work. In the
>> GitHub rtk-master downloaded last week, this method does not seem to be
>> present. There is only one method name beginning with Generate..., and it
>> is GenerateOutputInformation(). What is the new method name for
>> GenerateData(). If it cannot be called directly, how else is it to be
>> invoked? Will calling of Update() internally call GenerateData()?
>>
>> Thanks and regards
>> - Amarnath
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From colddiesun at gmail.com  Tue Jan 29 19:22:44 2019
From: colddiesun at gmail.com (tao sun)
Date: Tue, 29 Jan 2019 19:22:44 -0500
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
Message-ID: <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>

Hi again,

Finally I got time to work on this. I was able to compile the program this
time using the Graft() function. However, there's a runtime error when I
run the program:


/home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
@ unknown : Cuda Error #3
    terminate called after throwing an instance of 'itk::ExceptionObject'
    what():
/home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
    Cuda Error # 3
    Aborted

It happens when a new gpu backprojector is created:
    bp = rtk::CudaRayCastBackProjectionImageFilter::New();

Any insights for this?

Thanks,
Tao

tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???

> Thank you all! I will give a try using your solutions.
> Tao
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ?? ??12:26???
>
>> Hi,
>> That's one solution. Two other:
>> - graft the output to a Cuda image
>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float, 3>::New();
>> cuImg->Graft(projectionReader->GetOutput())
>> - use the rtk::ImportImageFilter which is templated over image type to
>> allow precisely this (I used it in Gate here
>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>> ).
>> Best regards,
>> Simon
>>
>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <andreasga22 at gmail.com>
>> wrote:
>>
>>> Hi Tao,
>>>
>>> I think you want the CastImageFilter
>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html> from
>>> ITK.
>>>
>>> Something like this:
>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
>>> itk::CudaImage<float,3>>;
>>> typename castToImageType::Pointer castfilter = castToImageType::New();
>>> castfilter->SetInput(projectionReader->GetOutput());
>>> castfilter->Update();
>>> auto cuda_image = castfilter->GetOutput();
>>>
>>> Best regards Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     agravgaard at protonmail.com
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have read in some image using  itk::ImportImageFilter.
>>>>  ImportFilterType::Pointer projectionReader = ImportFilterType::New();
>>>> ...
>>>>  projectionReader->Update();
>>>>
>>>> The type of the image is itk:::Image<float,3>. I wonder if there is any
>>>> way I can cast it to itk::CudaImage<float,3>?
>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>> CudaImageType so there is no such problem.
>>>>
>>>> Thanks,
>>>> Tao
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>
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From simon.rit at creatis.insa-lyon.fr  Wed Jan 30 01:25:22 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 30 Jan 2019 07:25:22 +0100
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
Message-ID: <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>

Hi,
No, not really. In my experience, this occurs mainly when you don't have a
GPU properly configured for CUDA. Can you check the value of CUDA_HAVE_GPU
in cmake ? If it's OFF, then this is indeed the problem.
Simon

On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com> wrote:

> Hi again,
>
> Finally I got time to work on this. I was able to compile the program this
> time using the Graft() function. However, there's a runtime error when I
> run the program:
>
>
> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
> @ unknown : Cuda Error #3
>     terminate called after throwing an instance of 'itk::ExceptionObject'
>     what():
> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>     Cuda Error # 3
>     Aborted
>
> It happens when a new gpu backprojector is created:
>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>
> Any insights for this?
>
> Thanks,
> Tao
>
> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>
>> Thank you all! I will give a try using your solutions.
>> Tao
>>
>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ?? ??12:26???
>>
>>> Hi,
>>> That's one solution. Two other:
>>> - graft the output to a Cuda image
>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>> 3>::New();
>>> cuImg->Graft(projectionReader->GetOutput())
>>> - use the rtk::ImportImageFilter which is templated over image type to
>>> allow precisely this (I used it in Gate here
>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>> ).
>>> Best regards,
>>> Simon
>>>
>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <andreasga22 at gmail.com>
>>> wrote:
>>>
>>>> Hi Tao,
>>>>
>>>> I think you want the CastImageFilter
>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html> from
>>>> ITK.
>>>>
>>>> Something like this:
>>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
>>>> itk::CudaImage<float,3>>;
>>>> typename castToImageType::Pointer castfilter = castToImageType::New();
>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>> castfilter->Update();
>>>> auto cuda_image = castfilter->GetOutput();
>>>>
>>>> Best regards Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     agravgaard at protonmail.com
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>  ImportFilterType::Pointer projectionReader = ImportFilterType::New();
>>>>> ...
>>>>>  projectionReader->Update();
>>>>>
>>>>> The type of the image is itk:::Image<float,3>. I wonder if there is
>>>>> any way I can cast it to itk::CudaImage<float,3>?
>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>> CudaImageType so there is no such problem.
>>>>>
>>>>> Thanks,
>>>>> Tao
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From colddiesun at gmail.com  Wed Jan 30 11:04:43 2019
From: colddiesun at gmail.com (tao sun)
Date: Wed, 30 Jan 2019 11:04:43 -0500
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
 <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
Message-ID: <CABaNCKqxxKH9kAD-kuY6tWEfBum_yJRZSLYvsifsRGWEKWN6jQ@mail.gmail.com>

Hi Simon,

CUDA_HAVE_GPU is on. So is CUDA_FOUND. I can run examples like rtkfdk with
gpu on without any problem though,
By the way I am using CUDA 9.2.88.

Tao





Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??1:25???

> Hi,
> No, not really. In my experience, this occurs mainly when you don't have a
> GPU properly configured for CUDA. Can you check the value of CUDA_HAVE_GPU
> in cmake ? If it's OFF, then this is indeed the problem.
> Simon
>
> On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com> wrote:
>
>> Hi again,
>>
>> Finally I got time to work on this. I was able to compile the program
>> this time using the Graft() function. However, there's a runtime error when
>> I run the program:
>>
>>
>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
>> @ unknown : Cuda Error #3
>>     terminate called after throwing an instance of 'itk::ExceptionObject'
>>     what():
>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>>     Cuda Error # 3
>>     Aborted
>>
>> It happens when a new gpu backprojector is created:
>>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>>
>> Any insights for this?
>>
>> Thanks,
>> Tao
>>
>> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>>
>>> Thank you all! I will give a try using your solutions.
>>> Tao
>>>
>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ?? ??12:26???
>>>
>>>> Hi,
>>>> That's one solution. Two other:
>>>> - graft the output to a Cuda image
>>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>>> 3>::New();
>>>> cuImg->Graft(projectionReader->GetOutput())
>>>> - use the rtk::ImportImageFilter which is templated over image type to
>>>> allow precisely this (I used it in Gate here
>>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>>> ).
>>>> Best regards,
>>>> Simon
>>>>
>>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <
>>>> andreasga22 at gmail.com> wrote:
>>>>
>>>>> Hi Tao,
>>>>>
>>>>> I think you want the CastImageFilter
>>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html> from
>>>>> ITK.
>>>>>
>>>>> Something like this:
>>>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
>>>>> itk::CudaImage<float,3>>;
>>>>> typename castToImageType::Pointer castfilter = castToImageType::New();
>>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>>> castfilter->Update();
>>>>> auto cuda_image = castfilter->GetOutput();
>>>>>
>>>>> Best regards Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     agravgaard at protonmail.com
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>>  ImportFilterType::Pointer projectionReader = ImportFilterType::New();
>>>>>> ...
>>>>>>  projectionReader->Update();
>>>>>>
>>>>>> The type of the image is itk:::Image<float,3>. I wonder if there is
>>>>>> any way I can cast it to itk::CudaImage<float,3>?
>>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>>> CudaImageType so there is no such problem.
>>>>>>
>>>>>> Thanks,
>>>>>> Tao
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
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From simon.rit at creatis.insa-lyon.fr  Wed Jan 30 11:13:33 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 30 Jan 2019 17:13:33 +0100
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CABaNCKqxxKH9kAD-kuY6tWEfBum_yJRZSLYvsifsRGWEKWN6jQ@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
 <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
 <CABaNCKqxxKH9kAD-kuY6tWEfBum_yJRZSLYvsifsRGWEKWN6jQ@mail.gmail.com>
Message-ID: <CAF0oig04PN+s72drZFVPP1AhAW=QdPDESbqkd5RSGPyaQy0_LQ@mail.gmail.com>

Are you using the HEAD version of the git ? Because I recently corrected a
bug in the Graft function (commit b2d73642ce171ba9890af2c107a1a31f923454b5).
Simon

On Wed, Jan 30, 2019 at 5:05 PM tao sun <colddiesun at gmail.com> wrote:

> Hi Simon,
>
> CUDA_HAVE_GPU is on. So is CUDA_FOUND. I can run examples like rtkfdk with
> gpu on without any problem though,
> By the way I am using CUDA 9.2.88.
>
> Tao
>
>
>
>
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??1:25???
>
>> Hi,
>> No, not really. In my experience, this occurs mainly when you don't have
>> a GPU properly configured for CUDA. Can you check the value of
>> CUDA_HAVE_GPU in cmake ? If it's OFF, then this is indeed the problem.
>> Simon
>>
>> On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com> wrote:
>>
>>> Hi again,
>>>
>>> Finally I got time to work on this. I was able to compile the program
>>> this time using the Graft() function. However, there's a runtime error when
>>> I run the program:
>>>
>>>
>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
>>> @ unknown : Cuda Error #3
>>>     terminate called after throwing an instance of 'itk::ExceptionObject'
>>>     what():
>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>>>     Cuda Error # 3
>>>     Aborted
>>>
>>> It happens when a new gpu backprojector is created:
>>>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>>>
>>> Any insights for this?
>>>
>>> Thanks,
>>> Tao
>>>
>>> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>>>
>>>> Thank you all! I will give a try using your solutions.
>>>> Tao
>>>>
>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ?? ??12:26???
>>>>
>>>>> Hi,
>>>>> That's one solution. Two other:
>>>>> - graft the output to a Cuda image
>>>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>>>> 3>::New();
>>>>> cuImg->Graft(projectionReader->GetOutput())
>>>>> - use the rtk::ImportImageFilter which is templated over image type to
>>>>> allow precisely this (I used it in Gate here
>>>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>>>> ).
>>>>> Best regards,
>>>>> Simon
>>>>>
>>>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <
>>>>> andreasga22 at gmail.com> wrote:
>>>>>
>>>>>> Hi Tao,
>>>>>>
>>>>>> I think you want the CastImageFilter
>>>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html> from
>>>>>> ITK.
>>>>>>
>>>>>> Something like this:
>>>>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
>>>>>> itk::CudaImage<float,3>>;
>>>>>> typename castToImageType::Pointer castfilter = castToImageType::New();
>>>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>>>> castfilter->Update();
>>>>>> auto cuda_image = castfilter->GetOutput();
>>>>>>
>>>>>> Best regards Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     agravgaard at protonmail.com
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>>>  ImportFilterType::Pointer projectionReader =
>>>>>>> ImportFilterType::New();
>>>>>>> ...
>>>>>>>  projectionReader->Update();
>>>>>>>
>>>>>>> The type of the image is itk:::Image<float,3>. I wonder if there is
>>>>>>> any way I can cast it to itk::CudaImage<float,3>?
>>>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>>>> CudaImageType so there is no such problem.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Tao
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>
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From colddiesun at gmail.com  Wed Jan 30 11:20:56 2019
From: colddiesun at gmail.com (tao sun)
Date: Wed, 30 Jan 2019 11:20:56 -0500
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CAF0oig04PN+s72drZFVPP1AhAW=QdPDESbqkd5RSGPyaQy0_LQ@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
 <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
 <CABaNCKqxxKH9kAD-kuY6tWEfBum_yJRZSLYvsifsRGWEKWN6jQ@mail.gmail.com>
 <CAF0oig04PN+s72drZFVPP1AhAW=QdPDESbqkd5RSGPyaQy0_LQ@mail.gmail.com>
Message-ID: <CABaNCKo5TaxJaRGK=BOXW=nqXiBeF+vnJssun-gYtGs=L+eUPA@mail.gmail.com>

No I am not using that. But the error was thrown before GRAFT() function
was called. It happens when I initialized the backprojector:
 bp = rtk::CudaRayCastBackProjectionImageFilter::New().

Tao

Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??11:13???

> Are you using the HEAD version of the git ? Because I recently corrected a
> bug in the Graft function (commit b2d73642ce171ba9890af2c107a1a31f923454b5).
> Simon
>
> On Wed, Jan 30, 2019 at 5:05 PM tao sun <colddiesun at gmail.com> wrote:
>
>> Hi Simon,
>>
>> CUDA_HAVE_GPU is on. So is CUDA_FOUND. I can run examples like
>> rtkfdk with gpu on without any problem though,
>> By the way I am using CUDA 9.2.88.
>>
>> Tao
>>
>>
>>
>>
>>
>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??1:25???
>>
>>> Hi,
>>> No, not really. In my experience, this occurs mainly when you don't have
>>> a GPU properly configured for CUDA. Can you check the value of
>>> CUDA_HAVE_GPU in cmake ? If it's OFF, then this is indeed the problem.
>>> Simon
>>>
>>> On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com> wrote:
>>>
>>>> Hi again,
>>>>
>>>> Finally I got time to work on this. I was able to compile the program
>>>> this time using the Graft() function. However, there's a runtime error when
>>>> I run the program:
>>>>
>>>>
>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
>>>> @ unknown : Cuda Error #3
>>>>     terminate called after throwing an instance of
>>>> 'itk::ExceptionObject'
>>>>     what():
>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>>>>     Cuda Error # 3
>>>>     Aborted
>>>>
>>>> It happens when a new gpu backprojector is created:
>>>>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>>>>
>>>> Any insights for this?
>>>>
>>>> Thanks,
>>>> Tao
>>>>
>>>> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>>>>
>>>>> Thank you all! I will give a try using your solutions.
>>>>> Tao
>>>>>
>>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ?? ??12:26???
>>>>>
>>>>>> Hi,
>>>>>> That's one solution. Two other:
>>>>>> - graft the output to a Cuda image
>>>>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>>>>> 3>::New();
>>>>>> cuImg->Graft(projectionReader->GetOutput())
>>>>>> - use the rtk::ImportImageFilter which is templated over image type
>>>>>> to allow precisely this (I used it in Gate here
>>>>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>>>>> ).
>>>>>> Best regards,
>>>>>> Simon
>>>>>>
>>>>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <
>>>>>> andreasga22 at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Tao,
>>>>>>>
>>>>>>> I think you want the CastImageFilter
>>>>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html>
>>>>>>> from ITK.
>>>>>>>
>>>>>>> Something like this:
>>>>>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
>>>>>>> itk::CudaImage<float,3>>;
>>>>>>> typename castToImageType::Pointer castfilter =
>>>>>>> castToImageType::New();
>>>>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>>>>> castfilter->Update();
>>>>>>> auto cuda_image = castfilter->GetOutput();
>>>>>>>
>>>>>>> Best regards Andreas
>>>>>>>
>>>>>>> __________________________________
>>>>>>>
>>>>>>> Andreas Gravgaard Andersen
>>>>>>>
>>>>>>> Department of Oncology,
>>>>>>>
>>>>>>> Aarhus University Hospital
>>>>>>>
>>>>>>> N?rrebrogade 44,
>>>>>>>
>>>>>>> 8000, Aarhus C
>>>>>>>
>>>>>>> Mail:     agravgaard at protonmail.com
>>>>>>>
>>>>>>> Cell:      +45 3165 8140
>>>>>>>
>>>>>>>
>>>>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>>>>  ImportFilterType::Pointer projectionReader =
>>>>>>>> ImportFilterType::New();
>>>>>>>> ...
>>>>>>>>  projectionReader->Update();
>>>>>>>>
>>>>>>>> The type of the image is itk:::Image<float,3>. I wonder if there is
>>>>>>>> any way I can cast it to itk::CudaImage<float,3>?
>>>>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>>>>> CudaImageType so there is no such problem.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Tao
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>
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From simon.rit at creatis.insa-lyon.fr  Wed Jan 30 11:29:08 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 30 Jan 2019 17:29:08 +0100
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CABaNCKo5TaxJaRGK=BOXW=nqXiBeF+vnJssun-gYtGs=L+eUPA@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
 <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
 <CABaNCKqxxKH9kAD-kuY6tWEfBum_yJRZSLYvsifsRGWEKWN6jQ@mail.gmail.com>
 <CAF0oig04PN+s72drZFVPP1AhAW=QdPDESbqkd5RSGPyaQy0_LQ@mail.gmail.com>
 <CABaNCKo5TaxJaRGK=BOXW=nqXiBeF+vnJssun-gYtGs=L+eUPA@mail.gmail.com>
Message-ID: <CAF0oig1kkmWcsZuO4o93cE-oYNRi+mM8ud__qhWtxFQnXYH6GQ@mail.gmail.com>

Can you send the code if you want us to help?

On Wed, Jan 30, 2019 at 5:21 PM tao sun <colddiesun at gmail.com> wrote:

> No I am not using that. But the error was thrown before GRAFT() function
> was called. It happens when I initialized the backprojector:
>  bp = rtk::CudaRayCastBackProjectionImageFilter::New().
>
> Tao
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??11:13???
>
>> Are you using the HEAD version of the git ? Because I recently corrected
>> a bug in the Graft function (commit
>> b2d73642ce171ba9890af2c107a1a31f923454b5).
>> Simon
>>
>> On Wed, Jan 30, 2019 at 5:05 PM tao sun <colddiesun at gmail.com> wrote:
>>
>>> Hi Simon,
>>>
>>> CUDA_HAVE_GPU is on. So is CUDA_FOUND. I can run examples like
>>> rtkfdk with gpu on without any problem though,
>>> By the way I am using CUDA 9.2.88.
>>>
>>> Tao
>>>
>>>
>>>
>>>
>>>
>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??1:25???
>>>
>>>> Hi,
>>>> No, not really. In my experience, this occurs mainly when you don't
>>>> have a GPU properly configured for CUDA. Can you check the value of
>>>> CUDA_HAVE_GPU in cmake ? If it's OFF, then this is indeed the problem.
>>>> Simon
>>>>
>>>> On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com> wrote:
>>>>
>>>>> Hi again,
>>>>>
>>>>> Finally I got time to work on this. I was able to compile the program
>>>>> this time using the Graft() function. However, there's a runtime error when
>>>>> I run the program:
>>>>>
>>>>>
>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
>>>>> @ unknown : Cuda Error #3
>>>>>     terminate called after throwing an instance of
>>>>> 'itk::ExceptionObject'
>>>>>     what():
>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>>>>>     Cuda Error # 3
>>>>>     Aborted
>>>>>
>>>>> It happens when a new gpu backprojector is created:
>>>>>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>>>>>
>>>>> Any insights for this?
>>>>>
>>>>> Thanks,
>>>>> Tao
>>>>>
>>>>> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>>>>>
>>>>>> Thank you all! I will give a try using your solutions.
>>>>>> Tao
>>>>>>
>>>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ?? ??12:26???
>>>>>>
>>>>>>> Hi,
>>>>>>> That's one solution. Two other:
>>>>>>> - graft the output to a Cuda image
>>>>>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>>>>>> 3>::New();
>>>>>>> cuImg->Graft(projectionReader->GetOutput())
>>>>>>> - use the rtk::ImportImageFilter which is templated over image type
>>>>>>> to allow precisely this (I used it in Gate here
>>>>>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>>>>>> ).
>>>>>>> Best regards,
>>>>>>> Simon
>>>>>>>
>>>>>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <
>>>>>>> andreasga22 at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Tao,
>>>>>>>>
>>>>>>>> I think you want the CastImageFilter
>>>>>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html>
>>>>>>>> from ITK.
>>>>>>>>
>>>>>>>> Something like this:
>>>>>>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>,
>>>>>>>> itk::CudaImage<float,3>>;
>>>>>>>> typename castToImageType::Pointer castfilter =
>>>>>>>> castToImageType::New();
>>>>>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>>>>>> castfilter->Update();
>>>>>>>> auto cuda_image = castfilter->GetOutput();
>>>>>>>>
>>>>>>>> Best regards Andreas
>>>>>>>>
>>>>>>>> __________________________________
>>>>>>>>
>>>>>>>> Andreas Gravgaard Andersen
>>>>>>>>
>>>>>>>> Department of Oncology,
>>>>>>>>
>>>>>>>> Aarhus University Hospital
>>>>>>>>
>>>>>>>> N?rrebrogade 44,
>>>>>>>>
>>>>>>>> 8000, Aarhus C
>>>>>>>>
>>>>>>>> Mail:     agravgaard at protonmail.com
>>>>>>>>
>>>>>>>> Cell:      +45 3165 8140
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>>>>>  ImportFilterType::Pointer projectionReader =
>>>>>>>>> ImportFilterType::New();
>>>>>>>>> ...
>>>>>>>>>  projectionReader->Update();
>>>>>>>>>
>>>>>>>>> The type of the image is itk:::Image<float,3>. I wonder if there
>>>>>>>>> is any way I can cast it to itk::CudaImage<float,3>?
>>>>>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>>>>>> CudaImageType so there is no such problem.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Tao
>>>>>>>>> _______________________________________________
>>>>>>>>> Rtk-users mailing list
>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>
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From andreasga22 at gmail.com  Wed Jan 30 11:33:49 2019
From: andreasga22 at gmail.com (Andreas Andersen)
Date: Wed, 30 Jan 2019 17:33:49 +0100
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CAF0oig1kkmWcsZuO4o93cE-oYNRi+mM8ud__qhWtxFQnXYH6GQ@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
 <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
 <CABaNCKqxxKH9kAD-kuY6tWEfBum_yJRZSLYvsifsRGWEKWN6jQ@mail.gmail.com>
 <CAF0oig04PN+s72drZFVPP1AhAW=QdPDESbqkd5RSGPyaQy0_LQ@mail.gmail.com>
 <CABaNCKo5TaxJaRGK=BOXW=nqXiBeF+vnJssun-gYtGs=L+eUPA@mail.gmail.com>
 <CAF0oig1kkmWcsZuO4o93cE-oYNRi+mM8ud__qhWtxFQnXYH6GQ@mail.gmail.com>
Message-ID: <CAE0aawE7u-510pW6nHvTK3SvqSDJh=L6dOWUrcCJ9SzFULs8iw@mail.gmail.com>

I've encountered the "Cuda Error # 3" issue two times.
As far as I remember, both were caused by the GPU being unreachable at
runtime:
* A missing or outdated (relative to CUDA version) nVidia driver
* The code running within a non-native environment.
The second point can also be triggered if the binary is located on remote
storage.

However, both of these cases were on Windows, and by the path
"/home/tsun/bin/" I would guess you're on some Linux distro.

/Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     agravgaard at protonmail.com

Cell:      +45 3165 8140


On Wed, 30 Jan 2019 at 17:29, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Can you send the code if you want us to help?
>
> On Wed, Jan 30, 2019 at 5:21 PM tao sun <colddiesun at gmail.com> wrote:
>
>> No I am not using that. But the error was thrown before GRAFT() function
>> was called. It happens when I initialized the backprojector:
>>  bp = rtk::CudaRayCastBackProjectionImageFilter::New().
>>
>> Tao
>>
>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??11:13???
>>
>>> Are you using the HEAD version of the git ? Because I recently corrected
>>> a bug in the Graft function (commit
>>> b2d73642ce171ba9890af2c107a1a31f923454b5).
>>> Simon
>>>
>>> On Wed, Jan 30, 2019 at 5:05 PM tao sun <colddiesun at gmail.com> wrote:
>>>
>>>> Hi Simon,
>>>>
>>>> CUDA_HAVE_GPU is on. So is CUDA_FOUND. I can run examples like
>>>> rtkfdk with gpu on without any problem though,
>>>> By the way I am using CUDA 9.2.88.
>>>>
>>>> Tao
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??1:25???
>>>>
>>>>> Hi,
>>>>> No, not really. In my experience, this occurs mainly when you don't
>>>>> have a GPU properly configured for CUDA. Can you check the value of
>>>>> CUDA_HAVE_GPU in cmake ? If it's OFF, then this is indeed the problem.
>>>>> Simon
>>>>>
>>>>> On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com> wrote:
>>>>>
>>>>>> Hi again,
>>>>>>
>>>>>> Finally I got time to work on this. I was able to compile the program
>>>>>> this time using the Graft() function. However, there's a runtime error when
>>>>>> I run the program:
>>>>>>
>>>>>>
>>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
>>>>>> @ unknown : Cuda Error #3
>>>>>>     terminate called after throwing an instance of
>>>>>> 'itk::ExceptionObject'
>>>>>>     what():
>>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>>>>>>     Cuda Error # 3
>>>>>>     Aborted
>>>>>>
>>>>>> It happens when a new gpu backprojector is created:
>>>>>>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>>>>>>
>>>>>> Any insights for this?
>>>>>>
>>>>>> Thanks,
>>>>>> Tao
>>>>>>
>>>>>> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>>>>>>
>>>>>>> Thank you all! I will give a try using your solutions.
>>>>>>> Tao
>>>>>>>
>>>>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ??
>>>>>>> ??12:26???
>>>>>>>
>>>>>>>> Hi,
>>>>>>>> That's one solution. Two other:
>>>>>>>> - graft the output to a Cuda image
>>>>>>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>>>>>>> 3>::New();
>>>>>>>> cuImg->Graft(projectionReader->GetOutput())
>>>>>>>> - use the rtk::ImportImageFilter which is templated over image type
>>>>>>>> to allow precisely this (I used it in Gate here
>>>>>>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>>>>>>> ).
>>>>>>>> Best regards,
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <
>>>>>>>> andreasga22 at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Tao,
>>>>>>>>>
>>>>>>>>> I think you want the CastImageFilter
>>>>>>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html>
>>>>>>>>> from ITK.
>>>>>>>>>
>>>>>>>>> Something like this:
>>>>>>>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>
>>>>>>>>> , itk::CudaImage<float,3>>;
>>>>>>>>> typename castToImageType::Pointer castfilter =
>>>>>>>>> castToImageType::New();
>>>>>>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>>>>>>> castfilter->Update();
>>>>>>>>> auto cuda_image = castfilter->GetOutput();
>>>>>>>>>
>>>>>>>>> Best regards Andreas
>>>>>>>>>
>>>>>>>>> __________________________________
>>>>>>>>>
>>>>>>>>> Andreas Gravgaard Andersen
>>>>>>>>>
>>>>>>>>> Department of Oncology,
>>>>>>>>>
>>>>>>>>> Aarhus University Hospital
>>>>>>>>>
>>>>>>>>> N?rrebrogade 44,
>>>>>>>>>
>>>>>>>>> 8000, Aarhus C
>>>>>>>>>
>>>>>>>>> Mail:     agravgaard at protonmail.com
>>>>>>>>>
>>>>>>>>> Cell:      +45 3165 8140
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>>>>>>  ImportFilterType::Pointer projectionReader =
>>>>>>>>>> ImportFilterType::New();
>>>>>>>>>> ...
>>>>>>>>>>  projectionReader->Update();
>>>>>>>>>>
>>>>>>>>>> The type of the image is itk:::Image<float,3>. I wonder if there
>>>>>>>>>> is any way I can cast it to itk::CudaImage<float,3>?
>>>>>>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>>>>>>> CudaImageType so there is no such problem.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Tao
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Rtk-users mailing list
>>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Rtk-users mailing list
>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From colddiesun at gmail.com  Wed Jan 30 11:45:58 2019
From: colddiesun at gmail.com (tao sun)
Date: Wed, 30 Jan 2019 11:45:58 -0500
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CAF0oig1kkmWcsZuO4o93cE-oYNRi+mM8ud__qhWtxFQnXYH6GQ@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
 <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
 <CABaNCKqxxKH9kAD-kuY6tWEfBum_yJRZSLYvsifsRGWEKWN6jQ@mail.gmail.com>
 <CAF0oig04PN+s72drZFVPP1AhAW=QdPDESbqkd5RSGPyaQy0_LQ@mail.gmail.com>
 <CABaNCKo5TaxJaRGK=BOXW=nqXiBeF+vnJssun-gYtGs=L+eUPA@mail.gmail.com>
 <CAF0oig1kkmWcsZuO4o93cE-oYNRi+mM8ud__qhWtxFQnXYH6GQ@mail.gmail.com>
Message-ID: <CABaNCKoowu9vRxzw+o8BeHKun-0-mX5cQFB44=pBcc2JzQcfbw@mail.gmail.com>

Here it is the piece of codes:

  typedef float PixelType;
  const unsigned int Dimension = 3;
  typedef itk::CudaImage< PixelType, Dimension > CudaImageType;
  typedef itk::Image< PixelType, Dimension > ImageType;
  typedef itk::ImportImageFilter <PixelType, Dimension> ImportFilterType;

 extern "C"  int idlrtkbackprojection_gpu(int argc, float * argv[])
{
volume                =  (float *)  argv[0];
projection            =  (float *)  argv[1];
        debug                 =  *(unsigned int*) argv[2];
        gpu                   =  *(unsigned int*) argv[3];
        bp_arg                =  *(unsigned int*) argv[4];
//string((*(idls *) argv[4]).s);
       geometry              =  std::string((*(idls *) argv[5]).s);
       sizexv                =  *(unsigned int*) argv[6];
sizeyv                =  *(unsigned int*) argv[7];
sizezv                =  *(unsigned int*) argv[8];
spacingxv             =  *(float *) argv[9];
spacingyv             =  *(float *) argv[10];
spacingzv             =  *(float *) argv[11];
offsetxv              =  *(float *) argv[12];
offsetyv              =  *(float *) argv[13];
offsetzv              =  *(float *) argv[14];
sizexp                =  *(unsigned int*) argv[15];
sizeyp                =  *(unsigned int*) argv[16];
sizezp                =  *(unsigned int*) argv[17];
spacingxp             =  *(float *) argv[18];
spacingyp             =  *(float *) argv[19];
spacingzp             =  *(float *) argv[20];
offsetxp              =  *(float *) argv[21];
offsetyp              =  *(float *) argv[22];
offsetzp              =  *(float *) argv[23];

// Geometry
  rtk::ThreeDCircularProjectionGeometryXMLFileReader::Pointer
geometryReader;
  geometryReader =
rtk::ThreeDCircularProjectionGeometryXMLFileReader::New();
  geometryReader->SetFilename(geometry);
  TRY_AND_EXIT_ON_ITK_EXCEPTION(
geometryReader->GenerateOutputInformation() )

// Volume reader
        ImportFilterType::Pointer volumeReader = ImportFilterType::New();

        ImageType::SizeType sizev;// = {{sizexv,sizeyv,sizezv}};
sizev[0] = sizexv; //406;        //int(dim[0]);
sizev[1] = sizeyv; //408;        //int(dim[1]);
sizev[2] = sizezv;

        ImageType::IndexType start;// = {{0,0,0}};
start[0] = 0;
start[1] = 0;
start[2] = 0;
        ImageType::RegionType regionv;
regionv.SetSize(sizev);
regionv.SetIndex(start);
        volumeReader->SetRegion(regionv);

       double spacingv[3];
spacingv[0] = spacingxv;
spacingv[1] = spacingyv;
spacingv[2] = spacingzv;
volumeReader->SetSpacing(spacingv);

double originv[3];
originv[0] = offsetxv;
originv[1] = offsetyv;
originv[2] = offsetzv;
volumeReader->SetOrigin(originv);

// Projections reader
       ImportFilterType::Pointer projectionReader = ImportFilterType::New();
       ImageType::SizeType sizep;
sizep[0] = sizexp; //406;        //int(dim[0]);
sizep[1] = sizeyp; //408;        //int(dim[1]);
sizep[2] = sizezp;

       ImageType::RegionType regionp;
regionp.SetSize(sizep);
regionp.SetIndex(start);
       projectionReader->SetRegion(regionp);

       double spacingp[3];
spacingp[0] = spacingxp;
spacingp[1] = spacingyp;
spacingp[2] = spacingzp;
projectionReader->SetSpacing(spacingp);

double originp[3];
originp[0] = offsetxp;
originp[1] = offsetyp;
originp[2] = offsetzp;
       projectionReader->SetOrigin(originp);

// Create backprojection image filter
  rtk::CudaFDKBackProjectionImageFilter::Pointer bp;
  bp = rtk::CudaFDKBackProjectionImageFilter::New();
                   // where error was thrown out

  CudaImageType::Pointer cuImg1 = CudaImageType::New();
  cuImg1->Graft(projectionReader->GetOutput());
  CudaImageType::Pointer cuImg2 = CudaImageType::New();
  cuImg2->Graft(volumeReader->GetOutput());
  bp->SetInput( cuImg2 );
  bp->SetInput( 1, cuImg1 );

  bp->SetGeometry( geometryReader->GetOutputObject() );
  TRY_AND_EXIT_ON_ITK_EXCEPTION( bp->Update() )


Thanks,
Tao

Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??11:29???

> Can you send the code if you want us to help?
>
> On Wed, Jan 30, 2019 at 5:21 PM tao sun <colddiesun at gmail.com> wrote:
>
>> No I am not using that. But the error was thrown before GRAFT() function
>> was called. It happens when I initialized the backprojector:
>>  bp = rtk::CudaRayCastBackProjectionImageFilter::New().
>>
>> Tao
>>
>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??11:13???
>>
>>> Are you using the HEAD version of the git ? Because I recently corrected
>>> a bug in the Graft function (commit
>>> b2d73642ce171ba9890af2c107a1a31f923454b5).
>>> Simon
>>>
>>> On Wed, Jan 30, 2019 at 5:05 PM tao sun <colddiesun at gmail.com> wrote:
>>>
>>>> Hi Simon,
>>>>
>>>> CUDA_HAVE_GPU is on. So is CUDA_FOUND. I can run examples like
>>>> rtkfdk with gpu on without any problem though,
>>>> By the way I am using CUDA 9.2.88.
>>>>
>>>> Tao
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??1:25???
>>>>
>>>>> Hi,
>>>>> No, not really. In my experience, this occurs mainly when you don't
>>>>> have a GPU properly configured for CUDA. Can you check the value of
>>>>> CUDA_HAVE_GPU in cmake ? If it's OFF, then this is indeed the problem.
>>>>> Simon
>>>>>
>>>>> On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com> wrote:
>>>>>
>>>>>> Hi again,
>>>>>>
>>>>>> Finally I got time to work on this. I was able to compile the program
>>>>>> this time using the Graft() function. However, there's a runtime error when
>>>>>> I run the program:
>>>>>>
>>>>>>
>>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
>>>>>> @ unknown : Cuda Error #3
>>>>>>     terminate called after throwing an instance of
>>>>>> 'itk::ExceptionObject'
>>>>>>     what():
>>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>>>>>>     Cuda Error # 3
>>>>>>     Aborted
>>>>>>
>>>>>> It happens when a new gpu backprojector is created:
>>>>>>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>>>>>>
>>>>>> Any insights for this?
>>>>>>
>>>>>> Thanks,
>>>>>> Tao
>>>>>>
>>>>>> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>>>>>>
>>>>>>> Thank you all! I will give a try using your solutions.
>>>>>>> Tao
>>>>>>>
>>>>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ??
>>>>>>> ??12:26???
>>>>>>>
>>>>>>>> Hi,
>>>>>>>> That's one solution. Two other:
>>>>>>>> - graft the output to a Cuda image
>>>>>>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>>>>>>> 3>::New();
>>>>>>>> cuImg->Graft(projectionReader->GetOutput())
>>>>>>>> - use the rtk::ImportImageFilter which is templated over image type
>>>>>>>> to allow precisely this (I used it in Gate here
>>>>>>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>>>>>>> ).
>>>>>>>> Best regards,
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <
>>>>>>>> andreasga22 at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Tao,
>>>>>>>>>
>>>>>>>>> I think you want the CastImageFilter
>>>>>>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html>
>>>>>>>>> from ITK.
>>>>>>>>>
>>>>>>>>> Something like this:
>>>>>>>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>
>>>>>>>>> , itk::CudaImage<float,3>>;
>>>>>>>>> typename castToImageType::Pointer castfilter =
>>>>>>>>> castToImageType::New();
>>>>>>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>>>>>>> castfilter->Update();
>>>>>>>>> auto cuda_image = castfilter->GetOutput();
>>>>>>>>>
>>>>>>>>> Best regards Andreas
>>>>>>>>>
>>>>>>>>> __________________________________
>>>>>>>>>
>>>>>>>>> Andreas Gravgaard Andersen
>>>>>>>>>
>>>>>>>>> Department of Oncology,
>>>>>>>>>
>>>>>>>>> Aarhus University Hospital
>>>>>>>>>
>>>>>>>>> N?rrebrogade 44,
>>>>>>>>>
>>>>>>>>> 8000, Aarhus C
>>>>>>>>>
>>>>>>>>> Mail:     agravgaard at protonmail.com
>>>>>>>>>
>>>>>>>>> Cell:      +45 3165 8140
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>>>>>>  ImportFilterType::Pointer projectionReader =
>>>>>>>>>> ImportFilterType::New();
>>>>>>>>>> ...
>>>>>>>>>>  projectionReader->Update();
>>>>>>>>>>
>>>>>>>>>> The type of the image is itk:::Image<float,3>. I wonder if there
>>>>>>>>>> is any way I can cast it to itk::CudaImage<float,3>?
>>>>>>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>>>>>>> CudaImageType so there is no such problem.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Tao
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Rtk-users mailing list
>>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Rtk-users mailing list
>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>
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From wuchao04 at gmail.com  Wed Jan 30 12:17:04 2019
From: wuchao04 at gmail.com (Chao Wu)
Date: Wed, 30 Jan 2019 18:17:04 +0100
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CAE0aawE7u-510pW6nHvTK3SvqSDJh=L6dOWUrcCJ9SzFULs8iw@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
 <CAE0aawHJ2TwJekDdf2jqzA-YF+ix1JHnRfaN6CSrMwUJe1dEgw@mail.gmail.com>
 <CAF0oig0daRony4PnMd8K2eyF=+WdvzxMHbzRLVrCFq+O6gGGMw@mail.gmail.com>
 <CABaNCKoDqvpA+OT9q3124S16jP25LRpbq1H2rgC7yxPTWy8vZA@mail.gmail.com>
 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
 <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
 <CABaNCKqxxKH9kAD-kuY6tWEfBum_yJRZSLYvsifsRGWEKWN6jQ@mail.gmail.com>
 <CAF0oig04PN+s72drZFVPP1AhAW=QdPDESbqkd5RSGPyaQy0_LQ@mail.gmail.com>
 <CABaNCKo5TaxJaRGK=BOXW=nqXiBeF+vnJssun-gYtGs=L+eUPA@mail.gmail.com>
 <CAF0oig1kkmWcsZuO4o93cE-oYNRi+mM8ud__qhWtxFQnXYH6GQ@mail.gmail.com>
 <CAE0aawE7u-510pW6nHvTK3SvqSDJh=L6dOWUrcCJ9SzFULs8iw@mail.gmail.com>
Message-ID: <CAH+sHrW72-ejM901Ctd5AEjGAjLQogT19AVStiH_uxH965_ppA@mail.gmail.com>

L.S.,

I encouter recently the "Cuda Error # 3" with a Quadro P4000 when running
rtkfdk, but I am not sure if the cause is the same as Tao's problem.
CUDA_CHECK() marks Driver API error with a "#" whereas Runtime API error
with a ":", so it is CUresult 3 (CUDA_ERROR_NOT_INITIALIZED).
Indeed when I add CUDA_CHECK to cuInit(0) in itkCudaContextManager.cxx I
already got an CUresult 100 (CUDA_ERROR_NO_DEVICE) here.
In the same itkCudaContextManager.cxx file, itk::CudaGetAvailableDevices
(which calls Runtime API) works well, so only Driver API doesn't work
properly.
The same build works fine with a Tesla P40.

I don't have time to investigate further but I found on my computer a
previous build based on commit 5717b6d02675ee10f03200038566f06dfcc2ad19 in
May 2018 doesn't have this issue with the Quadro card.
So I guess it shouldn't be the problem of the card or the driver, but a
problem induced by a later commit.

Best regards,
Chao

Andreas Andersen <andreasga22 at gmail.com> ?2019?1?30??? ??5:33???

> I've encountered the "Cuda Error # 3" issue two times.
> As far as I remember, both were caused by the GPU being unreachable at
> runtime:
> * A missing or outdated (relative to CUDA version) nVidia driver
> * The code running within a non-native environment.
> The second point can also be triggered if the binary is located on remote
> storage.
>
> However, both of these cases were on Windows, and by the path
> "/home/tsun/bin/" I would guess you're on some Linux distro.
>
> /Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     agravgaard at protonmail.com
>
> Cell:      +45 3165 8140
>
>
> On Wed, 30 Jan 2019 at 17:29, Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Can you send the code if you want us to help?
>>
>> On Wed, Jan 30, 2019 at 5:21 PM tao sun <colddiesun at gmail.com> wrote:
>>
>>> No I am not using that. But the error was thrown before GRAFT() function
>>> was called. It happens when I initialized the backprojector:
>>>  bp = rtk::CudaRayCastBackProjectionImageFilter::New().
>>>
>>> Tao
>>>
>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??11:13???
>>>
>>>> Are you using the HEAD version of the git ? Because I recently
>>>> corrected a bug in the Graft function (commit
>>>> b2d73642ce171ba9890af2c107a1a31f923454b5).
>>>> Simon
>>>>
>>>> On Wed, Jan 30, 2019 at 5:05 PM tao sun <colddiesun at gmail.com> wrote:
>>>>
>>>>> Hi Simon,
>>>>>
>>>>> CUDA_HAVE_GPU is on. So is CUDA_FOUND. I can run examples like
>>>>> rtkfdk with gpu on without any problem though,
>>>>> By the way I am using CUDA 9.2.88.
>>>>>
>>>>> Tao
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??1:25???
>>>>>
>>>>>> Hi,
>>>>>> No, not really. In my experience, this occurs mainly when you don't
>>>>>> have a GPU properly configured for CUDA. Can you check the value of
>>>>>> CUDA_HAVE_GPU in cmake ? If it's OFF, then this is indeed the problem.
>>>>>> Simon
>>>>>>
>>>>>> On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com> wrote:
>>>>>>
>>>>>>> Hi again,
>>>>>>>
>>>>>>> Finally I got time to work on this. I was able to compile the
>>>>>>> program this time using the Graft() function. However, there's a runtime
>>>>>>> error when I run the program:
>>>>>>>
>>>>>>>
>>>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
>>>>>>> @ unknown : Cuda Error #3
>>>>>>>     terminate called after throwing an instance of
>>>>>>> 'itk::ExceptionObject'
>>>>>>>     what():
>>>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>>>>>>>     Cuda Error # 3
>>>>>>>     Aborted
>>>>>>>
>>>>>>> It happens when a new gpu backprojector is created:
>>>>>>>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>>>>>>>
>>>>>>> Any insights for this?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Tao
>>>>>>>
>>>>>>> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>>>>>>>
>>>>>>>> Thank you all! I will give a try using your solutions.
>>>>>>>> Tao
>>>>>>>>
>>>>>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ??
>>>>>>>> ??12:26???
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>> That's one solution. Two other:
>>>>>>>>> - graft the output to a Cuda image
>>>>>>>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>>>>>>>> 3>::New();
>>>>>>>>> cuImg->Graft(projectionReader->GetOutput())
>>>>>>>>> - use the rtk::ImportImageFilter which is templated over image
>>>>>>>>> type to allow precisely this (I used it in Gate here
>>>>>>>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>>>>>>>> ).
>>>>>>>>> Best regards,
>>>>>>>>> Simon
>>>>>>>>>
>>>>>>>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <
>>>>>>>>> andreasga22 at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Tao,
>>>>>>>>>>
>>>>>>>>>> I think you want the CastImageFilter
>>>>>>>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html>
>>>>>>>>>> from ITK.
>>>>>>>>>>
>>>>>>>>>> Something like this:
>>>>>>>>>> using castToImageType = itk::CastImageFilter<itk:::Image<float,3>
>>>>>>>>>> , itk::CudaImage<float,3>>;
>>>>>>>>>> typename castToImageType::Pointer castfilter =
>>>>>>>>>> castToImageType::New();
>>>>>>>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>>>>>>>> castfilter->Update();
>>>>>>>>>> auto cuda_image = castfilter->GetOutput();
>>>>>>>>>>
>>>>>>>>>> Best regards Andreas
>>>>>>>>>>
>>>>>>>>>> __________________________________
>>>>>>>>>>
>>>>>>>>>> Andreas Gravgaard Andersen
>>>>>>>>>>
>>>>>>>>>> Department of Oncology,
>>>>>>>>>>
>>>>>>>>>> Aarhus University Hospital
>>>>>>>>>>
>>>>>>>>>> N?rrebrogade 44,
>>>>>>>>>>
>>>>>>>>>> 8000, Aarhus C
>>>>>>>>>>
>>>>>>>>>> Mail:     agravgaard at protonmail.com
>>>>>>>>>>
>>>>>>>>>> Cell:      +45 3165 8140
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>>>>>>>  ImportFilterType::Pointer projectionReader =
>>>>>>>>>>> ImportFilterType::New();
>>>>>>>>>>> ...
>>>>>>>>>>>  projectionReader->Update();
>>>>>>>>>>>
>>>>>>>>>>> The type of the image is itk:::Image<float,3>. I wonder if there
>>>>>>>>>>> is any way I can cast it to itk::CudaImage<float,3>?
>>>>>>>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>>>>>>>> CudaImageType so there is no such problem.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Tao
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Rtk-users mailing list
>>>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Rtk-users mailing list
>>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From simon.rit at creatis.insa-lyon.fr  Wed Jan 30 16:22:25 2019
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 30 Jan 2019 22:22:25 +0100
Subject: [Rtk-users] cast itk:::Image to itk::CudaImage
In-Reply-To: <CAH+sHrW72-ejM901Ctd5AEjGAjLQogT19AVStiH_uxH965_ppA@mail.gmail.com>
References: <CABaNCKr8ZLgsYOqXWdvPQnuAe90zgCp6qO42GaqBna+nMp5j1g@mail.gmail.com>
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 <CABaNCKq06LDEFsxY1rP-nwbZBG0Xnh18e3xwpnJCDvVNk_0PDQ@mail.gmail.com>
 <CAF0oig123w0ze+9T1Qci=_tkCtfVf0YnjYdCdi1HU8VMZKqm3A@mail.gmail.com>
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 <CABaNCKo5TaxJaRGK=BOXW=nqXiBeF+vnJssun-gYtGs=L+eUPA@mail.gmail.com>
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Message-ID: <CAF0oig28a1rVCZcRu7c06iJ=dcui1DiMvv4ux1WbMXcBmRc50g@mail.gmail.com>

I don't see what has changed since this commit...
For Tao, I would suggest to try a minimal example in one separate main just
to be sure that this is indeed this line that causes the problem and not
some bad memory management before. I really don't see what is the issue
here since you are using CUDA code from the same RTK version.

On Wed, Jan 30, 2019 at 6:17 PM Chao Wu <wuchao04 at gmail.com> wrote:

> L.S.,
>
> I encouter recently the "Cuda Error # 3" with a Quadro P4000 when running
> rtkfdk, but I am not sure if the cause is the same as Tao's problem.
> CUDA_CHECK() marks Driver API error with a "#" whereas Runtime API error
> with a ":", so it is CUresult 3 (CUDA_ERROR_NOT_INITIALIZED).
> Indeed when I add CUDA_CHECK to cuInit(0) in itkCudaContextManager.cxx I
> already got an CUresult 100 (CUDA_ERROR_NO_DEVICE) here.
> In the same itkCudaContextManager.cxx file, itk::CudaGetAvailableDevices
> (which calls Runtime API) works well, so only Driver API doesn't work
> properly.
> The same build works fine with a Tesla P40.
>
> I don't have time to investigate further but I found on my computer a
> previous build based on commit 5717b6d02675ee10f03200038566f06dfcc2ad19 in
> May 2018 doesn't have this issue with the Quadro card.
> So I guess it shouldn't be the problem of the card or the driver, but a
> problem induced by a later commit.
>
> Best regards,
> Chao
>
> Andreas Andersen <andreasga22 at gmail.com> ?2019?1?30??? ??5:33???
>
>> I've encountered the "Cuda Error # 3" issue two times.
>> As far as I remember, both were caused by the GPU being unreachable at
>> runtime:
>> * A missing or outdated (relative to CUDA version) nVidia driver
>> * The code running within a non-native environment.
>> The second point can also be triggered if the binary is located on remote
>> storage.
>>
>> However, both of these cases were on Windows, and by the path
>> "/home/tsun/bin/" I would guess you're on some Linux distro.
>>
>> /Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     agravgaard at protonmail.com
>>
>> Cell:      +45 3165 8140
>>
>>
>> On Wed, 30 Jan 2019 at 17:29, Simon Rit <simon.rit at creatis.insa-lyon.fr>
>> wrote:
>>
>>> Can you send the code if you want us to help?
>>>
>>> On Wed, Jan 30, 2019 at 5:21 PM tao sun <colddiesun at gmail.com> wrote:
>>>
>>>> No I am not using that. But the error was thrown before GRAFT()
>>>> function was called. It happens when I initialized the backprojector:
>>>>  bp = rtk::CudaRayCastBackProjectionImageFilter::New().
>>>>
>>>> Tao
>>>>
>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??11:13???
>>>>
>>>>> Are you using the HEAD version of the git ? Because I recently
>>>>> corrected a bug in the Graft function (commit
>>>>> b2d73642ce171ba9890af2c107a1a31f923454b5).
>>>>> Simon
>>>>>
>>>>> On Wed, Jan 30, 2019 at 5:05 PM tao sun <colddiesun at gmail.com> wrote:
>>>>>
>>>>>> Hi Simon,
>>>>>>
>>>>>> CUDA_HAVE_GPU is on. So is CUDA_FOUND. I can run examples like
>>>>>> rtkfdk with gpu on without any problem though,
>>>>>> By the way I am using CUDA 9.2.88.
>>>>>>
>>>>>> Tao
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?30? ?? ??1:25???
>>>>>>
>>>>>>> Hi,
>>>>>>> No, not really. In my experience, this occurs mainly when you don't
>>>>>>> have a GPU properly configured for CUDA. Can you check the value of
>>>>>>> CUDA_HAVE_GPU in cmake ? If it's OFF, then this is indeed the problem.
>>>>>>> Simon
>>>>>>>
>>>>>>> On Wed, Jan 30, 2019 at 1:23 AM tao sun <colddiesun at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi again,
>>>>>>>>
>>>>>>>> Finally I got time to work on this. I was able to compile the
>>>>>>>> program this time using the Graft() function. However, there's a runtime
>>>>>>>> error when I run the program:
>>>>>>>>
>>>>>>>>
>>>>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38
>>>>>>>> @ unknown : Cuda Error #3
>>>>>>>>     terminate called after throwing an instance of
>>>>>>>> 'itk::ExceptionObject'
>>>>>>>>     what():
>>>>>>>> /home/tsun/bin/RTK-1.4.0/utilities/ITKCudaCommon/src/itkCudaDataManager.cxx:38:
>>>>>>>>     Cuda Error # 3
>>>>>>>>     Aborted
>>>>>>>>
>>>>>>>> It happens when a new gpu backprojector is created:
>>>>>>>>     bp = rtk::CudaRayCastBackProjectionImageFilter::New();
>>>>>>>>
>>>>>>>> Any insights for this?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Tao
>>>>>>>>
>>>>>>>> tao sun <colddiesun at gmail.com> ? 2019?1?19? ?? ??8:51???
>>>>>>>>
>>>>>>>>> Thank you all! I will give a try using your solutions.
>>>>>>>>> Tao
>>>>>>>>>
>>>>>>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2019?1?17? ??
>>>>>>>>> ??12:26???
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>> That's one solution. Two other:
>>>>>>>>>> - graft the output to a Cuda image
>>>>>>>>>> itk::CudaImage<float, 3>::Pointer cuImg = itk::CudaImage<float,
>>>>>>>>>> 3>::New();
>>>>>>>>>> cuImg->Graft(projectionReader->GetOutput())
>>>>>>>>>> - use the rtk::ImportImageFilter which is templated over image
>>>>>>>>>> type to allow precisely this (I used it in Gate here
>>>>>>>>>> <https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L1583>
>>>>>>>>>> ).
>>>>>>>>>> Best regards,
>>>>>>>>>> Simon
>>>>>>>>>>
>>>>>>>>>> On Wed, Jan 16, 2019 at 11:06 PM Andreas Andersen <
>>>>>>>>>> andreasga22 at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Tao,
>>>>>>>>>>>
>>>>>>>>>>> I think you want the CastImageFilter
>>>>>>>>>>> <https://itk.org/Doxygen/html/classitk_1_1CastImageFilter.html>
>>>>>>>>>>> from ITK.
>>>>>>>>>>>
>>>>>>>>>>> Something like this:
>>>>>>>>>>> using castToImageType = itk::CastImageFilter<
>>>>>>>>>>> itk:::Image<float,3>, itk::CudaImage<float,3>>;
>>>>>>>>>>> typename castToImageType::Pointer castfilter =
>>>>>>>>>>> castToImageType::New();
>>>>>>>>>>> castfilter->SetInput(projectionReader->GetOutput());
>>>>>>>>>>> castfilter->Update();
>>>>>>>>>>> auto cuda_image = castfilter->GetOutput();
>>>>>>>>>>>
>>>>>>>>>>> Best regards Andreas
>>>>>>>>>>>
>>>>>>>>>>> __________________________________
>>>>>>>>>>>
>>>>>>>>>>> Andreas Gravgaard Andersen
>>>>>>>>>>>
>>>>>>>>>>> Department of Oncology,
>>>>>>>>>>>
>>>>>>>>>>> Aarhus University Hospital
>>>>>>>>>>>
>>>>>>>>>>> N?rrebrogade 44,
>>>>>>>>>>>
>>>>>>>>>>> 8000, Aarhus C
>>>>>>>>>>>
>>>>>>>>>>> Mail:     agravgaard at protonmail.com
>>>>>>>>>>>
>>>>>>>>>>> Cell:      +45 3165 8140
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Wed, 16 Jan 2019 at 22:59, tao sun <colddiesun at gmail.com>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> I have read in some image using  itk::ImportImageFilter.
>>>>>>>>>>>>  ImportFilterType::Pointer projectionReader =
>>>>>>>>>>>> ImportFilterType::New();
>>>>>>>>>>>> ...
>>>>>>>>>>>>  projectionReader->Update();
>>>>>>>>>>>>
>>>>>>>>>>>> The type of the image is itk:::Image<float,3>. I wonder if
>>>>>>>>>>>> there is any way I can cast it to itk::CudaImage<float,3>?
>>>>>>>>>>>> In rtkforwardprojections.cxx the imageReaderType is defined as
>>>>>>>>>>>> CudaImageType so there is no such problem.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Tao
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Rtk-users mailing list
>>>>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Rtk-users mailing list
>>>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
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