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OpenGATE / Gate

Official public repository of Gate
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Problem in creating output #329

Open somayehasadi opened 4 years ago

somayehasadi commented 4 years ago

I want to run the ready program in Gate with the name of Thermal being in the folder of Imaging/Thermal in the subfolder of GateContrib-master. In the program, It was asked for the two outputs name: Mobydose.mhd and Statistics.txt written in the part related to Actor. I have installed ITK and put the part related to the optical photon in ON. When the program is running, core dumped accrues, n output created and the error in below is received:

terminate called after throwing an instance of 'itk::ImageFileReaderException' what(): /home/BuildFiles/ITK/InsightToolkit-5.0.0-Source/Modules/IO/ImageBase/include/itkImageFileReader.hxx:136: Could not create IO object for reading file output/Mobydose-AbsorptionMap.mhd Tried to create one of the following: GDCMImageIO You probably failed to set a file suffix, or set the suffix to an unsupported type.

Aborted (core dumped)

The program is this one (the part related to actro) /vis/open VRML2FILE /vis/drawVolume /vis/viewer/set/viewpointThetaPhi 90 0 /vis/viewer/zoom 1 /vis/drawVolume /vis/viewer/flush /vis/drawVolume /tracking/storeTrajectory 1 /vis/scene/add/trajectories /vis/scene/endOfEventAction accumulate 10 ################################################# /gate/actor/addActor ThermalActor nano /gate/actor/nano/save Mobydose.mhd /gate/actor/nano/attachTo Mouse /gate/actor/nano/stepHitType random /gate/actor/nano/setPosition 0. 0. 0. cm /gate/actor/nano/setVoxelSize 0.25 0.25 0.25 mm /gate/actor/nano/setDiffusionTime 2 s /gate/actor/nano/setThermalDiffusivity 0.190 mm2/s /gate/actor/nano/setBloodPerfusionRate 0.004 /gate/actor/nano/setBloodDensity 1.06E-6 /gate/actor/nano/setBloodHeatCapacity 3.6E6 /gate/actor/nano/setTissueDensity 1.04E-6 /gate/actor/nano/setTissueHeatCapacity 3.65E6 /gate/actor/nano/setSimulationScale 1E10 /gate/actor/nano/setNumberOfTimeFrames 60 /gate/actor/addActor SimulationStatisticActor Myactor /gate/actor/Myactor/save Statistics.txt /gate/actor/Myactor/attachTo Mouse /gate/actor/Myactor/save EveryNSeconds 0.5 ######################################################

Has any person had the same problem and know about the meaning of this error? Thank you very much for your reading and any suggestion.

SimonRit commented 4 years ago

This issue has been discussed here on ITK's discourse. I don't have time to test the suggestions but I had a similar issue on RTK and fixed it with SimonRit/RTK@cf77624. Do you have time to have a look @tbaudier?

tbaudier commented 4 years ago

I tried to reproduce this error on Mac with Gate (Optical ON and ITK ON) but I do not have the output for ThermalTherapy.mac. The only output availble is g4_00.wrl

somayehasadi commented 4 years ago

Yes exactly the same for me. I even asked another person who has Gate and ITK in his system and works with AGte to run the program and it was the same error. It is strange that nobody knows the reason for this problem. I would be so thankful if any person knows that or may understand the way t solve it, let me know.

Thank you for your time

Somayeh Asadi (PhD) Postdoctoral Researcher Department of Mechanical Engineering Politecnico di Milano, Italy

Via Giuseppe La Masa,1 20156 - Milano - Italy phone: +39 0223998572

somayeh.asadi@polimi.it

From: tbaudier notifications@github.com Sent: Tuesday, May 12, 2020 2:18 PM To: OpenGATE/Gate Gate@noreply.github.com Cc: Somayeh Asadi somayeh.asadi@polimi.it; Author author@noreply.github.com Subject: Re: [OpenGATE/Gate] Problem in creating output (#329)

I tried to reproduce this error on Mac with Gate (Optical ON and ITK ON) but I do not have the output for ThermalTherapy.mac. The only output availble is g4_00.wrl

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/OpenGATE/Gate/issues/329#issuecomment-627306769, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AO77Q57TOM2WE6BQ543CIU3RRE5BXANCNFSM4MIYD2QA.

tbaudier commented 4 years ago

I cannot help you for that example. The initial push was done by @albertine Maybe she can help you.

dsarrut commented 4 years ago

Albertine no longer works in this field ...

@tbaudier, maybe you could just try to see if it helps to add something like SET(ITK_COMPONENTS ITKImageIO;ITKThresholding;ITKFFT;ITKImageCompose;ITKSmoothing) like said in the ITK discourse to see if it is better?

somayehasadi commented 4 years ago

I have checked everything and consult with the ITK organizer too. For the ITK everything is correct. The only thing that now I think it may be because of that is the version. I think the version of ITK, Gate, Linux should be matched but I don't know it is true or not. I used the Linux 18.04, ITK 5, and Gate 8. I was wondering if any other person run the thermal program in her/his system and doesn't get the error, I can compare this issue between two systems to check if the version is important or not.

Somayeh Asadi (PhD) Postdoctoral Researcher Department of Mechanical Engineering Politecnico di Milano, Italy

Via Giuseppe La Masa,1 20156 - Milano - Italy phone: +39 0223998572

somayeh.asadi@polimi.it

From: David Sarrut notifications@github.com Sent: Tuesday, May 12, 2020 3:19 PM To: OpenGATE/Gate Gate@noreply.github.com Cc: Somayeh Asadi somayeh.asadi@polimi.it; Author author@noreply.github.com Subject: Re: [OpenGATE/Gate] Problem in creating output (#329)

Albertine no longer works in this field ...

@tbaudierhttps://github.com/tbaudier, maybe you could just try to see if it helps to add something like SET(ITK_COMPONENTS ITKImageIO;ITKThresholding;ITKFFT;ITKImageCompose;ITKSmoothing) like said in the ITK discourse to see if it is better?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/OpenGATE/Gate/issues/329#issuecomment-627339431, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AO77Q55D6Q3WIUXA5JOTQNDRRFEFPANCNFSM4MIYD2QA.

tbaudier commented 4 years ago

Albertine no longer works in this field ...

@tbaudier, maybe you could just try to see if it helps to add something like SET(ITK_COMPONENTS ITKImageIO;ITKThresholding;ITKFFT;ITKImageCompose;ITKSmoothing) like said in the ITK discourse to see if it is better?

It's already done https://github.com/OpenGATE/Gate/blob/develop/CMakeLists.txt#L240 and even if I added ITKImageIO in the list, I have the same results than before