[Rtk-users] unable to use CudaParkerShortScanImageFilter in python

Tue Jul 18 09:11:40 CEST 2023

Hi Simon,

Thank you for the clarification. It works.

But I am facing a cuda related issue right now.
I need to reinstall itk, itk-rtk and itk-rtk-cuda116 so as to generate exe
of the application using pyinstaller.
After the reinstallation, I am getting the following error:

[image: image.png]

Here are the installed packages details:

[image: image.png]

[image: image.png]

[image: image.png]

For cuda116,I am using the wheel files you shared for Cuda PSSF at
https://github.com/RTKConsortium/RTK/actions/runs/5448263998

Please let me know your observations.

Regards,
Akshara

On Thu, 13 Jul 2023 at 13:23, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> As I said, the output type (set by ttype) can only be float or double even
> if the projections are unsigned short.
> But you need to change the component type for the input to
> IOComponent_USHORT (2 bytes), IOComponent_INT is 4 bytes.
> Simon
>
> On Thu, Jul 13, 2023 at 7:27 AM Akshara P K <akshara at advitech.in> wrote:
>
>> Hi Simon,
>>
>> Thank you for the quick response.
>>
>> We already tried that conversion. Here is the updated snippet:
>> size_x = 1024
>> size_y = 1024
>> numberOfProjections = 512
>> rawio = itk.RawImageIO.New()
>> rawio.SetNumberOfDimensions(2)
>> rawio.SetPixelType(itk.CommonEnums.IOPixel_SCALAR)
>> rawio.SetComponentType(itk.CommonEnums.IOComponent_FLOAT)
>> rawio.SetDimensions(0, size_x)
>> rawio.SetDimensions(1, size_y)
>> rawio.SetSpacing(0, 1)
>> rawio.SetSpacing(1, 1)
>> rawio.SetByteOrderToLittleEndian()
>>
>> # List of filenames
>> fileNames = []
>> for i in range(numberOfProjections-1):
>>     fileNames.append(f'/subvolume00/{i:04d}.raw')
>>
>> pixelSpacing = 0.420002
>> projOrigin = [ -pixelSpacing*(size_x-1)/2, 0, -pixelSpacing*(size_y-1)/2
>> ] #input images are size_x x size_y pixels with a 0.42mm pixel size
>> projSpacing = [ pixelSpacing, 1, pixelSpacing ]
>> # Read projections
>> CPUImageType = itk.Image[itk.F,3]
>> proj = rtk.projections_reader(ttype=CPUImageType,
>> file_names=fileNames,ImageIO=rawio, Origin=projOrigin, Spacing=projSpacing)
>>
>> Then it is throwing below error:
>> *ITK ERROR: RawImageIO(0000027078EE8D00): File seek failed*
>>
>> Then tried setting header as below
>> rawio.SetHeaderSize(rawio.GetImageSizeInPixels() * 0)
>>
>> and got another error saying
>> *ITK ERROR: RawImageIO(000001A2C02FAB20): Read failed: Wanted 4194304
>> bytes, but read 2097152 bytes.*
>>
>> To read appropriate number of bytes from each file, we need to use an
>> unsigned int (16 bit) type:
>> rawio.SetComponentType(itk.CommonEnums.IOComponent_INT)
>> # Read projections
>> CPUImageType = itk.Image[itk.US,3]
>> proj = rtk.projections_reader(ttype=CPUImageType,
>> file_names=fileNames,ImageIO=rawio, Origin=projOrigin, Spacing=projSpacing)
>>
>> the above changes throws error saying template not found.
>>
>>
>>
>>
>> *No suitable template parameter can be found.Please specify an input via
>> the first argument, the 'ttype' keyword parameter,or via one of the
>> following keyword arguments: Input, InputImage, Input1*
>>
>> Regards,
>> Akshara
>>
>>
>>
>> On Wed, 12 Jul 2023 at 22:22, Simon Rit <simon.rit at creatis.insa-lyon.fr>
>> wrote:
>>
>>> Check this archive on the mailing list:
>>>
>>> https://www.creatis.insa-lyon.fr/pipermail/rtk-users/2023-January/001921.html
>>> ProjectionsReader supports any input raw but converts it to the required
>>> output, i.e., float or double.
>>>
>>> On Wed, Jul 12, 2023 at 2:06 PM Akshara P K <akshara at advitech.in> wrote:
>>>
>>>> Hi Simon,
>>>> Thank you for pointing that out. We made some corrections in the gantry
>>>> angle.
>>>> There was a bug in assuming the axis setting of ProjectionsReader
>>>> origin too. All those are corrected and reconstruction works perfectly fine
>>>> now.
>>>>
>>>> Currently we are reading projections as .tif images but ultimately we
>>>> need to read .raw images and apply reconstruction on them.
>>>> We have 512 unsigned short projections in .raw format each of with
>>>> 1024x1024 dimensions.
>>>> It seems unsigned short is not supported by ProjectionsReader.
>>>>
>>>> Two possible methods that we can think of:
>>>> 1. Read projections with ImageSeriesReader which supports unsigned
>>>> short, converts data to float and feeds to ProjectionsReader.
>>>>    If so, is there a method to set manipulated input to
>>>> ProjectionsReader? From the literature, only SetFileNames is possible.
>>>> 2. Is there any alternative method to convert projections to line
>>>> integral without using ProjectionsReader.
>>>>
>>>> Looking forward to your suggestions.
>>>>
>>>> Regards,
>>>> Akshara
>>>>
>>>> On Tue, 11 Jul 2023 at 02:09, Simon Rit <simon.rit at creatis.insa-lyon.fr>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>> The folder does not contain the angle.bin file. I looked at the
>>>>> projections. Maybe it's because the teeth are far from the central slice,
>>>>> where data are missing? This is known to cause problems, in particular for
>>>>> short scans.
>>>>> Simon
>>>>>
>>>>> On Mon, Jul 10, 2023 at 9:14 PM Akshara P K <akshara at advitech.in>
>>>>> wrote:
>>>>>
>>>>>> Hi Simon,
>>>>>>
>>>>>> Cuda PSSF is working fine with the wheel file you shared. But it
>>>>>> looks like something I missed from the reconstruction process and the
>>>>>> result is not up to mark as I expected.
>>>>>> The result looks like as below:
>>>>>> [image: image.png]
>>>>>> [image: image.png]
>>>>>> and the expected is more or less something like below:
>>>>>>
>>>>>> [image: image.png]
>>>>>>
>>>>>>
>>>>>> The input projections and the parameter file (Which I used to fill
>>>>>> the input parameters) are available here:
>>>>>>
>>>>>> https://drive.google.com/drive/folders/13EC2Lusyrx3HvkKJL80aSBHfled0FduT?usp=sharing
>>>>>>
>>>>>> Can you please check and provide your valuable suggestions on how I
>>>>>> can improve the result.
>>>>>>
>>>>>> Here is the updated code:
>>>>>>
>>>>>> # Defines the image type
>>>>>> ImageType = itk.Image[itk.F,3]
>>>>>> GPUImageType = itk.CudaImage[itk.F,3]
>>>>>>
>>>>>> # Defines the RTK geometry object
>>>>>> geometry = rtk.ThreeDCircularProjectionGeometry.New()
>>>>>> numberOfProjections = 512
>>>>>> firstAngle = -0.54853
>>>>>> angularArc = 270.66079712
>>>>>> sid = 537.09972 # source to isocenter distance
>>>>>> sdd = 908.00674 # source to detector distance
>>>>>> size_x = 1024
>>>>>> size_y = 1024
>>>>>> projOffsetX = -2.06667995
>>>>>> projOffsetY = -0.19235000
>>>>>> outOfPlaneAngle = 0
>>>>>> inPlaneAngle = 0
>>>>>> sourceOffsetX = 0
>>>>>> sourceOffsetY = 0
>>>>>>
>>>>>> angle_path = os.path.join("/skull/","angle.bin")
>>>>>> angles2 = []
>>>>>> with open(angle_path, 'rb') as file:
>>>>>>     while True:
>>>>>>         data = file.read(4)  # Read 4 bytes (32 bits) at a time
>>>>>>         if not data:
>>>>>>             break  # Reached end of file
>>>>>>         value = struct.unpack('f', data)[0]  # Unpack binary data as
>>>>>> a float
>>>>>>         angles2.append(value)
>>>>>> print("Read angles from bin completed")
>>>>>>
>>>>>> for x in angles2:
>>>>>>     geometry.AddProjection(sid,sdd,x,projOffsetX, projOffsetY,
>>>>>> outOfPlaneAngle, inPlaneAngle, sourceOffsetX, sourceOffsetY)
>>>>>>
>>>>>> tiffio = itk.TIFFImageIO.New()
>>>>>>
>>>>>> extension = ".tif"
>>>>>> fileNameFormat = "/binary/raw" + "%04d" + extension
>>>>>> fnames = itk.NumericSeriesFileNames.New()
>>>>>> fnames.SetStartIndex(0)
>>>>>> fnames.SetEndIndex(numberOfProjections-1)
>>>>>> fnames.SetIncrementIndex(1)
>>>>>> fnames.SetSeriesFormat(fileNameFormat)
>>>>>>
>>>>>> ProjectionsReaderType = rtk.ProjectionsReader[ImageType]
>>>>>> projectionsSource = ProjectionsReaderType.New()
>>>>>> projectionsSource.SetImageIO(tiffio)
>>>>>> projectionsSource.SetFileNames(fnames.GetFileNames())
>>>>>> projOrigin = [ -0.42*(size_x-1)/2, 0, -0.42*(size_y-1)/2 ] #input
>>>>>> images are size_x x size_y pixels with a 0.42mm pixel size
>>>>>> projSpacing = [ 0.42, 1, 0.42 ]
>>>>>> projectionsSource.SetOrigin( projOrigin )
>>>>>> projectionsSource.SetSpacing( projSpacing )
>>>>>>
>>>>>> # Graft the projections to an itk::CudaImage
>>>>>> projections = GPUImageType.New()
>>>>>> projectionsSource.Update()
>>>>>>
>>>>>> projections.SetPixelContainer(projectionsSource.GetOutput().GetPixelContainer())
>>>>>> projections.CopyInformation(projectionsSource.GetOutput())
>>>>>>
>>>>>> projections.SetBufferedRegion(projectionsSource.GetOutput().GetBufferedRegion())
>>>>>>
>>>>>> projections.SetRequestedRegion(projectionsSource.GetOutput().GetRequestedRegion())
>>>>>>
>>>>>> ParkerShortScanImageFilterType = rtk.CudaParkerShortScanImageFilter
>>>>>> ParkerFilter = ParkerShortScanImageFilterType.New()
>>>>>> ParkerFilter.SetInput(projections)
>>>>>> ParkerFilter.SetGeometry(geometry)
>>>>>> ParkerFilter.InPlaceOff()
>>>>>>
>>>>>> ConstantImageSourceType = rtk.ConstantImageSource[GPUImageType]
>>>>>> # Create reconstructed image
>>>>>> constantImageSource2 = ConstantImageSourceType.New()
>>>>>> render_x = 512
>>>>>> render_y = 512
>>>>>> sizeOutput = [ render_x, render_y, numberOfProjections ]
>>>>>> origin = [ -(render_x/2.0), 0 , -(render_y/2.0) ]
>>>>>> spacing = [ 1.0, 0.5, 1.0 ]
>>>>>> constantImageSource2.SetOrigin( origin )
>>>>>> constantImageSource2.SetSpacing( spacing )
>>>>>> constantImageSource2.SetSize( sizeOutput )
>>>>>> constantImageSource2.SetConstant(0.)
>>>>>>
>>>>>> #Displaced detector weighting
>>>>>> ddf = rtk.CudaDisplacedDetectorImageFilter.New()
>>>>>> ddf.SetInput(ParkerFilter.GetOutput())
>>>>>> ddf.SetGeometry(geometry)
>>>>>>
>>>>>> # FDK reconstruction
>>>>>> print("Reconstructing...")
>>>>>> FDKGPUType = rtk.CudaFDKConeBeamReconstructionFilter
>>>>>> feldkamp = FDKGPUType.New()
>>>>>> feldkamp.SetInput(0, constantImageSource2.GetOutput())
>>>>>> feldkamp.SetInput(1, ddf.GetOutput())
>>>>>> feldkamp.SetGeometry(geometry)
>>>>>> feldkamp.GetRampFilter().SetTruncationCorrection(0.0)
>>>>>> feldkamp.GetRampFilter().SetHannCutFrequency(0.0)
>>>>>>
>>>>>> # Field-of-view masking
>>>>>> FOVFilterType = rtk.FieldOfViewImageFilter[ImageType, ImageType]
>>>>>> fieldofview = FOVFilterType.New()
>>>>>> fieldofview.SetInput(0, feldkamp.GetOutput())
>>>>>> fieldofview.SetProjectionsStack(feldkamp.GetOutput())
>>>>>> fieldofview.SetGeometry(geometry)
>>>>>>
>>>>>> # Writer
>>>>>> print("Writing output image...")
>>>>>> WriterType = rtk.ImageFileWriter[ImageType]
>>>>>> writer = WriterType.New()
>>>>>> writer.SetFileName("image_output_skull00_ver1.3.tiff")
>>>>>> writer.SetInput(fieldofview.GetOutput())
>>>>>> writer.Update()
>>>>>>
>>>>>> Regards,
>>>>>> Akshara
>>>>>>
>>>>>> On Thu, 6 Jul 2023 at 18:23, Akshara P K <akshara at advitech.in> wrote:
>>>>>>
>>>>>>> Hi Simon,
>>>>>>>
>>>>>>> Thank you for the quick response.
>>>>>>> It works perfectly fine except some warnings as you mentioned.
>>>>>>> Thank you again for the support.
>>>>>>>
>>>>>>> Regards,
>>>>>>> Akshara
>>>>>>>
>>>>>>> On Wed, 5 Jul 2023 at 18:36, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>> Following a recent similar request (see here
>>>>>>>> <https://www.creatis.insa-lyon.fr/pipermail/rtk-users/2023-June/001979.html>),
>>>>>>>> I have added CudaParkerShortScanImageFilter with this PR
>>>>>>>> <https://www.creatis.insa-lyon.fr/pipermail/rtk-users/2023-June/001979.html>.
>>>>>>>> New Python packages are available as artifacts of the CI here
>>>>>>>> <https://github.com/RTKConsortium/RTK/actions/runs/5448263998>. I
>>>>>>>> haven't tested them, let me know whether they work... In any case, I have
>>>>>>>> noticed new warnings when using these wheels which must be fixed (see issue
>>>>>>>> #553 <https://github.com/RTKConsortium/RTK/issues/553>).
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> On Wed, Jul 5, 2023 at 2:20 PM Akshara P K <akshara at advitech.in>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I was trying to use FirstCudaReconstruction.py to reconstruct a
>>>>>>>>> set of tiff projections images using the python binary of itk-rtk. Since
>>>>>>>>> the angle coverage is around 268 degrees, I had to implement a
>>>>>>>>> ParkerShortScanImageFilter between the output of the ProjectionsReader and
>>>>>>>>> the FDK reconstruction and it is working fine with the CPU version of API.
>>>>>>>>> However, the use of CudaParkerShortScanImageFilter causes an error saying
>>>>>>>>> module 'RTK' has no attribute 'CudaParkerShortScanImageFilter' even though
>>>>>>>>> CudaParkerShortScanImageFilter is added and implemented in the cpp version.
>>>>>>>>> Can anyone provide an insight on how to solve this issue?
>>>>>>>>>
>>>>>>>>> Regards,
>>>>>>>>> Akshara
>>>>>>>>> _______________________________________________
>>>>>>>>> Rtk-users mailing list
>>>>>>>>> rtk-users at openrtk.org
>>>>>>>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/rtk-users
>>>>>>>>>
>>>>>>>>
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