From simon.rit at creatis.insa-lyon.fr  Wed Jan  4 12:23:19 2023
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 4 Jan 2023 13:23:19 +0100
Subject: [Rtk-users] How to use RTK to reconstruction 2D X- ray Scan
 projection images into 2D CT Slice image?
In-Reply-To: <CAKGJ_RWtB+yW+8E2hCi1iAiB3Kos+d7FUV7LcQCmGcsodKqwCw@mail.gmail.com>
References: <CAKGJ_RWtB+yW+8E2hCi1iAiB3Kos+d7FUV7LcQCmGcsodKqwCw@mail.gmail.com>
Message-ID: <CAF0oig3wxd0coZt+amLq5FxmmagTJm2AqUEgQ6KXSOKPCgdbPw@mail.gmail.com>

Hello,
1/ Yes, you can read images in raw format but you need to specify the meta
information for example in python
rawio = itk.RawImageIO.New()
rawio.SetNumberOfDimensions(2)
rawio.SetPixelType(itk.CommonEnums.IOPixel_SCALAR)
rawio.SetComponentType(itk.CommonEnums.IOComponent_FLOAT)
rawio.SetDimensions(0, 256)
rawio.SetDimensions(1, 256)
rawio.SetSpacing(0, 1)
rawio.SetSpacing(1, 1)
rawio.SetByteOrderToLittleEndian()

# List of filenames
fileNames = []
for i in range(100):
    fileNames.append(f'{i}.raw')

# Read projections
CPUImageType = itk.Image[itk.F,3]
proj = rtk.projections_reader(ttype=CPUImageType, file_names=fileNames,
ImageIO=rawio)

2/ We only work in 3D. You can reconstruct one 3D slice by using a size of
1 in the axial direction.
Simon

On Mon, Dec 26, 2022 at 10:40 AM ??? via Rtk-users <
rtk-users at public.kitware.com> wrote:

>
> Hello everyone
>
> I am a newbie in using RTK
>
> I have  two question to ask,
> 1. Can the projectionreader API read images in RAW format data set?
> 2. Which API or method does RTK provide to reconstruct the 2D X-ray scan
> data set projection image into a 2D CT Slice image ?Or is there any other
> reference document that can help me reconstruct CT slices in RTK?
>
> thanks for reply ?BR
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>
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From m10512067 at yuntech.org.tw  Thu Jan  5 09:26:28 2023
From: m10512067 at yuntech.org.tw (=?UTF-8?B?5L2V5piO5ZOy?=)
Date: Thu, 5 Jan 2023 17:26:28 +0800
Subject: [Rtk-users] How to use RTK to reconstruction 2D X- ray Scan
 projection images into 2D CT Slice image?
In-Reply-To: <CAF0oig3wxd0coZt+amLq5FxmmagTJm2AqUEgQ6KXSOKPCgdbPw@mail.gmail.com>
References: <CAKGJ_RWtB+yW+8E2hCi1iAiB3Kos+d7FUV7LcQCmGcsodKqwCw@mail.gmail.com>
 <CAF0oig3wxd0coZt+amLq5FxmmagTJm2AqUEgQ6KXSOKPCgdbPw@mail.gmail.com>
Message-ID: <CAKGJ_RXGsrLtm7XmynXKAEvMm+EduymLsZ36yVhCwh6=GAgSFQ@mail.gmail.com>

Hello Simon

Thanks for your reply,

I also have some question to ask ,

1.  I just tried your suggested code  to implement  projectionreader API ,
in C++ version and use CUDA too,
     but is will be crash on update parameters function ,  What steps am I
doing wrong?

 here is my code :
   ?  ?  ?  ?  ?  ?  ?  ?  ?  ?  ?
 using ImageIOType = itk::RawImageIO<unsigned short, 2>; //unsigned short
  using IutputImageType = itk::CudaImage<float, 3>; //float

  ImageIOType::Pointer io = ImageIOType::New();
  io->SetHeaderSize(2048);
  io->SetNumberOfDimensions(2);
  io->SetPixelType(itk::CommonEnums::IOPixel::SCALAR);
  io->SetDimensions(0, 1152);
  io->SetDimensions(1, 1152);
  io->SetByteOrderToLittleEndian();
  io->SetSpacing(0, 0.25);
  io->SetSpacing(1, 0.25);

  string nametostring = "";
  std::vector<std::string> newfilename(272);
  for (int fna = 1; fna < 273; fna++)
  {
    nametostring = std::to_string(fna);
    newfilename.push_back(subfolder);
    newfilename.push_back("\\");
    newfilename.push_back(nametostring + ".raw");
  }

  using ReaderType = rtk::ProjectionsReader<IutputImageType>;
//OutputImageType CPUimagetype
  ReaderType::Pointer reader = ReaderType::New();

  reader->SetFileNames(newfilename);

  reader->SetImageIO(io);

  reader->Update();  <- Crash on here
---------

2.  You can reconstruct one 3D slice by using a size of 1 in the axial
direction
-->  Do you mean Set Z in the size parameter to 1 ?
      for example --> Size (XYZ)=>(1024,1024,1)
     then I get the reconstruct image like this ?

[image: 250.jpg]


Thanks again in advance for your reply.

BR







Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2023?1?4? ?? ??8:23???

> Hello,
> 1/ Yes, you can read images in raw format but you need to specify the meta
> information for example in python
> rawio = itk.RawImageIO.New()
> rawio.SetNumberOfDimensions(2)
> rawio.SetPixelType(itk.CommonEnums.IOPixel_SCALAR)
> rawio.SetComponentType(itk.CommonEnums.IOComponent_FLOAT)
> rawio.SetDimensions(0, 256)
> rawio.SetDimensions(1, 256)
> rawio.SetSpacing(0, 1)
> rawio.SetSpacing(1, 1)
> rawio.SetByteOrderToLittleEndian()
>
> # List of filenames
> fileNames = []
> for i in range(100):
>     fileNames.append(f'{i}.raw')
>
> # Read projections
> CPUImageType = itk.Image[itk.F,3]
> proj = rtk.projections_reader(ttype=CPUImageType, file_names=fileNames,
> ImageIO=rawio)
>
> 2/ We only work in 3D. You can reconstruct one 3D slice by using a size of
> 1 in the axial direction.
> Simon
>
> On Mon, Dec 26, 2022 at 10:40 AM ??? via Rtk-users <
> rtk-users at public.kitware.com> wrote:
>
>>
>> Hello everyone
>>
>> I am a newbie in using RTK
>>
>> I have  two question to ask,
>> 1. Can the projectionreader API read images in RAW format data set?
>> 2. Which API or method does RTK provide to reconstruct the 2D X-ray scan
>> data set projection image into a 2D CT Slice image ?Or is there any other
>> reference document that can help me reconstruct CT slices in RTK?
>>
>> thanks for reply ?BR
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Jan  5 09:32:40 2023
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 5 Jan 2023 10:32:40 +0100
Subject: [Rtk-users] How to use RTK to reconstruction 2D X- ray Scan
 projection images into 2D CT Slice image?
In-Reply-To: <CAKGJ_RXGsrLtm7XmynXKAEvMm+EduymLsZ36yVhCwh6=GAgSFQ@mail.gmail.com>
References: <CAKGJ_RWtB+yW+8E2hCi1iAiB3Kos+d7FUV7LcQCmGcsodKqwCw@mail.gmail.com>
 <CAF0oig3wxd0coZt+amLq5FxmmagTJm2AqUEgQ6KXSOKPCgdbPw@mail.gmail.com>
 <CAKGJ_RXGsrLtm7XmynXKAEvMm+EduymLsZ36yVhCwh6=GAgSFQ@mail.gmail.com>
Message-ID: <CAF0oig2m0ABshBZzzNk2F2fYde4mU7HhjyxRmjEL-_=SxUoS-g@mail.gmail.com>

Hi,
1. Try to catch the exception on Update to know what is the problem.
2. In RTK, the default rotation axis is Y so I meant Y. See the doc
<http://www.openrtk.org/Doxygen/DocGeo3D.html>.
Simon


On Thu, Jan 5, 2023 at 10:27 AM ??? <m10512067 at yuntech.org.tw> wrote:

>
> Hello Simon
>
> Thanks for your reply,
>
> I also have some question to ask ,
>
> 1.  I just tried your suggested code  to implement  projectionreader API ,
> in C++ version and use CUDA too,
>      but is will be crash on update parameters function ,  What steps am I
> doing wrong?
>
>  here is my code :
>    ?  ?  ?  ?  ?  ?  ?  ?  ?  ?  ?
>  using ImageIOType = itk::RawImageIO<unsigned short, 2>; //unsigned short
>   using IutputImageType = itk::CudaImage<float, 3>; //float
>
>   ImageIOType::Pointer io = ImageIOType::New();
>   io->SetHeaderSize(2048);
>   io->SetNumberOfDimensions(2);
>   io->SetPixelType(itk::CommonEnums::IOPixel::SCALAR);
>   io->SetDimensions(0, 1152);
>   io->SetDimensions(1, 1152);
>   io->SetByteOrderToLittleEndian();
>   io->SetSpacing(0, 0.25);
>   io->SetSpacing(1, 0.25);
>
>   string nametostring = "";
>   std::vector<std::string> newfilename(272);
>   for (int fna = 1; fna < 273; fna++)
>   {
>     nametostring = std::to_string(fna);
>     newfilename.push_back(subfolder);
>     newfilename.push_back("\\");
>     newfilename.push_back(nametostring + ".raw");
>   }
>
>   using ReaderType = rtk::ProjectionsReader<IutputImageType>;
> //OutputImageType CPUimagetype
>   ReaderType::Pointer reader = ReaderType::New();
>
>   reader->SetFileNames(newfilename);
>
>   reader->SetImageIO(io);
>
>   reader->Update();  <- Crash on here
> ---------
>
> 2.  You can reconstruct one 3D slice by using a size of 1 in the axial
> direction
> -->  Do you mean Set Z in the size parameter to 1 ?
>       for example --> Size (XYZ)=>(1024,1024,1)
>      then I get the reconstruct image like this ?
>
> [image: 250.jpg]
>
>
> Thanks again in advance for your reply.
>
> BR
>
>
>
>
>
>
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr> ? 2023?1?4? ?? ??8:23???
>
>> Hello,
>> 1/ Yes, you can read images in raw format but you need to specify the
>> meta information for example in python
>> rawio = itk.RawImageIO.New()
>> rawio.SetNumberOfDimensions(2)
>> rawio.SetPixelType(itk.CommonEnums.IOPixel_SCALAR)
>> rawio.SetComponentType(itk.CommonEnums.IOComponent_FLOAT)
>> rawio.SetDimensions(0, 256)
>> rawio.SetDimensions(1, 256)
>> rawio.SetSpacing(0, 1)
>> rawio.SetSpacing(1, 1)
>> rawio.SetByteOrderToLittleEndian()
>>
>> # List of filenames
>> fileNames = []
>> for i in range(100):
>>     fileNames.append(f'{i}.raw')
>>
>> # Read projections
>> CPUImageType = itk.Image[itk.F,3]
>> proj = rtk.projections_reader(ttype=CPUImageType, file_names=fileNames,
>> ImageIO=rawio)
>>
>> 2/ We only work in 3D. You can reconstruct one 3D slice by using a size
>> of 1 in the axial direction.
>> Simon
>>
>> On Mon, Dec 26, 2022 at 10:40 AM ??? via Rtk-users <
>> rtk-users at public.kitware.com> wrote:
>>
>>>
>>> Hello everyone
>>>
>>> I am a newbie in using RTK
>>>
>>> I have  two question to ask,
>>> 1. Can the projectionreader API read images in RAW format data set?
>>> 2. Which API or method does RTK provide to reconstruct the 2D X-ray scan
>>> data set projection image into a 2D CT Slice image ?Or is there any other
>>> reference document that can help me reconstruct CT slices in RTK?
>>>
>>> thanks for reply ?BR
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>>
>>
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