[Rtk-users] Reconstructed Slice save as tiff

[Cyril Mory]

Thanks Chao Wu,

You're right, I was mistaken : the cast filter is not required in this 
case. It is needed, on the other hand, to increase the dimension of an 
image. So in this case, Amjad, you don't need it.

Cyril

On 05/04/2016 02:44 PM, Chao Wu wrote:
> A small add-on (copied from ITK document):
>
> ExtractImageFilter also collapses dimensions so that the input image 
> may have more dimensions than the output image (i.e. 4-D input image 
> to a 3-D output image). To specify what dimensions to collapse, the 
> ExtractionRegion must be specified. For any dimension dim where 
> ExtractionRegion.Size[dim] = 0, that dimension is collapsed. The index 
> to collapse on is specified by ExtractionRegion.Index[dim]. For 
> example, we have a image 4D = a 4x4x4x4 image, and we want to get a 3D 
> image, 3D = a 4x4x4 image, specified as [x,y,z,2] from 4D (i.e. the 
> 3rd "time" slice from 4D). The ExtractionRegion.Size = [4,4,4,0] and 
> ExtractionRegion.Index = [0,0,0,2].
>
> Regards,
> Chao
>
> 2016-05-04 13:27 GMT+02:00 Cyril Mory <cyril.mory at uclouvain.be 
> <mailto:cyril.mory at uclouvain.be>>:
>
>     Hi Amjad,
>
>     You can use an ITK extract filter to extract a region that
>     corresponds to one of your slices (along the axis you want). The 
>     output of the extract filter will be 3D, so you will need to cast
>     it into a 2D images using an ITK cast filter.
>
>     Cyril
>
>
>     On 05/04/2016 11:04 AM, AMJAD N wrote:
>>     Hi all,
>>
>>     I have wrote code for saving output volume stack as *.tiff.
>>     Currently I am getting output of XY axis. What should I do in
>>     order to get the other axes.
>>     My code is shown below.
>>
>>             typedef itk::StreamingImageFilter<FloatImageType,
>>     FloatImageType> StreamerType;
>>     StreamerType::Pointer streamerBP = StreamerType::New();
>>     streamerBP->SetInput(feldkampCUDA->GetOutput());
>>     streamerBP->SetNumberOfStreamDivisions(8);
>>
>>     typedef itk::Image< float, 2 >     Image2DType;
>>     typedef itk::ImageSeriesWriter< FloatImageType, Image2DType >
>>     WriterType;
>>     WriterType::Pointer writer = WriterType::New();
>>     writer->SetInput(streamerBP->GetOutput());
>>
>>     typedef itk::NumericSeriesFileNames  NameGeneratorType;
>>     NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>>     nameGenerator->SetSeriesFormat("Reconstructed_%06d.tif");
>>     nameGenerator->SetStartIndex(0);
>>     nameGenerator->SetEndIndex(sizeOutput[2] - 1); // sizeOutput[2]
>>     is the Z-axis value of //reconstructed volume
>>     nameGenerator->SetIncrementIndex(1);
>>     writer->SetFileNames(nameGenerator->GetFileNames());
>>     writer->SetUseCompression(true);
>>     writer->Update();
>>
>>     PS: My reconstruction works fine.
>>
>>     Thanks and Regards
>>
>>     AMJAD N
>>
>>
>>
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