[SCIFIO] SCIFIO post from phsiao at cs.unc.edu requires approval

[Joe Ping-Lin Hsiao]

Hi Mark,

The output dimension is 3, which is equal to the input's dimension. I also
tried "-d 5". Seems to me it doesn't change anything of the output. The
output dimension is still 3 and the pixel values are wrong.

Don't know if this helps. I put the following code after reader->Update()
to check the image's min and max pixel values:

typedef itk::MinimumMaximumImageCalculator <ImageType>
ImageCalculatorFilterType;
ImageCalculatorFilterType::Pointer imageCalculatorFilter =
ImageCalculatorFilterType::New ();
imageCalculatorFilter->SetImage(reader->GetOutput());
imageCalculatorFilter->Compute();
cout << "max intensity " << imageCalculatorFilter->GetMaximum() << endl;
cout << "min intensity " << imageCalculatorFilter->GetMinimum();

The value range is the full range of 'float' from -3.49e38 to 3.49e38,
which seems wrong. But if I comment out reader->SetImageIO(io), the values
look reasonable.

Thanks,
Joe


On Tue, Oct 15, 2013 at 3:50 PM, Mark Hiner <hinerm at gmail.com> wrote:

> Hi Joe,
>
>  Thanks for reporting this issue.
>
> reader->SetImageIO( io );
>>
>
>  Just so you know, this is just disabling SCIFIO I believe, and defaulting
> to the ITK DICOM ImageIO.
>
>  Does the output file have the correct number of total planes? If not, you
> might try "-d 5" just to test. The dimension order is XYCZT but XYZ are the
> dimensions with length more than 1. The SCIFIO plugin is supposed to
> account for that but it could be a bug.
>
>  Otherwise if the dimensions are correct it could be an issue with the
> dataset being interleaved.
>
>  I'll try to look at it soon.
>
> Thanks,
> Mark
>
>
>
> From: Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>
>> To: scifio at scif.io
>> Cc:
>> Date: Tue, 15 Oct 2013 14:29:23 -0400
>> Subject: Error reading a 32-bit nrrd image via ITK
>> I am having trouble using SCIFIO in ITK to read a 32-bit .nrrd image in
>> my own program. The attached is a 32-bit 3-dimensional test image.
>>
>> Then I used the following command to test with the SCIFIO test program:
>>
>> SCIFIOTestDriver.exe itkSCIFIOImageIOTest sample_5.nrrd 123.ome.tiff -w
>> -d 3 -t float
>>
>> The output '123.ome.tiff' has wrong pixel values and looks wrong in
>> ImageJ.
>>
>> After I dig deeper, I found that in in 'itkSCIFIOImageIOTest.cxx', if I
>> comment out this line
>>
>>    reader->SetImageIO( io );
>>
>> to use ITK's default ImageIO, the output image becomes normal.
>>
>> Thanks,
>> Joe
>>
>
>
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