[SCIFIO] Error reading a 32-bit nrrd image via ITK

[Mark Hiner]

Hi Joe,

 Just wanted to let you know I identified that this is an error with
endianness not being handled correctly in the SCIFIO ImageIO.

 I fixed it locally, but found some bugs with how indexed and RGB images
are being handled along the way. Once I have those fixed I'll update the
SCIFIO ImageIO module and let you know.

Thank you for reporting this, and for using the SCIFIO-ITK imageIO!

- Mark

On Tue, Oct 15, 2013 at 3:21 PM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>wrote:

> 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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