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

[Joe Ping-Lin Hsiao]

Thanks, Mike! The pixels values are correct now.


For the same sample image, I also found the SCIFIO reader reports different
'Voxel sizes', which is microns/pixels for x, y, and z, comparing to what I
see from Fiji's Image ->  Show information. If I don't do "reader->SetImageIO(
io );", ITK's DICOM ImageIO actually reports the same value as Fiji's.
Should I create another topic for this issue?



On Wed, Oct 23, 2013 at 4:19 PM, Mark Hiner <hiner at wisc.edu> wrote:

> Hi Joe,
>
>  I made my changes and pushed a new scifio-itk-bridge.jar. I didn't have
> to change the C++ side at all, so all you should have to do is delete the
> "scifio-itk-bridge-1.0.0.jar" in your local $ITK_BUILD/lib/jars, then clean
> and rebuild the SCIFIO module (which should trigger a download of the
> latest jar, but only if it's not already present in $ITK_BUILD/lib/jars).
>
>  You can also manually download<http://jenkins.imagej.net/view/SCIFIO/job/SCIFIOITKBridge/lastSuccessfulBuild/artifact/target/scifio-itk-bridge-1.0.0.jar>and replace the jar if you don't want to rebuild everything.
>
>  Let me know if you have any more problems, or if this fix doesn't work
> for you.
>
> Thanks,
> Mark
>
>
> On Wed, Oct 23, 2013 at 1:31 PM, Mark Hiner <hinerm at gmail.com> wrote:
>
>> 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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