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QIICR / QuantitativeReporting

Segmentation-based measurements with DICOM import and export of the results.
https://qiicr.gitbooks.io/quantitativereporting-guide
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BUG: referenced image in segmentation is not properly loaded from DICOMDatabase #149

Closed che85 closed 7 years ago

che85 commented 7 years ago

Getting the following error. Segmentation is loaded, but reference image is not.

image 

[DEBUG][Python] 02.03.2017 17:46:49 [Python] (/Users/christian/sources/py/Reporting/Py/DICOMTID1500Plugin.py:117) - DICOM SR TID1500 load()
[DEBUG][Python] 02.03.2017 17:46:49 [Python] (/Users/christian/sources/py/Reporting/Py/DICOMSegmentationPlugin.py:66) - DICOM SEG modality found
[DEBUG][Python] 02.03.2017 17:46:49 [Python] (/Users/christian/sources/py/Reporting/Py/DICOMSegmentationPlugin.py:87) - DICOM SEG load()
[DEBUG][Python] 02.03.2017 17:46:49 [Python] (/Users/christian/sources/py/Reporting/Py/DICOMSegmentationPlugin.py:90) - in load(): uid =
[DEBUG][Python] 02.03.2017 17:46:50 [Python] (/Users/christian/sources/py/Reporting/Py/DICOMSegmentationPlugin.py:142) - number of segmentation files = 2
[DEBUG][Python] 02.03.2017 17:46:50 [Python] (/Users/christian/sources/py/Reporting/Py/DICOMPluginBase.py:33) - Cleaning up temporarily created directory /var/folders/tc/wh9fygxd50d1sl6mmdj68vt80000gn/T/Slicer/QIICR/SEG/2017-03-02_174649/1.2.276.0.7230010.3.1.4.0.88839.1488494012.781924
[DEBUG][Python] 02.03.2017 17:46:51 [Python] (/Users/christian/sources/py/Reporting/Py/DICOMTID1500Plugin.py:164) - in load(): uid =
[DEBUG][Python] 02.03.2017 17:46:51 [Python] (/Users/christian/sources/py/Reporting/Py/DICOMPluginBase.py:33) - Cleaning up temporarily created directory /var/folders/tc/wh9fygxd50d1sl6mmdj68vt80000gn/T/Slicer/QIICR/SR/2017-03-02_174651/1.2.276.0.7230010.3.1.4.0.88840.1488494013.226433
[DEBUG][Qt] 02.03.2017 17:46:49 [] (unknown:0) - Found CommandLine Module, target is  /Users/christian/sources/cpp/Slicer/Build/Slicer-build/lib/Slicer-4.7/cli-modules/segimage2itkimage
[DEBUG][Qt] 02.03.2017 17:46:49 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 02.03.2017 17:46:49 [] (unknown:0) - Convert DICOM SEG into ITK image command line: 

/Users/christian/sources/cpp/Slicer/Build/Slicer-build/lib/Slicer-4.7/cli-modules/segimage2itkimage --inputDICOM /Users/christian/Documents/SlicerDICOMDatabase/dicom/2.16.840.1.113662.4.4168496325.1025305873.7118351817185979330/1.2.276.0.7230010.3.1.3.0.88839.1488494012.781923/1.2.276.0.7230010.3.1.4.0.88839.1488494012.781924 --outputDirectory /var/folders/tc/wh9fygxd50d1sl6mmdj68vt80000gn/T/Slicer/QIICR/SEG/2017-03-02_174649/1.2.276.0.7230010.3.1.4.0.88839.1488494012.781924 --outputType nrrd
[DEBUG][Qt] 02.03.2017 17:46:50 [] (unknown:0) - Convert DICOM SEG into ITK image standard output:

dcmqi repository URL: https://github.com/che85/dcmqi.git revision: 95fc576 tag: v1.0.4-26-g95fc576
Row direction: 0 1 0
Col direction: 0 0 -1
Z direction: -1 0 0
Total frames: 150
Total frames with unique IPP: 95
Total overlapping frames: 55
Origin: [63.245, -133.929, 116.786]
vtkDebugLeaks has found no leaks.
[ERROR][VTK] 02.03.2017 17:46:50 [vtkSlicerCLIModuleLogic (0x6000004919e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Base/QTCLI/vtkSlicerCLIModuleLogic.cxx:2161) - Convert DICOM SEG into ITK image standard error:

E: Invalid value for attribute Segmentation Fractional Type:
[DEBUG][Qt] 02.03.2017 17:46:50 [] (unknown:0) - Convert DICOM SEG into ITK image completed without errors
fedorov commented 7 years ago

E: Invalid value for attribute Segmentation Fractional Type:

this was showing up before, right?

Does this segmentation you are loading reference images?

che85 commented 7 years ago

I am going to try that again with the current nightly build

che85 commented 7 years ago

Ok it's still not loading the referenced image. Need to take a look into this

che85 commented 7 years ago

Getting the following error message:

Warning in DICOM plugin Scalar Volume when examining loadable 202: Measurement Report: There is no pixel data attribute for the DICOM objects, but they might be readable as secondary capture images.  Reference image in series does not contain geometry information.  Please use caution.

@fedorov any idea what's going on here? Any changes in the Scalar Volume Plugin?

cpinter commented 7 years ago

This warning is the result of changes related to http://www.na-mic.org/Bug/view.php?id=4347. Most probably this warning (not error) was already identified before, but now it is shown in the interactor. As there is no other difference, probably this is independent of your issue.

fedorov commented 7 years ago

@che85 it looks like the warning is caused by the scalar volume plugin trying to make sense out of the SR object. It is not expected to be able to do it.

cpinter commented 7 years ago

At the examine step, each plugin looks into the object, and it is normal. If it tries to load it, then it is a problem. I have had similar issues with the DMRI plugin recently.

che85 commented 7 years ago

duplicate of #153