On Mon, Jul 17, 2017 at 2:38 PM, Mathieu Malaterre <[email protected]> wrote: > On Thu, Jul 13, 2017 at 5:32 PM, Yaroslav Halchenko <[email protected]> wrote: >> >> On Thu, 13 Jul 2017, Mathieu Malaterre wrote: >>> Step: >> >>> $ cd /tmp >>> $ wget >>> "https://sourceforge.net/p/gdcm/gdcmdata/ci/master/tree/SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw"; >>> $ mkdir bug >>> $ gdcmconv --raw SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm* bug/raw.dcm >>> $ nib-dicomfs /tmp/bug /tmp/demo >> >>> In another shell: >> >>> $ find /tmp/demo/ >> >> >> Great -- thanks! but seems to work for me just fine > > Right. It seems my steps were missing an important parts. Full steps are as > > $ cd /tmp > $ wget > "https://sourceforge.net/p/gdcm/gdcmdata/ci/master/tree/SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw"; > $ mkdir bug1 > $ gdcmconv --raw SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm* bug1/raw.dcm > $ nib-dicomfs /tmp/bug1 /tmp/demo > $ find /tmp/demo > > At this point output should be clean. Now let's try again with an > intermediate step: > > $ sudo umount /tmp/demo > $ mkdir bug2 > $ cp ~/buggy.dcm bug2/jpeg.dcm > $ nib-dicomfs /tmp/bug2 /tmp/demo > $ find /tmp/demo > > At this point it is expected to get a funky output since it is > explitely mentionned that JPEG is not supported. But now that we have > made nib-dicomfs failed at least once, let's try original steps again: > > $ sudo umount /tmp/demo > $ nib-dicomfs /tmp/bug1 /tmp/demo > $ find /tmp/demo > Traceback (most recent call last): > File "/usr/lib/python2.7/dist-packages/fuse.py", line 362, in __call__ > return apply(self.func, args, kw) > File "/usr/bin/nib-dicomfs", line 141, in getattr > st.st_size = matched_path[0]() > File "/usr/lib/python2.7/dist-packages/nibabel/dft.py", line 156, in > png_size > return len(self.as_png(index=index, scale_to_slice=scale_to_slice)) > File "/usr/lib/python2.7/dist-packages/nibabel/dft.py", line 137, in as_png > data = d.pixel_array.copy() > File "/usr/lib/python2.7/dist-packages/dicom/dataset.py", line 417, > in pixel_array > return self._get_pixel_array() > File "/usr/lib/python2.7/dist-packages/dicom/dataset.py", line 399, > in _get_pixel_array > raise NotImplementedError("Pixel Data is compressed in a format > pydicom does not yet handle. Cannot return array") > NotImplementedError: Pixel Data is compressed in a format pydicom does > not yet handle. Cannot return array > Traceback (most recent call last): > File "/usr/lib/python2.7/dist-packages/fuse.py", line 362, in __call__ > return apply(self.func, args, kw) > File "/usr/bin/nib-dicomfs", line 141, in getattr > st.st_size = matched_path[0]() > File "/usr/lib/python2.7/dist-packages/nibabel/dft.py", line 156, in > png_size > return len(self.as_png(index=index, scale_to_slice=scale_to_slice)) > File "/usr/lib/python2.7/dist-packages/nibabel/dft.py", line 137, in as_png > data = d.pixel_array.copy() > File "/usr/lib/python2.7/dist-packages/dicom/dataset.py", line 417, > in pixel_array > return self._get_pixel_array() > File "/usr/lib/python2.7/dist-packages/dicom/dataset.py", line 399, > in _get_pixel_array > raise NotImplementedError("Pixel Data is compressed in a format > pydicom does not yet handle. Cannot return array") > NotImplementedError: Pixel Data is compressed in a format pydicom does > not yet handle. Cannot return array > > Let me try to find an example of dataset that I can share. > > -M
The original SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm reproduce the symptoms perfectly. Let me know if you can reproduce it now with the complete steps. -M
