On Thu, Jul 13, 2017 at 5:32 PM, Yaroslav Halchenko <y...@debian.org> 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
