FNNDSC / FNNDSC/med2image

some dcm files do not work

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Dominant language
Python
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Description

in chris/data:

cd data/VWFA_13_02-1691/2015.03.11-033Y-INVESTIGATORS_Kanwisher_Active-3003/

```
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: Converting DICOM image.
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: PatientName: VWFA_13_02
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: PatientAge: 033Y
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: PatientSex: M
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: PatientID: VWFA_13_02
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: SeriesDescription: DIFFUSION_HighRes_60dir_ColorFA
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: ProtocolName: DIFFUSION_HighRes_60dir
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: Converting middle slice in DICOM series: 32
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: Outputfile = ./0046-1.3.12.2.1107.5.2.32.35115.201503111041251465434043.jpg
Traceback (most recent call last):
File "/neuro/users/chris//arch/scripts/med2image.py", line 568, in
C_convert.run()
File "/neuro/users/chris//arch/scripts/med2image.py", line 263, in run
self.slice_save(str_outputFile)
File "/neuro/users/chris//arch/scripts/med2image.py", line 204, in slice_save
pylab.imsave(astr_outputFile, self._Mnp_2Dslice, cmap = cm.Greys_r)
File "/usr/lib/pymodules/python2.7/matplotlib/pyplot.py", line 2182, in imsave
return _imsave(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/image.py", line 1302, in imsave
fig.savefig(fname, dpi=dpi, format=format, transparent=True)
File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 1421, in savefig
self.canvas.print_figure(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 2220, in print_figure
**kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 2008, in print_jpg
buf, size = agg.print_to_buffer()
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 524, in print_to_buffer
FigureCanvasAgg.draw(self)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 451, in draw
self.figure.draw(self.renderer)
File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 1034, in draw
func(*args)
File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/image.py", line 1030, in draw
im = self.make_image(renderer.get_image_magnification())
File "/usr/lib/pymodules/python2.7/matplotlib/image.py", line 999, in make_image
x = self.to_rgba(self._A, bytes=True)
File "/usr/lib/pymodules/python2.7/matplotlib/cm.py", line 248, in to_rgba
raise ValueError("third dimension must be 3 or 4")
ValueError: third dimension must be 3 or 4
```

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the failure from the chris/data path using the affected DICOM series, then inspect med2image.py and its slice_save method around the pylab.imsave call. Done means the series converts without the reported ValueError and produces the expected JPEG output.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli, tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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