parse_and_group error

[satra]

when running parse and group - with master branch - i get an error whose end point is this:

error: unpack requires a string argument of length 2
> /software/python/anaconda/envs/devpype/lib/python2.7/site-packages/dcmstack-0.7.dev-py2.7.egg/dcmstack/extract.py(348)_get_elem_value()
    347             if elem.VM == 1:
--> 348                 return struct.unpack(unpack_vr_map[elem.VR], elem.value)[0]
    349             else:

when i peek i get:

ipdb> elem.VR
'US or SS'
ipdb> unpack_vr_map[elem.VR]
'H'
ipdb> elem.value 
'\x00\x10\x00\x00\x10\x00'
ipdb> elem.VM
1

[moloney]

Best I can tell, this DICOM file must be invalid.

With a VR of "US or SS" we know that each value should have two bytes, and with a VM of 1 we expect a single two byte value.

Could you give some more details? For example which DICOM element this corresponds with and what software created (or last touched) the file.

[satra]

this is the element:

(0028, 1101) Red Palette Color Lookup Table Desc US or SS: '\x00\x10\x00\x00\x10\x00'

https://www.dabsoft.ch/dicom/3/C.7.6.3.1.5/

from reading the description, it looks like it's a tuple

and this is what i can do in the debugger:

struct.unpack(unpack_vr_map[elem.VR]*3, elem.value)
(4096, 0, 16)

and hence my suggested fix.

[moloney]

So it appears that the VM is wrong as it should be 3. Your proposed fix would only return the first value.

I still think the DICOM file is invalid, but I suppose a change that accounts for the VM possibly being wrong would not harm valid files.

[satra]

where does the VM come from? pydicom? or from the file itself? perhaps i can look into that to see if there is an issue.

i can try to use dclunie's tools to check the validity of the file

also i pushed a small change to return the appropriate number of elements.

[moloney]

The VM should come from the file itself. You could also possibly check the output of the 'dcmdump' command from DCMTK.

The updated PR looks reasonable at first glance. I will think about it a little more and then do the pull if I don't see issues.