id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1662	DICOM key error bitsAllocated	Elaine Meng	Tom Goddard	"Narrowed down the problem with the head/neck study.  Within the attached folder (zip), the subdirectories with ""RT Plan""in their names cause the problems.  The ""RT Dose"" and other subdirs seem to be read OK.

from Log:

open 02-20*4 format dicom
Summary of feedback from opening 02-20-2000-522-26564
notes	Missing PixelSpacing, using value 1, /Users/meng/Desktop/02-20-2000-522-26564/4-RT Dose - fx1hetero-4.5.1/000000.dcm
Missing PixelSpacing, using value 1, /Users/meng/Desktop/02-20-2000-522-26564/6-RT Dose - fx2hetero-4.5.2/000000.dcm
Missing PixelSpacing, using value 1, /Users/meng/Desktop/02-20-2000-522-26564/8-RT Dose - totalhetero-4.5.3/000000.dcm
Traceback (most recent call last):
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py"", line 252, in execute
    cmd.run(cmd_text)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py"", line 2615, in run
    result = ci.function(session, **kw_args)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py"", line 41, in open
    from_database=from_database, ignore_cache=ignore_cache, **kw))
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py"", line 117, in open
    models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py"", line 62, in handle_unknown_kw
    return f(*args, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/models.py"", line 598, in open
    session, filenames, format=format, name=name, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/io.py"", line 456, in open_multiple_data
    models, status = open_func(session, paths, mname, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py"", line 3450, in open_map_format
    return open_map(session, stream, name=name, format=format, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py"", line 3066, in open_map
    verbose = kw.get('verbose'))
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/fileformats.py"", line 141, in open_file
    data = module.open(apath, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/__init__.py"", line 20, in open
    return dicom_grids(paths, log = log, verbose = verbose)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/dicom_grid.py"", line 24, in dicom_grids
    d = DicomData(s)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/dicom_format.py"", line 354, in __init__
    self.value_type = numpy_value_type(attrs['BitsAllocated'], attrs['PixelRepresentation'],
KeyError: 'BitsAllocated'

KeyError: 'BitsAllocated'

File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/dicom_format.py"", line 354, in __init__
self.value_type = numpy_value_type(attrs['BitsAllocated'], attrs['PixelRepresentation'],

See log for complete Python traceback."	defect	closed	moderate		Volume Data		fixed						all	ChimeraX