id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1663	DICOM value error 50 times but 2 found	Elaine Meng	Tom Goddard	"Narrowed down the mouse data to at least one example, attached as zip file. (It may still be a good idea for you to try downloading some of these full studies because you can see possible issues with nonunique or nonhelpful model names. One reason I liked using filename is that the user can see which is which, and they are unique if you also retain the directory hierarchy.)

open dicom/tcia/Mouse-Astrocytoma/TVD_GBM_IC1_070610_19 format dicomTraceback (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 21, in dicom_grids
    series = find_dicom_series(paths, 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_format.py"", line 24, in find_dicom_series
    series.extend(dicom_file_series(dpaths, 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_format.py"", line 53, in dicom_file_series
    s.order_slices()
  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 150, in order_slices
    self._validate_time_series()
  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 168, in _validate_time_series
    % (self.num_times, len(tset), files[0].path, len(files)))
ValueError: DICOM series says it has 50 times but 2 found, /Users/meng/Desktop/dicom/tcia/Mouse-Astrocytoma/TVD_GBM_IC1_070610_19/09-27-2010-338722691-GBMintracranial-369.3/701-3D12SlDyn22sAPTR9TE3-427.3/000009.dcm... 24 files.

ValueError: DICOM series says it has 50 times but 2 found, /Users/meng/Desktop/dicom/tcia/Mouse-Astrocytoma/TVD_GBM_IC1_070610_19/09-27-2010-338722691-GBMintracranial-369.3/701-3D12SlDyn22sAPTR9TE3-427.3/000009.dcm... 24 files.

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 168, in _validate_time_series
% (self.num_times, len(tset), files[0].path, len(files)))

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