id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1612 DICOM unsupported value type Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-01-15) Description trying to open DICOM directory, different example and error than before zip file of directory attached Log: > open /Users/meng/Desktop/startup.cxc > alias nucrib car style nucleic x oval width 1.6 thick 1.6 > alias cylinders car style protein modeh tube rad 2 sides 24 > alias licorice car style protein modeh default arrows f x oval width 1 thick 1 > alias rib1 car style modeh def arrows t wid 2 thick 0.4; car style (nucleic|strand) x rect > alias reset view orient; view initial > open presets.cxc > camera ortho > alias lungs vol all style solid; vol lev -902,0.6 lev -305,0.6 col #FF8080 col #FF8080 > alias airways2 vol all style solid btcorr t dimtransparent f; vol all lev -742,0.0 lev -683,0.049 lev -481,0.25 lev -333,0.0 col 0,61,71 col 0,61,71 col 0,61,71 col 0,61,71 > alias aw2alpha vol all style solid btcorr t dimtransparent f; vol all lev -742,0.0 lev -683,0.049 lev -481,0.25 lev -333,0.0 col 0,61,71,0 col 0,61,71,0.2 col 0,61,71,6.2 col 0,61,71,0 executed presets.cxc executed startup.cxc UCSF ChimeraX version: 0.9 (2019-01-15) How to cite UCSF ChimeraX > open /Users/meng/Desktop/11-06-2014-1-96508 format dicom Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2612, in run result = ci.function(session, **kw_args) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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/3.6/lib/python3.6/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/3.6/lib/python3.6/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/3.6/lib/python3.6/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/3.6/lib/python3.6/site- packages/chimerax/core/io.py"", line 457, in open_multiple_data models, status = open_func(session, paths, mname, **kw) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 3411, 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/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 3042, in open_map verbose = kw.get('verbose')) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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/3.6/lib/python3.6/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/3.6/lib/python3.6/site- packages/chimerax/map/data/dicom/dicom_grid.py"", line 29, in dicom_grids d = DicomData(s) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/dicom/dicom_format.py"", line 158, in __init__ self.rescale_slope, self.rescale_intercept) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/dicom/dicom_format.py"", line 239, in numpy_value_type raise ValueError('Unsupported value type, bits_allocated = ', bits_allocated) ValueError: ('Unsupported value type, bits_allocated = ', 1) ValueError: ('Unsupported value type, bits_allocated = ', 1) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/dicom/dicom_format.py"", line 239, in numpy_value_type raise ValueError('Unsupported value type, bits_allocated = ', bits_allocated) See log for complete Python traceback. OpenGL version: 4.1 INTEL-10.36.22 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. File attachment: 11-06-2014-1-96508.zip }}} [attachment:""11-06-2014-1-96508.zip""] " defect closed normal Volume Data fixed all ChimeraX