id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1657	DICOM singular matrix error	Elaine Meng	Tom Goddard	"Narrowed this one down to a subset of the QIN LUNG CT data.  Zip file attached. Prioritize as you like!

open R0098 format dicomTraceback (most recent call last):
  File ""/Users/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/dicom_grid.py"", line 43, in dicom_grids
    g = DicomGrid(d)
  File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/dicom_grid.py"", line 58, in __init__
    file_type = 'dicom', time = time, channel = channel)
  File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py"", line 100, in __init__
    self.update_transform()
  File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py"", line 186, in update_transform
    tf, tf_inv = transformation_and_inverse(self.origin, self.step, rsaxes)
  File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py"", line 428, in transformation_and_inverse
    tf_inv = tf.inverse()
  File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/geometry/place.py"", line 187, in inverse
    self._inverse = Place(m34.invert_matrix(self._matrix))
  File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/geometry/matrix.py"", line 130, in invert_matrix
    rinv[:, :] = matrix_inverse(r)
  File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py"", line 551, in inv
    ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
  File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py"", line 97, in _raise_linalgerror_singular
    raise LinAlgError(""Singular matrix"")
numpy.linalg.LinAlgError: Singular matrix

numpy.linalg.LinAlgError: Singular matrix

File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py"", line 97, in _raise_linalgerror_singular
raise LinAlgError(""Singular matrix"")"	defect	closed	moderate		Volume Data		nonchimerax						all	ChimeraX