id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1606 Singular matrix reading DICOM time series Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-01-14) Description For opening DICOM I haven't been able to specify a whole directory successfully. In this case the attached folder (after unzipping) contains 6 subdirectories, each with a dicom stack. It is subset of the mouse brain data from TCIA. Opening this folder gives a traceback, as shown in the log. Log: UCSF ChimeraX version: 0.9 (2019-01-14) How to cite UCSF ChimeraX > open /Users/meng/Desktop/10-01-2010-339068828-GBMintracranial-631.2 format dicom Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 3405, 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/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 3041, in open_map grids = data.open_file(map_path, file_type = format, verbose = kw.get('verbose')) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/fileformats.py"", line 139, in open_file data = module.open(apath, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.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, verbose = verbose) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/dicom/dicom_grid.py"", line 34, in dicom_grids grids.append(DicomGrid(d)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/dicom/dicom_grid.py"", line 48, in __init__ file_type = 'dicom', channel = channel) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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/3.6/lib/python3.6/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/3.6/lib/python3.6/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/3.6/lib/python3.6/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/3.6/lib/python3.6/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/3.6/lib/python3.6/site- packages/numpy/linalg/linalg.py"", line 532, in inv ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/numpy/linalg/linalg.py"", line 89, in _raise_linalgerror_singular raise LinAlgError(""Singular matrix"") numpy.linalg.linalg.LinAlgError: Singular matrix numpy.linalg.linalg.LinAlgError: Singular matrix File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/numpy/linalg/linalg.py"", line 89, in _raise_linalgerror_singular raise LinAlgError(""Singular matrix"") See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation File attachment: 10-01-2010-339068828-GBMintracranial-631.2.zip }}} [attachment:""10-01-2010-339068828-GBMintracranial-631.2.zip""] " defect closed normal Volume Data fixed all ChimeraX