id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1799 error reading DICOM SEG models: IndexError: tuple index out of range Elaine Meng Tom Goddard "Reading these files was working fine for a while, but another change must have broken it again... for example, trying to open same data as attached to ticket #1612 UCSF ChimeraX version: 0.9 (2019-03-25) open /Users/meng/Desktop/11-06-2014-1-96508 format dicom Traceback (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 253, 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 2616, 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 463, 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/dicom/dicom.py"", line 39, in open_dicom models, msg = dicom_volumes(session, image_series, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom.py"", line 117, in dicom_volumes gmodels, gmsg = open_grids(session, grid_group, gname, **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 3241, in open_grids v.initialize_thresholds() 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 520, in initialize_thresholds s = self.matrix_value_statistics() 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 1629, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) 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 1664, in displayed_matrices matrices.append(self.matrix(read_matrix)) 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 1179, in matrix m = self.region_matrix(r, read_matrix) 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 1203, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) 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 248, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) 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 267, in read_matrix m = self._read_full_planes(ijk_origin, ijk_size, ijk_step, progress) 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 296, in _read_full_planes m2d= self.read_xy_plane(k) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_grid.py"", line 118, in read_xy_plane m = self.dicom_data.read_plane(k, self.time, c) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_format.py"", line 540, in read_plane d = pydicom.dcmread(self.paths[p]) IndexError: tuple index out of range IndexError: tuple index out of range File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_format.py"", line 540, in read_plane d = pydicom.dcmread(self.paths[p]) See log for complete Python traceback. Traceback (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/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) 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 3489, in _update_drawings v.initialize_thresholds() 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 520, in initialize_thresholds s = self.matrix_value_statistics() 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 1629, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) 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 1664, in displayed_matrices matrices.append(self.matrix(read_matrix)) 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 1179, in matrix m = self.region_matrix(r, read_matrix) 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 1203, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) 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 248, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) 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 267, in read_matrix m = self._read_full_planes(ijk_origin, ijk_size, ijk_step, progress) 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 296, in _read_full_planes m2d= self.read_xy_plane(k) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_grid.py"", line 118, in read_xy_plane m = self.dicom_data.read_plane(k, self.time, c) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_format.py"", line 540, in read_plane d = pydicom.dcmread(self.paths[p]) IndexError: tuple index out of range Error processing trigger ""graphics update"": tuple index out of range: IndexError: tuple index out of range File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_format.py"", line 540, in read_plane d = pydicom.dcmread(self.paths[p]) See log for complete Python traceback." defect closed major Volume Data fixed all ChimeraX