Opened 7 years ago

Closed 7 years ago

#1799 closed defect (fixed)

error reading DICOM SEG models: IndexError: tuple index out of range

Reported by: Elaine Meng Owned by: Tom Goddard
Priority: major Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

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.

Change History (1)

comment:1 by Tom Goddard, 7 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

New code to read dicom maps a plane at a time didn't properly handle multi-frame dicom files.

Unfortunately the new code has made showing this full dicom file at step 2 about 50 times slower (50 seconds vs 1 second). Need to investigate that.

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