Opened 4 years ago

Closed 4 years ago

#6479 closed defect (can't reproduce)

Read EMAN HDF: could not broadcast input array from shape

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.13.0-35-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3.dev202109070604 (2021-09-07 06:04:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202109070604 (2021-09-07)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /media/liyahu/cryoEM/3_Tomo/Liya-
> try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__empty_seg_clip.hdf
> /media/liyahu/cryoEM/3_Tomo/Liya-
> try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2_preproc__DLP_seg_clip.hdf

Opened prasad_hexa_grid1_tilt8_bin2__empty_seg_clip.hdf as #1.1, grid size
1960,1024,60, pixel 22.8, shown at level 0.478, step 2, values float32  
Opened prasad_hexa_grid1_tilt8_bin2_preproc__DLP_seg_clip.hdf as #1.2, grid
size 1960,1024,60, pixel 22.8, shown at level 1.13, step 2, values float32  

> volume #1.1 level 0.5255

> volume #1.2 level 1.535

> volume #1.1 level 1.501

> volume #1.1 step 4

> volume #1.1 color #8ae234

> volume #1.1 color #fce94f

> volume #1.1 color deeppink

> volume #1.2 color #73d216

> volume #1.2 step 4

> volume #1.1 level 0.9394

> volume #1.1 level 1.026

> volume #1.1 level 1.241

> open /media/liyahu/cryoEM/3_Tomo/Liya-
> try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf

Opened prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf as #2, grid size
1960,1024,60, pixel 22.8, shown at level 0.918, step 2, values float32  

> volume #2 level 0.9951

> volume #2 level 0.9074

[Repeated 1 time(s)]

> volume #2 level 0.9512

> open /media/liyahu/cryoEM/3_Tomo/Liya-
> try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf

Opened prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf as #3, grid size
1960,1024,60, pixel 22.8, shown at level 0.918, step 2, values float32  

> close #2

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2146, in mousePressEvent  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 365, in select_marker_cb  
cb(self.markers[i])  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2215, in selected_marker_cb  
self.select_data_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 112, in
read_matrix  
array[(k-k0)//kstep,:,:] = plane  
ValueError: could not broadcast input array from shape (512,950) into shape
(512,980)  
  
ValueError: could not broadcast input array from shape (512,950) into shape
(512,980)  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 112, in
read_matrix  
array[(k-k0)//kstep,:,:] = plane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2148, in mouseMoveEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  

> volume #3 level 0.8361

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseReleaseEvent  
self._drag(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2152, in _drag  
cb(event)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2223, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 39, in read_matrix  
self.eman_hdf_data.read_matrix(ijk_origin, ijk_size, ijk_step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 103, in
read_matrix  
f = tables.open_file(self.path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
ValueError: The file '/media/liyahu/cryoEM/3_Tomo/Liya-
try3-20220325/segmentations/prasad_hexa_grid1_tilt8_bin2__MT_seg_clip.hdf' is
already opened. Please close it before reopening. HDF5 v.1.8.5-patch1,
FILE_OPEN_POLICY = 'strict'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/tables/file.py", line 288, in open_file  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Silicon Mechanics
Model: Structura_cryoSPARC-Certified_Config,_Single_Socket
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-1630 v4 @ 3.70GHz
Cache Size: 10240 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       2.3Gi        24Gi        40Mi        35Gi        59Gi
	Swap:         2.0Gi       517Mi       1.5Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation GP102 [TITAN Xp] [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109070604
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.12
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.11.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Read EMAN HDF: could not broadcast input array from shape

comment:2 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

The user opened an EMAN hdf5 map of size 1960 by 1024 by 60 initially displayed at step2 that seemed to work correctly

Opened prasad_hexa_grid1_tilt8_bin2MT_seg_clip.hdf as #3, grid size
1960,1024,60, pixel 22.8, shown at level 0.918, step 2, values float32

They then closed a different map, and tried moving the histogram level of this map getting an error. The code tried to read the map planes of size 980 x 512 (half full size because of step 2), but the PyTables read of the array gave a plane of size 950 x 512 generating an error. Then subsequent threshold changes gave a different error repeatedly because the first error caused the PyTables file to remain open, and apparently it does not allow opening an HDF5 file twice (weird).

I don't know how the read failed. My only guess is the user rewrote the file after it was opened in ChimeraX with a different size. This is so rare a problem I will not spend the time to protect against it unless I see it again.

Note: See TracTickets for help on using tickets.