Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#9635 closed defect (nonchimerax)

Read HDF5 during session restore: file signature not found

Reported by: dparrell@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Openinig file saved across two computers. And version of chimera X 1.5 to 1.6.(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Volumes/DP2/2023_PHB_seg/snaps/TS21_Cm.cxs

Opened 1506_G4_20kx_tilt_21_rec_normalize.hdf.mrc as #1, grid size
1694,2674,943, pixel 9.21,9.21,9.21, shown at step 1, values float32  
Opened 1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc__21_IM_2_seg.hdf as #5, grid
size 847,1337,471, pixel 18.4, shown at level 0.184, step 2, values float32  
Opened 1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc__21_OM_2_seg.hdf as #6, grid
size 847,1337,471, pixel 18.4, shown at level 0.113, step 2, values float32  
Opened IM_Clean_TS21.mrc as #7, grid size 847,1337,471, pixel 18.4,18.4,18.4,
shown at level 0.184, step 2, values float32  
Opened TS21_OM_clean.mrc as #8, grid size 847,1337,471, pixel 18.4,18.4,18.4,
shown at level 0.113, step 1, values float32  
Log from Thu Aug 24 11:51:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd /Volumes/DP2/2023_PHB_seg/snaps

Current working directory is: /Volumes/DP2/2023_PHB_seg/snaps  

> open /Volumes/DP2/2023_PHB_seg/Untreated/TS4.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 219, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 400, in grid_data_from_state  
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 471, in open_data  
grids, error_message = opendialog.open_grid_files(paths_and_types,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/opendialog.py", line 27, in open_grid_files  
glist = open_file(path, file_type, log = log)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 159, in open_file  
data = open_func(apath, **okw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 58, in __init__  
f = tables.open_file(path)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/file.py", line 300, in open_file  
return File(filename, mode, title, root_uep, filters, **kwargs)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/file.py", line 750, in __init__  
self._g_new(filename, mode, **params)  
File "tables/hdf5extension.pyx", line 486, in tables.hdf5extension.File._g_new  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "H5F.c", line 620, in H5Fopen  
unable to open file  
File "H5VLcallback.c", line 3502, in H5VL_file_open  
failed to iterate over available VOL connector plugins  
File "H5PLpath.c", line 579, in H5PL__path_table_iterate  
can't iterate over plugins in plugin path '(null)'  
File "H5PLpath.c", line 620, in H5PL__path_table_iterate_process_path  
can't open directory: /usr/local/hdf5/lib/plugin  
File "H5VLcallback.c", line 3351, in H5VL__file_open  
open failed  
File "H5VLnative_file.c", line 97, in H5VL__native_file_open  
unable to open file  
File "H5Fint.c", line 1990, in H5F_open  
unable to read superblock  
File "H5Fsuper.c", line 405, in H5F__super_read  
file signature not found  
  
End of HDF5 error back trace  
  
Unable to open/create file
'/Users/dparrell/Desktop/tomos2/1671_G3_20kx_tilt_4_aligned_rec.mrc_nad.mrc'  
  
opened ChimeraX session  

> open /Volumes/DP2/2023_PHB_seg/Untreated/TS6.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 219, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 400, in grid_data_from_state  
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 471, in open_data  
grids, error_message = opendialog.open_grid_files(paths_and_types,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/opendialog.py", line 27, in open_grid_files  
glist = open_file(path, file_type, log = log)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 159, in open_file  
data = open_func(apath, **okw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 58, in __init__  
f = tables.open_file(path)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/file.py", line 300, in open_file  
return File(filename, mode, title, root_uep, filters, **kwargs)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/file.py", line 750, in __init__  
self._g_new(filename, mode, **params)  
File "tables/hdf5extension.pyx", line 486, in tables.hdf5extension.File._g_new  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "H5F.c", line 620, in H5Fopen  
unable to open file  
File "H5VLcallback.c", line 3502, in H5VL_file_open  
failed to iterate over available VOL connector plugins  
File "H5PLpath.c", line 579, in H5PL__path_table_iterate  
can't iterate over plugins in plugin path '(null)'  
File "H5PLpath.c", line 620, in H5PL__path_table_iterate_process_path  
can't open directory: /usr/local/hdf5/lib/plugin  
File "H5VLcallback.c", line 3351, in H5VL__file_open  
open failed  
File "H5VLnative_file.c", line 97, in H5VL__native_file_open  
unable to open file  
File "H5Fint.c", line 1990, in H5F_open  
unable to read superblock  
File "H5Fsuper.c", line 405, in H5F__super_read  
file signature not found  
  
End of HDF5 error back trace  
  
Unable to open/create file
'/Users/dparrell/Desktop/tomos2/1671_G3_20kx_tilt_6_aligned_rec.mrc_nad.mrc'  
  
opened ChimeraX session  

> open /Volumes/DP2/2023_PHB_seg/Untreated/TS4_IM_Clean.mrc

Opened TS4_IM_Clean.mrc as #1, grid size 827,1259,400, pixel 18.4,18.4,18.4,
shown at step 1, values float32  

> open /Volumes/DP2/2023_PHB_seg/Untreated/TS4_OM_Clean.mrc

Opened TS4_OM_Clean.mrc as #2, grid size 827,1259,400, pixel 18.4,18.4,18.4,
shown at step 1, values float32  

> open
> /Volumes/DP2/2023_PHB_seg/Untreated/tomograms/1671_G3_20kx_tilt_4_aligned_rec_sirt_bin4_preproc.hdf

Opened 1671_G3_20kx_tilt_4_aligned_rec_sirt_bin4_preproc.hdf as #3, grid size
827,1259,400, pixel 18.4,18.4,18.4, shown at step 1, values float32  

> open /Volumes/DP2/2023_PHB_seg/Untreated/tomograms/TS4_PHB.mod

Read IMOD model /Volumes/DP2/2023_PHB_seg/Untreated/tomograms/TS4_PHB.mod,
pixel size 1.841, 1 surfaces  

> open /Volumes/DP2/2023_PHB_seg/Untreated/tomograms/TS4_PP.mod

Read IMOD model /Volumes/DP2/2023_PHB_seg/Untreated/tomograms/TS4_PP.mod,
pixel size 1.841, 1 surfaces  

> open
> /Volumes/DP2/2023_PHB_seg/normalized_tomos/1671_G3_20kx_tilt_4_aligned_rec_normalize.hdf.mrc

Opened 1671_G3_20kx_tilt_4_aligned_rec_normalize.hdf.mrc as #6, grid size
1654,2518,801, pixel 9.21,9.21,9.21, shown at step 1, values float32  

> select add #6

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,352.92,0,1,0,1205.2,0,0,1,3725.5

> view orient

> view matrix models #6,1,0,0,1194.6,0,1,0,2862.1,0,0,1,3725.5

> view matrix models #6,1,0,0,-5876.6,0,1,0,2290.1,0,0,1,3725.5

> volume #6 level -0.2732,0 level 0.5183,0.8 level 1.541,1

[Repeated 1 time(s)]

> volume #6 color black color #b3b3ff color #b3b3ff

> volume #6 level -0.2732,0 level 0.5183,0.8 level 1.541,1

> volume #6 color black color white color #b3b3ff

> volume #6 color black color white color white

> volume #6 level -3.916,0 level 0.5183,0.8 level 1.541,1

> volume #6 level -3.916,0 level 0.5183,0.8 level 2.72,1

> volume #6 level -3.916,0 level 0.1609,1 level 2.72,1

> volume #6 level -3.225,0.25 level 0.1609,1 level 2.72,1

> volume #6 level -3.225,0.25 level 0.6851,0.8971 level 2.72,1

> color #5 #7a81ffff

> color #4 #009051ff

> color #4 #008f00ff

> color #4 #009051ff

> color #3 #76d6ffff models

> color #2 #ffd479ff models

> volume #2 region 0,0,0,826,1258,399 step 4

[Repeated 1 time(s)]

> volume #1 region 0,0,0,826,1258,399 step 4

[Repeated 1 time(s)]

> ui tool show "Hide Dust"

> surface dust #1 size 2497.5

> surface dust #2 size 1165.7

> surface dust #2 size 1205.9

> surface dust #2 size 5350.6

> surface dust #2 size 5259

[Repeated 1 time(s)]

> surface dust #2 size 4367.2

> surface dust #1 size 2583.5

> surface dust #1 size 394.37

> surface dust #1 size 401.24

> surface dust #1 size 713.35

> surface dust #1 size 873.98

> surface dust #1 size 1107.7

> surface dust #1 size 1145.8

> surface dust #1 size 1404.8

> surface dust #1 size 1554.9

> surface dust #1 size 2539.2

> hide #4 models

> hide #5 models

> volume #6 level -3.225,0.25 level 1.218,1 level 2.72,1

> volume #6 level -3.225,0.25 level 0.8348,1 level 2.72,1

> volume #6 level -1.87,0.1176 level 0.8348,1 level 2.72,1

> volume #6 level -1.87,0.1176 level 0.4275,0.8529 level 2.72,1

> view orient

> volume #6 level -1.87,0.1176 level 0.3385,0.9706 level 2.72,1

> volume #6 level -2.292,0.1618 level 0.3385,0.9706 level 2.72,1

> volume #6 level -2.292,0.1618 level 0.391,1 level 2.72,1

> show #4 models

> show #5 models

> color #2 #ffd479ff models

> color #2 #76d6ffff models

> color #1 #ffd479ff models

> view orient

> cd /Volumes/DP2/2023_PHB_seg/snaps

Current working directory is: /Volumes/DP2/2023_PHB_seg/snaps  

> save /Volumes/DP2/2023_PHB_seg/snaps/TS4_Un.cxs

> view orient

> turn Z 90

> surface dust #1 size 2672.4

> surface dust #1 size 4593.1

> save /Users/dparrell/Desktop/image1.png supersample 3

> save /Volumes/DP2/2023_PHB_seg/snaps/TS4_Un.cxs

> close

> open
> /Volumes/DP2/2023_PHB_seg/normalized_tomos/1506_G4_20kx_tilt_21_rec_normalize.hdf.mrc

Opened 1506_G4_20kx_tilt_21_rec_normalize.hdf.mrc as #1, grid size
1694,2674,943, pixel 9.21,9.21,9.21, shown at step 1, values float32  

> open
> /Volumes/DP2/2023_PHB_seg/Cm_treated/tomograms/1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc.hdf

Opened 1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc.hdf as #2, grid size
847,1337,471, pixel 18.4, shown at step 1, values float32  

> open /Volumes/DP2/2023_PHB_seg/Cm_treated/tomograms/TS21_PHB.mod

Read IMOD model /Volumes/DP2/2023_PHB_seg/Cm_treated/tomograms/TS21_PHB.mod,
pixel size 1.841, 1 surfaces  

> open /Volumes/DP2/2023_PHB_seg/Cm_treated/tomograms/TS21_PP.mod

Read IMOD model /Volumes/DP2/2023_PHB_seg/Cm_treated/tomograms/TS21_PP.mod,
pixel size 1.841, 1 surfaces  

> select add #3

1 model selected  

> close #3

> open /Volumes/DP2/2023_PHB_seg/Cm_treated/tomograms/TS21_new.mod

Read IMOD model /Volumes/DP2/2023_PHB_seg/Cm_treated/tomograms/TS21_new.mod,
pixel size 1.841, 1 surfaces  

> open
> /Volumes/DP2/2023_PHB_seg/Cm_treated/segmentations/1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc__21_IM_2_seg.hdf

Opened 1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc__21_IM_2_seg.hdf as #5, grid
size 847,1337,471, pixel 18.4, shown at step 1, values float32  

> open
> /Volumes/DP2/2023_PHB_seg/Cm_treated/segmentations/1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc__21_OM_2_seg.hdf

Opened 1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc__21_OM_2_seg.hdf as #6, grid
size 847,1337,471, pixel 18.4, shown at step 1, values float32  

> volume #5 region 0,0,0,846,1336,470 step 4

[Repeated 1 time(s)]

> volume #6 level 0,0 level 0.5112,0.8 level 2.456,1

> volume #6 region 0,0,0,846,1336,470 step 4

[Repeated 1 time(s)]

> view orient

> turn Z 90

> turn x 90

> volume #2 level -1.051,0 level 2.398,0.8 level 3,1

> select add #1

2 models selected  

> view matrix models #1,1,0,0,-2.5714,0,1,0,199.61,0,0,1,4330.1

> view orient

> turn Z 90

> view matrix models #1,1,0,0,-5835.3,0,1,0,3195,0,0,1,4330.1

> select subtract #1

Nothing selected  

> view orient

> turn Z 90

> close #2

> volume #1 level -0.2559,0 level 0.5028,0.8 level 1.597,1

> volume #1 level -2.01,0 level 0.5028,0.8 level 1.597,1

> volume #1 level -2.01,0 level 0.2632,0.8088 level 1.597,1

> hide #4 models

> show #4 models

> hide #3 models

> volume #5 step 2

> volume #6 step 2

> save /Volumes/DP2/2023_PHB_seg/snaps/TS21_Cm.cxs

> color #3 #009051ff

> color #4 #7a81ffff

> show #3 models

> hide #3 models

> volume #5 change image level 0,0 level 0.3613,0.8 level 3.518,1

> volume #5 color #ffd479

> volume #6 color #76d6ff

> ui tool show "Hide Dust"

> surface dust #5 size 1185.2

> show #3 models

> surface dust #5 size 1268.2

> surface dust #5 size 2626.6

> volume #5 level 0.1671

> volume #5 level 0.1839

> surface dust #6 size 1185.2

> hide #3 models

> hide #4 models

> ui mousemode right "map eraser"

> volume erase #5 center 353.39,11099,4447.4 radius 3017.8

Opened 1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc__21_IM_2_seg.hdf copy as #7,
grid size 847,1337,471, pixel 18.4, shown at step 1, values float32  

> volume #7 step 2

> surface dust #7 size 644.47

> volume erase #7 center -375.16,6224.4,3801 radius 3018

> volume erase #7 center 56.947,11877,7129.8 radius 3018

> surface dust #7 size 655.69

> surface dust #7 size 1290.3

> volume erase #7 center -132.52,2502.2,4827 radius 3018

> volume erase #7 center -243.62,7858,5803.1 radius 3018

> volume erase #7 center -237.14,16472,9284.3 radius 3018

> volume erase #7 center 286.01,14001,1775.7 radius 3018

> volume erase #7 center 2709.7,19176,4930.8 radius 3018

> volume erase #7 center 15825,22722,1233.1 radius 3018

> volume erase #7 center -220.68,8462.3,2290.4 radius 3018

> volume erase #7 center 5751.2,3630.5,8925.8 radius 3018

> volume erase #7 center 7038,8288,5442.2 radius 1464.7

> volume erase #7 center 9670.7,16084,7691.8 radius 1464.7

> volume erase #7 center 7215.8,22860,4919.3 radius 1464.7

> volume erase #7 center 10118,24003,3844.1 radius 1464.7

> save /Volumes/DP2/2023_PHB_seg/snaps/IM_Clean_TS21.mrc models #7

> volume erase #6 center -2188.5,9203.4,2095 radius 5296.6

Opened 1506_G4_20kx_tilt_21_rec_sirt_bin4_preproc__21_OM_2_seg.hdf copy as #8,
grid size 847,1337,471, pixel 18.4, shown at step 1, values float32  

> surface dust #8 size 1851.8

> volume erase #8 center -1292.3,13817,7846.4 radius 5297

> volume erase #8 center -1461.3,3629.6,4269.4 radius 3680.2

> volume erase #8 center -1474.1,15940,1904.4 radius 3680.2

> volume erase #8 center -1371.3,22144,5693.3 radius 3680.2

> volume erase #8 center 16964,21606,7416.4 radius 3680.2

> volume erase #8 center 16810,16619,8461.5 radius 3680.2

> volume erase #8 center 16604,21247,1073.7 radius 3680.2

> volume erase #8 center 17383,16447,1413.1 radius 3680.2

> volume erase #8 center 9470.5,1732.8,9008.6 radius 3680.2

> volume erase #8 center 4529.8,5308.8,9413 radius 3680.2

> volume erase #8 center 1867,8234.4,9411.1 radius 3680.2

> volume erase #8 center 2399.7,20222,5839.1 radius 3680.2

> volume erase #8 center 4723.6,24264,4650.2 radius 3680.2

> volume erase #8 center 9939.8,26483,5712.7 radius 3680.2

> volume erase #8 center 7295,7903,5215.4 radius 1452.4

> save /Volumes/DP2/2023_PHB_seg/snaps/TS21_OM_clean.mrc models #8

> show #3 models

> show #4 models

> view orient

> turn Z 90

[Repeated 2 time(s)]

> save /Volumes/DP2/2023_PHB_seg/snaps/TS21_Cm.cxs

> hide #3 models

> volume #1 level -2.436,0.08824 level 0.2632,0.8088 level 1.597,1

> volume #1 level -2.436,0.08824 level 0.7039,0.8971 level 1.597,1

> volume #1 level -1.478,0.1765 level 0.7039,0.8971 level 1.597,1

> volume #1 level -1.478,0.1765 level 0.6583,0.9265 level 1.597,1

> volume #1 level -1.478,0.1765 level 0.5747,0.9853 level 1.597,1

> volume #1 level -1.478,0.1765 level 0.5747,0.9853 level 1.797,1

[Repeated 1 time(s)]

> volume #1 level -1.478,0.1765 level 0.6887,1 level 1.797,1

> show #3 models

> turn Z 90

[Repeated 3 time(s)]

> turn y 90

[Repeated 1 time(s)]

> turn Z 90

[Repeated 1 time(s)]

> turn y 90

[Repeated 1 time(s)]

> turn Z 90

[Repeated 1 time(s)]

> save /Users/dparrell/Desktop/image2.png supersample 3

> save /Volumes/DP2/2023_PHB_seg/snaps/TS21_Cm.cxs

——— End of log from Thu Aug 24 11:51:21 2023 ———

opened ChimeraX session  

> ui tool show "Scale Bar"

> scalebar

> scalebar 5000 color #000000

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 65, in _update_scalebar  
self._show_scalebar()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 70, in _show_scalebar  
options = self._changed_options()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 92, in _changed_options  
xpos, ypos = self._xpos.value, self._ypos.value  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
ValueError: could not convert string to float: '0..7'  
  
ValueError: could not convert string to float: '0..7'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
  
See log for complete Python traceback.  
  

> scalebar xpos 0.7

> scalebar ypos 0.05

> save /Users/dparrell/Desktop/image4.png supersample 3

> cd /Volumes/DP2/2023_PHB_seg/snaps

Current working directory is: /Volumes/DP2/2023_PHB_seg/snaps  

> save /Volumes/DP2/2023_PHB_seg/snaps/TS21_Cm.cxs

> close

> open /Volumes/DP2/2023_PHB_seg/snaps/TS14_cm.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 219, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 400, in grid_data_from_state  
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/session.py", line 471, in open_data  
grids, error_message = opendialog.open_grid_files(paths_and_types,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/opendialog.py", line 27, in open_grid_files  
glist = open_file(path, file_type, log = log)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 159, in open_file  
data = open_func(apath, **okw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 58, in __init__  
f = tables.open_file(path)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/file.py", line 300, in open_file  
return File(filename, mode, title, root_uep, filters, **kwargs)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/file.py", line 750, in __init__  
self._g_new(filename, mode, **params)  
File "tables/hdf5extension.pyx", line 486, in tables.hdf5extension.File._g_new  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "H5F.c", line 620, in H5Fopen  
unable to open file  
File "H5VLcallback.c", line 3502, in H5VL_file_open  
failed to iterate over available VOL connector plugins  
File "H5PLpath.c", line 579, in H5PL__path_table_iterate  
can't iterate over plugins in plugin path '(null)'  
File "H5PLpath.c", line 620, in H5PL__path_table_iterate_process_path  
can't open directory: /usr/local/hdf5/lib/plugin  
File "H5VLcallback.c", line 3351, in H5VL__file_open  
open failed  
File "H5VLnative_file.c", line 97, in H5VL__native_file_open  
unable to open file  
File "H5Fint.c", line 1990, in H5F_open  
unable to read superblock  
File "H5Fsuper.c", line 405, in H5F__super_read  
file signature not found  
  
End of HDF5 error back trace  
  
Unable to open/create file
'/Users/dparrell/Desktop/tomos2/1506_G4_20kx_tilt_14_rec.mrc_nad.mrc'  
  
opened ChimeraX session  




OpenGL version: 4.1 ATI-4.6.21
OpenGL renderer: AMD Radeon Pro Vega 64X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac Pro
      Model Identifier: iMacPro1,1
      Processor Name: 18-Core Intel Xeon W
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 18
      L2 Cache (per Core): 1 MB
      L3 Cache: 24.8 MB
      Hyper-Threading Technology: Enabled
      Memory: 256 GB
      System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.7.8 (20G1351)
      Kernel Version: Darwin 20.6.0
      Time since boot: 6:11

Graphics/Displays:

    Radeon Pro Vega 64X:

      Chipset Model: Radeon Pro Vega 64X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 16 GB
      Vendor: AMD (0x1002)
      Device ID: 0x686b
      Revision ID: 0x0000
      ROM Revision: 113-D0500D-114
      VBIOS Version: 113-D05001A1XX-021
      Option ROM Version: 113-D05001A1XX-021
      EFI Driver Version: 01.01.114
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LED Cinema Display:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2A11515U6JL 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0
File attachment: TS14_cm.cxs

TS14_cm.cxs​

Attachments (1)

TS14_cm.cxs​ (1013.6 KB ) - added by dparrell@… 2 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

by dparrell@…, 2 years ago

Attachment: TS14_cm.cxs​ added

Added by email2trac

comment:1 by pett, 2 years ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Read HDF5 during session restore: file signature not found

Reported by Daniel Parrell

comment:2 by Tom Goddard, 2 years ago

Resolution: → nonchimerax
Status: assigned → closed

When you try to open a ChimeraX session

open /Volumes/DP2/2023_PHB_seg/snaps/TS14_cm.cxs

it is producing various HDF5 errors. The session file contains paths to several HDF5 files and it appears that at least one of those HDF5 files is corrupted.

To help you see what files it is trying to load you might temporarily rename folders

/Users/dparrell/Desktop/2023_PHB_seg

/Users/dparrell/Desktop/tomo2

When I try to open your .cxs file it asks me to locate a bunch of HDF files in those directories. This may help you figure out which file has been corrupted. Unfortunately the horrible HDF5 error messages don't even tell you which file has the problem.

comment:3 by Tom Goddard, 2 years ago

After renaming the directories try to open the session in ChimeraX and it will ask you to locate each of the missing hdf files and hopefully you can figure out which one is corrupted. If you know the files in that session you can simply try to open each in ChimeraX using File / Open....

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