Opened 7 years ago

Closed 6 years ago

Last modified 6 years ago

#1867 closed defect (fixed)

Errors restoring session with TIFF stacks or directly opening them

Reported by: En.Cai@… 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:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-17)
Description
I installed the new daily build, and try to open TIFF files. No files were read. 

Log:
UCSF ChimeraX version: 0.9 (2019-04-17)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Yanxin/Box
Sync/Job/Research_Statement/Figure/isolated_cell1.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 594, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/session.py", line 218, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/session.py", line 355, in grid_data_from_state  
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/session.py", line 426, in open_data  
log = session.logger)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/opendialog.py", line 27, in open_grid_files  
glist = open_file(path, file_type, log = log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 151, in open_file  
data = open_func(apath, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/__init__.py", line 22, in open  
if not is_3d_image(paths[0]) and len(paths) > 1:  
IndexError: list index out of range  
  
opened ChimeraX session  

> open "/Users/Yanxin/Box
Sync/Grants/BWF/Interview/Slides/Figures/isolated_cell1.cxs"

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3488, in _update_drawings  
v.update_drawings()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 686, in update_drawings  
self._update_surfaces()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 701, in _update_surfaces  
s.update_surface(show_mesh, ro)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1873, in update_surface  
matrix = v.matrix()  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_grid.py", line 48, in
read_matrix  
m = s.read_matrix(ijk_origin, ijk_size, ijk_step, self.channel, progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 102, in
read_matrix  
return self.read_tiff_matrix(ijk_origin, ijk_size, ijk_step, channel,
progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 88, in
read_tiff_matrix  
a = tif.asarray(key = klist)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 2143, in asarray  
result = stack_pages(pages, out=out, maxworkers=maxworkers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 9691, in stack_pages  
page0.asarray(validate=None) # ThreadPoolExecutor swallows exceptions  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
ValueError: cannot decompress PACKBITS  
  
Error processing trigger "graphics update": cannot decompress PACKBITS:  
ValueError: cannot decompress PACKBITS  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2172, in mousePressEvent  
cb(event)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2230, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 304, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 330, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 374, in
show_using_dialog_settings  
dr.show()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 662, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_grid.py", line 48, in
read_matrix  
m = s.read_matrix(ijk_origin, ijk_size, ijk_step, self.channel, progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 102, in
read_matrix  
return self.read_tiff_matrix(ijk_origin, ijk_size, ijk_step, channel,
progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 88, in
read_tiff_matrix  
a = tif.asarray(key = klist)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 2143, in asarray  
result = stack_pages(pages, out=out, maxworkers=maxworkers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 9691, in stack_pages  
page0.asarray(validate=None) # ThreadPoolExecutor swallows exceptions  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
ValueError: cannot decompress PACKBITS  
  
ValueError: cannot decompress PACKBITS  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2172, in mousePressEvent  
cb(event)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2230, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 304, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 330, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 374, in
show_using_dialog_settings  
dr.show()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 662, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_grid.py", line 48, in
read_matrix  
m = s.read_matrix(ijk_origin, ijk_size, ijk_step, self.channel, progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 102, in
read_matrix  
return self.read_tiff_matrix(ijk_origin, ijk_size, ijk_step, channel,
progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 88, in
read_tiff_matrix  
a = tif.asarray(key = klist)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 2143, in asarray  
result = stack_pages(pages, out=out, maxworkers=maxworkers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 9691, in stack_pages  
page0.asarray(validate=None) # ThreadPoolExecutor swallows exceptions  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
ValueError: cannot decompress PACKBITS  
  
ValueError: cannot decompress PACKBITS  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1859, in <lambda>  
sm.addAction(style, lambda s=style: self.representation_changed_cb(s))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2375, in
representation_changed_cb  
self.set_map_style(v, style)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2395, in set_map_style  
v.show(representation = style, show = v.shown())  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 662, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_grid.py", line 48, in
read_matrix  
m = s.read_matrix(ijk_origin, ijk_size, ijk_step, self.channel, progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 102, in
read_matrix  
return self.read_tiff_matrix(ijk_origin, ijk_size, ijk_step, channel,
progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 88, in
read_tiff_matrix  
a = tif.asarray(key = klist)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 2143, in asarray  
result = stack_pages(pages, out=out, maxworkers=maxworkers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 9691, in stack_pages  
page0.asarray(validate=None) # ThreadPoolExecutor swallows exceptions  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
ValueError: cannot decompress PACKBITS  
  
ValueError: cannot decompress PACKBITS  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
  
See log for complete Python traceback.  
  

> close #1

> open "/Users/Yanxin/Box
Sync/Figures/Fig0/Isolated_cell/BMDC488_SL8_OTI_CD45A647_25_ch0_stack0000_642nm_0000000msec_0009352364msecAbs_decon.tif"

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 464, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1248, in _open_dropped_file  
run(session, 'open %s' % quote_if_necessary(path))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2631, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 602, in open  
session, filenames, format=format, name=name, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 473, in open_multiple_data  
models, status = open_func(session, paths, mname, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3518, in open_map_format  
return open_map(session, stream, name=name, format=format, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3140, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3239, in open_grids  
v.initialize_thresholds()  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_grid.py", line 48, in
read_matrix  
m = s.read_matrix(ijk_origin, ijk_size, ijk_step, self.channel, progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 102, in
read_matrix  
return self.read_tiff_matrix(ijk_origin, ijk_size, ijk_step, channel,
progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 88, in
read_tiff_matrix  
a = tif.asarray(key = klist)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 2143, in asarray  
result = stack_pages(pages, out=out, maxworkers=maxworkers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 9691, in stack_pages  
page0.asarray(validate=None) # ThreadPoolExecutor swallows exceptions  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
ValueError: cannot decompress PACKBITS  
  
ValueError: cannot decompress PACKBITS  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
  
See log for complete Python traceback.  
  

> open "/Users/Yanxin/Box
Sync/Figures/Fig0/Isolated_cell/BMDC488_SL8_OTI_CD45A647_25_ch0_stack0000_642nm_0000000msec_0009352364msecAbs_decon.tif"

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 552, in _qt_safe  
run(session, "open " + quote_if_necessary(paths[0]))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2631, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 602, in open  
session, filenames, format=format, name=name, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 473, in open_multiple_data  
models, status = open_func(session, paths, mname, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3518, in open_map_format  
return open_map(session, stream, name=name, format=format, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3140, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3239, in open_grids  
v.initialize_thresholds()  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_grid.py", line 48, in
read_matrix  
m = s.read_matrix(ijk_origin, ijk_size, ijk_step, self.channel, progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 102, in
read_matrix  
return self.read_tiff_matrix(ijk_origin, ijk_size, ijk_step, channel,
progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 88, in
read_tiff_matrix  
a = tif.asarray(key = klist)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 2143, in asarray  
result = stack_pages(pages, out=out, maxworkers=maxworkers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 9691, in stack_pages  
page0.asarray(validate=None) # ThreadPoolExecutor swallows exceptions  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
ValueError: cannot decompress PACKBITS  
  
ValueError: cannot decompress PACKBITS  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
  
See log for complete Python traceback.  
  

> help help:user/tools/cli.html#history

> open "/Users/Yanxin/Box
Sync/Figures/Fig0/Isolated_cell/BMDC488_SL8_OTI_CD45A647_25_ch0_stack0000_642nm_0000000msec_0009352364msecAbs_decon.tif"

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 552, in _qt_safe  
run(session, "open " + quote_if_necessary(paths[0]))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2631, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 602, in open  
session, filenames, format=format, name=name, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 473, in open_multiple_data  
models, status = open_func(session, paths, mname, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3518, in open_map_format  
return open_map(session, stream, name=name, format=format, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3140, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3239, in open_grids  
v.initialize_thresholds()  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_grid.py", line 48, in
read_matrix  
m = s.read_matrix(ijk_origin, ijk_size, ijk_step, self.channel, progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 102, in
read_matrix  
return self.read_tiff_matrix(ijk_origin, ijk_size, ijk_step, channel,
progress)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/imagestack/imagestack_format.py", line 88, in
read_tiff_matrix  
a = tif.asarray(key = klist)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 2143, in asarray  
result = stack_pages(pages, out=out, maxworkers=maxworkers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 9691, in stack_pages  
page0.asarray(validate=None) # ThreadPoolExecutor swallows exceptions  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
ValueError: cannot decompress PACKBITS  
  
ValueError: cannot decompress PACKBITS  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tifffile/tifffile.py", line 3888, in asarray  
'cannot decompress %s' % self.compression.name)  
  
See log for complete Python traceback.  
  

Window position outside any known screen, using primary screen  




OpenGL version: 4.1 INTEL-10.36.19
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.

Change History (8)

comment:1 by pett, 7 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Errors restoring session with TIFF stacks or directly opening them

comment:2 by Tom Goddard, 7 years ago

Hi En,

The problem opening you ChimeraX session is that the tiff files it is trying to read use a compression scheme called PACKBITS that the TIFF file reader does not handle. Of course, you saved this session before so it should read it since it read it before. But I changed the TIFF file reader in ChimeraX because the one I was using from the Python Image Library had so many problems and limitations. The new one from Chris Gohlke is tifffile.py from Chris Gohlke at the laboratory for fluorescence dynamics has been specifically made for light microscopy, is 5 times faster and handles the weird microscopy formats like 16-bit integers. Your files with PACKBITS compression are the first I have seen that it does not handle.

If your ChimeraX sessions were made with version 0.8 (december 2018) you can open them with that older ChimeraX. If they were made with a newer ChimeraX they probably will not open in the older version 0.8. We used to have some older March 9, 2019 version of ChimeraX that uses the older TIFF reading code. I don't see it on the download page, so I will have to ask my lab what happened to it. I'll see if we can get you a ChimeraX version that opens your sessions.

For a longer term solution, it is difficult because TIFF is a complicated file format and the available file readers all seem to have problems.

Tom

comment:3 by Tom Goddard, 7 years ago

Hi En,

If you have older ChimeraX on your machine it may read these files. You can have multiple versions of ChimeraX installed, they do not conflict with each other.

Tom

comment:4 by Tom Goddard, 7 years ago

Looking at the tifffile code I found it is supposed to handle PACKBITS compression, but it requires an additonal library imagecodecs or imagecodecs-lite to be installed. I put imagecodecs-lite in ChimeraX and tested on a packbits compressed tiff and it is working.

This will hopefully fix your opening of tiff files. Let me know if it works or not. Fix will be in tonight's ChimeraX builds.

I also fixed some other issues. Files with suffix ".tif" were read with tifffile but ones with suffix ".tiff" used Pillow. I made them both use tifffile. Restoring a session with a volume time series it will ask about every single map in the series with a separate dialog if you choose not to replace the maps (ie. no longer have the maps, or not on this computer). Now it will only ask you to locate the first map in the series and if you cancel it won't ask about the others.

comment:5 by Tom Goddard, 7 years ago

Last night's ChimeraX builds failed on Mac and Linux, worked on Windows. So the fix is not yet in the current Mac and Linux ChimeraX.

comment:6 by Tom Goddard, 6 years ago

Do you still get errors in ChimeraX builds from the past 2 weeks opening TIFF files? I added a library needed to decompress TIFF files that I believe should fix the problem, but I do not have an example file with the compression (PACKBITS) your files are using.

comment:7 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

Fixed. Tested with a compressed TIFF file I created, but don't know if reporter's file works.

in reply to:  8 ; comment:8 by En.Cai@…, 6 years ago 

Hi Tom,
Sorry for the late response. I was travelling. 
Yes, the TIFF stacks opens fine now. 
Best,
En
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