id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1867 Errors restoring session with TIFF stacks or directly opening them En.Cai@… Tom Goddard "{{{ 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 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. }}} " defect closed normal Volume Data fixed all ChimeraX