Hi Christophe, This is a bug in ChimeraX. I have fixed it in ChimeraX daily builds dated May 4, 2024 and newer. If you rename your file to not include "ch2" in the name then it will work with your current ChimeraX 1.7.1. Your tiff file had in the file name "ch2" and when ChimeraX reads Tiff stacks it looks for "chN" in the file name and assigns that channel number to the open data. In this case it assigned channel 2. But the file only contains a single channel. And that broke the ImageJ reader because it uses the channel number to figure out which 2d planes of the file to extract. So I fixed the code so it does not look at the file name for ImageJ TIFF files. When you get a traceback in ChimeraX you should use the "Report a Bug" button on the error dialog so we get all information about your ChimeraX setup and computer operating system. Tom
On May 3, 2024, at 12:15 AM, Christophe Leterrier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I have two 32-bit tiff stacks (generated by ImageJ) and I try to open both to overlay two channels. When opening the second one or trying to open both at the same time (see paths below), I get the following error with the latest stable and daily ChimeraX macOS versions:
UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open "/Users/christo/Travail/Data NSTORM/230811 Patt#56/Figure 4 Article (actin DNA-Paint bass)/3um aligned 3D/Recs TS ROIs 3um aligned (Gxy4z4)/Roi002_C2_N04_ch1_ph647_bas643_sypto_map_3D_48K_DC1C_(22688,12672)_TS3D.tif" "/Users/christo/Travail/Data NSTORM/230811 Patt#56/Figure 4 Article (actin DNA-Paint bass)/3um aligned 3D/Recs TS ROIs 3um aligned (Gxy4z4)/Roi002_C2_N04_ch2_ph647_bas643_sypto_map_3D_7,63K_DC1C_transfo_(22688,12672)_TS3D.tif"Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 334, in _qt_safe run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + ("" File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 191, in provider_open models, status = collated_open(session, None, paths, data_format, _add_models, log_errors, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/__init__.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 182, in open return open_map(session, path, format=_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 3621, in open_map smodels, smsg = open_grids(session, sgrids, name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 3723, in open_grids v.update_drawings() File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 813, in update_drawings self.image_levels, self.image_colors = self.initial_image_levels() ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 633, in initial_image_levels mstats = self.matrix_value_statistics() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 1734, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 1769, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 1252, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 1276, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/griddata.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/imagestack/imagej_tiff.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 74, in read_matrix a = pi.planes_data(klist, cc, ch, self.time) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/imagestack/imagej_tiff.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 199, in planes_data a = tif.asarray(key = plist) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 4272, in asarray pages = pages._getlist(key) ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 7532, in _getlist pages = [getitem(i, validate=validhash) for i in key] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 7532, in <listcomp> pages = [getitem(i, validate=validhash) for i in key] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 7578, in _getitem self._seek(key) File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 7481, in _seek raise IndexError('index out of range') IndexError: index out of range
IndexError: index out of range
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py <http://chimerax-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versi...>", line 7481, in _seek raise IndexError('index out of range')
See log for complete Python traceback.
Any idea of what is going wrong?
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/