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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", line 7481, in _seek
raise IndexError('index out of range')

See log for complete Python traceback.

Any idea of what is going wrong?


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