Reading 2D ImageJ microscopy: IndexError: index out of range

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.dev202211252110 (2022-11-25 21:10:28 UTC)
Description
Error reading 2D ImageJ microscopy.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.6.dev202211252110 (2022-11-25)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/goddard/ucsf/people/orszag/archea_2d/MAX_BSA 1 500 a SegA 1 750
> GAG561 150X_11_MMStack_Pos0.ome.tif - deconvolution-1.tif"

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 175, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 460, in collated_open  
return remember_data_format()  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 431, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 169, in open  
return open_map(session, path, format=_name, **kw)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3597, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3692, in open_grids  
v.update_drawings()  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 791, in update_drawings  
self.image_levels, self.image_colors = self.initial_image_levels()  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 611, in initial_image_levels  
mstats = self.matrix_value_statistics()  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1711, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_tiff.py", line 69, in read_matrix  
a = pi.planes_data(klist, cc, ch, self.time)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_tiff.py", line 194, in
planes_data  
a = tif.asarray(key = plist)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 3957, in asarray  
pages = pages._getlist(key)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 6724, in _getlist  
pages = [getitem(i, validate=validhash) for i in key]  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 6724, in <listcomp>  
pages = [getitem(i, validate=validhash) for i in key]  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 6770, in _getitem  
self._seek(key)  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 6673, in _seek  
raise IndexError('index out of range')  
IndexError: index out of range  
  
IndexError: index out of range  
  
File "/Users/goddard/Desktop/ChimeraX Nov 28
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 6673, in _seek  
raise IndexError('index out of range')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 451.140.1.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 68 days 20:40

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
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    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.43.4
    ChimeraX-AtomicLibrary: 8.0.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
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    ChimeraX-CellPack: 1.0
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    ChimeraX-Contacts: 1.0.1
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    ChimeraX-CoreFormats: 1.1
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    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-Dssp: 2.0
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    ChimeraX-FileHistory: 1.0.1
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    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
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[Tom Goddard]

File from Arthur Charles-Orszag that causes read error, 2D ImageJ, 3 channels

[Tom Goddard]

Fixed.

The code was using zsize equal to the number of tiff pages there is no ImageJ "slices" parameter in the TIFF file. That made it think there were 3 z-planes, but those were in fact the 3 channels. So it incorrectly tried to read 9 planes (3 z, 3 channels). I changed it so if slices is not specified in an ImageJ tiff then it assumes 1 z-plane.