id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8010 Image stack:tuple index out of range dakoner@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.5rc202211091945 (2022-11-09 19:45:07 UTC) Description Tried to load a volume from a collection of images (pattern image_{t}_{c}_{z}. Received error: File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map_data\imagestack\imagestack_format.py"", line 90, in a = imread([self.paths[k] for k in klist]) IndexError: tuple index out of range which then reported Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\graphics\opengl.py"", line 3034, in __del__ raise OpenGLError('OpenGL texture was not deleted before graphics.Texture destroyed') chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before graphics.Texture destroyed Log: UCSF ChimeraX version: 1.5rc202211091945 (2022-11-09) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open z:\src\microscope_ui\chimerax\image_{t}_{c}.tiff Opened multichannel map series image_{t}_{c}.tiff as #1, 3 channels, 57 images per channel, grid size 10100,3,1, pixel 1, shown at step 1, values uint8 > volume #1.1.1 level 163,0 level 180,0.8 level 191,1 > volume #1.1.1 level 80.01,0 level 180,0.8 level 191,1 > volume #1.2.1 level 201,0 level 219,0.8 level 225,1 > volume #1.2.1 level 93.23,0.03077 level 219,0.8 level 225,1 > volume #1.3.1 level 213,0 level 231,0.8 level 238,1 > volume #1.3.1 level 101.6,0 level 231,0.8 level 238,1 > close all > open z:\src\microscope_ui\chimerax\image_{t}_{c}_{z}.tiff Opened multichannel map series image_{t}_{c}_{z}.tiff as #1, 3 channels, 19 images per channel, grid size 11300,10100,3, pixel 1, shown at step 4, values uint8 An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. tuple index out of range Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\graphics\view.py"", line 177, in draw self._draw_scene(camera, drawings) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\graphics\view.py"", line 254, in _draw_scene draw_transparent(r, transparent_drawings) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1543, in draw_transparent r.draw_transparent( File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 1252, in draw_transparent draw() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1545, in lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1551, in _draw_multiple d.draw(renderer, draw_pass) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 773, in draw bi.draw(renderer, draw_pass) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 1364, in draw Image3d.draw(self, renderer, draw_pass) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 783, in draw pd = self._update_planes(renderer) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 551, in _update_planes pd = self._update_2d_texture_planes(view_dir) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 559, in _update_2d_texture_planes pd = self._texture_2d_planes(axis) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 585, in _texture_2d_planes pd = self._make_planes(axis) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 713, in _make_planes d = Texture2dPlanes(self, axis) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 984, in __init__ self._update_textures(planes) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 1056, in _update_textures textures = [self._plane_texture(k, axis) for k,axis in planes] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 1056, in textures = [self._plane_texture(k, axis) for k,axis in planes] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 1063, in _plane_texture self._fill_plane_texture(k, axis, t) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 1082, in _fill_plane_texture data = ir._color_plane(plane, axis) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 1378, in _color_plane dp = ir._color_plane(k, axis, color_3d=color_3d, require_color=True) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 234, in _color_plane m = self._matrix_plane(plane, axis) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\image3d.py"", line 209, in _matrix_plane m = self._data.matrix(ijk_origin, ijk_size, ijk_step) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map_data\griddata.py"", line 306, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) File ""C:\Program Files\ChimeraX\bin\lib\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 ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map_data\imagestack\imagestack_format.py"", line 106, in read_matrix return self.read_tiff_matrix(ijk_origin, ijk_size, ijk_step, channel, progress) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map_data\imagestack\imagestack_format.py"", line 90, in read_tiff_matrix a = imread([self.paths[k] for k in klist]) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map_data\imagestack\imagestack_format.py"", line 90, in a = imread([self.paths[k] for k in klist]) IndexError: tuple index out of range Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 3034, in __del__ raise OpenGLError('OpenGL texture was not deleted before graphics.Texture destroyed') chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before graphics.Texture destroyed OpenGL version: 3.3.0 NVIDIA 516.40 OpenGL renderer: NVIDIA GeForce RTX 3080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: System manufacturer Model: System Product Name OS: Microsoft Windows 10 Pro (Build 19044) Memory: 68,649,721,856 MaxProcessMemory: 137,438,953,344 CPU: 32 AMD Ryzen 9 3950X 16-Core Processor OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 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 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5rc202211091945 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.0.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.3 prompt-toolkit: 3.0.32 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.0 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.10.0 }}} " defect closed normal Volume Data can't reproduce Eric Pettersen all ChimeraX