id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1949 Problem reading TIFF planes: index out of range chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.9 (2019-05-16) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.9 (2019-05-16) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/JKuo/Desktop/worm1_GutUpper-Airyscan Processing-01.czi"" Unrecognized file suffix '.czi' Unrecognized file suffix '.czi' > open ""C:/Users/JKuo/Desktop/New folder/worm1_GutUpper-Airyscan Processing-01.tif"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 564, in _qt_safe run(session, ""open "" + quote_if_necessary(paths[0])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2632, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 64, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 602, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 473, in open_multiple_data models, status = open_func(session, paths, mname, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 3581, in open_map_format return open_map(session, path, name=name, format=format, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 3202, in open_map smodels, smsg = open_grids(session, sgrids, name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 3301, in open_grids v.update_drawings() File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 708, in update_drawings self.image_levels, self.image_colors = self.initial_image_levels() File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 533, in initial_image_levels mstats = self.matrix_value_statistics() File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1590, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1625, in displayed_matrices matrices.append(self.matrix(read_matrix)) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1140, in matrix m = self.region_matrix(r, read_matrix) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1164, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\data\griddata.py"", line 248, 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\imagej_tiff.py"", line 69, in read_matrix a = pi.planes_data(klist, cc, ch, self.time) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\data\imagestack\imagej_tiff.py"", line 186, in planes_data a = tif.asarray(key = plist) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 2112, in asarray pages = self.pages._getlist(key) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3419, in _getlist self.keyframe = next(key) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3259, in keyframe self._keyframe = self._getitem(index) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3457, in _getitem self._seek(key) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3381, in _seek raise IndexError('index out of range') IndexError: index out of range IndexError: index out of range File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3381, in _seek raise IndexError('index out of range') See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 3551, in _update_drawings v.update_drawings() File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 708, in update_drawings self.image_levels, self.image_colors = self.initial_image_levels() File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 533, in initial_image_levels mstats = self.matrix_value_statistics() File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1590, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1625, in displayed_matrices matrices.append(self.matrix(read_matrix)) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1140, in matrix m = self.region_matrix(r, read_matrix) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1164, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\data\griddata.py"", line 248, 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\imagej_tiff.py"", line 69, in read_matrix a = pi.planes_data(klist, cc, ch, self.time) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\data\imagestack\imagej_tiff.py"", line 186, in planes_data a = tif.asarray(key = plist) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 2112, in asarray pages = self.pages._getlist(key) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3419, in _getlist self.keyframe = next(key) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3259, in keyframe self._keyframe = self._getitem(index) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3457, in _getitem self._seek(key) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3381, in _seek raise IndexError('index out of range') IndexError: index out of range Error processing trigger ""graphics update"": index out of range: IndexError: index out of range File ""C:\Program Files\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3381, in _seek raise IndexError('index out of range') See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 388.13 OpenGL renderer: GeForce GTX 745/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data fixed all ChimeraX