id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1994 Volume cropping: index out of range brandon.scott@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.9 (2019-06-03) Description Cropping down the image to look at a small feature caused an index out of range error. Log: UCSF ChimeraX version: 0.9 (2019-06-03) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Opened multichannel map series cell_CamB_ch0_stack0000_488nm_0000000msec_0003964235msecAbs_COR_decon.tif, 2 channels, 100 images per channel, grid size 602,584,248, pixel 1, shown at step 2, values uint16 > volume #1 projectionMode 3d > ui mousemode rightMode ""crop volume"" > volume #1.1.1 region 30,0,0,601,583,247 > volume #1.1.1 region 30,0,0,601,431,247 > volume #1.1.1 region 30,146,0,601,431,247 > volume #1.1.17 region 30,146,0,250,431,247 > volume #1.1.17 region 30,146,0,199,431,247 > view cofr false Traceback (most recent call last): File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 3554, in _update_drawings v.update_drawings() File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 721, in update_drawings self._keep_displayed_data = self.displayed_matrices() File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1628, in displayed_matrices matrices.append(self.matrix(read_matrix)) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1143, in matrix m = self.region_matrix(r, read_matrix) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py"", line 1167, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) File ""C:\Apps\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:\Apps\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:\Apps\ChimeraX\bin\lib\site- packages\chimerax\map\data\imagestack\imagej_tiff.py"", line 194, in planes_data a = tif.asarray(key = plist) File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 2112, in asarray pages = self.pages._getlist(key) File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3425, in _getlist pages = [getitem(i, validate) for i in key] File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3425, in pages = [getitem(i, validate) for i in key] File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3457, in _getitem self._seek(key) File ""C:\Apps\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:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3381, in _seek raise IndexError('index out of range') See log for complete Python traceback. 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. Traceback (most recent call last): File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\core\updateloop.py"", line 72, in draw_new_frame view.draw(check_for_changes = False) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\core\graphics\view.py"", line 162, in draw self._draw_scene(camera, drawings) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\core\graphics\view.py"", line 227, in _draw_scene draw_transparent(r, transparent_drawings) File ""C:\Apps\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1400, in draw_transparent lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)) File ""C:\Apps\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 1101, in draw_transparent draw() File ""C:\Apps\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1400, in lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)) File ""C:\Apps\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1405, in _draw_multiple d.draw(renderer, draw_pass) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 704, in draw bi.draw(renderer, draw_pass) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 1152, in draw Image3d.draw(self, renderer, draw_pass) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 714, in draw pd = self._update_planes(renderer) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 484, in _update_planes pd = self._update_view_aligned_planes(view_dir) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 536, in _update_view_aligned_planes pd = self._view_planes() File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 546, in _view_planes pd = ViewAlignedPlanes(self) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 985, in __init__ self._fill_textures() File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 1031, in _fill_textures self.texture = t = self._texture_3d() File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 1040, in _texture_3d td = self._texture_3d_data() File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 1064, in _texture_3d_data td[i,:] = ir._color_plane(k0+i*kstep, z_axis, view_aligned=True) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 1161, in _color_plane dp = ir._color_plane(k, axis, view_aligned=view_aligned, require_color=True) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 206, in _color_plane m = self._matrix_plane(plane, axis) File ""C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\map\image3d.py"", line 188, in _matrix_plane m = self._data.matrix(ijk_origin, ijk_size, ijk_step) File ""C:\Apps\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:\Apps\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:\Apps\ChimeraX\bin\lib\site- packages\chimerax\map\data\imagestack\imagej_tiff.py"", line 194, in planes_data a = tif.asarray(key = plist) File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 2112, in asarray pages = self.pages._getlist(key) File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3419, in _getlist self.keyframe = next(key) File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3259, in keyframe self._keyframe = self._getitem(index) File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3457, in _getitem self._seek(key) File ""C:\Apps\ChimeraX\bin\lib\site-packages\tifffile\tifffile.py"", line 3381, in _seek raise IndexError('index out of range') IndexError: index out of range OpenGL version: 3.3.0 NVIDIA 430.86 OpenGL renderer: Quadro M4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data can't reproduce all ChimeraX