id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1694 error trying to use 3D projection mode with dicom CT + SEG models Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-02-08) Description error trying to use 3D projection mode with dicom CT + SEG models I opened the data and showed a 3D region, then tried to apply 3D projection mode. This is the same data with SEGs that you've already seen, but for convenience I attach a zip that has just 3 of the segmentation models plus the CT scan. Log: UCSF ChimeraX version: 0.9 (2019-02-08) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/meng/Desktop/4-24533-segs format dicom Opened multi-channel map CHEST CT 4, 4 channels, grid size 512,512,236, pixel 0.576,0.576,1.25, shown at step 1, values int16 > volume #1.1.1.1 region 105,310,139,210,413,188 > view > volume all projectionMode 3d 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 ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 72, in draw_new_frame view.draw(check_for_changes = False) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 159, in draw self._draw_scene(camera, drawings) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 221, in _draw_scene draw_transparent(r, transparent_drawings) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1373, in draw_transparent lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 1043, in draw_transparent draw() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1373, in lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1378, in _draw_multiple d.draw(renderer, draw_pass) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/grayscale.py"", line 241, in draw bi.draw(renderer, draw_pass) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/grayscale.py"", line 633, in draw GrayScaleDrawing.draw(self, renderer, draw_pass) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/grayscale.py"", line 251, in draw pd = self._update_planes(renderer) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/grayscale.py"", line 284, in _update_planes pd = self._update_view_aligned_planes(view_dir) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/grayscale.py"", line 328, in _update_view_aligned_planes pd.load_texture() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/grayscale.py"", line 574, in load_texture self.texture = t = self._texture_3d() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/grayscale.py"", line 579, in _texture_3d td = self._texture_3d_data() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/grayscale.py"", line 587, in _texture_3d_data p = self._color_plane(0, z_axis, view_aligned=True) TypeError: color_plane() got an unexpected keyword argument 'view_aligned' OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation File attachment: 4-24533-segs.zip }}} [attachment:""4-24533-segs.zip""] " defect closed normal Volume Data fixed all ChimeraX