error trying to use 3D projection mode with dicom CT + SEG models

[Elaine Meng]

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>  
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

4-24533-segs.zip​

[Elaine Meng]

Added by email2trac

[Tom Goddard]

Fixed.

3d projection mode was not handling blending.