Volume color, ValueError: The truth value of an array with more than one element is ambiguous.

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.0.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-02)
Description
Changing image color by clicking volume viewer color button.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-12-02)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/data/dicom/11-06-2014-1-96508 format dicom

Opened multi-channel map CHEST CT 4, 10 channels, grid size 512,512,236, pixel
0.576,0.576,1.25, shown at step 1, values int16  
Opened CHEST CT 8, grid size 512,512,213, pixel 0.588,0.588,1.25, shown at
step 1, values int16  

> close

> open /Users/goddard/ucsf/data/dicom/4-24533 format dicom

Opened CHEST CT 4, grid size 512,512,236, pixel 0.576,0.576,1.25, shown at
step 1, values int16  

> volume #1.1.1.1 region 0,0,0,511,511,235 step 2

> volume #1.1.1.1 region 0,0,0,511,511,235 step 2

> volume appearance "Airways II"

> ui mousemode rightMode windowing

> volume #1.1.1.1 level -702.6,0 level -656.3,0.04932 level -498.1,0.2497
level -382.6,0

> volume #1.1.1.1 level -25.32,0 level 20.87,0.04932 level 178.7,0.2497 level
293.9,0

> volume appearance CT_Skin

> volume #1.1.1.1 level -906,1 level -506.4,1 level -188.5,1 level -179.4,1
level -120.4,1 level -15.93,1 level 43.11,1 level 79.44,1 level 111.2,1 level
147.6,1 level 206.6,1 level 252,1 color transparent color #87aba232 color
#e996dc34 color transparent color #ff942878 color transparent color #8000003f
color #9f382968 color #ff5a4687 color #ff0000a6 color #ffff00c7 color
#ffffffe4

> volume #1.1.1.1 level -506.4,1 level -188.5,1 level -179.4,1 level -120.4,1
level -15.93,1 level 43.11,1 level 79.44,1 level 111.2,1 level 147.6,1 level
206.6,1 level 252,1 color #87aba232 color #e996dc34 color transparent color
#ff942878 color transparent color #8000003f color #9f382968 color #ff5a4687
color #ff0000a6 color #ffff00c7 color #ffffffe4

> volume #1.1.1.1 level -188.5,1 level -179.4,1 level -120.4,1 level -15.93,1
level 43.11,1 level 79.44,1 level 111.2,1 level 147.6,1 level 206.6,1 level
252,1 color #e996dc34 color transparent color #ff942878 color transparent
color #8000003f color #9f382968 color #ff5a4687 color #ff0000a6 color
#ffff00c7 color #ffffffe4

> volume #1.1.1.1 level -188.5,1 level -120.4,1 level -15.93,1 level 43.11,1
level 79.44,1 level 111.2,1 level 147.6,1 level 206.6,1 level 252,1 color
#e996dc34 color #ff942878 color transparent color #8000003f color #9f382968
color #ff5a4687 color #ff0000a6 color #ffff00c7 color #ffffffe4

> volume #1.1.1.1 level -120.4,1 level -15.93,1 level 43.11,1 level 79.44,1
level 111.2,1 level 147.6,1 level 206.6,1 level 252,1 color #ff942878 color
transparent color #8000003f color #9f382968 color #ff5a4687 color #ff0000a6
color #ffff00c7 color #ffffffe4

> volume appearance "Airways II"

> volume #1.1.1.1 level -742.1,0 level -683,0.04932 level -481,0.2497 level
-333.5,0

> volume #1.1.1.1 level -742.1,0 level -683,0.04932 level -481,0.2497 level
-333.5,0

> volume #1.1.1.1 level -565.2,0 level -506.1,0.04932 level -304.3,0.2497
level -156.9,0

> volume #1.1.1.1 level -463.6,0 level -437.5,0.04932 level -348.3,0.2497
level -283.1,0

> volume #1.1.1.1 level -463.6,0 level -437.5,0.04932 level -348.3,0.9706
level -283.1,0

> volume #1.1.1.1 level -92.98,0 level -66.82,0.04932 level 22.54,0.9706 level
87.79,0

> ui mousemode rightMode "crop volume"

> volume #1.1.1.1 region 0,0,115,511,511,235

> volume #1.1.1.1 region 0,0,115,511,511,157

> volume #1.1.1.1 region 0,0,115,511,511,197

> volume #1.1.1.1 region 0,0,139,511,511,197

> ui mousemode rightMode windowing

> volume #1.1.1.1 level -226.3,0 level -200.1,0.04932 level -110.5,0.9706
level -45.11,0

> volume #1.1.1.1 step 1

> ui mousemode rightMode windowing

> volume #1.1.1.1 level 407.2,0 level 433.5,0.04932 level 523.3,0.9706 level
588.8,0

> volume #1.1.1.1 level 129.1,0 level 155.4,0.04932 level 245.3,0.9706 level
311,0

> volume #1.1.1.1 level 20.79,0 level 47.13,0.04932 level 137.1,0.9706 level
202.9,0

> volume #1.1.1.1 level -302.3,0 level -275.8,0.04932 level -185.2,0.9706
level -119.1,0

> ui mousemode rightMode "crop volume"

> volume #1.1.1.1 region 0,0,139,511,511,188

> volume #1.1.1.1 region 0,0,156,511,511,188

> volume #1 projectionMode 2d-z

> volume #1.1.1.1 region 0,0,156,511,511,184

> ui mousemode rightMode windowing

> volume #1.1.1.1 level -16.54,0 level 10.06,0.04932 level 100.9,0.9706 level
167.3,0

> volume #1.1.1.1 level 20.41,0 level 35.02,0.04932 level 84.94,0.9706 level
121.4,0

> volume #1.1.1.1 level 34.34,0 level 43.14,0.04932 level 73.2,0.9706 level
95.16,0

> volume #1.1.1.1 level 14.71,0 level 23.52,0.04932 level 53.6,0.9706 level
75.57,0

> volume #1.1.1.1 level -18.23,0 level 1.263,0.04932 level 67.86,0.9706 level
116.5,0

> volume #1.1.1.1 level -69.24,0 level -33.2,0.04932 level 89.95,0.9706 level
179.9,0

> volume #1.1.1.1 region 0,0,170,511,511,170 step 1

> ui mousemode rightMode windowing

> volume #1.1.1.1 level -304.9,0 level -268.7,0.04932 level -145.3,0.9706
level -55.1,0

> volume #1.1.1.1 level -240.4,0 level -225.2,0.04932 level -173.2,0.9706
level -135.2,0

> volume #1.1.1.1 level -40.47,0 level -25.27,0.04932 level 26.67,0.9706 level
64.59,0

> volume #1.1.1.1 level -52.47,0 level -37.39,0.04932 level 14.14,0.9706 level
51.77,0

> volume #1.1.1.1 level -20.26,0 level -5.011,0.04932 level 47.07,0.9706 level
85.11,0

> ui mousemode rightMode "crop volume"

> volume #1.1.1.1 region 0,0,170,511,511,195

> volume #1.1.1.1 region 0,0,150,511,511,195

> volume #1.1.1.1 region 0,0,150,511,511,178

> ui mousemode rightMode windowing

> volume #1.1.1.1 level -651.7,0 level -636.5,0.04932 level -584.4,0.9706
level -546.4,0

> volume #1.1.1.1 level 45.83,0 level 61.08,0.04932 level 113.2,0.9706 level
151.3,0

> volume #1.1.1.1 level -3.714,0 level 11.53,0.04932 level 63.61,0.9706 level
101.6,0

> color #1 pink

> volume #1 color pink

> volume #1.1.1.1 level -3.714,0 level 11.53,0.04932 level 63.61,0.9706 level
101.6,0 level -641.7,0.04412 color pink color pink color pink color pink color
pink

> volume #1.1.1.1 level -3.714,0 level 11.53,0.04932 level 63.61,0.9706 level
101.6,0 level -641.7,0.04412 level -553.5,0.9706 color pink color pink color
pink color pink color pink color pink

> volume #1.1.1.1 level -3.714,0 level 11.53,0.04932 level 63.61,0.9706 level
101.6,0 level -641.7,0.04412 level -553.5,0.9706 level -443.2,1.11e-16 color
pink color pink color pink color pink color pink color pink color pink

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2564, in _color_chosen  
self.set_threshold_parameters_from_gui(show = True)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2759, in
set_threshold_parameters_from_gui  
if icolors != v.image_colors:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2759, in
set_threshold_parameters_from_gui  
if icolors != v.image_colors:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.2.24
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

Fixed.

The usual non-sense comparing a tuple to a numpy array gave gave a numpy array of bool.