Opened 2 years ago

Closed 2 years ago

#9736 closed defect (fixed)

Opening point cloud gltf file: Second array dimension must have size 3, got 1

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.5.2-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202308222255 (2023-08-22 22:55:59 UTC)
Description
Opening a GLTF files consisting of a point cloud.  Apparently the triangle array has shape (N) while ChimeraX wants it to have shape (N,1).  And ChimeraX is trying to compute normals which it should only do for actual triangles (ie shape (N,3)).

Log:
UCSF ChimeraX version: 1.7.dev202308222255 (2023-08-22)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/people/li/243vs274_c1_fit03_scale.cxs format
> session

Opened map 256957 points as #2, grid size 356,142,352, pixel 1, shown at level
0.307,0.528,1.05, step 1, values float32  
Opened map 256957 points as #3, grid size 356,142,352, pixel 1, shown at level
0.181,0.368,0.693, step 1, values float32  
Log from Fri Sep 1 18:01:47 2023Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.7.dev202308222255 (2023-08-22)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/people/li/points.py

executed points.py  

> points openPath /Users/goddard/ucsf/people/li/08vs09_c1_energy.npy

1488590 points shown, xyz ranges (-180.0, 180.0) (-89.8, 89.8) (-180.0,
180.0), color range (0, 1)  

> view

> points #1 minValue 0.2

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.7

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.1 range 0.2,0.6

1210284 points shown, xyz ranges (-179.9, 179.9) (-75.2, 75.2) (-179.0,
179.0), color range (0.1, 1)  

> points #1 minValue 0.2 range 0.2,0.6

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.7

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette redblue

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette bluered

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> 0.2:#0000ff,0.6:#ff0000

Invalid "palette" argument: Color must be 3 or 4 comma-separated numbers 0-100  

> points #1 minValue 0.2 range 0.2,0.6 palette 0.2,#0000ff:0.6,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette 0.2,#0000ff00:0.6,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette 0.2,#0000ff80:0.6,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette 0.2,#0000ff80:0.8,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette 0.2,#0000ff80:0.9,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff80:0.6,#ffff00:0.9,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff80:0.6,#ffff0080:0.9,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff80:0.6,#ffff0080:1,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff80:0.6,#ffff0080:2,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff80:0.6,#ffff0080:1.5,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff80:0.6,#ffff0080:1,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff80:0.6,#ffff0080:0.8,#00ff00:1,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff40:0.6,#ffff0080:0.8,#00ff00:1,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range 0.2,0.6 palette
> 0.2,#0000ff40:0.6,#ffff0080:0.8,#00ff00a0:1,#ff0000

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> set bgColor white

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> set bgColor black

> lighting full

> points #1 minValue 0.2 range 0.2,0.6

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> lighting simple

> points #1 minValue 0.5 range 0.2,0.6

166532 points shown, xyz ranges (-45.8, 58.2) (-49.8, 49.8) (-26.3, 26.3),
color range (0.5, 1)  

> points #1 minValue 0.5

166532 points shown, xyz ranges (-45.8, 58.2) (-49.8, 49.8) (-26.3, 26.3),
color range (0.5, 1)  

> points #1 minValue 0.5 range 0.5,0.8

166532 points shown, xyz ranges (-45.8, 58.2) (-49.8, 49.8) (-26.3, 26.3),
color range (0.5, 1)  

> points #1 minValue 0.5 range 0.5,0.7

166532 points shown, xyz ranges (-45.8, 58.2) (-49.8, 49.8) (-26.3, 26.3),
color range (0.5, 1)  

> points #1 minValue 0.5 range 0.5,0.6

166532 points shown, xyz ranges (-45.8, 58.2) (-49.8, 49.8) (-26.3, 26.3),
color range (0.5, 1)  

> points #1 minValue 0.8 range 0.5,0.6

806 points shown, xyz ranges (-10.1, 18.4) (-11.9, 11.9) (-18.5, 18.5), color
range (0.80014, 1)  

> points #1 minValue 0.8

806 points shown, xyz ranges (-10.1, 18.4) (-11.9, 11.9) (-18.5, 18.5), color
range (0.80014, 1)  

> points #1 minValue 0.1

1210284 points shown, xyz ranges (-179.9, 179.9) (-75.2, 75.2) (-179.0,
179.0), color range (0.1, 1)  

> points #1 minValue 0

1488590 points shown, xyz ranges (-180.0, 180.0) (-89.8, 89.8) (-180.0,
180.0), color range (0, 1)  

> points #1 minValue 0.2

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> points #1 minValue 0.2 range .2,.6

988782 points shown, xyz ranges (-171.0, 105.7) (-70.5, 70.5) (-45.6, 45.6),
color range (0.2, 1)  

> open /Users/goddard/ucsf/people/li/points.py

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/scripting.py", line 83, in open_python_script  
code = compile(data, stream.name, 'exec')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/ucsf/people/li/points.py", line 97  
weights = ones((len(xyz),) float32) # weight each point equally.  
^^^^^^^^^^^^^^^^^^^  
SyntaxError: invalid syntax. Perhaps you forgot a comma?  
  
Error opening python file /Users/goddard/ucsf/people/li/points.py  

> open /Users/goddard/ucsf/people/li/points.py

FYI: command is replacing existing command: "points"  
executed points.py  

> points map #1

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/ucsf/people/li/points.py", line 99, in points_map  
from . import volume_from_grid_data  
ImportError: attempted relative import with no known parent package  
  
ImportError: attempted relative import with no known parent package  
  
File "/Users/goddard/ucsf/people/li/points.py", line 99, in points_map  
from . import volume_from_grid_data  
  
See log for complete Python traceback.  
  

> open /Users/goddard/ucsf/people/li/points.py

FYI: command is replacing existing command: "points"  
FYI: command is replacing existing command: "points map"  
executed points.py  

> points map #1

Opened as #2, grid size 277,141,92, pixel 1, shown at step 1, values float32  

> volume #2 level 4.615

> hide #1 models

> volume #2 level 0.6171

> lighting soft

> volume #2 level 1.145

> volume #2 style mesh

> volume #2 level 1.145 level 2.263 color #b2b2b2 color #b2b2b2

> volume #2 color #b2b2b2 color #b2b213

> volume #2 color #b2b21358 color #b2b213

> volume #2 color #b2b2b658 color #b2b213

> volume #2 level 1.145 level 2.263 level 3.752 color #b2b2b658 color #b2b213
> color #b2b2b658

> volume #2 color #b2b2b658 color #b2b213 color #b20eb658

> volume #2 color #b2b2b658 color #b2b213 color #b20eb6fe

> volume #2 level 1.145 level 2.263 level 6.185

> lighting simple

> lighting soft

> lighting full

> lighting soft

> volume #2 style surface

> volume #2 color #b2b2b658 color #b2b21399 color #b20eb6fe

> volume #2 color #b2b2b658 color #b2b21399 color #b2b213

> volume #2 color #b2b2b658 color #b2b21399 color #b21a13

> volume #2 style mesh

> set bgColor white

> set bgColor gray

> set bgColor black

> volume #2 level 0.9753 level 2.263 level 6.185

> show #1 models

> hide #!2 models

> lighting simple

> lighting soft

> lighting simple

> show #!2 models

> hide #1 models

> lighting full

> lighting soft

> hide #!2 models

> show #1 models

> lighting full

> lighting soft

> lighting simple

> close

> points openPath /Users/goddard/ucsf/people/li/243vs274_c1_fit03_scale.star

659304 points shown, xyz ranges (-180.0, 180.0) (-89.9, 89.9) (-180.0, 180.0),
color range (0.062964, 1.0625)  

> points #1 minValue 0.2

484565 points shown, xyz ranges (-180.0, 180.0) (-75.1, 75.1) (-180.0, 180.0),
color range (0.2, 1.0625)  

> points #1 minValue 0.3

256957 points shown, xyz ranges (-177.4, 178.2) (-70.6, 70.7) (-175.9, 175.8),
color range (0.3, 1.0625)  

> points #1 minValue 0.3 range 0.3,0.6

256957 points shown, xyz ranges (-177.4, 178.2) (-70.6, 70.7) (-175.9, 175.8),
color range (0.3, 1.0625)  

> points #1 minValue 0.3 range 0.3,0.7

256957 points shown, xyz ranges (-177.4, 178.2) (-70.6, 70.7) (-175.9, 175.8),
color range (0.3, 1.0625)  

> open /Users/goddard/ucsf/people/li/points.py

FYI: command is replacing existing command: "points"  
FYI: command is replacing existing command: "points map"  
executed points.py  

> points map #1

Opened as #2, grid size 356,142,352, pixel 1, shown at step 1, values float32  

> hide #1 models

> volume #2 style mesh

> volume #2 level 0.307 level 0.6384 color #b2b2b2 color #b2b2b2

> volume #2 level 0.307 level 0.6384 level 1.17 color #b2b2b2 color #b2b2b2
> color #b2b2b2

> volume #2 color #b2b2b2 color #b2b2b2 color #b208b2

> volume #2 color #b2b2b2 color #b2b2b2 color #b20815

> volume #2 color #b2081529 color #b2b2b2 color #b20815

> volume #2 color #b2b11529 color #b2b2b2 color #b20815

> volume #2 color #b2b1b329 color #b2b2b2 color #b20815

> volume #2 color #b2b1b35f color #b2b2b2 color #b20815

> volume #2 color #b2b1b33a color #b2b2b2 color #b20815

> volume #2 color #b2b1b360 color #b2b2b2 color #b20815

> volume #2 color #b2b1b360 color #b2b21d color #b20815

> volume #2 color #b2b1b360 color #b2b21d9d color #b20815

> volume #2 level 0.307 level 0.6384 level 0.952

> lighting soft

> points map #1 sdev 3

Opened as #3, grid size 356,142,352, pixel 1, shown at step 1, values float32  

> volume #3 level 0.2775 level 0.3684 color #ffffb2 color #ffffb2

> volume #3 level 0.2775 level 0.3684 level 0.5915 color #ffffb2 color #ffffb2
> color #ffffb2

> volume #3 style mesh

> volume #3 color #ffffb2 color #ffffb2 color #ff05b2

> volume #3 color #ffffb2 color #ffffb2 color #ff0504

> volume #3 color #ffffb2 color #ffffb25a color #ff0504

> volume #3 level 0.1807 level 0.3684 level 0.5915

> volume #3 color white color #ffffb25a color #ff0504

> volume #3 color #ffffff5c color #ffffb25a color #ff0504

> volume #3 level 0.1807 level 0.3684 level 0.6925

> volume #3 color #ffffff5c color #ffff755a color #ff0504

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> show #1 models

> hide #!3 models

> show #!3 models

> hide #1 models

> show #!2 models

> hide #!3 models

> lighting soft

> volume #2 color #b2b1b360 color #b2b21d9d color #f10815

> volume #2 level 0.307 level 0.6384 level 1.048

> volume #2 level 0.307 level 0.5277 level 1.048

> volume #2 color #b2b1b360 color #fcb21d9d color #f10815

> volume #2 color #b2b1b360 color #fcfa1d9d color #f10815

> volume #2 color #b2b1b360 color #fcfa1d6c color #f10815

> lighting soft

> volume #2 color #b2f9b360 color #fcfa1d6c color #f10815

> volume #2 color #f6f9b360 color #fcfa1d6c color #f10815

> volume #2 color #f6f9fe60 color #fcfa1d6c color #f10815

> volume #2 color #f6f9fe4e color #fcfa1d6c color #f10815

> volume #2 color #f6f9fe27 color #fcfa1d6c color #f10815

> volume #2 color #f6f9fe45 color #fcfa1d6c color #f10815

> show #!2 models

> show #1 models

> lighting simple

> tile

3 models tiled  

> tile columns 3

3 models tiled  

> lighting soft

> tile columns 3 pad .1

Expected a keyword  

> usage tile

tile [models] [columns an integer] [spacingFactor a number] [viewAll true or
false] [independentRotation true or false]  
— tile models onto grid

tile off [models] [viewAll true or false]  
— untile models  

> tile columns 3 space .5

Expected a keyword  

> tile columns 3 spacingFactor .5

3 models tiled  

> tile off

> tile columns 3 spacingFactor .5

3 models tiled  

> lighting soft

> usage material

material [preset] [reflectivity a number] [specularReflectivity a number]
[exponent a number] [ambientReflectivity a number] [transparentCastShadows
true or false] [meshesCastShadows true or false]  
— report or alter material parameters  
preset: one of chimera, default, dull, or shiny  

> transparency #1 50

> transparency #1 1

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/goddard/Desktop/movie1.mp4

Movie saved to /Users/goddard/Desktop/movie1.mp4  
  

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> select add #1

1 model selected  

> view matrix models
> #1,0.9444,-0.098635,-0.31365,27.158,0.087922,0.99496,-0.048157,8.3855,0.31682,0.017903,0.94832,4.7679

> select subtract #1

Nothing selected  

> movie record

> turn y 1 360 models #1 center #1

> turn y 1 360 models #2 center #2

> turn y 1 360 models #3 center #3

> wait 360

> movie encode points.mp4

Movie saved to points.mp4  
  

> save 243vs274_c1_fit03_scale.cxs

——— End of log from Fri Sep 1 18:01:47 2023 ———

opened ChimeraX session  

> open /Users/goddard/ucsf/people/li/points.py

executed points.py  

> close

> points openPath /Users/goddard/ucsf/people/li/08vs09_c1_energy.npy

1488590 points shown, xyz ranges (-180.0, 180.0) (-89.8, 89.8) (-180.0,
180.0), color range (0, 1)  

> lighting simple

> close

> usage points

points [pointsModel] [openPath name of a file to open/read; a name of 'browse'
will bring up a file browser] [xyzColumns xyzColumns] [colorColumn an integer]
[palette a colormap] [range range] [minValue a number] [maxValue a number]  
— Read point cloud data from multi-column text file or numpy array file  
xyzColumns: some integers  
range: some numbers or full

points map pointsModel [sdev a number] [gridSpacing a number]  
— Create a map by placing a Gaussian at each point of a point cloud.  

> points openPath /Users/goddard/ucsf/people/li/243vs274_c1_fit03_scale.npy

659304 points shown, xyz ranges (-180.0, 180.0) (-89.9, 89.9) (-180.0, 180.0),
color range (0.062964, 1.0625)  

> save test.glb

> open test.glb

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/gltf/__init__.py", line 35, in open  
return gltf.read_gltf(session, data, file_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/gltf/gltf.py", line 81, in read_gltf  
mesh_drawings = meshes_as_models(session, j['meshes'], colors, textures, ba,
bv)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/gltf/gltf.py", line 221, in meshes_as_models  
na = surface.calculate_vertex_normals(va, ta)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: Second array dimension must have size 3, got 1  
  
TypeError: Second array dimension must have size 3, got 1  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/gltf/gltf.py", line 221, in meshes_as_models  
na = surface.calculate_vertex_normals(va, ta)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 515.0.0.0.0
      OS Loader Version: 577.140.2~15
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.5.2 (22G91)
      Kernel Version: Darwin 22.6.0
      Time since boot: 18 hours, 18 minutes

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.47.2
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202308222255
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NIHPresets: 1.1.9
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.31.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.41.1
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.7
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.9.1
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6: 6.3.1
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 6.3.1
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.4
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8

Change History (2)

comment:1 by Tom Goddard, 2 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Opening point cloud gltf file: Second array dimension must have size 3, got 1

Also the GLTF point cloud viewed in Quest VR with LookSee suggests that the points have normal vectors when in fact they should not have directional lighting.

comment:2 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

The gltf reader was trying to compute lighting normals for triangle sets and mistakenly tried to do that for dots and mesh lines. I made it not try to compute normals for dots and mesh lines.

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