Opened 7 years ago

Closed 7 years ago

#1870 closed defect (fixed)

"measure volume" when style isn't surface gives TypeError: Array argument has non-numeric values

Reported by: Elaine Meng Owned by: Tom Goddard
Priority: minor Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Although it is a user error to try to use "measure volume" when the volume is not shown in an isosurface style, the result should be friendlier than the traceback in the Log:

UCSF ChimeraX version: 0.9 (2019-04-18)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open "/Users/meng/Desktop/dicom/tcia/RIDER Lung CT/RIDER-1129164940/11-06-2014-1-96508/4-24533/*.dcm"Opened CHEST CT 4, grid size 512,512,236, pixel 0.576,0.576,1.25, shown at step 1, values int16

info
6 models
#1, 4-24533, shown
#1.1, Patient RIDER-1129164940, shown
#1.1.1, 20060920, shown
#1.1.1.1, CHEST CT 4, shown size 512,512,236, step 1, voxel size 0.57617,0.57617,1.25, level/intensity -1000 (0.00), 300 (0.90), 3000 (1.00), value range -1024 - 1893, value type int16, 0 symmetry operators
#1.1.1.1.1, level 659, shown
#1.1.1.1.2, image, shown

measure volume #1.1.1
Traceback (most recent call last):

File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 253, in execute

cmd.run(cmd_text)

File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2631, in run

result = ci.function(session, kw_args)

File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/surface/area.py", line 73, in measure_volume

v, nholes = enclosed_volume(va, ta)

File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/surface/area.py", line 34, in enclosed_volume

vol, hole_count = enclosed_volume(varray, tarray)

TypeError: Array argument has non-numeric values

TypeError: Array argument has non-numeric values

File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/surface/area.py", line 34, in enclosed_volume
vol, hole_count = enclosed_volume(varray, tarray)

Change History (1)

comment:1 by Tom Goddard, 7 years ago

Resolution: fixed
Status: assignedclosed

Fixed.

Surface that never had geometry set was giving error when measuring volume or area. Now reports 0 volume and area.

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