id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2315	fitmap fails when no surface exists	goddard@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-08-13)
Description
Fitting a CT map to another gives this error because no surface has been shown so no surface level exists, and fitmap by default uses the surface level.

Should probably default ""envelope false"" in fitmap if no surface level exists.

Log:
UCSF ChimeraX version: 0.91 (2019-08-13)  
© 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  

> fitmap #1.1.1.1.1 inMap #1.1.1.2

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/cmd_line/tool.py"", line 254, in execute  
cmd.run(cmd_text)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py"", line 2655, in run  
result = ci.function(session, **kw_args)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/fit/fitcmd.py"", line 136, in fitmap  
max_steps, grid_step_min, grid_step_max, log)]  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/fit/fitcmd.py"", line 300, in fit_map_in_map  
points, point_weights = map_fitting_points(v, envelope)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/fit/fitcmd.py"", line 514, in map_fitting_points  
point_to_scene_transform)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/fit/fitmap.py"", line 544, in map_points_and_weights  
points_int = high_indices(m, threshold)  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/fit/fitmap.py"", line 544, in map_points_and_weights  
points_int = high_indices(m, threshold)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

}}}
"	defect	closed	normal		Volume Data		fixed		Elaine Meng				all	ChimeraX