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Opened 6 years ago
Closed 6 years ago
#2699 closed defect (duplicate)
Problem with Map Eraser closing models during session close
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.91 (2019-07-27) Description Was looking at a sample in VR (oculus) and then tried to close session so I could load a new view. Log: UCSF ChimeraX version: 0.91 (2019-07-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "D:/WorkDir/Stack 4 - Tomo EDS stack Gen2/Output2bin/ManyElementsinChimeraXquant.cxc" > open Aligned/C_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/C_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\C_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened C_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.157, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #2 style surface color red > volume #2 projectionMode 3d > volume #2 hide > open Aligned/Al_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Al_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Al_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Al_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.255, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #3 style surface color yellow level 0.255 > volume #3 projectionMode 3d > volume #3 show > open Aligned/Fe_Ka_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Fe_Ka_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Fe_Ka_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Fe_Ka_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.512, step 1, values float32 > view orient cofr false > volume voxelSize 1 > volume median #1 binSize 5 > close #1 > volume #4 style surface color red level 0.86 > volume #4 projectionMode 3d > volume #4 show > open Aligned/Ca_Ka_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Ca_Ka_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Ca_Ka_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Ca_Ka_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.157, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #5 style surface color purple level 0.233 > volume #5 projectionMode 3d > volume #5 show > open Aligned/Mg_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Mg_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Mg_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Mg_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.929, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #6 style surface color limegreen transparency 0.66 level 0.435 > volume #6 projectionMode 3d > volume #6 show > open Aligned/Ni_Ka_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Ni_Ka_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Ni_Ka_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Ni_Ka_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.0484, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #7 style surface color limegreen level 0.502 > volume #7 projectionMode 3d > volume #7 show > open Aligned/S_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/S_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\S_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened S_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.21, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #8 style surface color royalblue level 5.56 > volume #8 projectionMode 3d > volume #8 show > open Aligned/Cr_Ka_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Cr_Ka_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Cr_Ka_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Cr_Ka_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.064, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #9 style surface color royalblue level 0.064 > volume #9 projectionMode 3d > volume #9 show > open Aligned/HAADF_reconstruction_cropped.mrc Summary of feedback from opening Aligned/HAADF_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\HAADF_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened HAADF_reconstruction_cropped.mrc, grid size 256,256,256, pixel 0.00391, shown at level 445, step 1, values float32 > volume bin #1 binSize 2 > volume #10 voxelSize 1.0 > view orient cofr false > close #1 > volume #10 style surface color white > volume #10 projectionMode 3d > volume #10 hide > open Aligned/O_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/O_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\O_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened O_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 1.07, step 1, values float32 > volume #1 voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #11 style surface color gray transparency 0.66 level 8.14 > volume #11 projectionMode 3d > volume #11 show > open Aligned/Si_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Si_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Si_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Si_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 1.01, step 1, values float32 > volume #1 voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #12 style image color gray > volume #12 style image level 0.0,0.0 level 0.5,0.9 level 1.76,1.0 > volume #12 projectionMode 3d > volume #12 show > view matrix camera 0.0,0.0,1,287.35,1,0.0,0.0,47.006,0,1,0,53.78 > lighting shadows true intensity 0.5 > cofr 64,50,54 showPivot false executed ManyElementsinChimeraXquant.cxc > vr on started SteamVR rendering VR mode crop volume > volume #3 region 0,0,43,127,127,127 > volume #3 region 0,0,43,127,127,127 > volume #3 region 0,53,43,127,127,127 > volume #3 region 66,53,43,127,127,127 > volume #3 region 66,53,43,127,127,98 > volume #3 region 66,53,43,127,127,54 > volume #3 region 66,53,43,127,75,54 > volume #3 region 66,65,43,127,75,54 > volume #3 region 66,65,43,78,75,54 > volume #3 region 66,68,43,78,75,54 > volume #3 region 68,68,43,78,75,54 > volume #3 region 68,68,46,78,75,54 > volume #3 region 68,68,46,73,75,54 > volume #3 region 68,68,46,73,75,51 > volume #3 region 68,68,46,73,72,51 > volume #3 region 68,68,47,73,72,51 > volume #3 region 68,68,48,73,72,51 > volume #3 region 68,68,47,73,72,51 > volume #3 region 68,70,47,73,72,51 VR mode map eraser VR mode map eraser VR mode zone > measure mapstats Map C_K_reconstruction_cropped.mrc median #2, minimum 0, maximum 0.3238, mean 0.000842, SD 0.01017, RMS 0.01021 Map Al_K_reconstruction_cropped.mrc median #3, minimum 0, maximum 0.001275, mean 1.417e-05, SD 0.0001337, RMS 0.0001344 Map Fe_Ka_reconstruction_cropped.mrc median #4, minimum 0, maximum 0.7762, mean 0.116, SD 0.2221, RMS 0.2506 Map Ca_Ka_reconstruction_cropped.mrc median #5, minimum 0, maximum 0.1224, mean 0.007736, SD 0.0267, RMS 0.0278 Map Mg_K_reconstruction_cropped.mrc median #6, minimum 0, maximum 0.4919, mean 0.04852, SD 0.1015, RMS 0.1125 Map Ni_Ka_reconstruction_cropped.mrc median #7, minimum 0, maximum 0, mean 0, SD 0, RMS 0 Map S_K_reconstruction_cropped.mrc median #8, minimum 0, maximum 0.1886, mean 0.00749, SD 0.02875, RMS 0.02971 Map Cr_Ka_reconstruction_cropped.mrc median #9, minimum 0, maximum 0.3842, mean 0.1092, SD 0.1132, RMS 0.1573 Map HAADF_reconstruction_cropped.mrc binned #10, minimum 0, maximum 2072, mean 25.01, SD 85.11, RMS 88.71 Map O_K_reconstruction_cropped.mrc median #11, minimum 0, maximum 0.4342, mean 0.1082, SD 0.1407, RMS 0.1775 Map Si_K_reconstruction_cropped.mrc median #12, minimum 0, maximum 0.2893, mean 0.02441, SD 0.06262, RMS 0.06721 > volume #3 region 68,70,47,71,72,51 > volume #3 region 68,69,47,71,72,51 > volume #3 region 68,71,47,71,72,51 VR mode crop volume > volume #3 region 68,71,47,71,72,51 > volume #3 region 68,71,47,71,72,51 > volume #3 region 68,71,47,71,72,51 > volume #3 region 68,71,47,71,72,51 VR mode crop volume > volume #3 region 68,71,47,71,74,51 > volume #3 region 68,71,47,71,72,51 > volume #3 region 68,71,47,71,71,51 > volume #3 region 68,69,47,71,69,51 > volume #3 region 68,58,47,71,72,51 > volume #3 region 68,58,47,71,72,67 > volume #3 region 53,58,47,71,72,67 > volume #3 region 53,58,32,71,72,67 > volume #3 region 53,58,32,71,72,67 > volume #3 region 53,0,32,71,72,67 > volume #3 region 53,0,0,71,72,67 > volume #3 region 53,0,0,112,72,67 > volume #3 region 53,0,0,85,72,67 > volume #3 region 53,0,0,104,72,67 > volume #3 region 53,0,0,104,119,67 > volume #3 region 53,48,0,104,119,67 > volume #3 region 53,48,0,104,56,67 > volume #3 region 53,48,0,81,56,67 > volume #3 region 53,48,0,81,56,30 > volume #3 region 53,48,20,81,56,30 > volume #3 region 67,48,20,81,56,30 > volume #3 region 67,48,20,79,56,30 > volume #3 region 67,48,23,79,56,30 > volume #3 region 67,48,23,79,51,30 > volume #3 region 74,48,23,79,51,30 > volume #3 region 74,48,23,79,51,26 > volume #3 region 74,48,23,79,51,26 > volume #3 region 74,48,23,79,51,27 > volume #3 region 74,48,23,79,51,27 > volume #3 region 74,49,23,79,51,27 > volume #3 region 74,49,23,77,51,27 > volume #3 region 74,49,23,77,51,27 > volume #3 region 74,49,23,77,51,25 > volume #3 region 74,49,23,77,51,25 > volume #3 region 74,50,23,77,51,25 > volume #3 region 74,49,23,77,51,25 > volume #3 region 74,49,23,77,51,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 74,49,24,77,52,25 > volume #3 region 74,49,24,77,52,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 74,49,24,77,51,25 > volume #3 region 71,49,24,77,51,25 > volume #3 region 71,49,24,77,51,25 > volume #3 region 71,49,24,77,51,25 > volume #3 region 71,49,24,77,51,27 > volume #3 region 71,49,24,77,51,27 > volume #3 region 71,49,24,77,52,27 > volume #3 region 71,49,24,77,51,27 > volume #3 region 71,49,24,77,51,27 > volume #3 region 74,49,24,77,51,27 > volume #3 region 74,49,24,77,51,27 > volume #3 region 74,49,24,77,51,27 > volume #3 region 74,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,27 > volume #3 region 76,49,24,77,51,26 > volume #3 region 77,49,24,77,51,26 > measure mapstats Map C_K_reconstruction_cropped.mrc median #2, minimum 0, maximum 0.3238, mean 0.000842, SD 0.01017, RMS 0.01021 Map Al_K_reconstruction_cropped.mrc median #3, minimum 0.1083, maximum 0.2525, mean 0.1964, SD 0.04957, RMS 0.2026 Map Fe_Ka_reconstruction_cropped.mrc median #4, minimum 0, maximum 0, mean 0, SD 0, RMS 0 Map Ca_Ka_reconstruction_cropped.mrc median #5, minimum 0, maximum 0, mean 0, SD 0, RMS 0 Map Mg_K_reconstruction_cropped.mrc median #6, minimum 0, maximum 0.3207, mean 0.1684, SD 0.1155, RMS 0.2042 Map Ni_Ka_reconstruction_cropped.mrc median #7, minimum 0, maximum 0, mean 0, SD 0, RMS 0 Map S_K_reconstruction_cropped.mrc median #8, minimum 0, maximum 0, mean 0, SD 0, RMS 0 Map Cr_Ka_reconstruction_cropped.mrc median #9, minimum 0.0636, maximum 0.08416, mean 0.06868, SD 0.006358, RMS 0.06897 Map HAADF_reconstruction_cropped.mrc binned #10, minimum 0, maximum 2072, mean 25.01, SD 85.11, RMS 88.71 Map O_K_reconstruction_cropped.mrc median #11, minimum 0.5002, maximum 0.5471, mean 0.5211, SD 0.01394, RMS 0.5212 Map Si_K_reconstruction_cropped.mrc median #12, minimum 0.5471, maximum 0.6511, mean 0.5963, SD 0.03664, RMS 0.5974 > close session Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 869, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_close_cb(sess)) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 599, in file_close_cb run(session, 'close session') File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2655, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\std_commands\close.py", line 60, in close_session session.reset() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py", line 442, in reset sm.reset_state(container, self) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py", line 313, in reset_state tool_inst.delete() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map_eraser\eraser.py", line 230, in delete ses.models.close([self._sphere_model]) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 589, in close mremoved = self.remove(models) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in remove mlist.sort(key=lambda m: len(m.id), reverse=True) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in <lambda> mlist.sort(key=lambda m: len(m.id), reverse=True) TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in mlist.sort(key=lambda m: len(m.id), reverse=True) See log for complete Python traceback. > open "D:/WorkDir/Stack 4 - Tomo EDS stack Gen2/Output2bin/ManyElementsinChimeraXquant.cxc" > open Aligned/C_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/C_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\C_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened C_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.157, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 3 > close #1 > volume #2 style surface color red No volumes specified > vr off > close session Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 869, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_close_cb(sess)) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 599, in file_close_cb run(session, 'close session') File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2655, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\std_commands\close.py", line 60, in close_session session.reset() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py", line 442, in reset sm.reset_state(container, self) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py", line 313, in reset_state tool_inst.delete() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map_eraser\eraser.py", line 230, in delete ses.models.close([self._sphere_model]) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 589, in close mremoved = self.remove(models) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in remove mlist.sort(key=lambda m: len(m.id), reverse=True) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in <lambda> mlist.sort(key=lambda m: len(m.id), reverse=True) TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in mlist.sort(key=lambda m: len(m.id), reverse=True) See log for complete Python traceback. > open "D:/WorkDir/Stack 4 - Tomo EDS stack Gen2/Output2bin/ManyElementsinChimeraXquant.cxc" > open Aligned/C_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/C_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\C_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened C_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.157, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 3 > close #1 > volume #2 style surface color red > volume #2 projectionMode 3d > volume #2 hide > open Aligned/Al_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Al_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Al_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Al_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.255, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 3 > close #1 > volume #3 style surface color yellow level 0.255 > volume #3 projectionMode 3d > volume #3 show > open Aligned/Fe_Ka_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Fe_Ka_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Fe_Ka_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Fe_Ka_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.512, step 1, values float32 > view orient cofr false > volume voxelSize 1 > volume median #1 binSize 3 > close #1 > volume #4 style surface color red level 0.86 > volume #4 projectionMode 3d > volume #4 show > open Aligned/Ca_Ka_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Ca_Ka_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Ca_Ka_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Ca_Ka_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.157, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 3 > close #1 > volume #5 style surface color purple level 0.233 > volume #5 projectionMode 3d > volume #5 show > open Aligned/Mg_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Mg_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Mg_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Mg_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.929, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 3 > close #1 > volume #6 style surface color limegreen transparency 0.66 level 0.435 > volume #6 projectionMode 3d > volume #6 show > open Aligned/Ni_Ka_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Ni_Ka_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Ni_Ka_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Ni_Ka_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.0484, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 3 > close #1 > volume #7 style surface color limegreen level 0.502 > volume #7 projectionMode 3d > volume #7 show > open Aligned/S_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/S_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\S_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened S_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.21, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 3 > close #1 > volume #8 style surface color royalblue level 5.56 > volume #8 projectionMode 3d > volume #8 show > open Aligned/Cr_Ka_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Cr_Ka_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Cr_Ka_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Cr_Ka_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 0.064, step 1, values float32 > volume voxelSize 1 > view orient cofr false > volume median #1 binSize 3 > close #1 > volume #9 style surface color royalblue level 0.064 > volume #9 projectionMode 3d > volume #9 show > open Aligned/HAADF_reconstruction_cropped.mrc Summary of feedback from opening Aligned/HAADF_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\HAADF_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened HAADF_reconstruction_cropped.mrc, grid size 256,256,256, pixel 0.00391, shown at level 445, step 1, values float32 > volume bin #1 binSize 2 > volume #10 voxelSize 1.0 > view orient cofr false > close #1 > volume #10 style surface color white > volume #10 projectionMode 3d > volume #10 hide > open Aligned/O_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/O_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\O_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened O_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 1.07, step 1, values float32 > volume #1 voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #11 style surface color gray transparency 0.66 level 8.14 > volume #11 projectionMode 3d > volume #11 show > open Aligned/Si_K_reconstruction_cropped.mrc Summary of feedback from opening Aligned/Si_K_reconstruction_cropped.mrc --- note | D:\WorkDir\Stack 4 - Tomo EDS stack Gen2\Output2bin\Aligned\Si_K_reconstruction_cropped.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened Si_K_reconstruction_cropped.mrc, grid size 128,128,128, pixel 0.00781, shown at level 1.01, step 1, values float32 > volume #1 voxelSize 1 > view orient cofr false > volume median #1 binSize 5 > close #1 > volume #12 style image color gray > volume #12 style image level 0.0,0.0 level 0.5,0.9 level 1.76,1.0 > volume #12 projectionMode 3d > volume #12 show > view matrix camera 0.0,0.0,1,287.35,1,0.0,0.0,47.006,0,1,0,53.78 > lighting shadows true intensity 0.5 > cofr 64,50,54 showPivot false executed ManyElementsinChimeraXquant.cxc > vr on started SteamVR rendering > measure mapstats Map C_K_reconstruction_cropped.mrc median #2, minimum 0, maximum 0.4669, mean 0.001255, SD 0.01332, RMS 0.01338 Map Al_K_reconstruction_cropped.mrc median #3, minimum 0, maximum 0.9795, mean 0.004237, SD 0.04227, RMS 0.04248 Map Fe_Ka_reconstruction_cropped.mrc median #4, minimum 0, maximum 6.911, mean 0.01166, SD 0.1344, RMS 0.1349 Map Ca_Ka_reconstruction_cropped.mrc median #5, minimum 0, maximum 0.8489, mean 0.001381, SD 0.01849, RMS 0.01854 Map Mg_K_reconstruction_cropped.mrc median #6, minimum 0, maximum 2.002, mean 0.02847, SD 0.1392, RMS 0.1421 Map Ni_Ka_reconstruction_cropped.mrc median #7, minimum 0, maximum 0.3968, mean 0.0002009, SD 0.00492, RMS 0.004924 Map S_K_reconstruction_cropped.mrc median #8, minimum 0, maximum 2.738, mean 0.005605, SD 0.08463, RMS 0.08482 Map Cr_Ka_reconstruction_cropped.mrc median #9, minimum 0, maximum 1.069, mean 6.51e-05, SD 0.003765, RMS 0.003766 Map HAADF_reconstruction_cropped.mrc binned #10, minimum 0, maximum 2072, mean 25.01, SD 85.11, RMS 88.71 Map O_K_reconstruction_cropped.mrc median #11, minimum 0, maximum 1.743, mean 0.05029, SD 0.1665, RMS 0.1739 Map Si_K_reconstruction_cropped.mrc median #12, minimum 0, maximum 1.759, mean 0.0391, SD 0.1468, RMS 0.1519 VR mode crop volume VR mode crop volume > volume #3 region 0,0,0,127,126,127 > volume #3 region 0,0,0,127,98,127 > volume #3 region 0,0,0,93,98,127 > volume #3 region 44,0,0,93,98,127 > volume #3 region 44,0,21,93,98,127 > volume #3 region 44,0,21,93,78,127 > volume #3 region 44,0,21,93,78,62 > volume #3 region 44,42,21,93,78,62 > volume #3 region 44,42,21,93,47,62 > volume #3 region 44,42,57,93,47,62 > volume #3 region 44,42,57,73,47,62 > volume #3 region 44,42,57,73,47,62 > volume #3 region 70,42,57,73,47,62 > volume #3 region 70,42,59,73,47,62 > volume #3 region 70,42,59,73,47,62 > volume #3 region 70,42,59,73,45,62 > volume #3 region 70,44,59,73,45,62 > measure mapstats Map C_K_reconstruction_cropped.mrc median #2, minimum 0, maximum 0.4669, mean 0.001255, SD 0.01332, RMS 0.01338 Map Al_K_reconstruction_cropped.mrc median #3, minimum 0, maximum 0.202, mean 0.03436, SD 0.0717, RMS 0.07951 Map Fe_Ka_reconstruction_cropped.mrc median #4, minimum 0, maximum 0.007813, mean 0.0002442, SD 0.001359, RMS 0.001381 Map Ca_Ka_reconstruction_cropped.mrc median #5, minimum 0, maximum 0.2172, mean 0.07367, SD 0.0716, RMS 0.1027 Map Mg_K_reconstruction_cropped.mrc median #6, minimum 0, maximum 0.2884, mean 0.01781, SD 0.06898, RMS 0.07124 Map Ni_Ka_reconstruction_cropped.mrc median #7, minimum 0, maximum 0, mean 0, SD 0, RMS 0 Map S_K_reconstruction_cropped.mrc median #8, minimum 0, maximum 0, mean 0, SD 0, RMS 0 Map Cr_Ka_reconstruction_cropped.mrc median #9, minimum 0, maximum 0.4876, mean 0.2236, SD 0.1561, RMS 0.2727 Map HAADF_reconstruction_cropped.mrc binned #10, minimum 0, maximum 2072, mean 25.01, SD 85.11, RMS 88.71 Map O_K_reconstruction_cropped.mrc median #11, minimum 0.4134, maximum 0.7042, mean 0.5828, SD 0.07891, RMS 0.5882 Map Si_K_reconstruction_cropped.mrc median #12, minimum 0.004232, maximum 0.3219, mean 0.1618, SD 0.07688, RMS 0.1791 > volume #3 region 70,33,59,73,45,62 > volume #3 region 70,33,59,83,45,62 > volume #3 region 70,33,53,83,45,62 > volume #3 region 62,33,53,83,45,62 > volume #3 region 62,33,53,83,48,90 > volume #3 region 62,33,53,83,90,90 > volume #3 region 62,33,37,83,90,90 > volume #3 region 62,33,37,83,90,44 > volume #3 region 62,33,37,83,51,44 > volume #3 region 62,47,37,83,51,44 > volume #3 region 62,45,37,83,51,44 > volume #3 region 62,45,37,73,51,44 > volume #3 region 67,45,37,73,51,44 > volume #3 region 67,45,17,73,51,44 > volume #3 region 67,24,17,73,81,44 > volume #3 region 77,24,17,84,81,44 > volume #3 region 78,24,17,99,81,44 > volume #3 region 78,24,17,99,81,44 > volume #3 region 78,24,17,99,52,44 > volume #3 region 78,51,17,99,52,44 > volume #3 region 78,52,17,99,52,44 > volume #3 region 78,52,17,99,55,44 > volume #3 region 78,52,17,81,55,44 > volume #3 region 78,52,17,83,55,44 > volume #3 region 78,52,28,83,55,44 > volume #3 region 77,52,28,83,55,44 > volume #3 region 77,52,28,83,55,31 > volume #3 region 77,50,28,83,55,31 > volume #3 region 77,50,28,83,55,31 > volume #3 region 77,50,28,80,55,31 > vr off > close session Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 869, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_close_cb(sess)) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 599, in file_close_cb run(session, 'close session') File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2655, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\std_commands\close.py", line 60, in close_session session.reset() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py", line 442, in reset sm.reset_state(container, self) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py", line 313, in reset_state tool_inst.delete() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map_eraser\eraser.py", line 230, in delete ses.models.close([self._sphere_model]) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 589, in close mremoved = self.remove(models) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in remove mlist.sort(key=lambda m: len(m.id), reverse=True) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in <lambda> mlist.sort(key=lambda m: len(m.id), reverse=True) TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in mlist.sort(key=lambda m: len(m.id), reverse=True) See log for complete Python traceback. > close session Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 869, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_close_cb(sess)) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 599, in file_close_cb run(session, 'close session') File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2655, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\std_commands\close.py", line 60, in close_session session.reset() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py", line 442, in reset sm.reset_state(container, self) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py", line 313, in reset_state tool_inst.delete() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map_eraser\eraser.py", line 230, in delete ses.models.close([self._sphere_model]) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 589, in close mremoved = self.remove(models) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in remove mlist.sort(key=lambda m: len(m.id), reverse=True) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in <lambda> mlist.sort(key=lambda m: len(m.id), reverse=True) TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 564, in mlist.sort(key=lambda m: len(m.id), reverse=True) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 441.12 OpenGL renderer: GeForce RTX 2060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem with Map Eraser closing models during session close |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This was fixed Nov 14, 2019. Get the daily build.
Duplicate of #2577
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Reported by Zack Gainsforth