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Opened 8 months ago
Closed 8 months ago
#16931 closed defect (wontfix)
Problem saving segmentations
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Zach Pearson | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.7.2-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
In Segment Map (segger) > File > Open Segmentation
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/garciae/Documents/CT scan/Dicom/PAT0/STUDY0/SERIES0" format
> dicom
Summary of feedback from opening /Users/garciae/Documents/CT
scan/Dicom/PAT0/STUDY0/SERIES0
---
note | Opened 1 CT (Topograma 1.0 Tr20) as #1.1.1, grid size 512,512,1, pixel 1, shown at step 1, values float32
> hide #!1.1.1 models
> show #!1.1.1 models
> open "/Users/garciae/Documents/CT scan/Dicom/PAT0/STUDY0/SERIES1" format
> dicom
Summary of feedback from opening /Users/garciae/Documents/CT
scan/Dicom/PAT0/STUDY0/SERIES1
---
warning | Merged incoming unique studies with existing patient with same ID
note | Opened 2 CT (Torax 5.0 Bf37 3) as #1.1.2, grid size 512,512,73, pixel 1,1,4.93, shown at step 1, values float32
> open "/Users/garciae/Documents/CT scan/Dicom/PAT0/STUDY0/SERIES2" format
> dicom
Summary of feedback from opening /Users/garciae/Documents/CT
scan/Dicom/PAT0/STUDY0/SERIES2
---
warning | Merged incoming unique studies with existing patient with same ID
note | Opened 3 CT (Torax 5.0 Br59 3) as #1.1.3, grid size 512,512,73, pixel 1,1,4.93, shown at step 1, values float32
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.1 models
> show #!1.1.1 models
> open "/Users/garciae/Documents/CT scan/Dicom/PAT0/STUDY0/SERIES3" format
> dicom
Summary of feedback from opening /Users/garciae/Documents/CT
scan/Dicom/PAT0/STUDY0/SERIES3
---
warning | Merged incoming unique studies with existing patient with same ID
note | Opened 4 CT (Torax 1.0 Bv38 3) as #1.1.4, grid size 512,512,520, pixel 1,1,0.699, shown at step 1, values float32
> open "/Users/garciae/Documents/CT scan/Dicom/PAT0/STUDY0/SERIES4" format
> dicom
Summary of feedback from opening /Users/garciae/Documents/CT
scan/Dicom/PAT0/STUDY0/SERIES4
---
warning | Merged incoming unique studies with existing patient with same ID
note | Opened 5 CT (Torax 1.0 Br59 AR) as #1.1.5, grid size 512,512,520, pixel 1,1,0.699, shown at step 1, values float32
> open "/Users/garciae/Documents/CT scan/Dicom/PAT0/STUDY0/SERIES5" format
> dicom
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/__init__.py", line 36, in run_provider
actions.run_provider(session, name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/actions.py", line 29, in run_provider
open_dicom(session)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/actions.py", line 37, in open_dicom
show_open_folder_dialog(session)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 349, in
show_open_folder_dialog
_folder_dlg.display(session)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 110, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_opener.py", line 7, in open
dcm = DICOM.from_paths(session, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 54, in from_paths
return cls(path, session=session)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 49, in __init__
self.find_dicom_files(self.paths)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 102, in find_dicom_files
patients = self.dicom_patients(dfiles)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 156, in dicom_patients
patient.studies_from_files(series)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_hierarchy.py", line 57, in studies_from_files
study.series_from_files(files)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_hierarchy.py", line 165, in series_from_files
s = Series(self.session, self, files)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_hierarchy.py", line 323, in __init__
self.dicom_data.append(DicomData(self.session, self, file_list))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_hierarchy.py", line 526, in __init__
self.value_type = self.numpy_value_type(
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_hierarchy.py", line 999, in numpy_value_type
raise ValueError("Unsupported value type, bits_allocated = %d" %
bits_allocated)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
TypeError: %d format: a real number is required, not NoneType
TypeError: %d format: a real number is required, not NoneType
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_hierarchy.py", line 999, in numpy_value_type
raise ValueError("Unsupported value type, bits_allocated = %d" %
bits_allocated)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
See log for complete Python traceback.
> open "/Users/garciae/Documents/CT scan/Dicom/PAT0/STUDY0/SERIES6" format
> dicom
Summary of feedback from opening /Users/garciae/Documents/CT
scan/Dicom/PAT0/STUDY0/SERIES6
---
warning | Merged incoming unique studies with existing patient with same ID
note | Opened 502 CT (Protocolo de paciente) as #1.1.6, grid size 512,512,1, pixel 1, shown at step 1, values uint16
> hide #!1.1.6 models
> show #!1.1.6 models
> close #1.1.6
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1.1 models
> volume #1.1.5 region 0,0,0,511,511,519 step 4
[Repeated 1 time(s)]
> volume #1.1.5 step 1
> lighting soft
> volume #1.1.5 level 465.4
> ui tool show "Side View"
> surface dust #1.1.5 size 10
[Repeated 3 time(s)]
> volume #1.1.5 level 442.7
> volume #1.1.5 level 397.3
> volume #1.1.5 level 208.1
> surface dust
Missing or invalid "surfaces" argument: empty atom specifier
> surface dust update f
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust update false
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust update false
Missing or invalid "surfaces" argument: invalid surfaces specifier
> volume #1.1.5 level 33.97
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> volume #1.1.5 level 624.4
> volume #1.1.3 region 0,0,0,511,511,72 step 2
[Repeated 1 time(s)]
> volume #1.1.3 style image
> volume #1.1.3 maximumIntensityProjection true
> volume #1.1.3 style surface maximumIntensityProjection false
> volume #1.1.3 level 265.8
> volume #1.1.3 level 39.86
> volume #1.1.5 level 215.6
> volume #1.1.5 level 170.2
> volume #1.1.5 level 56.67
> volume #1.1.5 level 253.5
> volume #1.1.3 level 228.8
> volume #1.1.2 region 0,0,0,511,511,72 step 2
[Repeated 1 time(s)]
> volume #1.1.2 level 173.4
> volume #1.1.4 region 0,0,0,511,511,519 step 4
[Repeated 1 time(s)]
> volume #1.1.4 level 93.84
> volume #1.1.4 level -19.89
> volume #1.1.4 level 86.26
> volume #1.1.4 level 124.2
> volume #1.1.4 level 78.68
> volume #1.1.5 level 299.1
> volume #1.1.5 level 337
> ui tool show "Segment Map"
Segmenting 4 CT (Torax 1.0 Bv38 3), density threshold 78.678608
Only showing 60 of 4791 regions.
Showing 60 of 4791 region surfaces
183516 watershed regions, grouped to 4791 regions
Showing 4 CT (Torax 1 Bv38 3).seg - 4791 regions, 60 surfaces
Segmenting 4 CT (Torax 1.0 Bv38 3), density threshold 78.678608
Only showing 1000 of 100413 regions.
Showing 1000 of 100413 region surfaces
Showing 607 region surfaces
100413 watershed regions, grouped to 607 regions
Showing 4 CT (Torax 1 Bv38 3).seg - 607 regions, 607 surfaces
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right select
> select #2.74
1 model selected
> select #2.74
1 model selected
Ungrouped to 2 regions
Grouped 2 regions
> hide #!2 models
> surface dust #1.1.4 size 10
[Repeated 1 time(s)]
> surface dust #1.1.4 size 20
> volume #1.1.4 level 93.84
> volume #1.1.4 level 71.1
> surface dust #1.1.4 size 10
> volume #1.1.4 level 78.68
> surface dust #1.1.4 size 15
> show #!2 models
Segmenting 4 CT (Torax 1.0 Bv38 3), density threshold 78.678608
Only showing 1000 of 100413 regions.
Showing 1000 of 100413 region surfaces
Showing 607 region surfaces
100413 watershed regions, grouped to 607 regions
Showing 4 CT (Torax 1 Bv38 3).seg - 607 regions, 607 surfaces
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume gaussian
Missing or invalid "volumes" argument: empty atom specifier
> volume gaussian #1.1.4
Opened 4 CT (Torax 1.0 Bv38 3) gaussian as #3, grid size 512,512,520, pixel
1,1,0.699, shown at step 1, values float32
> volume #3 level 29.08
QGestureManager::deliverEvent: could not find the target for gesture
> volume #3 level 808.9
> volume #3 level 265.2
> show #!2 models
> hide #!2 models
Drag select of 1.1.5 5 CT (Torax 1.0 Br59 AR)
Drag select of 1.1.4 4 CT (Torax 1.0 Bv38 3)
> ui mousemode right rotate
> ui mousemode right zoom
> ~select
Nothing selected
> show #!3 models
> hide #!1.1.4 models
> volume #3 level 222.2
> volume #3 level 172.2
> volume #3 level 157.9
> volume #3 level 129.2
> volume #3 level 100.6
> volume #3 level 86.32
> volume #3 level 72.01
> volume #3 level 75
> volume #3 level 80
> volume #3 level 85
> volume #3 level 90
> volume #3 level 85
Segmenting 4 CT (Torax 1.0 Bv38 3) gaussian, density threshold 85.000000
Only showing 1000 of 20307 regions.
Showing 1000 of 20307 region surfaces
Showing 587 region surfaces
20307 watershed regions, grouped to 587 regions
Showing 4 CT (Torax 1 Bv38 3) gaussian.seg - 587 regions, 587 surfaces
> ui mousemode right select
Drag select of 33837, 33853, 33842, 33875, 33845, 33832, 33910, 110513 of
118912 triangles, 33870, 33681, 50362 of 54988 triangles, 33903, 33906, 33913,
12624 of 45376 triangles, 33702, 2470 of 41440 triangles, 33916, 33854, 334 of
39500 triangles, 33912, 33897, 1403 of 35732 triangles, 33885, 33901, 482 of
24940 triangles, 33909, 8538 of 20336 triangles, 33921, 33856, 459 of 17108
triangles, 33533, 33864, 33665, 33867, 860 of 12060 triangles, 33697, 33892,
33851, 33232, 33199, 33800, 33677, 33915, 33285, 7858 of 9792 triangles,
33442, 11009 of 11036 triangles, 33390, 33814, 33568, 33360, 33529, 33882,
33798, 33551, 6619 of 8832 triangles, 33010, 32888, 33387, 33113, 33230,
33176, 33660, 32067, 33133, 33829, 33245, 33175, 8778 of 8980 triangles,
33148, 3469 of 6824 triangles, 33250, 32894, 33552, 32930, 32785, 33183,
33745, 33277, 33164, 33104, 32526, 32774, 33249, 32256, 33874, 33272, 32426,
32441, 33141, 32861, 32899, 32991, 31971, 2680 of 5612 triangles, 32297,
32185, 32460, 33444, 31157, 33640, 5788 of 5808 triangles, 33501, 4517 of 4884
triangles, 33607, 32156, 32945, 32933, 2942 of 5868 triangles, 33143, 33079,
32766, 2176 of 4588 triangles, 32392, 32887, 1971 of 5836 triangles, 33185,
32609, 32476, 32817, 31209, 33174, 32724, 32310, 32214, 33446, 4274 of 5464
triangles, 32094, 3752 of 4824 triangles, 31300, 33318, 31797, 31950, 33065,
33859, 32062, 5571 of 5616 triangles, 33452, 754 of 4020 triangles, 32783,
1009 of 4196 triangles, 29858, 32354, 32509, 31954, 32890, 1500 of 3732
triangles, 31552, 32120, 31129, 32379, 78 of 3224 triangles, 31924, 33509, 871
of 3624 triangles, 33438, 29439, 32317, 217 of 3484 triangles, 32247, 32204,
1659 of 3376 triangles, 29611, 30298, 31772, 32964, 2144 of 3964 triangles,
23827, 32339, 1974 of 3948 triangles, 31647, 30201, 30400, 32681, 29348,
31397, 22160, 32396, 27733, 30340, 26038, 32103, 33902, 32401, 27719, 32221,
32183, 29544, 27331, 383 of 2980 triangles, 30218, 31208, 29860, 29552, 30190,
30164, 30408, 32253, 438 of 2744 triangles, 32580, 922 of 2800 triangles,
25217, 27231, 30085, 32255, 546 of 2652 triangles, 31987, 257 of 2168
triangles, 31611, 184 of 2504 triangles, 31601, 4942, 28551, 27288, 31829, 10
of 2308 triangles, 23388, 28999, 1507 of 1624 triangles, 26893, 24644, 24584,
4938, 736 of 1192 triangles, 24696, 214, 24605, 28541, 3 4 CT (Torax 1.0 Bv38
3) gaussian
Deleted 187 regions
> ~select
Nothing selected
Drag select of 33914, 28029
Deleted 2 regions
Drag select of 33830, 33826, 18842 of 56516 triangles, 33825, 33831, 33855,
20532 of 26060 triangles, 33922, 25103 of 26112 triangles, 33841, 5768 of
22000 triangles, 33685, 7440 of 21744 triangles, 33865, 6282 of 16368
triangles, 33846, 33756, 9758 of 16344 triangles, 33860, 5643 of 9332
triangles, 33852, 33510, 33476, 33872, 1128 of 5196 triangles, 33683, 33770,
4772 of 5072 triangles, 33783, 32722, 1652 of 5868 triangles, 33682, 33686,
33849, 32954, 1054 of 4588 triangles, 32981, 3624 of 4332 triangles, 32703,
3490 of 4596 triangles, 33693, 33929, 33117, 4358 of 4424 triangles, 32865,
963 of 4268 triangles, 33399, 51 of 4492 triangles, 33385, 33871, 32610,
33373, 33163, 33306, 4291 of 4300 triangles, 32966, 33923, 33732, 32967,
32955, 33372, 32882, 32734, 32970, 32999, 1384 of 4136 triangles, 33698,
33866, 1313 of 2840 triangles, 33899, 3576 of 4132 triangles, 32998, 32713,
32692, 32806, 1733 of 3128 triangles, 33058, 31710, 30283, 33700, 33087,
32055, 33068, 32735, 33464, 31858, 32917, 32984, 32474, 32056, 32907, 33369,
65 of 2968 triangles, 33261, 32089, 32803, 25995, 32976, 33157, 33670, 32795,
32665, 31020, 33077, 33083, 32376, 33597, 32566, 32626, 32864, 32090, 33699,
33410, 33216, 32867, 33495, 32370, 32492, 32982, 32729, 32855, 28783, 26301,
4924, 4923, 4745, 4922
Deleted 104 regions
Drag select of 33873, 23477 of 92876 triangles, 33803, 33627, 14923 of 59052
triangles, 33513, 8198 of 48140 triangles, 33847, 6185 of 40856 triangles,
33154, 4130 of 36340 triangles, 33862, 33348, 4788 of 28028 triangles, 33781,
33869, 33879, 33499, 3223 of 23972 triangles, 33437, 2923 of 19844 triangles,
33810, 1829 of 19144 triangles, 33646, 33833, 33900, 32680, 33827, 29698,
33601, 33868, 33273, 33786, 33675, 33610, 31342, 33703, 31886, 33470, 33581,
33429, 33898, 33835, 33511, 33188, 33771, 33523, 32772, 33672, 32133, 32802,
33260, 33443, 33400, 32697, 30598, 31466, 31110, 32963, 30518, 31192, 30288,
32836, 32763, 23685, 21937, 21872, 33069, 33403, 21720, 31940, 32084, 32670,
33421, 33424, 33425, 31876, 21611, 32961, 30278, 32282, 32553, 32968, 33371,
27507, 31720, 33018, 33402, 33887, 31032, 33422, 18764, 24213, 29925, 27519,
24989, 23432
Deleted 88 regions
Drag select of 33848, 33925, 33861, 33889, 33896, 33824, 33844, 33880, 33894,
33288, 33304, 33689, 33728, 33919, 33907, 33816, 33927, 33877, 33289, 33708,
33904, 33782, 32462, 33534, 33467, 33893, 33876, 18741 of 21524 triangles,
33821, 33802, 32938, 33819, 33505, 16254 of 16576 triangles, 31949, 32866,
33664, 33863, 33858, 33823, 29646, 33891, 33571, 33753, 33709, 33292, 33657,
33592, 31692, 32479, 33680, 33659, 33926, 32947, 32069, 33317, 33405, 33063,
33580, 33168, 33619, 32851, 33001, 33820, 33878, 32741, 32578, 33612, 33404,
30761, 33477, 6180 of 8228 triangles, 26635, 32477, 31265, 32039, 27260,
32277, 27182, 30265, 29654, 30022, 28329, 30228, 30500, 28259, 28544, 32088,
27740, 28995, 30053, 30023, 31354, 20824, 23893, 30868
Deleted 93 regions
> select #2.4
1 model selected
> ui mousemode right zoom
Ungrouped to 5 regions
> ~select
Nothing selected
> ui mousemode right select
> select #2.69
1 model selected
Ungrouped to 4 regions
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #2.73
1 model selected
Ungrouped to 2 regions
> select #2.82
1 model selected
Deleted 1 regions
Drag select of 33888, 355 of 250216 triangles, 33812, 11344 of 115196
triangles, 33217, 820 of 121356 triangles, 33097, 14012 of 61980 triangles,
33722, 462 of 51968 triangles, 31864, 526 of 32000 triangles, 33687, 294 of
31212 triangles
> select #2.44
1 model selected
Ungrouped to 3 regions
> select #2.36
1 model selected
Ungrouped to 3 regions
> select #2.93
1 model selected
Ungrouped to 5 regions
Drag select of 33917, 380 of 208152 triangles, 33920, 1773 of 138696
triangles, 33755, 2103 of 72992 triangles, 29642, 298 of 45576 triangles,
32870, 7 of 56952 triangles, 33730, 1638 of 20088 triangles, 32769, 2445 of
82100 triangles, 31899, 378 of 32452 triangles, 33540, 4830 of 163732
triangles
> select #2.100
1 model selected
Ungrouped to 4 regions
> select #2.107
1 model selected
Ungrouped to 2 regions
> select #2.100
1 model selected
Ungrouped to 2 regions
> select #2.107
1 model selected
Drag select of 33805, 732 of 178860 triangles, 33918, 27298 of 108596
triangles, 33695, 33231 of 167776 triangles, 33788, 32774 of 168652 triangles,
33625, 31478 of 72964 triangles, 33836, 4139 of 89740 triangles, 33259, 131 of
55940 triangles, 33062, 2327 of 54292 triangles, 33577, 14622 of 44940
triangles, 33748, 223 of 42856 triangles, 33777, 5454 of 53720 triangles,
33767, 22069 of 255284 triangles, 32769, 7413 of 82100 triangles, 31899, 13254
of 32452 triangles, 33413, 4550 of 28032 triangles
> ui mousemode right zoom
> ~select
Nothing selected
> save "/Users/garciae/Documents/CT scan/costelles_4CT_gaussian.seg" models #2
> hide #!2 models
> ui mousemode right translate
> ui mousemode right zoom
> hide #!1.1.2 models
> show #!1.1.3 models
> hide #!1.1.3 models
> show #!1.1.4 models
> hide #!1.1.4 models
> show #!1.1.5 models
> volume #1.1.5 level 93.93
> volume #1.1.5 step 2
> volume #1.1.5 level 55.95
> volume #1.1.5 step 1
> volume gaussian #1.1.5
Opened 5 CT (Torax 1.0 Br59 AR) gaussian as #4, grid size 512,512,520, pixel
1,1,0.699, shown at step 1, values float32
> volume #4 level 318.6
> volume #4 level 94.59
> volume #4 level 52.21
> volume #4 level -32.55
Segmenting 5 CT (Torax 1.0 Br59 AR) gaussian, density threshold -32.553135
Only showing 1000 of 230149 regions.
Showing 1000 of 230149 region surfaces
Only showing 1000 of 229600 regions.
Showing 1000 of 229600 region surfaces
Showing 599 region surfaces
229600 watershed regions, grouped to 599 regions
Showing 5 CT (Torax 1 Br59 AR) gaussian.seg - 599 regions, 599 surfaces
> ui mousemode right select
> select #2.34
1 model selected
> select #2.67
1 model selected
> select #2.34
1 model selected
> select #2.91
1 model selected
> select add #2.34
2 models selected
> select add #2.42
3 models selected
> select add #2.7
4 models selected
> select add #2.67
5 models selected
Grouped 5 regions
> select #2.46
1 model selected
> select add #2.21
2 models selected
> select add #2.76
3 models selected
> select add #2.119
4 models selected
> select add #2.35
5 models selected
> select add #2.84
6 models selected
> select add #2.94
7 models selected
> select add #2.113
8 models selected
> select add #2.102
9 models selected
> select add #2.23
10 models selected
> select add #2.12
11 models selected
> select add #2.4
12 models selected
> select subtract #2.4
11 models selected
> select add #2.27
12 models selected
> select add #2.63
13 models selected
> select add #2.81
14 models selected
> select subtract #2.94
13 models selected
> select subtract #2.84
12 models selected
> select add #2.40
13 models selected
> select add #2.89
14 models selected
> select add #2.24
15 models selected
> select add #2.93
16 models selected
> select add #2.73
17 models selected
Grouped 17 regions
> select #2.84
1 model selected
> select add #2.94
2 models selected
> select add #2.97
3 models selected
> select add #2.12
4 models selected
> select add #2.7
5 models selected
Grouped 5 regions
> select #2.7
1 model selected
> select #2.31
1 model selected
Drag select of 316877, 7 of 326796 triangles
> hide #!2 models
> select add #2
576 models selected
> select subtract #2
Nothing selected
> show #!1.1.5 models
> volume #1.1.5 level -187.2
> volume #1.1.5 level -696.2
> volume #1.1.5 level -1024
Drag select of 1.1.5 5 CT (Torax 1.0 Br59 AR)
> ui mousemode right zoom
> ~select
Nothing selected
> volume #1.1.5 level -900
> save /Users/garciae/Desktop/image1030.png supersample 3
> volume #1.1.5 level -910
> volume #1.1.5 level -850
> volume #1.1.5 level -800
> volume #1.1.5 level -700
> volume #1.1.5 level -600
> volume #1.1.5 level -650
> volume #1.1.5 level -700
> volume #1.1.5 level -750
> volume #1.1.5 level -650
Segmenting 5 CT (Torax 1.0 Br59 AR), density threshold -650.000000
Only showing 2000 of 1007490 regions.
Showing 2000 of 1007490 region surfaces
Only showing 2000 of 34545 regions.
Showing 2000 of 34545 region surfaces
1007490 watershed regions, grouped to 34545 regions
Showing 5 CT (Torax 1 Br59 AR).seg - 34545 regions, 2000 surfaces
> ui mousemode right select
> select #2.9
1 model selected
Drag select of 2146451, 386 of 6598428 triangles, 2146459, 142 of 1308696
triangles, 2146460, 80 of 1095100 triangles, 2146491, 169 of 427924 triangles,
2146490, 200 of 163188 triangles, 2143486, 96 of 24172 triangles, 2145761, 189
of 9484 triangles, 2132102, 67 of 3092 triangles
> ui mousemode right zoom
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_raw.seg" models #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
> ui mousemode right select
> ~select
Nothing selected
> select #2.4
1 model selected
Deleted 1 regions
> select #2.3
1 model selected
Deleted 1 regions
> select clear
Drag select of 2132316, 2100974, 2132429, 2052159, 2101972, 2103203, 1910576,
2054017, 2100408, 2099010, 2100972, 2100425, 1015 of 2008 triangles, 1925383,
2058919, 1899042, 2062962, 1947681, 521 of 1800 triangles, 2065681, 1935902,
2102256, 2060831, 1914370, 1946712, 2101297, 698 of 1500 triangles, 1951336,
1983419, 1980517, 1964543, 2058471, 953 of 1368 triangles, 1687007, 1954171,
1661026, 1988095, 1982291, 1715394, 467 of 1336 triangles, 1984221, 2062034,
1987160, 2102352, 29 of 1532 triangles, 2065738, 1989387, 1983778, 2063956,
2062767, 1997473, 1815224, 1811922, 2067983, 1974177, 2066105
Deleted 50 regions
> select #2.5
1 model selected
> select #2.5
1 model selected
> select #2.6
1 model selected
Drag select of 2146450, 7152 of 5853100 triangles, 2146451, 2981 of 6598428
triangles, 2146463, 2014 of 1270624 triangles, 2146458, 12718 of 927212
triangles, 2146457, 1573 of 134156 triangles, 2146495, 234 of 58600 triangles,
2146509, 576 of 50164 triangles, 2146020, 11 of 17608 triangles, 2132283, 321
of 3628 triangles, 2122778, 1386 of 7596 triangles, 2132742, 109 of 3552
triangles, 2132980, 323 of 6568 triangles, 2121859, 2128 of 2928 triangles,
2102296, 329 of 2564 triangles, 2132984, 761 of 4380 triangles, 2133063, 792
of 4308 triangles, 2067027, 284 of 1680 triangles, 1967427, 207 of 1516
triangles, 2064573, 187 of 1876 triangles, 1979913, 130 of 1292 triangles
> select #2.6
1 model selected
> select #2.6
1 model selected
Deleted 1 regions
Drag select of 2141463, 1714 of 4488 triangles, 2121340, 2049120, 1955657,
1938734, 2102319, 1705552, 609 of 1208 triangles
Deleted 7 regions
Drag select of 1983096
Deleted 1 regions
Drag select of 2146451, 2225 of 6598428 triangles, 2146460, 338 of 1095100
triangles, 2146446, 545 of 62200 triangles, 2101642, 431 of 4164 triangles,
2138698, 277 of 9028 triangles, 2141772, 505 of 3572 triangles, 2122613, 645
of 6640 triangles, 2064391, 88 of 3140 triangles, 2049193, 585 of 2272
triangles, 2103710, 390 of 4880 triangles, 2103418, 301 of 3296 triangles,
2103416, 658 of 3644 triangles, 2103725, 347 of 2876 triangles, 2067929, 91 of
2308 triangles
> select #2.5
1 model selected
> select #2.121
1 model selected
Deleted 1 regions
> select #2.105
1 model selected
Deleted 1 regions
Drag select of 2146450, 11568 of 5853100 triangles, 2146458, 16636 of 927212
triangles, 2146456, 603 of 136588 triangles, 2146482, 1380 of 183820
triangles, 2146481, 344 of 175376 triangles, 2146159, 14 of 38864 triangles,
2146495, 917 of 58600 triangles, 2146505, 1934 of 35744 triangles, 2145973,
1490 of 10408 triangles, 2121990, 905 of 5136 triangles, 2138689, 69 of 7036
triangles, 2095927, 1026 of 3008 triangles, 2122761, 697 of 3820 triangles,
2122589, 247 of 5036 triangles, 1960100, 566 of 2128 triangles, 2122773, 1104
of 4024 triangles, 2122580, 241 of 3052 triangles, 2103680, 384 of 2960
triangles, 1994408, 367 of 2124 triangles, 1999472, 421 of 2672 triangles,
1964451, 101 of 1400 triangles
> ui mousemode right zoom
> ~select
Nothing selected
Only showing 2000 of 34482 regions.
Showing 2000 of 34482 region surfaces
> ui mousemode right select
> select #2.1425
1 model selected
> select zone sel 50
Selected 66 surfaces
Drag select of 2146450, 13456 of 5853100 triangles, 2146451, 8905 of 6598428
triangles, 2146458, 22726 of 927212 triangles, 2146482, 8107 of 183820
triangles, 2146487, 2770 of 21300 triangles, 2146159, 9 of 38864 triangles,
2146495, 5761 of 58600 triangles, 2146509, 1786 of 50164 triangles, 2145139,
1291 of 13108 triangles, 2146442, 321 of 35448 triangles, 2146505, 2662 of
35744 triangles, 2143393, 662 of 6864 triangles, 2146017, 2291 of 17140
triangles, 2121990, 1611 of 5136 triangles, 2103669, 1043 of 4796 triangles,
2122589, 434 of 5036 triangles, 2122595, 482 of 3712 triangles, 2067881, 719
of 3756 triangles, 2103684, 808 of 3176 triangles, 2122742, 223 of 3572
triangles, 2103013, 214 of 3092 triangles, 1994408, 456 of 2124 triangles,
1964451, 527 of 1400 triangles, 2067797, 281 of 2600 triangles
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> select #2.1425
1 model selected
> select zone sel 20 extend true
Selected 22 surfaces
> select #2.44
1 model selected
> select #2.9
1 model selected
> select #2.943
1 model selected
> select zone sel 20 extend true
Selected 24 surfaces
Drag select of 2146450, 516 of 5853100 triangles, 2146451, 645 of 6598428
triangles
> ui mousemode right zoom
> ui mousemode right select
> select #2.1
1 model selected
Ungrouped to 2 regions
Drag select of 2146450, 280 of 5853100 triangles, 2146371, 26 of 5098348
triangles
Drag select of 2146450, 8421 of 5853100 triangles, 2146371, 27 of 5098348
triangles
Drag select of 2146450, 27528 of 5853100 triangles, 2146493, 13697 of 208732
triangles, 2146447, 4130 of 25736 triangles, 2146371, 13798 of 5098348
triangles, 2146374, 8816 of 1987148 triangles
> ui mousemode right zoom
> ui mousemode right select
> select #2.943
1 model selected
> select #2.9
1 model selected
> ui mousemode right zoom
> ui mousemode right select
> select #2.44
1 model selected
Region has 20 adjacent regions
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_v2.seg" models #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
> ~select
Nothing selected
No regions selected
> select #2.2002
1 model selected
> ui mousemode right zoom
Ungrouped to 2 regions, but did not show all surfaces, see Options
> select #2.1
1 model selected
> select #2.1
1 model selected
Ungrouped to 2 regions, but did not show all surfaces, see Options
Region has 2607 adjacent regions
> ~select
Nothing selected
> select #2.2001
1 model selected
Ungrouped to 2 regions, but did not show all surfaces, see Options
> select #2.1
1 model selected
Ungrouped to 2 regions, but did not show all surfaces, see Options
Only showing 2000 of 34487 regions.
Showing 2000 of 34487 region surfaces
> select #2.2003
1 model selected
Ungrouped to 2 regions, but did not show their surfaces, see Options
Only showing 1000 of 34488 regions.
Showing 1000 of 34488 region surfaces
> select #2.8
1 model selected
Region has 516 adjacent regions
> select #2.9
1 model selected
> select #2.1
1 model selected
> select #2.2
1 model selected
Drag select of 2146460, 2146491, 2146486, 2146470, 2146490, 2146503, 2146496,
2146446, 2146508, 2146504, 2146510, 2146366, 2146444, 2145831, 2145553,
2146273, 2144526, 2146270, 2145825, 2146023, 2144537, 2138328, 2145823,
2133101, 2143513, 2143514, 2133089, 2138599, 2138674, 2122714, 2133083,
2145161, 2138698, 2133067, 2133059, 2103605, 2122613, 2132992, 2133103,
2122719, 2133076, 2103611, 2103387, 2103717, 2103298, 2122591, 2133068,
2000736, 2103710, 2103655, 2103635, 2132990
> select subtract #2.27
51 models selected
> select subtract #2.8
50 models selected
> ~select
Nothing selected
> select #2.280
1 model selected
> select add #2.27
2 models selected
> select #2.27
1 model selected
Region has 38 adjacent regions
> select #2.9
1 model selected
> select #2.8
1 model selected
Region has 516 adjacent regions
> select #2.9
1 model selected
> select #2.1
1 model selected
> select #2.2
1 model selected
> select #2.1965
1 model selected
> select #2.1964
1 model selected
Drag select of 2146460, 2146491, 417839 of 427924 triangles, 2146486, 2146470,
2146490, 2146503, 2146496, 2146446, 2146508, 2146504, 2146510, 2146366,
2146444, 2145831, 2145553, 2146507, 2146273, 2144526, 2146270, 2145825,
2146023, 2144537, 2138328, 2145823, 2133101, 2143513, 2143514, 2133089,
2138599, 2138674, 2122714, 2133083, 2145161, 2138698, 2133067, 2133059,
2103605, 2122613, 2132992, 2133103, 2122719, 2133076, 2103611, 2103387,
2103717, 2103298, 2122591, 2133068, 2000736, 2103710, 2103655, 2103635,
2132990
> select subtract #2.27
52 models selected
> save /Users/garciae/Desktop/image1031.png supersample 3
Grouped 52 regions
> ~select
Nothing selected
> select #2.3
1 model selected
Region has 872 adjacent regions
> select #2.2
1 model selected
> select #2.21
1 model selected
> select #2.1
1 model selected
> select #2.1965
1 model selected
> select #2.9
1 model selected
> select #2.2001
1 model selected
> select #2.1964
1 model selected
Drag select of 2146477, 2146470, 2146497, 2146276, 2146157, 2145561, 2138627,
2138682, 2141760, 2103374, 2132994, 2133098, 2122807, 2133071, 2122771,
2103745, 2133077, 2103351, 2122786, 2133117, 2146513
> select subtract #2.27
20 models selected
Grouped 20 regions
> ~select
Nothing selected
> select #2.3
1 model selected
Region has 941 adjacent regions
> select #2.1
1 model selected
> select #2.9
1 model selected
> select #2.2
1 model selected
> select #2.1965
1 model selected
> select #2.1964
1 model selected
> select #2.2001
1 model selected
Drag select of 2146470, 2145839, 2145569, 2132997, 2138700, 2138701, 2103729,
2122810, 2146514, 3118995 of 3155716 triangles
> select subtract #2.27
8 models selected
Grouped 8 regions
> ~select
Nothing selected
> select #2.3
1 model selected
Region has 936 adjacent regions
> select #2.9
1 model selected
Region has 13393 adjacent regions
> select #2.2005
1 model selected
> select #2.44
1 model selected
Region has 20 adjacent regions
> select add #2.76
2 models selected
Grouped 2 regions
Region has 24 adjacent regions
> select #2.9
1 model selected
> select #2.4
1 model selected
> select add #2.20
2 models selected
Grouped 2 regions
Region has 125 adjacent regions
> select #2.9
1 model selected
> select #2.1965
1 model selected
> select #2.1964
1 model selected
Drag select of 2146458, 2146493, 2145840, 2146168, 2146026, 2138656, 2122205,
2141789, 2133130, 2122483, 2133125, 2133013, 2067500, 2141747, 2102843,
2068005, 2146517, 323110 of 323144 triangles
> select #2.10
1 model selected
Drag select of 2146458, 927024 of 927212 triangles, 2146493, 2145840, 2146168,
2146026, 2138656, 2122205, 2141789, 2133130, 2122483, 2133125, 2133013,
2067500, 2141747, 2102843, 2068005, 2146517, 322919 of 323144 triangles
Grouped 17 regions
Region has 698 adjacent regions
> select #2.9
1 model selected
> select #2.2001
1 model selected
> select #2.2002
1 model selected
> select #2.1965
1 model selected
> select #2.1964
1 model selected
Drag select of 2146482, 2146506, 2146495, 2146499, 2146442, 2146505, 2145796,
2146512, 2145573, 2145176, 2145158, 2146017, 2146018, 2146020, 2143524,
2141784, 2145566, 2145102, 2143528, 2145560, 2141758, 2133112, 2141735,
2122778, 2122781, 2141733, 2133056, 2103484, 2133002, 2132980, 2122798,
2103082, 2122839, 2141764, 2122722, 2122814, 2138676, 2122737, 2132951,
2122799, 2122598, 2122630, 2122817, 2122797, 2103612, 2103315, 2067915,
2133063, 2122795, 2065716, 2122595, 2103086, 2146518
Grouped 53 regions
Region has 725 adjacent regions
> select #2.2002
1 model selected
> select #2.9
1 model selected
> select #2.2001
1 model selected
> select #2.1964
1 model selected
> select #2.1965
1 model selected
> select #2.41
1 model selected
> select #2.4
1 model selected
Ungrouped to 53 regions
> select #2.76
1 model selected
Ungrouped to 17 regions
> select #2.280
1 model selected
Ungrouped to 2 regions
> select #2.76
1 model selected
Ungrouped to 2 regions
> select #2.280
1 model selected
> select #2.280
1 model selected
Ungrouped to 2 regions
> select #2.76
1 model selected
> select #2.76
1 model selected
Ungrouped to 2 regions
> select #2.280
1 model selected
Ungrouped to 2 regions
> select #2.216
1 model selected
Drag select of 2122717, 2122720, 2066647, 2133112, 2143524, 2141733, 2141758,
2133002, 2122598, 2122630, 2145158, 2143528, 2122839, 2146017, 2103484,
2146506, 2103315, 2122778, 2141735, 2145176, 2145573, 2122795, 2133056,
2146020, 2146482, 2145796, 2122781, 2122797, 2141764, 2146512, 2146505,
2122798, 2122814, 2146499, 2103082, 2141784, 2122799, 2145102, 2132980,
2067915, 2065716, 2122737, 2122817, 2145560, 2146442, 2132951, 2122722,
2145566, 2146495, 2133063, 2138676, 2146018, 2122595, 2103086, 2103612,
2067500, 2146493, 2138656, 2146517, 2133013, 2145840, 2133125, 2146026,
2146168, 2133130, 2122483, 2102843, 2141747, 2068005, 2141789, 2122205,
2146429, 2146326, 1989236, 2146104, 2145905, 1991906
Grouped 77 regions
Region has 722 adjacent regions
> select #2.2002
1 model selected
> select #2.2001
1 model selected
> select #2.1964
1 model selected
> select #2.1965
1 model selected
> select #2.9
1 model selected
> select #2.41
1 model selected
> select clear
> select #2.4
1 model selected
Region has 722 adjacent regions
> select #2.9
1 model selected
Region has 13372 adjacent regions
> select #2.9
1 model selected
> select #2.2
1 model selected
> select #2.12
1 model selected
> select #2.1
1 model selected
> select #2.2002
1 model selected
> select #2.4
1 model selected
> select add #2.3
2 models selected
> ~select
Nothing selected
> select #2.3
1 model selected
Region has 936 adjacent regions
> select #2.2
1 model selected
> select #2.9
1 model selected
> select #2.1
1 model selected
> select #2.1965
1 model selected
> select #2.3
1 model selected
> select #2.58
1 model selected
> select add #2.306
2 models selected
> select add #2.178
3 models selected
> select add #2.3
4 models selected
Grouped 4 regions
> select #2.136
1 model selected
> select add #2.33
2 models selected
> select add #2.3
3 models selected
Grouped 3 regions
> select #2.93
1 model selected
> select add #2.318
2 models selected
> select add #2.596
3 models selected
> select add #2.524
4 models selected
> select add #2.152
5 models selected
> select add #2.323
6 models selected
> select add #2.798
7 models selected
> select add #2.3
8 models selected
Grouped 8 regions
> ~select
Nothing selected
> select #2.248
1 model selected
> select add #2.837
2 models selected
> select add #2.957
3 models selected
> select add #2.835
4 models selected
> select add #2.847
5 models selected
> select add #2.522
6 models selected
> select add #2.741
7 models selected
Region has 10 adjacent regions
> select #2.1
1 model selected
> select #2.9
1 model selected
Ungrouped to 2 regions
> select #2.8
1 model selected
> select #2.6
1 model selected
> select #2.8
1 model selected
Region has 9028 adjacent regions
> select #2.8
1 model selected
> select #2.2
1 model selected
> select #2.6
1 model selected
> select #2.52
1 model selected
> select #2.8
1 model selected
> select #2.25
1 model selected
Region has 27 adjacent regions
> select #2.8
1 model selected
> select #2.4
1 model selected
> select #2.4
1 model selected
Region has 722 adjacent regions
> select #2.8
1 model selected
> select #2.12
1 model selected
> select #2.2005
1 model selected
> select #2.2004
1 model selected
> select #2.2002
1 model selected
> select #2.2004
1 model selected
> select #2.7
1 model selected
> select #2.1964
1 model selected
> select #2.1965
1 model selected
> select #2.2001
1 model selected
> select #2.41
1 model selected
> select #2.242
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.377
1 model selected
> select add #2.69
2 models selected
> select add #2.532
3 models selected
> select add #2.283
4 models selected
> select add #2.544
5 models selected
> select add #2.120
6 models selected
> select add #2.25
7 models selected
> select add #2.943
8 models selected
> select add #2.461
9 models selected
> select add #2.538
10 models selected
> select add #2.682
11 models selected
> select add #2.660
12 models selected
> select add #2.505
13 models selected
> select add #2.144
14 models selected
> select add #2.4
15 models selected
> select add #2.171
16 models selected
> select add #2.182
17 models selected
Grouped 17 regions
> ~select
Nothing selected
> select #2.1014
1 model selected
> select add #2.134
2 models selected
> select add #2.401
3 models selected
> select add #2.571
4 models selected
> select add #2.705
5 models selected
> select add #2.898
6 models selected
> select add #2.594
7 models selected
> select add #2.4
8 models selected
Grouped 8 regions
> ~select
Nothing selected
> select #2.4
1 model selected
> ~select
Nothing selected
> select #2.301
1 model selected
> select add #2.4
2 models selected
Grouped 2 regions
> ~select
Nothing selected
> select #2.356
1 model selected
> select add #2.60
2 models selected
> select add #2.215
3 models selected
> select add #2.545
4 models selected
> select subtract #2.545
3 models selected
> select add #2.4
4 models selected
> select subtract #2.60
3 models selected
Grouped 3 regions
> ~select
Nothing selected
> select #2.60
1 model selected
Ungrouped to 2 regions
> select #2.9
1 model selected
> select #2.1017
1 model selected
> select add #2.4
2 models selected
Grouped 2 regions
> select #2.4
1 model selected
> select #2.9
1 model selected
> ~select
Nothing selected
> select #2.846
1 model selected
> select add #2.743
2 models selected
> select add #2.4
3 models selected
Grouped 3 regions
> ~select
Nothing selected
> select #2.27
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> ~select
Nothing selected
> select #2.1965
1 model selected
Region has 1216 adjacent regions
> select #2.2
1 model selected
> select #2.8
1 model selected
> select #2.1965
1 model selected
Ungrouped to 2 regions
> select #2.16
1 model selected
Region has 576 adjacent regions
> select #2.8
1 model selected
> select #2.4
1 model selected
> select add #2.3
2 models selected
> ~select
Nothing selected
> select #2.3
1 model selected
Ungrouped to 2 regions
> ~select
Nothing selected
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_v3.seg" models #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
> select #2.20
1 model selected
Region has 1010 adjacent regions
> select #2.8
1 model selected
> select #2.1964
1 model selected
Ungrouped to 2 regions
> select #2.3
1 model selected
Region has 719 adjacent regions
> select #2.8
1 model selected
> select #2.4
1 model selected
> select #2.22
1 model selected
Ungrouped to 2 regions
> select #2.24
1 model selected
Ungrouped to 2 regions
> select #2.22
1 model selected
Ungrouped to 2 regions
> select #2.24
1 model selected
Ungrouped to 2 regions
> select #2.22
1 model selected
Ungrouped to 2 regions
> select #2.24
1 model selected
Ungrouped to 2 regions
> select #2.22
1 model selected
Ungrouped to 2 regions
Drag select of 2141786, 2143497, 2141782, 2137964, 2137967
Grouped 5 regions
> select #2.22
1 model selected
Region has 64 adjacent regions
> select #2.3
1 model selected
> select #2.27
1 model selected
> select #2.28
1 model selected
> select #2.2002
1 model selected
> select #2.22
1 model selected
> select add #2.483
2 models selected
> select add #2.4
3 models selected
Grouped 3 regions
> select #2.4
1 model selected
> select add #2.587
2 models selected
Grouped 2 regions
> ~select
Nothing selected
> select #2.4
1 model selected
Region has 805 adjacent regions
> select #2.8
1 model selected
> select #2.4
1 model selected
> select #2.9
1 model selected
Ungrouped to 2 regions
> select #2.22
1 model selected
Ungrouped to 2 regions
> select #2.9
1 model selected
Ungrouped to 2 regions
> select #2.22
1 model selected
Ungrouped to 2 regions
> select #2.9
1 model selected
Ungrouped to 2 regions
> select #2.49
1 model selected
> select #2.22
1 model selected
> select #2.662
1 model selected
> select add #2.33
2 models selected
> select add #2.49
3 models selected
> select add #2.48
4 models selected
> select add #2.44
5 models selected
Grouped 5 regions
Region has 6 adjacent regions
> select #2.8
1 model selected
> select #2.9
1 model selected
> select add #2.4
2 models selected
Grouped 2 regions
Region has 806 adjacent regions
> select #2.2002
1 model selected
> select #2.4
1 model selected
> select #2.22
1 model selected
> select add #2.8
2 models selected
Grouped 2 regions
> select #2.8
1 model selected
Ungrouped to 2 regions
> select #2.3
1 model selected
> select #2.2001
1 model selected
> select #2.41
1 model selected
> select #2.16
1 model selected
> select #2.25
1 model selected
> select add #2.27
2 models selected
Grouped 2 regions
> select #2.22
1 model selected
> select #2.22
1 model selected
Ungrouped to 2 regions
> select #2.25
1 model selected
> select #2.27
1 model selected
Ungrouped to 2 regions
> select #2.22
1 model selected
> select #2.33
1 model selected
Ungrouped to 2 regions
> select #2.27
1 model selected
> select #2.44
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
Ungrouped to 2 regions
> select #2.44
1 model selected
Ungrouped to 2 regions
> select #2.49
1 model selected
> select add #2.48
2 models selected
> select #2.22
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
> select #2.44
1 model selected
> select #2.58
1 model selected
Ungrouped to 2 regions
> select #2.22
1 model selected
Ungrouped to 2 regions
> select #2.61
1 model selected
Drag select of 2145870, 7579 of 812556 triangles, 2145653, 11226 of 502832
triangles, 2145658, 1923 of 308240 triangles
Drag select of 2145255, 283849 of 315708 triangles, 2145870, 686652 of 812556
triangles, 2145653, 491853 of 502832 triangles, 2145658
Ungrouped to 8 regions
> select #2.65
1 model selected
> select #2.67
1 model selected
> select #2.69
1 model selected
> select #2.65
1 model selected
Region has 435 adjacent regions
> select #2.44
1 model selected
> select #2.67
1 model selected
> select #2.49
1 model selected
> select #2.65
1 model selected
> select #2.16
1 model selected
> select #2.8
1 model selected
> select #2.3
1 model selected
> select #2.69
1 model selected
Region has 348 adjacent regions
> select #2.2
1 model selected
> select add #2.6
2 models selected
> select add #2.67
3 models selected
> select add #2.44
4 models selected
> select #2.3
1 model selected
Drag select of 2146536, 466 of 3087316 triangles, 2145643, 914 of 460436
triangles
> ~select
Nothing selected
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_v4.seg" models #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
> select #2.4
1 model selected
> select #2.20
1 model selected
> ~select
Nothing selected
> select #2.69
1 model selected
> ~select
Nothing selected
Only showing 1000 of 34312 regions.
Showing 1000 of 34312 region surfaces
> select #2.239
1 model selected
> select add #2.941
2 models selected
> select add #2.162
3 models selected
> select add #2.717
4 models selected
> select add #2.316
5 models selected
> select add #2.265
6 models selected
Deleted 6 regions
> select #2.82
1 model selected
> select add #2.417
2 models selected
> select add #2.408
3 models selected
Deleted 3 regions
> select #2.921
1 model selected
> select add #2.2005
2 models selected
> select subtract #2.2005
1 model selected
> select add #2.512
2 models selected
> select add #2.397
3 models selected
> select add #2.14
4 models selected
Deleted 4 regions
> select #2.194
1 model selected
Deleted 1 regions
> select #2.2005
1 model selected
Ungrouped to 2 regions
> select #2.10
1 model selected
Deleted 1 regions
> select #2.1
1 model selected
Ungrouped to 2 regions
> select #2.10
1 model selected
> ~select
Nothing selected
> save /Users/garciae/Desktop/image1032.png supersample 3
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_v5.seg" models #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
> select #2.20
1 model selected
[deleted to fit within ticket size limits]
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_-650_v1.seg" models
> #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
Showing 10803 region surfaces
Drag select of 2068140, 2000181, 822 of 1164 triangles, 1559392, 1627700,
1127362, 159 of 420 triangles, 1112775, 982815, 656625, 223 of 276 triangles,
1110605, 1129404, 242 of 328 triangles, 732724, 1135618, 152 of 248 triangles,
1137642, 281 of 364 triangles, 1054709, 1161496, 1025290, 1166641, 1170080,
1114905, 1161498, 1050084, 1159669, 1159668, 168 of 340 triangles, 1106266,
1093214, 1088643, 1173115, 1166640, 1041172, 987348, 814556, 1086291, 237 of
260 triangles, 1043313, 66 of 236 triangles, 1050129, 1149807, 991823
Drag select of 1579154, 240 of 600 triangles, 1539224, 1593758, 324 of 580
triangles, 1593277, 1115224, 1133882, 1592971, 1627310, 498 of 608 triangles,
1016614, 208 of 480 triangles, 1607586, 1126129, 1061581, 1130247, 103 of 380
triangles, 1132196, 1108677, 1146326, 1132184, 1039105, 1115477, 1007635, 224
of 312 triangles, 1082149, 1025509, 1032445, 188 of 316 triangles, 1113047,
1082251, 1136356, 1158489, 1141936, 1005324, 1134176, 1109132, 1075271,
1125441, 1106655, 1079665, 1025520, 1054866, 1000952, 107 of 240 triangles,
1075272, 1146577, 1123892, 95 of 264 triangles, 1172500, 1057283, 1054870, 106
of 252 triangles, 1100459, 1043610, 45 of 248 triangles, 1091194, 1021076, 121
of 232 triangles, 1070488, 1152629, 1018759, 1059643, 21 of 272 triangles,
1089010, 30 of 240 triangles, 1134325, 128 of 240 triangles, 1144651, 1098147
Drag select of 1590466, 320 of 468 triangles, 1133636, 1110675, 904272,
1025375, 16 of 292 triangles, 1149852, 1117002, 1020925, 1090991, 1102240,
1137710, 1133574, 130 of 292 triangles, 1065869, 1072653, 1114983, 1112843,
1072677, 1127459, 893570, 36 of 244 triangles, 1052396, 844365, 129 of 284
triangles, 1125311, 1038982, 1147874, 1123182, 1135592, 1121193, 1137735,
976161, 143 of 216 triangles, 1018602, 1036693, 153 of 216 triangles, 1099953,
1133615, 1133601, 76 of 240 triangles, 980675
Deleted 127 regions
Drag select of 1538321, 26 of 552 triangles, 1627781, 187 of 676 triangles,
1468824, 353 of 496 triangles, 1592211, 413 of 684 triangles, 887348, 400 of
500 triangles, 859648, 138 of 456 triangles, 1626411, 1626717, 263 of 460
triangles, 1042203, 282 of 360 triangles, 1592178, 1043999, 937046, 1070915,
935228, 1064431, 994593, 218 of 320 triangles, 933102, 211 of 332 triangles,
1118438, 89 of 316 triangles, 1018970, 994373, 1066949, 284 of 308 triangles,
1051223, 46 of 248 triangles, 1026052, 39 of 284 triangles, 1171351, 290 of
304 triangles, 1115864, 97 of 248 triangles, 1077819, 123 of 252 triangles,
1026272, 168 of 240 triangles, 658028, 253 of 296 triangles, 1089556, 220 of
244 triangles, 676743, 10 of 248 triangles, 1098982, 1075816, 958816, 1142829,
106 of 244 triangles, 1124173, 961073, 1016877, 1001645, 1044429, 1030402, 165
of 256 triangles, 867902, 996465
Drag select of 812463, 14 of 452 triangles, 880514, 1038955, 938906, 296 of
436 triangles, 1159676, 387 of 412 triangles, 1121102, 936714, 238 of 276
triangles, 1000702, 303 of 304 triangles, 1143692, 38 of 312 triangles,
1074769, 254 of 272 triangles, 1023012, 1147846, 1131451, 195 of 300
triangles, 1090796, 30 of 256 triangles, 900002, 1108461, 304 of 308
triangles, 1086301, 994041, 199 of 292 triangles, 1034451, 1084085, 965169,
224 of 344 triangles, 971737, 825193, 204 of 276 triangles, 1114918, 908623,
1125255, 910714, 16 of 244 triangles, 991756, 203 of 256 triangles, 1002929,
1014188, 919477, 915215, 1114933, 1061394, 1020896, 1133542, 1077167, 980625,
1072608, 987337, 164 of 252 triangles, 1137616, 1121138, 1108456, 1097733,
1149787, 1084069, 1020888
Drag select of 1116936, 1168399, 1133532, 1020883, 170 of 328 triangles,
1155807, 1170067, 1108480, 1163239, 1173046, 176 of 236 triangles
Deleted 98 regions
Drag select of 1153848, 1139722, 1163202, 234 of 372 triangles, 1106228,
1141713, 1137617, 134 of 340 triangles, 1110537, 1168377, 1127380, 1137628,
1141664, 1159647, 1121066, 1168408, 1163224, 1127366, 221 of 244 triangles,
1116859, 165 of 264 triangles
Drag select of 1102081, 255 of 280 triangles, 1102100, 295 of 300 triangles,
971765, 221 of 288 triangles, 1137618, 991837, 106 of 352 triangles, 1059088,
178 of 264 triangles, 947731, 62 of 264 triangles, 965203, 90 of 264 triangles
Drag select of 1038909, 85 of 288 triangles, 1166584, 1143679, 1088588,
1050073, 62 of 324 triangles, 1166562
Drag select of 1114799, 1067932, 121 of 272 triangles, 1063419, 37 of 284
triangles, 1131315, 1104035, 1168329, 1171576, 180 of 260 triangles
Deleted 38 regions
> select #2.4
1 model selected
Ungrouped to 2 regions
> select #2.90
1 model selected
Ungrouped to 2 regions
> select #2.73
1 model selected
> select #2.4
1 model selected
Region has 849 adjacent regions
> select #2.8
1 model selected
> select #2.9
1 model selected
> select add #2.3
2 models selected
> select add #2.2
3 models selected
> select #2.73
1 model selected
> select add #2.93
2 models selected
> select #2.7031
1 model selected
> select #2.4479
1 model selected
> select #2.4
1 model selected
Drag select of 2146324, 2121549, 2120988, 2138340, 2101605, 2033646, 2132581,
2102546, 2102314, 2121635, 2101952, 2060404, 2067762, 2103600, 2102979,
1973900, 1986396, 2064342, 1989074, 1981811, 1975721, 2061270, 2067175,
1986256, 2066614, 2065196, 2067116, 2067666, 2065670, 1991611, 2122394,
1715190, 2067214, 1811904, 1984873, 1987660, 1994100, 1999294, 1988840,
1989013, 1699619, 1992824, 1984764, 1723296, 1765291, 1978836, 1996638,
1812284, 1812373, 1774480, 1866821, 1989018, 1818694, 1818653, 1996600,
2000575, 1818760, 1774333, 1766472, 1841287, 1988985, 2000562, 1825105,
1855526, 1836100, 1998043, 1996627, 1437453, 1390095, 1866949, 1995496,
1846650, 1825007, 1995341, 1775321, 483143, 1586338, 1859269, 1873015,
1458398, 1846447, 1830189, 1830704, 1791159, 1836319, 1413511, 1824563,
1825082, 1999069, 1841326, 1863207, 1999220, 1999359, 2000639, 1862531,
1862944, 1507314, 1996685, 2000450, 1391015, 1824692, 1529731, 1846361,
1866884, 1873145, 1850997, 1346615, 1851167, 1507271, 1485182, 1566834,
1873281, 1507764, 1411468, 1480789, 1866664, 1850563, 1851085, 1483812,
1873109, 1859538, 1586408, 1568656, 1366161, 1867034, 1870200, 1584954,
1855361, 1549936, 1873387, 1870239, 1855430, 1389186, 1367227, 354884,
1459856, 1484174, 1621055, 1854741, 1846042, 1550851, 1873459, 1507647,
1630591, 1437670, 517791, 502146, 1611327, 1611863, 1859131, 1413760, 486358,
547141, 1568427, 1461531, 1863061, 1528736, 1584659, 370214, 1866631, 337301,
1529446, 1507762, 1505830, 373169, 531604, 1630853, 1503031, 527530, 522087,
1568589, 1612086, 430027, 1462088, 1507912, 1568646, 1549001, 558157, 1620942,
445562, 359678, 296427, 509063, 1550223, 536149, 1866843, 1612733, 1601062,
346906, 475808, 497597, 508813, 1586353, 428465, 1547944, 1629489, 1530073,
478534, 1570070, 328942, 498836, 1549170, 497440, 1630228, 445661, 387328,
1621197, 1529024, 510908, 1599937, 365491, 423189, 1550849, 378482, 352088,
511007, 1567483, 450275, 495924, 497487, 409045, 1612773, 389200, 459700,
1600958, 1413725, 504612, 1630851, 334602, 1611381, 1506915, 1506833, 1586085,
1586044, 1585568, 459255, 540338, 475564, 484741, 1612325, 1597660, 1585816,
461187, 1567425, 1567284, 459791, 1630860, 1630025, 520828, 423940, 1611695,
446582, 541951, 401786, 1600184, 518947, 399650, 477081, 517695, 1630744,
465845, 528974, 1598093, 464869, 464900, 418752, 470560, 500806, 441626,
1621880, 1621795, 1621352, 523825, 462947, 462632, 1598132, 404242, 1584516,
464198, 511967, 365162, 332374, 401451, 540476, 561762, 425616, 1622340,
1621692, 523790, 1611126, 504370, 423688, 446797, 373759, 299499, 454264,
508766, 507034, 526149, 543276, 1550226, 519111, 406860, 356928, 491098,
458188, 488329, 1600010, 375785, 492527, 332692, 510672, 1569438, 483799,
529750, 538158, 450399, 491102, 495875, 524357, 529295, 529289, 545053,
448727, 1586007, 485327, 326036, 1569095, 1568364, 1567930, 489875, 504587,
499559, 417258, 1631004, 1621689, 426651, 549339, 386357, 420945, 412282,
492487, 442801, 489775, 490089, 510985, 494249, 423475, 332361, 535049,
447402, 490998, 497744, 557784, 497874, 513931, 482061, 439456, 467333,
443129, 523811, 494099, 401576, 374678, 492694, 465919, 469552, 335914,
467792, 366366, 481769, 543497, 440658, 467366, 536092, 443491, 378581,
548930, 532677, 356783, 397281, 514203, 465649, 487798, 459519, 449057,
475135, 480042, 484698, 470982, 552925, 502597, 438657, 439444, 513938,
391520, 318103, 378455, 395321, 320362, 461572, 449413, 536914, 531250,
467920, 427877, 472633, 314599, 450607, 452920, 558438, 320733, 416974,
417582, 452877, 524025, 465665, 428403, 478599, 480236, 522416, 517564,
547267, 290650, 383841, 407366, 481609, 378459, 447475, 461582, 509168,
442568, 456056, 504347, 491193, 448537, 448579, 454234, 474076, 554372,
329440, 454870, 468863, 466398, 450824, 506199, 486855, 554262, 386110,
478635, 461132, 496291, 565283, 527755, 454539, 520548, 438365, 383667,
383734, 561490, 321251, 324257, 349641, 296848, 434566, 511132, 533299,
456355, 340289, 401863, 491318, 473620, 374473, 409906, 493147, 373157,
475186, 418901, 568903, 362408, 477015, 444766, 378919, 438509, 542079,
407452, 455031, 519371, 486637, 452808, 393955, 417353, 285142, 284936,
480502, 573375, 374211, 402747, 422096, 502162, 406817, 367947, 472696,
406978, 406890, 486252, 480187, 288575, 512294, 529248, 541513, 415091,
400246, 459937, 554843, 510689, 483489, 472575, 462847, 466443, 329035,
329016, 416289, 373660, 533322, 392015, 421471, 474265, 394107, 492684,
522120, 407123, 504490, 547225, 426585, 523871, 440492, 509200, 467273,
382518, 548963, 491093, 518980, 416817, 330219, 499357, 359705, 397237,
376653, 448408, 452569, 320243, 454074, 464209, 368456, 491714, 456637,
450675, 486763, 413995, 522552, 521160, 381125, 438357, 507698, 296712,
540370, 440971, 395062, 480556, 475461, 504517, 432419, 302374, 338480,
429909, 426583, 524267, 560240, 433116, 512195, 480696, 428857, 462575,
422151, 467555, 473544, 432267, 494380, 516229, 478825, 359718, 359729,
507293, 525675, 414452, 345936, 525858, 456389, 505706, 362507, 494236,
397459, 405161, 402481, 365131, 373123, 479993, 535050, 366367, 388930,
531111, 554467, 481961, 540425, 380984, 308859, 508979, 513868, 425549,
425613, 437508, 404847, 569514, 423982, 563112, 491564, 379302, 511162,
468974, 457701, 481711, 481722, 497300, 495871, 404144, 434872, 512215,
371589, 434745, 419314, 287640, 532854, 553004, 370488, 524021, 384281,
492758, 404048, 483507, 494830, 376503, 491664, 472569, 460973, 455939,
509115, 501355, 373124, 475759, 501184, 559652, 496037, 460903, 388913,
566952, 499211, 381156, 536070, 432337, 475254, 448832, 407552, 401641,
487950, 489422, 443201, 467452, 511187, 436586, 412105, 529645, 507406,
483892, 480231, 531034, 446594, 458147, 343722, 375821, 382416, 529561,
502464, 512267, 360830, 432620, 430239, 459290, 550806, 502726, 532782,
532793, 527303, 492868, 359600, 435269, 517226, 428738, 370391, 348604,
487801, 475318, 411714, 470531, 455854, 449046, 409673, 439002, 478720,
488509, 508781, 460870, 477394, 538806, 438900, 524364, 294015, 516960,
438738, 311391, 419262, 561661, 399452, 545789, 430899, 513780, 383831,
464719, 432398, 536882, 513693, 378610, 441217, 565019, 494426, 480591,
480636, 533156, 483286, 428787, 386359, 373023, 488383, 290954, 495894,
478524, 502443, 457716, 454671, 505450, 505456, 394547, 525920, 464255,
401673, 449128, 465771, 478371, 461381, 461011, 421098, 348865, 472020,
447319, 503809, 407651, 405015, 521178, 517555, 477332, 524132, 440776,
480377, 475281, 418616, 519369, 495802, 495715, 497426, 497454, 335438,
407789, 429860, 331882, 360249, 314374, 484728, 396592, 569541, 517043,
467488, 529627, 427871, 514114, 445126, 494447, 409222, 531049, 521000,
428519, 499089, 418856, 314570, 428850, 314255, 541970, 480081, 482157,
365260, 550594, 425416, 404618, 507056, 472174, 354082, 538340, 527326,
456558, 464185, 516084, 516110, 510966, 435261, 483530, 428684, 337775,
489649, 472617, 457821, 455906
Deleted 840 regions
Showing 9702 region surfaces
> select #2.73
1 model selected
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_-650_v1.seg" models
> #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
Ungrouped to 2 regions
> select #2.11
1 model selected
> select #2.25
1 model selected
> select #2.11
1 model selected
Region has 1131 adjacent regions
> select #2.9
1 model selected
> select add #2.4
2 models selected
> select add #2.2
3 models selected
> select #2.25
1 model selected
> select #2.9597
1 model selected
> select add #2.540
2 models selected
> select #2.7956
1 model selected
> select add #2.5602
2 models selected
> select add #2.9103
3 models selected
> select #2.53
1 model selected
> select #2.2720
1 model selected
> select #2.1164
1 model selected
> select #2.1112
1 model selected
> select #2.93
1 model selected
Drag select of 2065229, 746 of 1740 triangles, 1841617, 1508440, 503 of 604
triangles, 1613009, 1601057, 572907, 594312, 602131, 135 of 328 triangles,
550770, 545403, 567194, 2146044, 21378 of 1093256 triangles
> ~select
Nothing selected
> select #2.11
1 model selected
Drag select of 2146483, 2145060, 2145119, 2145005, 2145549, 2145154, 2141526,
2141513, 2141691, 2144463, 2143518, 2138235, 2138377, 2120692, 2102138,
2141773, 2121115, 2138508, 2099350, 2122587, 2098915, 2102356, 2132697,
2103093, 2101293, 2062700, 2065714, 2122585, 2102340, 2101809, 2101780,
2122270, 2062616, 2055101, 1960100, 2122609, 1897700, 2062116, 2061216,
2065760, 2065229, 2060827, 2064334, 2063870, 1961927, 2057837, 2063062,
2060941, 2062758, 1966732, 2060953, 1947441, 2065739, 2067455, 2065355,
2067376, 1993253, 1999075, 1975965, 2103373, 2103464, 1683028, 2061416,
2062668, 1989128, 1990750, 1990642, 1982042, 2067812, 1996508, 1966434,
1999526, 1716611, 1986729, 1994498, 1997132, 1989464, 2066773, 1777737,
1508091, 1805901, 1977683, 2001051, 1714437, 1987652, 1983641, 2062735,
1985072, 1836788, 1991937, 2067861, 1994326, 1776842, 1807630, 1807437,
1991810, 1806668, 1819582, 1998245, 1986426, 1851360, 1873819, 1996909,
1985042, 1866893, 1995727, 1819572, 1767009, 2000808, 1806316, 1999444,
1998330, 2000961, 1842126, 1995819, 1818525, 1750863, 1825655, 1326695,
1999540, 1807323, 1998313, 1807979, 1513586, 1832795, 1814298, 1999672,
1864433, 1855188, 1997242, 1309270, 1867300, 1831292, 1836954, 1851778,
1792091, 1416804, 1863908, 1874405, 1860733, 572591, 1851771, 1273373,
1856301, 1991730, 1832532, 1859983, 1851784, 1871211, 1443813, 1864081,
1463976, 1462532, 1531263, 1417392, 1415086, 1305270, 1873678, 1326473,
1489976, 1463375, 1485183, 1624417, 1847290, 1631885, 1373516, 2000710,
1611357, 1295164, 1396083, 1842027, 1445338, 1515176, 720425, 1874291,
1848082, 448737, 1852160, 1842326, 1841617, 1347674, 1418491, 1510273,
1508440, 1589009, 1349854, 1536559, 1552910, 1856718, 1531755, 842725,
1489679, 1575673, 1552117, 1440085, 1623857, 589803, 478405, 1536314, 1873539,
1614434, 1613009, 1859338, 1510814, 1818700, 750593, 789045, 1533056, 1623258,
1511975, 1589931, 1632021, 1864469, 1600645, 776357, 590064, 1630488, 1613657,
657445, 882922, 407404, 876415, 502338, 1611893, 1415180, 1869740, 1588378,
1575391, 656789, 1572621, 585814, 1623799, 555755, 1514351, 1864261, 1503856,
1590836, 1590146, 614734, 1569420, 1874009, 491410, 1534863, 1867382, 726777,
1509413, 1489946, 797609, 1574374, 1533760, 1532010, 1510184, 956529, 1588308,
624269, 1574877, 1462457, 1530955, 711225, 1612488, 1603229, 401867, 878506,
1588700, 1586763, 1586169, 1574937, 332777, 1571547, 511944, 568908, 481768,
754734, 1624797, 1533654, 1623037, 706903, 565055, 1605085, 1587589, 793388,
1572453, 1570929, 1570601, 518761, 1347392, 675906, 340394, 1601057, 750328,
541466, 684136, 1462441, 825319, 1439846, 1530953, 1416420, 1602996, 1589663,
412138, 696403, 622225, 1464786, 440918, 1631734, 1631407, 1622861, 1615850,
965375, 709208, 481878, 1602073, 1598969, 1589735, 1492786, 774064, 1574906,
1573262, 522067, 1631546, 836131, 767836, 1622860, 1622611, 757288, 867978,
600176, 1590687, 572907, 1575637, 900217, 572442, 696947, 1554720, 1633346,
1632685, 1631705, 1631012, 1630977, 1624563, 688342, 1589044, 739446, 1586745,
923972, 657267, 1575844, 1574930, 590121, 679977, 846641, 600281, 756943,
690728, 705223, 1513922, 1602776, 1602048, 771820, 570643, 376448, 638665,
1588101, 1601164, 563169, 1573819, 599783, 1552388, 694765, 1632068, 593724,
840249, 1625925, 1615317, 682601, 644625, 878544, 829596, 771848, 1590437,
574445, 622743, 1586909, 591768, 917672, 530664, 394068, 527318, 776210,
1569542, 921838, 737263, 522472, 607964, 767619, 853071, 838550, 374070,
561737, 1631746, 715970, 593820, 557636, 1612455, 859583, 795652, 857408,
1585255, 1572893, 1572411, 520859, 735106, 582394, 594312, 515751, 561511,
590295, 1631208, 654800, 707510, 726548, 726560, 1601234, 926080, 778666,
679683, 653569, 838233, 559876, 634393, 748315, 669869, 612660, 602131,
683895, 685874, 528890, 895962, 586063, 628310, 657077, 249389, 454115,
1572010, 669569, 622220, 819188, 561266, 788977, 683946, 730699, 769703,
634997, 1588740, 1586953, 582326, 648728, 844515, 523762, 548849, 555805,
525778, 612236, 616079, 797667, 722436, 692510, 919753, 597822, 878622,
726791, 706890, 802045, 1612840, 821220, 642609, 357186, 1587618, 1586220,
908979, 541684, 591777, 671988, 671902, 778668, 776291, 1570237, 893853,
496036, 586248, 612036, 677781, 799987, 692566, 624341, 692257, 603865,
726367, 1622555, 756907, 827515, 1613408, 1601236, 442687, 717902, 936962,
698610, 746622, 719934, 913203, 795914, 612115, 557972, 1631515, 654774,
698459, 246523, 840259, 726702, 726468, 690529, 523827, 436495, 787157,
934936, 329781, 529002, 491177, 574364, 867867, 604350, 492549, 659008,
320902, 680353, 510745, 797802, 698562, 859443, 759107, 737299, 594305,
678164, 833902, 527158, 419135, 676246, 825327, 683871, 686029, 728588,
842711, 730856, 819231, 702840, 769966, 814711, 741671, 855197, 808462,
580493, 739429, 652861, 574348, 939237, 656877, 608316, 893944, 776281,
850952, 616239, 614821, 503799, 846621, 561542, 898003, 697020, 724153,
812629, 851070, 603963, 682485, 346623, 612502, 688097, 636446, 771881,
808472, 774031, 574330, 580064, 655207, 667951, 823383, 778452, 620296,
421102, 611992, 601714, 323971, 583895, 409277, 800130, 724215, 789056,
434361, 715949, 606175, 603893, 780758, 724322, 752564, 887292, 705109,
819051, 757368, 827496, 731051, 628628, 878791, 853252, 650656, 614197,
430041, 908808, 609990, 646647, 548556, 656886, 865769, 585898, 913332,
669276, 565167, 741968, 550770, 246598, 518714, 583882, 624844, 870042,
694375, 644580, 595914, 784773, 643164, 812597, 928280, 468981, 756874,
757358, 406767, 819379, 703067, 462931, 851314, 648600, 821272, 765469,
510434, 688136, 570601, 544965, 620216, 814999, 949976, 950059, 561385,
900294, 823315, 778466, 520418, 737403, 816936, 348870, 522402, 614461,
665117, 789257, 797719, 784782, 595816, 614560, 607924, 784961, 709017,
876416, 726756, 791115, 786998, 602085, 624508, 373901, 624208, 947874,
700972, 688441, 632991, 709601, 910925, 512219, 928408, 652855, 505431,
346044, 718022, 258146, 859345, 921865, 741767, 817164, 402295, 634882,
767631, 870024, 677833, 589742, 722399, 915482, 784882, 836220, 593748,
653179, 570559, 872164, 563122, 639053, 705145, 728598, 730834, 769748,
555750, 660983, 486233, 887201, 771865, 874500, 732960, 739691, 536507,
954346, 646606, 657341, 919651, 880832, 656857, 746177, 698833, 698497,
269874, 719880, 679703, 588006, 844721, 599770, 545081, 550436, 323248,
572739, 722065, 677681, 632449, 598117, 452233, 748289, 624321, 618386,
821109, 654856, 726382, 707036, 661413, 639032, 532899, 705302, 842430,
802093, 930411, 769745, 769741, 731032, 545403, 947953, 685855, 774147,
418806, 681822, 789166, 804189, 688725, 829588, 337921, 831860, 867815,
636859, 507106, 610030, 632303, 733414, 939218, 510730, 698505, 859451,
850938, 679615, 763377, 713955, 376577, 924062, 454367, 642985, 737325,
814921, 665581, 795498, 844569, 522642, 765558, 546850, 694864, 555999,
722033, 694535, 249312, 610394, 321135, 522667, 645288, 724560, 724586,
825315, 425574, 683889, 706928, 556065, 902396, 704941, 705002, 507207,
601990, 581999, 603927, 296552, 717673, 889460, 821320, 454201, 919877,
630781, 642548, 622406, 848880, 863886, 739962, 732827, 496081, 836359,
715780, 718132, 823255, 823238, 900188, 469252, 750681, 778467, 719829,
863756, 913354, 626251, 735404, 816993, 855449, 795707, 489813, 742075,
611968, 620869, 778416, 844561, 844501, 539975, 550371, 495929, 783065,
677748, 789258, 797751, 595782, 622584, 692180, 780603, 534592, 618213,
744307, 675708, 684349, 726324, 726599, 557604, 728670, 819048, 237915,
703257, 484926, 673927, 702815, 340319, 673361, 682003, 821068, 821091,
628604, 343784, 829788, 688323, 857524, 688006, 669395, 667583, 529129,
772108, 659160, 658947, 658948, 544984, 507377, 620448, 620408, 923896,
733001, 492930, 485034, 750757, 917545, 939164, 865732, 698570, 716005,
831909, 893935, 746331, 719824, 256235, 270756, 913148, 678150, 523759,
365360, 782717, 608120, 587740, 677654, 722547, 759151, 419178, 825334,
616063, 789039, 748330, 748358, 508880, 724161, 784804, 784934, 615958,
597812, 593742, 752938, 675546, 567118, 878588, 683954, 814836, 661486,
641202, 728570, 651003, 515722, 604082, 769773, 770026, 713645, 581952,
329791, 682274, 682037, 673473, 737665, 296618, 748386, 829703, 688144,
688133, 643360, 910912, 529123, 772002, 876521, 659272, 928396, 923990,
381547, 598242, 428181, 646629, 919639, 561346, 557701, 548531, 656812,
831933, 679579, 612599, 893780, 715639, 696502, 638811, 669181, 631042,
667671, 720172, 334825, 340629, 865859, 522371, 578019, 838264, 833887,
522078, 834202, 778695, 530810, 665229, 546802, 665110, 783043, 677646,
632425, 616065, 885133, 885141, 754728, 789435, 825583, 756935, 676201,
411833, 676015, 715971, 744365, 604184, 603887, 780783, 780759, 593714,
709016, 473677, 812628, 840322, 707439, 567194, 567157, 565076, 755136,
755083, 639117, 902402, 801892, 802084, 690188, 604036, 602081, 934904,
673793, 814779, 568864, 673417, 457959, 681981, 821139, 616627, 891602,
891578, 859462, 718235, 804110, 688123, 654900, 771855, 570598, 887390,
290947, 659447, 772030, 492532, 541491, 652829, 652797, 733422, 848842,
584328, 686315, 880815, 656895, 895827, 671812, 797625, 671528, 510695,
589859, 655501, 711767, 850968, 793682, 719782, 679659, 455912
Deleted 1117 regions
Showing 8586 region surfaces
Drag select of 1596945, 99 of 556 triangles, 1619905, 108 of 584 triangles,
213690, 84 of 472 triangles, 213720, 23 of 340 triangles, 116668, 254754,
281270, 129 of 244 triangles, 304813, 162 of 220 triangles, 83732, 161694,
216684, 44 of 284 triangles, 237346, 216693, 31 of 248 triangles, 231309
Drag select of 969260, 143 of 508 triangles, 1538867, 232 of 488 triangles,
1029753, 366 of 496 triangles, 1018396, 128 of 488 triangles, 1633878, 962934,
995896, 897686, 893379, 286 of 396 triangles, 1591114, 425 of 504 triangles,
938759, 980423, 1065323, 138 of 416 triangles, 901980, 91 of 324 triangles,
919220, 212 of 304 triangles, 967198, 884834, 925716, 317 of 364 triangles,
980187, 288 of 368 triangles, 886820, 984811, 923643, 19 of 340 triangles,
936323, 237 of 316 triangles, 925800, 1011650, 256 of 316 triangles, 1085989,
233 of 300 triangles, 969297, 137 of 312 triangles, 873727, 104 of 380
triangles, 971573, 954039, 216 of 280 triangles, 1011640, 31 of 284 triangles,
995851, 1076693, 110 of 304 triangles, 949635, 949664, 1054105, 47 of 296
triangles, 947437, 110 of 312 triangles, 1016232, 969309, 916892, 880416,
1013983, 938547, 938679, 1022846, 910672, 1027475, 191 of 296 triangles,
1072498, 18 of 308 triangles, 1020627, 980372, 221 of 308 triangles, 962791,
276 of 284 triangles, 1020386, 956075, 1031964, 67 of 240 triangles, 949532,
1006961, 943026, 934471, 978179, 128 of 284 triangles, 1071975, 121 of 220
triangles, 1104043, 181 of 248 triangles, 940783, 984529, 235 of 236
triangles, 906344, 311 of 312 triangles, 1043251, 27 of 244 triangles, 921616,
1009456, 1018395, 1029674, 906010, 6 of 216 triangles, 1000185, 228 of 244
triangles, 1074644, 1020524, 1101929, 107 of 236 triangles, 964938, 880175, 5
of 236 triangles, 1038651, 1002712, 971414
Deleted 93 regions
> select #2.515
1 model selected
> select add #2.1042
2 models selected
> select add #2.2941
3 models selected
> select add #2.4796
4 models selected
> select add #2.815
5 models selected
> select add #2.2415
6 models selected
> select subtract #2.2415
5 models selected
> select add #2.3
6 models selected
> select add #2.1818
7 models selected
> select add #2.2756
8 models selected
> select add #2.4322
9 models selected
> select add #2.4794
10 models selected
> select add #2.2301
11 models selected
> select add #2.2754
12 models selected
> select add #2.1263
13 models selected
> select add #2.25
14 models selected
> select add #2.2469
15 models selected
> select add #2.3672
16 models selected
> select add #2.514
17 models selected
> select add #2.1188
18 models selected
> select add #2.1795
19 models selected
> select add #2.1405
20 models selected
> select add #2.1622
21 models selected
Grouped 21 regions
> select #2.8
1 model selected
Drag select of 1865308, 1870987, 754 of 772 triangles, 1852329, 1865011,
1867788, 2001120, 1623153, 159 of 772 triangles, 1421667, 1874700, 787 of 844
triangles, 1493107, 1871596, 1590951, 1554363, 1492306, 336 of 572 triangles,
1558549, 157 of 476 triangles, 673069, 611790, 743425, 1576638, 812192,
1592654, 693907, 1871414, 1535611, 660596, 747832, 92 of 492 triangles,
570224, 220 of 480 triangles, 1536299, 458 of 512 triangles, 737008, 786577,
775821, 882319, 257 of 492 triangles, 1625399, 644271, 769364, 287 of 432
triangles, 1632259, 1625767, 636101, 786523, 982618, 901775, 180 of 428
triangles, 1613427, 833543, 1616286, 848282, 354 of 420 triangles, 973943,
681567, 778243, 1633759, 1626643, 842090, 1603390, 760972, 908201, 656578,
971394, 152 of 412 triangles, 844211, 938894, 76 of 384 triangles, 829329,
1603500, 932279, 1587838, 568436, 715226, 763064, 683687, 677286, 1625659,
998400, 290 of 352 triangles, 664855, 1633962, 780141, 172 of 396 triangles,
1079255, 338 of 468 triangles, 1615246, 987339, 941066, 790950, 715291,
865325, 382 of 400 triangles, 1631953, 662633, 928115, 1018336, 268 of 360
triangles, 919468, 1590750, 814191, 277 of 312 triangles, 656477, 329 of 332
triangles, 702447, 803870, 803637, 917097, 292 of 296 triangles, 893565,
897571, 638325, 980478, 1034177, 331 of 356 triangles, 793085, 763098, 765042,
865281, 960667, 801577, 827015, 127 of 304 triangles, 593507, 760810, 574095,
216 of 332 triangles, 646206, 13 of 316 triangles, 812397, 704525, 993658, 83
of 300 triangles, 814345, 820896, 927861, 241 of 368 triangles, 648249, 180 of
256 triangles, 844294, 850781, 763043, 844189, 833563, 587467, 233 of 256
triangles, 736847, 708787, 902169, 904050, 801418, 211 of 292 triangles,
704584, 857030, 748026, 973736, 1034140, 198 of 292 triangles, 792972, 837832,
159 of 296 triangles, 591346, 84 of 296 triangles, 734682, 852564, 852733,
632081, 925592, 893453, 812368, 989550, 841973, 773747, 803830, 1038747, 211
of 320 triangles, 954022, 876262, 1034416, 1045668, 797353, 880403, 880372,
886684, 938694, 585654, 899771, 621969, 1133480, 1000601, 771344, 171 of 276
triangles, 958610, 1108447, 53 of 292 triangles, 837996, 921611, 644180,
891271, 601516, 579825, 587487, 810017, 175 of 276 triangles, 784442, 756522,
628070, 962985, 799497, 1016310, 848545, 617711, 829337, 871683, 681524,
1023072, 1045570, 246 of 332 triangles, 793180, 1104117, 656469, 698134,
1007009, 27 of 248 triangles, 971415, 20 of 252 triangles, 816761, 818763,
833574, 921513, 846469, 780354, 825079, 636166, 904247, 934375, 745566, 128 of
248 triangles, 1002787, 998083, 17 of 248 triangles, 1093082, 119 of 316
triangles, 1014105, 978364, 1038605, 252 of 268 triangles, 607632, 854803,
808051, 719628, 775851, 648326, 713068, 1002531, 90 of 244 triangles, 782383,
867586, 934686, 1020603, 159 of 220 triangles, 839987, 564736, 149 of 244
triangles, 803900, 803608, 261 of 268 triangles, 803670, 673113, 908590, 6 of
244 triangles, 863493, 805957, 816797, 668946, 1013864, 215 of 272 triangles,
668827, 120 of 236 triangles, 1095449, 969369, 921511, 619889, 945304, 901811,
65 of 252 triangles, 878239, 737009, 1029877, 1054677, 934377, 29 of 232
triangles, 947359, 702423, 1000554, 859123, 820731, 882602, 803811, 1074566,
61 of 240 triangles, 831271, 40 of 220 triangles, 891394, 956109, 908307, 50
of 220 triangles, 666820, 875857, 125 of 268 triangles, 1007350, 846212, 59 of
236 triangles, 936733, 763022, 741380, 765149, 852813, 1020789, 973933,
945258, 568352, 254 of 260 triangles, 758629, 1054508, 745754, 617733, 925850,
829069, 124 of 216 triangles, 829430, 1043310, 146 of 264 triangles, 771463,
954161, 790785, 998442, 858875, 797362, 1104122, 670983, 179 of 280 triangles,
880387, 969437, 880527
Deleted 286 regions
Drag select of 1862665, 437882, 1599432, 1585928, 1530701, 462 of 560
triangles, 1587010, 52 of 636 triangles, 1507398, 195 of 540 triangles,
465177, 1599808, 1586531, 147 of 532 triangles, 1483874, 1483799, 114 of 416
triangles, 1567833, 456994, 313 of 376 triangles, 444075, 471428, 408480, 351
of 368 triangles, 492159, 446089, 403745, 482582, 234 of 388 triangles,
477785, 111 of 344 triangles, 451615, 433767, 482691, 557220, 153 of 292
triangles, 501867, 510052, 431724, 528477, 180 of 296 triangles, 501877,
490515, 163 of 304 triangles, 445971, 215 of 348 triangles, 495215, 242 of 300
triangles, 508314, 560833, 135 of 312 triangles, 435749, 194 of 280 triangles,
485798, 489114, 458784, 447942, 510096, 532052, 203 of 252 triangles, 429391,
398691, 501652, 490591, 391238, 462158, 420597, 506745, 495170
Drag select of 1592622, 598 of 620 triangles, 1607337, 1036099, 438 of 460
triangles, 1558835, 1020366, 1018155, 1069752, 1107945, 1036144, 1122747,
1626931, 1047255, 195 of 340 triangles, 1101677, 1088224, 1067736, 1065311,
1009049, 296 of 300 triangles, 1103800, 1118725, 1127078, 1101685, 1161257,
1027126, 1049620, 1090370, 1078781, 1116565, 1108123, 1051827, 1172962,
1094823, 1131159, 1143528, 1056557, 1051982, 1027125, 1069770, 1092962,
1101687, 1029426, 1090633, 1038249, 54 of 216 triangles, 1053922, 101 of 236
triangles, 1049439, 182 of 276 triangles
Deleted 44 regions
Drag select of 1044874, 379 of 600 triangles, 1066975, 1132523, 1089861,
1111442, 1146789, 1113739, 1089848, 1011061, 281 of 308 triangles, 1053589,
1024582, 984461, 66 of 372 triangles, 1094392, 1096457, 1152799, 1100742, 43
of 256 triangles, 1004282, 243 of 280 triangles, 1040107, 233 of 284
triangles, 1103074, 1136591, 1116049, 1126236, 1115886, 1049336, 1124080,
1146716, 1049053, 1140758, 1080460, 122 of 240 triangles
Drag select of 1868470, 1860580, 134 of 736 triangles, 1591651, 1591811, 129
of 532 triangles, 822731, 196 of 496 triangles, 1575631, 1515037, 75 of 532
triangles, 925363, 901755, 5 of 440 triangles, 1576373, 238 of 456 triangles,
1011212, 995687, 987057, 1004794, 982560, 1008947, 1576192, 997824, 882378,
251 of 396 triangles, 949382, 863104, 1020287, 1004795, 1036113, 1043078,
989064, 899448, 341 of 408 triangles, 934391, 852555, 1171548, 982236, 964590,
6 of 304 triangles, 895331, 818616, 1133435, 1088485, 1149670, 884429, 28 of
256 triangles, 982276, 1159545, 1022567, 1042892, 1112676, 960313, 975533,
1056724, 1009301, 1086145, 932113, 1083879, 1054369, 1029394, 998056, 995670,
1122987, 1129279, 1004609, 1155760, 986998, 987055, 816439, 206 of 244
triangles, 1112675, 980267, 1097627, 1074703, 1120937, 1002431, 1006918,
991444
Deleted 98 regions
Drag select of 1626019, 618 of 652 triangles, 1615769, 300 of 624 triangles,
1576409, 237 of 564 triangles, 977819, 358 of 528 triangles, 997849, 1591701,
1038162, 106 of 484 triangles, 1576052, 240 of 460 triangles, 927604, 339 of
448 triangles, 916905, 975695, 960390, 973471, 982204, 181 of 504 triangles,
877908, 65 of 308 triangles, 938447, 947163, 923244, 308 of 356 triangles,
953600, 113 of 344 triangles, 1040518, 276 of 312 triangles, 951449, 251 of
276 triangles, 951535, 993617, 886597, 49 of 284 triangles, 986698, 184 of 284
triangles, 1011183, 973550, 899524, 28 of 240 triangles, 993477, 947054, 127
of 304 triangles, 1006692, 142 of 252 triangles, 860951, 6 of 252 triangles,
1017888, 237 of 252 triangles, 942774, 942959, 1013508
> select add #2.5920
37 models selected
> select add #2.7141
38 models selected
> select add #2.13861
39 models selected
> select add #2.9903
40 models selected
> select add #2.11896
41 models selected
> select add #2.2384
42 models selected
> select add #2.6430
43 models selected
> select add #2.13862
44 models selected
> select add #2.3145
45 models selected
> select add #2.7135
46 models selected
> select add #2.12406
47 models selected
> select add #2.7074
48 models selected
Drag select of 1491474, 433 of 620 triangles, 1466718, 466 of 600 triangles,
1370979, 1602335, 1587703, 1490924, 35 of 588 triangles, 1631986, 700899,
813196, 1614728, 1534135, 1873994, 774577, 294 of 540 triangles, 711653, 343
of 524 triangles, 757340, 825787, 688369, 763339, 787386, 1603338, 46 of 496
triangles, 584260, 645003, 291 of 500 triangles, 785036, 724733, 855623, 323
of 488 triangles, 1588667, 815130, 38 of 488 triangles, 836652, 242 of 440
triangles, 849221, 203 of 440 triangles, 868232, 1612775, 325 of 492
triangles, 682226, 690442, 159 of 392 triangles, 748597, 748602, 765739,
771979, 817210, 565290, 132 of 368 triangles, 679736, 319 of 368 triangles,
618591, 844657, 759253, 626661, 735373, 872342, 759329, 791214, 652958,
705240, 782822, 898450, 254 of 348 triangles, 715724, 66 of 296 triangles,
614443, 709136, 690365, 770042, 855555, 335 of 336 triangles, 849363, 269 of
300 triangles, 679743, 539990, 181 of 344 triangles, 673831, 789547, 808585,
838796, 69 of 316 triangles, 919677, 787108, 954538, 37 of 344 triangles,
673820, 644962, 667274, 201 of 296 triangles, 889617, 711593, 197 of 320
triangles, 761577, 857679, 111 of 336 triangles, 716124, 616291, 275 of 324
triangles, 536356, 58 of 332 triangles, 709447, 632899, 272 of 304 triangles,
707461, 682174, 765498, 593942, 268 of 308 triangles, 655161, 876698, 752583,
610490, 913445, 808649, 742080, 783109, 266 of 272 triangles, 810657, 707225,
729125, 842705, 821426, 750617, 665480, 796215, 624871, 699109, 696758,
784862, 724624, 724672, 724732, 767844, 684118, 730928, 95 of 256 triangles,
770139, 582341, 596352, 283 of 308 triangles, 680207, 650805, 84 of 264
triangles, 735591, 765561, 223 of 284 triangles, 782768, 838790, 744105,
726698, 705218, 65 of 256 triangles, 673936, 639169, 739551, 61 of 268
triangles, 655357, 806965, 586284, 676011, 690441, 730766, 731314, 703118,
730970, 761913, 170 of 228 triangles, 772031, 791513, 732980, 883118, 578314,
779015, 110 of 304 triangles, 735372, 720502
Deleted 191 regions
Drag select of 1856244, 727183, 133 of 312 triangles, 776921, 828071, 260 of
300 triangles, 768405, 804749, 295 of 340 triangles, 693060, 111 of 244
triangles, 720651, 819844, 707839, 802720, 251 of 252 triangles, 787568
Drag select of 667775, 1570748, 41 of 488 triangles, 600377, 165 of 432
triangles, 618540, 61 of 316 triangles, 580729, 313 of 348 triangles, 590487,
141 of 336 triangles, 632886, 680135, 639291, 610573, 93 of 292 triangles,
645384, 98 of 252 triangles, 558397, 78 of 260 triangles, 519640, 16 of 256
triangles, 522998, 567500, 682562, 240 of 268 triangles, 633064, 516193,
618818, 592585
Drag select of 437758, 528239, 84 of 624 triangles, 1529378, 418 of 500
triangles, 1507398, 485 of 540 triangles, 613268, 423 of 564 triangles,
490382, 61 of 484 triangles, 506453, 456994, 366 of 376 triangles, 1551272,
122 of 392 triangles, 629498, 6 of 332 triangles, 482582, 477785, 30 of 344
triangles, 451615, 433767, 52 of 344 triangles, 588998, 376 of 408 triangles,
649885, 482691, 654021, 672528, 111 of 348 triangles, 445971, 508314, 590932,
546134, 504778, 469654, 86 of 260 triangles, 519640, 460187, 126 of 248
triangles, 482372, 71 of 264 triangles, 522998, 501652, 560457, 490591, 159 of
232 triangles, 511384, 119 of 244 triangles, 516193, 521407, 134 of 268
triangles, 641699, 443919, 707839, 581065, 61 of 228 triangles, 495170,
501497, 232 of 256 triangles
> select add #2.4531
66 models selected
> select add #2.13467
67 models selected
> select add #2.8116
68 models selected
> select add #2.13678
69 models selected
> select add #2.9286
70 models selected
> select add #2.457
71 models selected
> select add #2.2426
72 models selected
> select add #2.3449
73 models selected
> select add #2.12567
74 models selected
> select add #2.7007
75 models selected
> select add #2.380
76 models selected
> select add #2.2982
77 models selected
> select add #2.8936
78 models selected
> select add #2.7903
79 models selected
> select add #2.4345
80 models selected
> select add #2.13007
81 models selected
> select add #2.13592
82 models selected
> select add #2.10941
83 models selected
> select add #2.7620
84 models selected
Drag select of 1617048, 619 of 624 triangles, 1128777, 1634607, 142 of 640
triangles, 1080994, 1448252, 323 of 484 triangles, 1424820, 137 of 432
triangles, 1168064, 1067276, 131 of 436 triangles, 1107741, 1164442, 1054072,
1065357, 1060849, 256 of 308 triangles, 1065288, 1132864, 1101404, 1141150,
1071864, 1045106, 197 of 272 triangles, 1139032, 1033889, 144 of 268
triangles, 1060775, 1051740, 173 of 248 triangles, 1133288, 1128752, 1114331,
1101238, 11 of 220 triangles, 1107773, 1054132, 1099584, 1096844, 97 of 228
triangles, 1094565, 59 of 240 triangles, 1107625, 1067329, 100 of 236
triangles, 1063014
Drag select of 1559755, 1593861, 1578446, 390 of 396 triangles, 1121988,
1098813, 1089715, 1062497, 151 of 344 triangles, 1144615, 1096599, 180 of 352
triangles, 1113723, 1128284, 1089603, 1126269, 1146657, 1132224, 1051306, 84
of 248 triangles, 1132294, 1140570
Drag select of 1577240, 1043263, 1539489, 1538553, 118 of 604 triangles,
1049910, 1616528, 509 of 544 triangles, 1043169, 1634236, 962918, 291 of 384
triangles, 1090707, 938880, 68 of 348 triangles, 962886, 40 of 388 triangles,
1043262, 958559, 985022, 971644, 967327, 1011622, 1032060, 987088, 109 of 304
triangles, 965129, 1051899, 1013994, 1027352, 962927, 172 of 252 triangles,
1079074, 1072413, 1027313, 1027470, 951965, 1076807, 203 of 280 triangles,
1116898, 1007356, 1083953, 1027595, 1009495
Drag select of 640368, 605705, 624078, 619997
Drag select of 2065259, 1631469, 404 of 708 triangles, 1874141, 805487, 541 of
544 triangles, 698114, 1614280, 1572945, 14 of 632 triangles, 1613971, 648018,
754375, 1604396, 1631382, 183 of 652 triangles, 1553242, 737022, 1623678,
706590, 1874140, 803279, 63 of 524 triangles, 745882, 805995, 1573176,
1632312, 1624193, 672806, 805852, 792736, 643938, 123 of 408 triangles,
754321, 764835, 619752, 617487, 650167, 758519, 84 of 388 triangles, 712645,
126 of 420 triangles, 805765, 581366, 354 of 364 triangles, 769295, 765015,
704316, 658369, 779977, 814388, 788587, 758483, 698121, 573746, 273 of 384
triangles, 865328, 13 of 316 triangles, 738742, 784340, 825077, 704333, 233 of
356 triangles, 743209, 726097, 782505, 848370, 304 of 360 triangles, 756510,
764804, 704079, 732431, 790764, 734384, 741040, 225 of 304 triangles, 629807,
797199, 581317, 121 of 264 triangles, 683388, 786345, 797041, 831497, 591063,
129 of 268 triangles, 734632, 685526, 649903, 74 of 248 triangles, 646008,
765178, 664314, 560684, 247 of 296 triangles, 706344, 726073, 856996, 803715,
828991, 155 of 264 triangles, 850745, 865555, 833632, 579450, 557051, 131 of
272 triangles, 812260, 674903, 706459, 683191, 188 of 236 triangles, 719246,
732618, 758463, 816307, 611331, 305 of 312 triangles, 835866, 741244, 751766,
751676, 852787, 809830, 708365, 803677, 627583, 108 of 236 triangles, 672784,
790917, 633808, 633853, 775662, 831423, 779876, 788427, 765139, 607326,
784321, 627697, 676944, 581424, 723706, 756022, 123 of 240 triangles, 717303,
775625, 805825, 794766, 243 of 264 triangles
Drag select of 1834993, 237139, 222464, 317 of 364 triangles, 213628, 301616,
307638, 269206, 284042, 234129
Drag select of 1631009, 124 of 740 triangles, 1585981, 575 of 592 triangles,
1630792, 165 of 548 triangles, 471472, 1599965, 466859, 460445, 462094,
474693, 431636, 53 of 292 triangles, 465137, 509927, 437961, 533754, 504978,
508296, 267 of 272 triangles, 508331, 468364, 518219, 473225, 476271, 455297,
85 of 240 triangles, 446061, 521645, 433756, 147 of 236 triangles, 385911
Deleted 337 regions
Drag select of 398652, 296 of 456 triangles, 1566477, 348151, 348164, 364454,
375292
Drag select of 476573, 185 of 368 triangles, 482987
Drag select of 2102890, 1840 of 1936 triangles, 1860798, 1515453, 1604990,
895477, 904121, 1633491, 923530, 1625808, 1576237, 928021, 893371, 1615656,
955888, 192 of 356 triangles, 949500, 256 of 400 triangles, 943218, 934365, 11
of 252 triangles, 923423, 250 of 284 triangles, 886956, 861024, 283 of 300
triangles, 1009059, 213 of 324 triangles, 962560, 108 of 272 triangles,
860970, 978172, 905942, 53 of 340 triangles, 887001, 921584, 936572, 915013,
934618, 871677, 927850, 70 of 244 triangles, 878082
Drag select of 437882, 1585841, 266 of 636 triangles, 1599432, 465177,
1599808, 83 of 608 triangles, 1866710, 499877, 80 of 520 triangles, 1483874,
463401, 182 of 524 triangles, 1599645, 437780, 471428, 1630652, 446089,
403745, 272 of 336 triangles, 480911, 431724, 490515, 286 of 304 triangles,
495215, 232 of 300 triangles, 435749, 485798, 451433, 447763, 458784, 447942,
257 of 260 triangles, 519640, 429391, 225 of 276 triangles, 522998, 516193,
420597, 445943, 2146548, 19 of 5792116 triangles
> select subtract #2.3
72 models selected
Drag select of 707839
Deleted 73 regions
> select #2.2
1 model selected
Drag select of 2066587, 1389130, 1529168, 470849, 349 of 588 triangles,
1569192, 471 of 580 triangles, 477235, 38 of 600 triangles, 379861, 443 of 480
triangles, 1630599, 400645, 414967, 501189, 524776, 86 of 412 triangles,
430568, 48 of 360 triangles, 512804, 380083, 529857, 335 of 352 triangles,
1612420, 298 of 368 triangles, 499578, 515933, 501323, 430990, 456517, 382615,
280 of 380 triangles, 330615, 540250, 247 of 292 triangles, 553104, 366733,
382956, 45 of 288 triangles, 414830, 488265, 545862, 477217, 517889, 510949,
480747, 542050, 437463, 435393, 463314, 529642, 355502, 461664, 536757,
493337, 538817, 517820, 424699, 200 of 244 triangles, 398333, 463109, 507747,
352969, 482231, 468055, 212 of 276 triangles, 483743, 419577, 540402, 435168,
482081, 186 of 216 triangles, 363910, 124 of 244 triangles, 478821, 501263,
523068, 142 of 216 triangles
Drag select of 1551452, 602258, 1623358, 576 of 668 triangles, 1463148,
540106, 70 of 412 triangles, 596697, 465 of 472 triangles, 600187, 102 of 408
triangles, 637331, 608363, 250 of 380 triangles, 549161, 236 of 340 triangles,
538326, 151 of 304 triangles, 558043, 559730, 557846, 545397, 32 of 352
triangles, 580919, 557817, 151 of 272 triangles, 602198, 602877, 51 of 260
triangles, 604800, 573183, 617091, 604736, 539782, 567465
Drag select of 1619952, 290159, 216667, 216668, 213705, 216694, 207861,
207902, 216664
Drag select of 1565186, 1629221, 167 of 564 triangles, 1501203, 1525696,
1583372, 368 of 508 triangles, 215022, 355 of 372 triangles, 238600, 1610169,
252993, 319 of 400 triangles, 267597, 181 of 328 triangles, 188609, 200365,
235398, 206084, 220946, 250207, 59 of 272 triangles, 241490, 200315, 261738,
69 of 220 triangles, 264852, 209 of 220 triangles, 241288, 7 of 244 triangles
> select add #2.8548
118 models selected
> select add #2.945
119 models selected
> select add #2.13601
120 models selected
> select add #2.5827
121 models selected
> select add #2.1898
122 models selected
> select add #2.5425
123 models selected
> select add #2.262
124 models selected
Deleted 124 regions
Drag select of 1862665, 1530701, 524 of 560 triangles, 1587010, 315 of 636
triangles, 1586531, 188 of 532 triangles, 1567833, 234 of 400 triangles,
444075, 289 of 384 triangles, 408480, 250 of 368 triangles, 380346, 557220,
243 of 292 triangles, 510052, 528477, 197 of 296 triangles, 501877, 403428,
560833, 261 of 312 triangles, 385624, 388192, 32 of 248 triangles, 532052, 240
of 252 triangles, 398691, 506745
Deleted 19 regions
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_-650_v1.seg" models
> #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
> select #2.2888
1 model selected
> select add #2.10304
2 models selected
> select add #2.5466
3 models selected
> select add #2.1928
4 models selected
> select add #2.13346
5 models selected
Deleted 5 regions
> select #2.11
1 model selected
Drag select of 1538057, 793758, 1397311, 808584, 1874813, 138 of 708
triangles, 1591822, 1616359, 99 of 592 triangles, 1602458, 314 of 608
triangles, 810625, 692304, 1632119, 576 of 600 triangles, 1623721, 983025,
737592, 1394715, 1624223, 823602, 429 of 536 triangles, 711597, 1511973,
771993, 772119, 716056, 300 of 416 triangles, 868161, 761342, 1009777, 111 of
456 triangles, 870175, 679752, 748333, 1616514, 331 of 484 triangles, 656943,
897977, 767871, 1589855, 628583, 806588, 258 of 448 triangles, 759276, 744171,
1626191, 661063, 895955, 949972, 851351, 324 of 508 triangles, 865925, 949965,
34 of 344 triangles, 791386, 821440, 917679, 934839, 752828, 682068, 847016,
113 of 424 triangles, 851161, 765824, 172 of 372 triangles, 752683, 728733,
307 of 320 triangles, 804129, 778571, 763333, 952258, 825497, 705185, 624428,
776351, 898272, 793541, 748311, 767863, 821215, 622489, 688227, 622416,
657011, 974146, 648730, 800084, 726553, 789141, 865746, 720206, 853358,
640831, 755090, 688254, 814975, 817381, 53 of 268 triangles, 686094, 724413,
754855, 846900, 184 of 308 triangles, 859622, 694408, 785081, 840465, 711609,
136 of 220 triangles, 934890, 874432, 735444, 690400, 757047, 983005, 851075,
737583, 791281, 815171, 153 of 292 triangles, 936909, 694527, 752632, 872144,
707161, 889596, 767995, 930459, 673526, 815046, 717953, 939366, 954364, 963299
Drag select of 1874769, 1874813, 978684, 1558411, 43 of 512 triangles,
1616359, 1003203, 1627030, 1043697, 1057137, 1577509, 983025, 154 of 548
triangles, 1045945, 1057281, 110 of 444 triangles, 1064190, 1043733, 1084357,
473 of 516 triangles, 1577044, 1557954, 352 of 452 triangles, 1082108, 57 of
492 triangles, 1009777, 1032482, 1616514, 1059530, 1079961, 291 of 420
triangles, 1048228, 992432, 273 of 352 triangles, 1606680, 1037107, 163 of 412
triangles, 1023344, 289 of 336 triangles, 1003558, 347 of 356 triangles,
949965, 21 of 344 triangles, 1048180, 1084730, 46 of 364 triangles, 1017008,
265 of 364 triangles, 1055051, 981177, 364 of 392 triangles, 1052749, 1095926,
1048173, 208 of 316 triangles, 996841, 269 of 324 triangles, 1066092, 969842,
158 of 292 triangles, 1046051, 1036958, 1023285, 1030658, 1016492, 1048277,
294 of 316 triangles, 1057422, 974146, 77 of 324 triangles, 976310, 1030392,
1034776, 1012228, 1055103, 1050555, 996439, 173 of 252 triangles, 1043960,
1062080, 227 of 264 triangles, 1059532, 1039290, 1055193, 1075426, 1075546,
1007822, 1021176, 1037087, 1012410, 152 of 264 triangles, 1014647, 1048298,
1061791, 994326, 1026084, 231 of 280 triangles, 1050342, 1072944, 967589, 61
of 260 triangles, 1021412, 1048685, 1046222, 88 of 216 triangles, 1007733
Drag select of 1868594, 533 of 688 triangles, 1093777, 323 of 460 triangles,
1082108, 176 of 492 triangles, 1578366, 317 of 440 triangles, 1066748, 126 of
304 triangles, 1113429, 58 of 504 triangles, 1084730, 161 of 364 triangles,
1084806, 227 of 276 triangles, 1077773, 12 of 268 triangles, 1095901, 261 of
288 triangles, 1096262, 1089433, 168 of 240 triangles
Drag select of 1616359, 246 of 592 triangles, 926368, 416 of 420 triangles,
937142, 459 of 460 triangles, 949965, 241 of 344 triangles, 930727, 224 of 252
triangles
Drag select of 1590967, 237 of 536 triangles, 876822, 427 of 460 triangles,
861858, 142 of 336 triangles
Drag select of 1874721, 961181, 411 of 512 triangles, 1537729, 153 of 500
triangles, 956697, 420 of 448 triangles, 961415, 183 of 460 triangles, 965396,
948323, 207 of 380 triangles, 946052, 67 of 384 triangles, 976365, 105 of 268
triangles, 954577, 230 of 264 triangles
Drag select of 1084491, 160 of 404 triangles, 1098161, 1102616, 1091379,
1079764, 153 of 244 triangles, 1075217
Drag select of 1862797, 378106, 401316, 459111
Drag select of 1600720, 548200, 174 of 464 triangles, 548262, 159 of 248
triangles, 581606, 68 of 260 triangles
> select add #2.1966
225 models selected
> select add #2.13441
226 models selected
Deleted 226 regions
Drag select of 784839, 728613, 761228
Drag select of 1874813, 1633995, 983025, 1009777, 1616514, 961062, 309 of 412
triangles, 956601, 146 of 340 triangles, 941416, 967566, 954397, 939499, 130
of 292 triangles, 959008, 974146, 920051, 994349, 206 of 284 triangles
Drag select of 1082108
Drag select of 1510230, 373 of 528 triangles, 1463057, 676873, 615257, 676787,
264 of 292 triangles, 655967, 118 of 304 triangles, 650003, 664338, 601006, 66
of 320 triangles, 633825, 601027, 130 of 248 triangles, 655832, 150 of 244
triangles, 676803, 647869, 635740, 591074, 666350, 234 of 256 triangles
Drag select of 798974
Drag select of 1617206, 230 of 408 triangles, 1078508, 1073934, 1064981, 203
of 252 triangles, 1080829, 159 of 232 triangles
Drag select of 1096703, 124 of 304 triangles, 1098945, 139 of 276 triangles
Drag select of 957902, 993409, 228 of 292 triangles
> select add #2.10289
47 models selected
Drag select of 1851400, 1531111, 483 of 544 triangles, 1463057, 476 of 500
triangles, 575473, 237 of 516 triangles, 1613269, 1551533, 351 of 424
triangles, 581149, 284 of 348 triangles, 600926, 598892, 568019, 590811, 235
of 308 triangles, 607060, 595006, 600854, 154 of 288 triangles, 575532,
569885, 601027, 181 of 248 triangles, 598862, 597064, 584996, 159 of 288
triangles, 591074, 117 of 216 triangles, 590873
> select add #2.5305
64 models selected
> select add #2.10168
65 models selected
Drag select of 1605751, 32 of 588 triangles, 1557580, 90 of 584 triangles,
1008978, 76 of 376 triangles, 997844, 69 of 400 triangles, 1017722, 243 of 312
triangles, 1008745, 205 of 284 triangles
Deleted 71 regions
Drag select of 1593081, 1084730, 1089453, 1085065, 161 of 260 triangles,
1082883, 209 of 248 triangles
Drag select of 1015874, 281 of 428 triangles, 1015883, 219 of 368 triangles,
1022270, 1011215, 82 of 300 triangles, 1008878, 15 of 284 triangles
Drag select of 1533381, 1603547, 423 of 544 triangles, 811734, 322 of 392
triangles, 680935, 325 of 348 triangles, 742739, 109 of 272 triangles, 732139,
723292, 716732, 224 of 280 triangles, 678844, 135 of 252 triangles, 693569, 18
of 300 triangles, 758045, 826450, 96 of 216 triangles, 685090, 683238,
2146546, 22 of 3458336 triangles
> select subtract #2.9
24 models selected
Deleted 24 regions
> select #2.53
1 model selected
Drag select of 1570134, 594864, 118 of 556 triangles, 1570788, 107 of 464
triangles, 504831, 463527, 562124, 247 of 392 triangles, 477762, 213 of 416
triangles, 472989, 506555, 1570304, 495121, 471370, 491953, 431596, 190 of 340
triangles, 573489, 645448, 275 of 344 triangles, 588653, 519902, 495162,
558746, 437869, 192 of 240 triangles, 461960, 449750, 542416, 268 of 328
triangles, 465058, 573689, 121 of 264 triangles, 431562, 555130, 469759,
506472, 564309, 130 of 264 triangles, 499928, 591074, 451547
> select add #2.1610
35 models selected
Drag select of 627436, 302 of 648 triangles, 1601849, 232 of 620 triangles,
1531501, 691161, 600265, 1551316, 264 of 448 triangles, 596502, 1631588,
670419, 594608, 691210, 1571086, 584548, 655849, 655818, 305 of 332 triangles,
629143, 622852, 592383, 569075, 604690, 600514, 645448, 610967, 614942,
633333, 645028, 113 of 296 triangles, 641705, 52 of 276 triangles, 625010,
626980, 612941, 628750, 150 of 296 triangles, 592303, 610399, 618824, 592441,
592222, 637014, 622605, 631217, 574726, 616678, 625085
> select add #2.3506
76 models selected
Drag select of 1558605, 1577974, 1055408, 1494614, 1069030, 448 of 480
triangles, 1048815, 59 of 348 triangles, 1578093, 1634061, 978745, 1019115,
1044060, 1042055, 255 of 368 triangles, 1073216, 1028226, 1032876, 1037521, 41
of 356 triangles, 1050988, 1044199, 1050734, 1073018, 258 of 300 triangles,
1068680, 1001319, 1057759, 1057615, 1046474, 1048683, 1016908, 95 of 300
triangles, 1003493, 80 of 236 triangles, 1057411, 1048775, 142 of 252
triangles, 996645, 1005543, 1037470, 15 of 228 triangles, 1039827, 113 of 280
triangles, 1064525
Drag select of 1603182, 375 of 484 triangles, 798585, 748727, 125 of 352
triangles, 716121, 783367, 785308, 802812, 707431, 813613, 282 of 292
triangles, 740039, 783742, 847212, 100 of 248 triangles, 733547, 2146546, 23
of 3458336 triangles
> select subtract #2.9
124 models selected
Deleted 124 regions
Drag select of 580878, 1873566, 1600820, 547737, 526378, 556589, 1550614,
541923, 545831, 575096, 556289, 554723, 545618, 547372, 516192, 569665,
547662, 540391, 571544, 560390, 558202, 586718, 540326, 569230, 580768,
551344, 514280, 579070, 529765, 558136, 573367, 560326, 586862, 606970,
567572, 533419, 571635, 558259, 563736
Drag select of 1860603
> select add #2.2511
41 models selected
Drag select of 1573431, 1487675, 972024, 376 of 492 triangles, 1623543,
757057, 980901, 1613668, 702778, 694321, 709250, 178 of 348 triangles, 656972,
173 of 312 triangles, 998714, 197 of 380 triangles, 675576, 1016583, 1012183,
15 of 360 triangles, 694338, 998737, 48 of 348 triangles, 696440, 722129,
661008, 732939, 1007721, 214 of 292 triangles, 863781, 686069, 245 of 336
triangles, 810690, 865957, 675543, 956757, 1027831, 904511, 748532, 4 of 316
triangles, 874483, 932732, 883083, 715703, 865910, 998746, 182 of 276
triangles, 780723, 767797, 707081, 885202, 900393, 963322, 958905, 696458,
1012156, 1025626, 139 of 316 triangles, 836269, 684032, 702797, 681986,
733018, 926242, 1032464, 119 of 284 triangles, 1032473, 179 of 248 triangles,
887319, 889505, 928425, 965499, 921846, 874366, 696545, 737425, 737426,
989794, 952215, 998735, 268 of 280 triangles, 789282, 663054, 654767, 878586,
754842, 769849, 1023397, 9 of 280 triangles, 812853, 59 of 252 triangles,
750401, 302 of 304 triangles, 750523, 1023363, 741692, 844716, 998697, 825565,
797725, 744013, 836226, 709105, 906602, 859515, 985387, 698621, 759175,
722265, 836132, 814858, 754820, 769855, 648606, 638554, 857379, 791244,
638658, 300 of 312 triangles, 667157, 965537, 1016507, 836133, 1014442,
660979, 806395, 967612, 750499, 935006, 123 of 228 triangles, 950064, 969851,
926158, 936916
Drag select of 981081, 996534, 195 of 432 triangles, 930688, 304 of 340
triangles, 937033, 110 of 356 triangles, 1005573, 878822, 89 of 316 triangles,
939424, 978826, 996520, 277 of 300 triangles, 965671, 350 of 356 triangles,
981045, 894045, 56 of 252 triangles, 948046, 817252, 6 of 276 triangles,
1025672, 937130
Deleted 172 regions
Drag select of 470950, 49 of 612 triangles, 1530213, 406 of 572 triangles,
1621593, 182 of 440 triangles, 1621992, 120 of 480 triangles, 512496, 126 of
320 triangles, 514036, 111 of 280 triangles, 783649, 173 of 264 triangles,
742653, 43 of 244 triangles, 809275, 722991
> select add #2.1460
11 models selected
Drag select of 1018945, 253 of 436 triangles, 1626471, 481 of 488 triangles,
1032520, 963363, 217 of 372 triangles, 998824, 40 of 336 triangles, 1072959,
919838, 25 of 296 triangles, 969937, 195 of 272 triangles, 1057190, 1025771,
81 of 260 triangles
Drag select of 1001554, 28 of 576 triangles, 1046168, 999019, 1591545, 426 of
572 triangles, 1634144, 378 of 588 triangles, 1592460, 1057319, 458 of 460
triangles, 1626713, 956989, 243 of 416 triangles, 1016930, 59 of 380
triangles, 1030355, 972249, 981032, 935048, 1003352, 965705, 1014707, 1014708,
939436, 198 of 328 triangles, 950216, 945984, 252 of 280 triangles, 1041549,
994530, 1034922, 1017014, 987791, 981251, 1021375, 1066682, 902596, 102 of 244
triangles, 1003334, 1055510, 220 of 248 triangles, 1075588, 990048, 928495,
125 of 240 triangles, 983400, 956873, 1003712, 58 of 284 triangles, 1005843,
229 of 280 triangles, 965702, 1055373, 1059724, 994565, 1023616
Drag select of 907393, 170 of 248 triangles, 883549, 233 of 292 triangles,
874930
Drag select of 896186, 247 of 644 triangles, 913563, 957092, 300 of 448
triangles, 909179, 76 of 360 triangles, 941864, 322 of 328 triangles, 939698,
928666, 238 of 272 triangles, 981462, 227 of 280 triangles, 972496
Drag select of 946064, 16 of 544 triangles, 996742, 66 of 480 triangles,
911272, 206 of 476 triangles, 935211, 264 of 296 triangles, 1012430, 140 of
296 triangles, 956906
Drag select of 1869886, 311 of 1392 triangles, 612363, 297 of 716 triangles,
1417438, 1623945, 563 of 576 triangles, 1624080, 1613075, 529042, 636838,
612151, 1571916, 597933, 634625, 532550, 545122, 648810, 349 of 364 triangles,
626473, 606026, 567058, 146 of 340 triangles, 622391, 735395, 654941, 656982,
313 of 324 triangles, 630544, 109 of 328 triangles, 599887, 510482, 552286,
652940, 527263, 646759, 81 of 276 triangles, 606005, 539833, 694532, 614190,
640723, 591859
Deleted 118 regions
Drag select of 1616480, 567 of 628 triangles, 1633881, 924309, 250 of 444
triangles, 1616566, 32 of 452 triangles, 1039536, 1591093, 913531, 105 of 344
triangles, 992674, 976574, 166 of 296 triangles, 1014622, 894088, 19 of 308
triangles, 1008249, 1030738, 1062488, 139 of 300 triangles, 1006065, 273 of
284 triangles, 1030862, 948268, 898264, 125 of 276 triangles, 974645, 985840,
144 of 248 triangles, 990016, 217 of 244 triangles, 1010504, 14 of 244
triangles, 996912, 1062287
> select add #2.705
25 models selected
Drag select of 1534700, 252 of 596 triangles, 1574336, 728785, 304 of 368
triangles, 800047, 200 of 384 triangles, 1554564, 85 of 428 triangles, 823652,
62 of 356 triangles, 844841, 218 of 372 triangles, 752761, 870321, 325 of 332
triangles, 911179, 148 of 288 triangles, 780959, 761427, 259 of 260 triangles,
791483, 207 of 264 triangles, 889739, 941653, 318 of 328 triangles, 640620,
126 of 284 triangles, 744136, 211 of 248 triangles, 859729, 243 of 292
triangles, 817292, 132 of 264 triangles, 844769, 878843, 939529, 37 of 220
triangles, 750637, 644733, 24 of 268 triangles, 821352, 861848, 909012
Drag select of 1534700, 29 of 596 triangles, 874597, 53 of 544 triangles,
1575061, 178 of 420 triangles, 1554564, 130 of 428 triangles, 842715, 222 of
364 triangles, 817269, 724415, 688268, 327 of 332 triangles, 652889, 315 of
324 triangles, 698690, 52 of 372 triangles, 844835, 236 of 252 triangles,
829928, 77 of 312 triangles, 776522, 190 of 284 triangles, 603952, 261 of 268
triangles, 614080, 737529, 741897, 823581, 257 of 272 triangles, 855523, 80 of
268 triangles, 759301, 192 of 260 triangles, 720123, 42 of 248 triangles
> select add #2.555
70 models selected
> select add #2.4240
71 models selected
> select add #2.1636
72 models selected
> select add #2.3243
73 models selected
Drag select of 832124, 216 of 496 triangles, 1604320, 111 of 372 triangles,
834319, 163 of 296 triangles, 956974, 160 of 296 triangles, 840635, 48 of 216
triangles
> select add #2.11932
79 models selected
> select add #2.5628
80 models selected
> select add #2.13029
81 models selected
Deleted 81 regions
Drag select of 1601571, 368 of 480 triangles, 632839, 308 of 372 triangles,
690690, 682345, 157 of 316 triangles, 696852, 174 of 284 triangles
> select add #2.656
6 models selected
> select add #2.6698
7 models selected
> select add #2.8526
8 models selected
> select add #2.12137
9 models selected
> select add #2.13943
10 models selected
Drag select of 1015265, 326 of 616 triangles, 1040136, 160 of 252 triangles,
1042258, 1051322, 243 of 300 triangles, 1053515, 118 of 272 triangles, 1033258
> select add #2.1175
17 models selected
> select add #2.12796
18 models selected
> select add #2.9019
19 models selected
> select add #2.11754
20 models selected
> select add #2.7913
21 models selected
Deleted 21 regions
> select #2.4
1 model selected
Drag select of 1546806, 1629583, 515 of 580 triangles, 244280, 1565180,
309149, 291419, 314861, 190 of 276 triangles, 300153, 294316, 282395, 315055,
267373, 291324
Deleted 13 regions
> select #2.93
1 model selected
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_-650_v1.seg" models
> #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
Ungrouped to 2 regions
> select #2.15
1 model selected
Ungrouped to 2 regions
> select #2.20
1 model selected
Ungrouped to 2 regions
> select #2.24
1 model selected
Ungrouped to 2 regions
> select #2.25
1 model selected
Ungrouped to 2 regions
> select #2.20
1 model selected
Ungrouped to 2 regions
> select #2.25
1 model selected
Ungrouped to 2 regions
> select #2.37
1 model selected
Ungrouped to 2 regions
> select #2.25
1 model selected
> select add #2.24
2 models selected
Grouped 2 regions
Drag select of 2145613, 54351 of 368852 triangles, 2145285, 93619 of 263496
triangles, 2143723, 53903 of 82240 triangles, 2144033, 58422 of 59628
triangles, 2142515, 48168 of 65284 triangles, 2140550, 1390 of 24048 triangles
Grouped 6 regions
> select #2.17
1 model selected
Ungrouped to 2 regions
Ungrouped to 4 regions
> select #2.33
1 model selected
Ungrouped to 2 regions
> select #2.20
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
Ungrouped to 2 regions
> select #2.38
1 model selected
Ungrouped to 2 regions
> select #2.39
1 model selected
Ungrouped to 2 regions
> select #2.40
1 model selected
Ungrouped to 2 regions
> select #2.39
1 model selected
Ungrouped to 2 regions
> select #2.43
1 model selected
Ungrouped to 2 regions
> select #2.44
1 model selected
Ungrouped to 2 regions
> select #2.45
1 model selected
Ungrouped to 2 regions
> select #2.46
1 model selected
> select #2.37
1 model selected
Ungrouped to 2 regions
> select #2.47
1 model selected
Ungrouped to 2 regions
> select #2.37
1 model selected
Ungrouped to 2 regions
> select #2.52
1 model selected
Ungrouped to 2 regions
> select #2.54
1 model selected
Ungrouped to 2 regions
> select #2.57
1 model selected
Ungrouped to 2 regions
> select #2.54
1 model selected
Ungrouped to 2 regions
> select #2.57
1 model selected
Ungrouped to 2 regions
> select #2.66
1 model selected
> select #2.32
1 model selected
Ungrouped to 2 regions
> select #2.57
1 model selected
Ungrouped to 2 regions
> select #2.32
1 model selected
Ungrouped to 2 regions
> select #2.57
1 model selected
Ungrouped to 2 regions
> select #2.32
1 model selected
Ungrouped to 2 regions
> select #2.57
1 model selected
Ungrouped to 2 regions
> select #2.73
1 model selected
Ungrouped to 2 regions
> select #2.75
1 model selected
Ungrouped to 2 regions
> select #2.73
1 model selected
Ungrouped to 2 regions
> select #2.77
1 model selected
Ungrouped to 2 regions
> select #2.78
1 model selected
Ungrouped to 2 regions
> select #2.77
1 model selected
Ungrouped to 2 regions
> select #2.75
1 model selected
> select add #2.78
2 models selected
> select add #2.81
3 models selected
> select add #2.79
4 models selected
> select add #2.76
5 models selected
Grouped 5 regions
> select #2.23
1 model selected
Ungrouped to 2 regions
> select #2.77
1 model selected
Ungrouped to 2 regions
> select #2.23
1 model selected
Ungrouped to 2 regions
> select #2.79
1 model selected
Ungrouped to 2 regions
> select #2.23
1 model selected
Ungrouped to 2 regions
> select #2.79
1 model selected
Ungrouped to 2 regions
> select #2.23
1 model selected
> select #2.23
1 model selected
Ungrouped to 2 regions
> select #2.79
1 model selected
Ungrouped to 2 regions
> select #2.23
1 model selected
Ungrouped to 2 regions
> select #2.76
1 model selected
> select #2.79
1 model selected
Drag select of 2146550, 2145370, 1980552, 2141927, 2139099, 2136294, 2131595,
2118328, 2077406, 2043341, 1846731, 2142394, 2139554, 2136268, 2131355,
2107404, 2066197, 2012065, 1995603, 2132631, 2144355, 2142188, 2140641,
2134856, 2123857, 2120035, 1944168, 2143564, 2142667, 2139854, 2133851,
2131899, 2109405, 2094041, 2007951, 1962278
Grouped 36 regions
> select #2.15
1 model selected
Region has 836 adjacent regions
> select #2.8
1 model selected
> select add #2.2
2 models selected
> select add #2.9
3 models selected
> select add #2.11
4 models selected
> select add #2.3
5 models selected
> select #2.2605
1 model selected
> select add #2.11487
2 models selected
> select add #2.15
3 models selected
> select subtract #2.15
2 models selected
> select add #2.1420
3 models selected
> select add #2.3647
4 models selected
> select add #2.75
5 models selected
> select add #2.79
6 models selected
> select add #2.5362
7 models selected
> select add #2.4661
8 models selected
> select add #2.46
9 models selected
> select add #2.66
10 models selected
> select add #2.1716
11 models selected
> select add #2.8683
12 models selected
> select add #2.12300
13 models selected
> select add #2.8191
14 models selected
> select add #2.10771
15 models selected
> select add #2.7452
16 models selected
> select add #2.85
17 models selected
> select add #2.8104
18 models selected
Grouped 18 regions
> select #2.24
1 model selected
> select add #2.693
2 models selected
> select add #2.5364
3 models selected
> select #2.5449
1 model selected
> select #2.102
1 model selected
> select #2.3629
1 model selected
> select #2.12200
1 model selected
> select #2.1134
1 model selected
> select #2.3232
1 model selected
> select add #2.7634
2 models selected
> select #2.1164
1 model selected
> select add #2.4501
2 models selected
> select #2.12132
1 model selected
> select #2.3629
1 model selected
> select #2.4
1 model selected
> select #2.15
1 model selected
Drag select of 2145827, 2143314, 2143393, 2132811, 2121990, 2138462, 2132502,
2122762, 2133087, 2095927, 2101055, 2102818, 2060480, 2062192, 2066630,
2133099, 2062208, 2066198, 2122187, 1944370, 1968367, 1950000, 2103683,
1741867, 1983614, 2065195, 2067773, 1992895, 2067346, 2065727, 1996753,
2000811, 1767456, 1748836, 1995478, 2066191, 1813264, 1999420, 1830918,
2000697, 1999615, 1851299, 2067832, 1836708, 1867230, 1995429, 1791123,
1791498, 1748897, 1791669, 1825027, 1775375, 1985022, 1855857, 1999460,
1791004, 2000787, 1860096, 1846477, 1999517, 1998165, 1863766, 1783246,
1841463, 1867515, 1863578, 1851257, 1846651, 1863477, 1859736, 1819170,
1873521, 1859567, 1995480, 1831074, 1995538, 1367614, 2000765, 1873802,
1847034, 1836740, 1859895, 1326848, 1998161, 1867092, 1507154, 1439213,
1836343, 1440506, 1870734, 1463029, 1533475, 1855746, 1462287, 1438776,
1416169, 1846725, 503920, 1530179, 1863767, 1855734, 1836377, 1570352,
1863202, 1855773, 1569509, 1867161, 1530147, 1509189, 1855883, 1509844,
630816, 1484669, 1863247, 669700, 1439906, 1438458, 1867286, 1532589, 1873423,
1602621, 1601020, 629402, 1553306, 1551969, 1855527, 1572729, 514389, 1531624,
1867155, 1507641, 1486073, 1463564, 1550938, 1863567, 1531537, 1587175,
1867394, 1846385, 1601287, 1571770, 1552384, 1530680, 1846547, 1601018,
1600380, 1485165, 606638, 1551221, 1509137, 1414632, 1532729, 1510776,
1569119, 1551421, 1510879, 1571532, 1550490, 1863455, 1586271, 1552912,
1348943, 588259, 682723, 1600037, 533004, 663866, 1631961, 1532280, 1602463,
1601023, 1587729, 1486959, 496297, 1550579, 1529505, 1612553, 1601811,
1601467, 1599975, 1588200, 1587114, 525628, 1570250, 1622452, 1530849,
1612510, 1602408, 1507394, 620925, 582352, 492846, 1612626, 1611970, 1571442,
1569441, 692578, 1622806, 1587637, 1586168, 1630585, 1534205, 1532656,
1622544, 1612793, 529545, 1586544, 523973, 1551690, 1631781, 1532981, 653340,
1508974, 1588835, 1587452, 618896, 576639, 1551531, 1612382, 457923, 475630,
1587330, 1570278, 1569060, 506172, 1550468, 693017, 1622708, 507867, 1612280,
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698864, 604607, 563817, 1551142, 630903, 1630881, 485145, 544016, 588640,
625021, 597914, 1600957, 1600623, 529562, 529136, 622384, 515826, 1463245,
694858, 592157, 1630646, 578525, 612478, 1586696, 525634, 543604, 1569731,
593955, 648940, 596229, 645454, 522747, 520785, 565575, 552795, 540170,
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638959, 524386, 480412, 550679, 499562, 558095, 639265, 614600, 576941,
566867, 641211, 598376, 501034, 1613960, 529052, 552633, 568895, 499063,
574466, 608251, 539751, 547718, 515462, 510960, 612180, 646896, 568952,
614449, 522652, 524107, 548767, 542060, 507595, 651344, 519409, 675972,
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519246, 505611, 695070, 541664, 543802, 612798, 618520, 562067, 565579,
560233, 515694, 499093, 616591, 559781, 527696, 512595, 580485, 478791,
569207, 610457, 553006, 580080, 472529, 550569, 565780, 501222, 559569,
604702, 519339, 519323, 524193, 499499, 663919, 561625, 634815, 561750,
684307, 499153, 467661, 532697, 491392, 592028, 493036, 567312, 550834,
538216, 538248, 596371, 665771, 506181, 584106, 586321, 524543, 583960,
524112, 472240, 558284, 502655, 525763, 481981, 612279, 628581, 507500,
506079, 601988, 582814, 634991, 572881, 502837, 550813, 574579, 527305,
671763, 516042, 643263, 517163, 616289, 614889, 506179, 547591, 600654,
573115, 509357, 653037, 547305, 558296, 521092, 521085, 651163, 676248,
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491166, 629166, 594546, 529554, 473979, 539803, 667488, 667527, 618894,
525696, 538261, 532873, 526020, 524063, 483544, 645016, 641136, 571030,
547670, 604648, 584122, 614536, 522601, 574647, 553989, 692538, 538094,
536203, 663503, 522729, 475481, 753122, 538731, 545149, 556116, 604038,
608296, 614784, 492955, 565481, 547704, 561411, 557686, 543652, 538558,
510693, 488128, 631075, 653627, 637002, 499265, 586281, 620511, 596490,
584190, 699023, 626756, 722647, 595941, 507537, 561457, 561725, 653152,
568731, 640999, 598326, 515703, 653244, 626884, 510893, 637255, 512046,
572898, 507357, 543892, 538237, 527396, 526080, 525952, 469287, 517301,
751108, 608486, 571472, 536244, 696918, 720431, 606634, 503909, 626550,
509312, 544144, 545885, 560084, 561612, 684705, 590235, 640996, 626709,
549452, 518860, 604115, 604087, 582163, 716474, 602287, 622539, 480070,
459455, 459459, 698894, 563697, 608219, 659657, 659529, 512268, 620415,
621142, 627175, 565418, 584408, 657349, 647031, 539906, 672220, 509539,
671787, 538546, 686609, 565847, 565406, 606589, 547632, 594313, 614522,
499257, 594715, 517600, 586717, 524127, 524341, 552486, 555939, 649285,
598796, 612316, 612823, 651312, 684669, 663476, 545785, 669804, 618195,
604177, 645255, 580623, 725047, 690697, 549541, 517038, 544013, 705714,
489939, 651077, 604078, 703137, 673882, 462909, 531054, 586335, 529103,
529105, 649424, 616842, 653403, 620711, 628719, 634959, 630783, 495866,
539730, 549033, 549029, 578142, 477110, 588359, 569186, 594114, 610470,
493024, 484963, 657685, 563444, 496088, 548606, 545602, 515339, 534724,
494551, 686574, 515289, 514185, 649043, 565870, 563414, 478700, 552625,
596652, 600685, 587972, 478926, 533317, 596485, 538451, 543524, 694937,
556648, 571207, 481967, 547379, 592126, 639280, 692644, 684722, 669795,
618373, 509407, 480462, 486555, 580569, 564014, 491544, 554553, 549249,
519104, 512124, 502336, 514150, 616405, 527199, 602328, 697166, 616808,
615091, 688581, 688485, 635048, 582936, 569136, 578230, 543871, 646996,
515446, 733768, 571485, 647300, 598459, 665717, 631074, 533053, 596593,
665661, 584098, 503903, 527855, 500825, 573018, 499410, 499461, 544116,
543801, 554480, 600605, 509025, 497877, 481986, 663771, 692889, 536192,
684686, 556390, 648865, 573325, 584873, 578826, 604742, 604599, 661587,
510552, 505879, 635139, 502359, 586362, 529104, 541988, 635014, 563779,
529555, 586202, 592431, 598231, 618803, 565448, 657365, 657415, 565195,
456272, 573483, 545534, 545626, 502809, 516091, 486340, 585940, 602612,
610220, 720370
Deleted 799 regions
Showing 5635 region surfaces
Drag select of 999462, 177 of 348 triangles, 997287
Deleted 2 regions
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_650_v2.seg" models #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
> select #2.3
1 model selected
Ungrouped to 21 regions
> select #2.21
1 model selected
> select #2.27
1 model selected
> select add #2.38
2 models selected
Drag select of 2067793, 1871069, 2103658, 2066619, 2067972, 2146544, 1999422,
2143516, 1874183, 2122790, 2001091, 2133064, 2000007, 2067753, 1873949,
2103427, 1874476, 1873437
Grouped 18 regions
Region has 312 adjacent regions
> select #2.2
1 model selected
> select add #2.8
2 models selected
> select #2.21
1 model selected
> select add #2.6
2 models selected
> select add #2.4
3 models selected
> select #2.279
1 model selected
Drag select of 864448, 806869, 513018, 479403, 590823, 1006595, 832615,
537192, 924785, 832815, 619015, 517650, 695238, 783952, 641453, 766436,
789956, 460116, 427164, 669847, 566116, 675938, 781150, 844998, 661819,
475934, 652169, 979915, 828183, 623221, 682761, 556782, 602276, 877279,
867067, 995467, 952986, 933517, 918188, 835003, 680709, 680676, 931555,
849993, 621416, 1001764, 1026405, 809473, 522323, 551437, 590672, 783169,
512858, 313428, 559799, 811171, 429044, 504183, 866475, 598652, 672769,
907548, 775512, 775471, 671950, 496859, 944398, 712361, 948745, 670828,
491836, 720768, 826381, 851730, 519135, 462676, 535168, 564302, 798545,
542367, 494790, 749330, 1030927, 983606, 336576, 828449, 770419, 529550,
590513, 1019408, 621635, 830837, 611151, 997631, 898986, 496516, 764625,
472836, 480821, 720724, 721236, 504636, 712297, 913840, 796223, 538830,
461962, 860773, 723245, 839356, 979722, 712143, 431143, 521528, 731893,
927111, 746940, 870399, 1010744, 468056, 571769, 813603, 558908, 774900,
804793, 506642, 478875, 509787, 796628, 548029, 560750, 946819, 680583,
538987, 712417, 988675, 807230, 627055, 488256, 832633, 735701, 809122,
614506, 738676, 964068, 523224, 579476, 966118, 566118, 798565, 435769,
599281, 862111, 578980, 707938, 870997, 484121, 594827, 866847, 347630,
507451, 937872, 1040369, 701778, 975279, 1026788, 805275, 881549, 630800,
605175, 653801, 628919, 1013026, 592420, 657950, 517865, 740091, 914434,
562267, 999784, 509545, 935844, 514707, 385243, 283716, 526453, 1017314,
463307, 566241, 667720, 833242, 736348, 809665, 747264, 439839, 501690,
779802, 651174, 649730, 988787, 464741, 639475, 708549, 647525, 818345,
725454, 560593, 417917, 868284, 905007, 641729, 512822, 537286, 556783,
492035, 608819, 881580, 498118, 942025, 770960, 975414, 888320, 879567,
563545, 622684, 992645, 772451, 861945, 492942, 775104, 575534, 886004,
536724, 516347, 361626, 957752, 647746, 496673, 856556, 647287, 713949,
776989, 469623, 881962, 873434, 643598, 501390, 720936, 763770, 552579,
601207, 600942, 310469, 879103, 504305, 926683, 471215, 550676, 968265,
592186, 602814, 558533, 693179, 1008332, 627471, 562169, 724841, 623413,
556843, 903073, 801197, 843032, 506413, 981873, 731917, 468177, 673890,
491993, 592545, 390463, 1044850, 878980, 879710, 1004013, 617263, 926767,
687101, 896488, 761789, 502832, 805482, 339334, 495007, 873109, 845914,
551305, 452888, 982121, 493333, 590910, 493421, 487324, 793904, 602527,
776922, 2146554
Grouped 306 regions
Region has 7 adjacent regions
> select #2.8
1 model selected
> select add #2.21
2 models selected
> select add #2.4
3 models selected
> select add #2.2
4 models selected
> select #2.6
1 model selected
> select #2.279
1 model selected
Drag select of 2146555
Grouped 1 regions
Region has 7 adjacent regions
> select #2.21
1 model selected
Region has 894 adjacent regions
> select #2.9
1 model selected
Region has 316 adjacent regions
> select #2.11
1 model selected
> select add #2.4
2 models selected
> select add #2.2
3 models selected
> select add #2.8
4 models selected
> select #2.21
1 model selected
> select add #2.15
2 models selected
> select #2.12
1 model selected
> select #2.1
1 model selected
Ungrouped to 2 regions
> select #2.20
1 model selected
Ungrouped to 2 regions
> select #2.25
1 model selected
Ungrouped to 2 regions
> select #2.20
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
Ungrouped to 2 regions
> select #2.20
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
Ungrouped to 2 regions
> select #2.20
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
Ungrouped to 2 regions
> select #2.34
1 model selected
> select add #2.37
2 models selected
> select add #2.20
3 models selected
> select add #2.39
4 models selected
> select #2.40
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
Ungrouped to 2 regions
> select #2.40
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
Ungrouped to 0 regions
> select #2.33
1 model selected
Ungrouped to 0 regions
> select #2.34
1 model selected
> select add #2.37
2 models selected
> select add #2.20
3 models selected
> select add #2.44
4 models selected
> select add #2.39
5 models selected
Deleted 5 regions
> select #2.43
1 model selected
> select add #2.41
2 models selected
Deleted 2 regions
> select #2.33
1 model selected
Ungrouped to 0 regions
> select #2.33
1 model selected
Deleted 1 regions
> select #2.178
1 model selected
Ungrouped to 2 regions
> select #2.33
1 model selected
Deleted 1 regions
> select #2.24
1 model selected
Drag select of 2066315, 1874392, 1625870, 1871361, 1633732, 1867970, 1616661,
854110, 1871359, 1625683, 872504, 1556625, 1632793, 979175, 1626134, 1626509,
1632998, 539779, 791511, 465721, 807058, 926986, 1625624, 868406, 1575211,
885728, 1614928, 939910, 1615482, 2001125, 842909, 891992, 1625972, 542477,
970514, 787876, 541058, 734561, 823738, 408415, 594979, 868809, 766360,
501541, 1630669, 1613655, 802584, 673669, 929117, 832760, 593070, 464877,
487080, 641876, 666487, 972958, 666241, 879268, 599272, 844872, 418022,
745500, 758247, 611454, 881029, 951143, 872631, 613343, 972969, 571796,
468254, 835009, 792734, 856259, 471194, 766600, 890587, 785964, 753837,
480856, 739925, 507945, 1033121, 400891, 573761, 648117, 727557, 470829,
375062, 616658, 1037985, 588953, 646036, 508032, 480954, 864082, 924788,
523220, 954972, 519701, 481950, 685258, 643942, 828043, 635598, 639790,
873339, 770332, 633905, 742835, 847667, 909412, 777317, 670577, 419677,
393358, 721511, 664261, 693269, 759357, 811080, 663210, 944199, 725280,
841172, 551588, 725552, 706217, 903201, 970431, 853476, 786140, 772285,
854172, 1017745, 602951, 999646, 433622, 775294, 849660, 914412, 390794,
981509, 807101, 510632, 734474, 779653, 678666, 763714, 742616, 533610,
922528, 440738, 1037661, 901557, 691175, 684093, 690957, 556855, 754126,
759482, 804512, 599136, 774552, 872701, 894677, 571766, 460449, 516425,
595056, 621696, 615272, 485331, 986074, 615530, 751287, 721074, 514571,
619572, 587269, 551446, 1005961, 869035, 607386, 927328, 729813, 483893,
757883, 631487, 805193, 926802, 894841, 529242, 1049022, 981972, 993050,
400818, 892796, 531842, 495034, 494195, 621478, 485189, 457847, 885715,
594453, 601195, 1026462, 556894, 868736, 935519, 872817, 841306, 953470,
749628, 627500, 870634, 613395, 595259, 1019738, 879797, 447612, 503994,
884362, 805463, 579429, 686209, 872603, 733362, 461258, 836904, 740502,
463219, 916167, 738587, 639007, 557056, 796518, 940090, 723710, 612411,
799081, 562358, 924602, 933698, 528333, 408493, 731876, 468203, 567933,
783173, 856130, 783871, 881039, 488601, 962045, 830522, 815128, 494964,
657534, 719282, 615525, 700173, 837096, 514725, 1051568, 640027, 451539,
649854, 735558, 555320, 475692, 619610, 568161, 695618, 546324, 512897,
915760, 693419, 838848, 877520, 877576, 754043, 704359, 845610, 457966,
771124, 920828, 742845, 942013, 830672, 990815, 770918, 847086, 939920,
478496, 886129, 658225, 775144, 775504, 834843, 996970, 970528, 776761,
2146546, 2146553, 2141786, 2143321, 1000098, 2138655, 1605939, 2122851
Grouped 312 regions
Region has 69 adjacent regions
> select #2.11
1 model selected
> select add #2.8
2 models selected
> select add #2.2
3 models selected
> select add #2.4
4 models selected
> select #2.15
1 model selected
> select #2.21
1 model selected
> select #2.12
1 model selected
> select #2.24
1 model selected
Drag select of 2133129, 2122465, 2103396, 2103774, 2103767, 2103713, 2067428,
1860964, 1867876, 1999955, 1874704, 1999836, 1616109, 1867817, 1999632,
862787, 1874477, 1511472, 1871557, 1624788, 1615570, 1615305, 1624887,
1871591, 1614790, 1604633, 1871454, 1605252, 1590290, 835090, 1604110,
1625072, 1604840, 1625246, 803032, 1633039, 781816, 912346, 871012, 907874,
841639, 833107, 1625073, 869052, 907978, 783756, 818137, 841396, 892826,
964431, 718819, 852083, 805292, 918581, 794578, 955609, 852255, 832919,
809446, 854234, 2146557
Grouped 61 regions
Region has 9 adjacent regions
> select add #2.8
2 models selected
> select add #2.12
3 models selected
> select add #2.11
4 models selected
> select add #2.2
5 models selected
> select #2.24
1 model selected
Region has 60 adjacent regions
> select #2.2
1 model selected
> select add #2.4
2 models selected
> select #2.15
1 model selected
> select #2.21
1 model selected
> select add #2.24
2 models selected
> select #2.1
1 model selected
Region has 9 adjacent regions
> select #2.4
1 model selected
> select add #2.15
2 models selected
> select add #2.11
3 models selected
> select add #2.2
4 models selected
> select #2.24
1 model selected
> select add #2.21
2 models selected
> select add #2.8
3 models selected
> select #2.12
1 model selected
Drag select of 2146558
Grouped 1 regions
Region has 9 adjacent regions
> select #2.21
1 model selected
> save "/Users/garciae/Documents/CT scan/arbre_bronquial_650_v2.seg" models #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1157, in SaveSegmentationAs
segfile.show_save_dialog(smod, self.path_changed_cb)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog
show_save_file_dialog(seg.session, format = 'Segmentation',
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save
save_segmentation(session, path, models = models)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation
write_segmentation(seg, path)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
TypeError: can only concatenate str (not "tuple") to str
TypeError: can only concatenate str (not "tuple") to str
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 91, in write_segmentation
debug(" - map path: " + d.path)
~~~~~~~~~~~~~~~~^~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1077, in OpenSegmentation
dir = os.path.dirname(dmap.data.path) if dmap else None
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen posixpath>", line 152, in dirname
TypeError: expected str, bytes or os.PathLike object, not tuple
TypeError: expected str, bytes or os.PathLike object, not tuple
File "", line 152, in dirname
See log for complete Python traceback.
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.12093.0.0,0)
OS Loader Version: 580.140.1~51
Software:
System Software Overview:
System Version: macOS 14.7.2 (23H311)
Kernel Version: Darwin 23.6.0
Time since boot: 22 days, 17 hours, 20 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
python-gdcm: 3.0.24.1
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Volume Data |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem saving segmentations |
comment:2 by , 8 months ago
| Resolution: | → wontfix |
|---|---|
| Status: | assigned → closed |
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The user tried to save a segmentation done with Zach's segmentation tool using Segger. Segger only saves Segger segmentations, so what they were trying was not going to save their segmentation. Still it is an error in Segger that it cannot handle maps that are defined by multiple data file paths (usually one path per xy plane). This is a limitation of Segger and it should be fixed. But I'm not going to fix it unless someone who is actually using Segger encounters it because use of multi-file maps is so rare it is has probably never been tried with Segger.