Opened 2 years ago

Closed 9 months ago

#9437 closed defect (fixed)

DICOM: bits_allocated is None

Reported by: Scooter Morris Owned by: Zach Pearson
Priority: normal Milestone:
Component: DICOM Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.7.dev202307220101 (2023-07-22 01:01:24 UTC)
Description
Download of RIDER-8509201188, all series

Log:
Startup Messages  
---  
warning | Registration file '/Users/scooter/Library/Application
Support/ChimeraX/registration' has expired  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.dev202307220101 (2023-07-22)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Registration file '/Users/scooter/Library/Application
Support/ChimeraX/registration' has expired  

> ui tool show Registration

> ui tool show "Download DICOM"

> open 1.3.6.1.4.1.9328.50.1.48441840081578419409180519840073808100
> fromDatabase tcia format dicom

Summary of feedback from opening
1.3.6.1.4.1.9328.50.1.48441840081578419409180519840073808100 fetched from tcia  
---  
note | Opened 8 CT (No Description) as #1.1.1, grid size 512,512,213, pixel
0.588,0.588,1.24, shown at step 1, values int16  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.3.6.1.4.1.9328.50.1.83304264089411327530730818890072724533
> fromDatabase tcia format dicom

Summary of feedback from opening
1.3.6.1.4.1.9328.50.1.83304264089411327530730818890072724533 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 4 CT (No Description) as #1.1.2, grid size 512,512,236, pixel
0.576,0.576,1.24, shown at step 1, values int16  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8180.1415310847.593766 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8180.1415310847.593766 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg01 run1segmentation result) as
#1.1.3, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8207.1415310875.888278 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8207.1415310875.888278 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg01 run2segmentation result) as
#1.1.4, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8229.1415310904.705216 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8229.1415310904.705216 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg01 run3segmentation result) as
#1.1.5, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8257.1415310937.239787 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8257.1415310937.239787 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg02 run1segmentation result) as
#1.1.6, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8279.1415310969.742678 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8279.1415310969.742678 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg02 run2segmentation result) as
#1.1.7, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8302.1415311002.136804 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8302.1415311002.136804 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg02 run3segmentation result) as
#1.1.8, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8331.1415311023.603234 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8331.1415311023.603234 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg03 run1segmentation result) as
#1.1.9, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8363.1415311056.610053 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8363.1415311056.610053 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg03 run2segmentation result) as
#1.1.10, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.8395.1415311088.560335 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.8395.1415311088.560335 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1000 SEG (QIN CT challenge: alg03 run3segmentation result) as
#1.1.11, grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5,
step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.246.352.71.2.494841863751.4253278.20190214221526 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.246.352.71.2.494841863751.4253278.20190214221526 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.8323329.20780.1554842143.193341 fromDatabase
> tcia format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.8323329.20780.1554842143.193341 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 300 SEG (RIDER-1129164940_20190402_RETEST) as #1.1.13, grid size
512,512,426, pixel 0.588,0.588,0.622, shown at level 0.5, step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.8323329.2021.1554822307.24503 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.8323329.2021.1554822307.24503 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 300 SEG (RIDER-1129164940_20190220_TEST) as #1.1.14, grid size
512,512,472, pixel 0.576,0.576,0.622, shown at level 0.5, step 2, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.246.352.71.2.494841863751.4253279.20190214221610 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.246.352.71.2.494841863751.4253279.20190214221610 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.505801377.2044.1345983847.24 fromDatabase tcia
> format dicom

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 230, in <lambda>  
self.open_button.clicked.connect(lambda: self._on_open_button_clicked())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 373, in
_on_open_button_clicked  
self._on_series_table_double_clicked(self.series_entries.selected)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 377, in
_on_series_table_double_clicked  
run(self.session, f"open {item.seriesUid} fromDatabase tcia format dicom")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_fetcher.py", line 6, in fetch  
return TCIADatabase.getImages(session, ident, ignore_cache)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/databases/tcia.py", line 147, in getImages  
models, msg = DICOM.from_paths(session, final_download_dir).open()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 44, in from_paths  
return cls(path, session = session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 39, in __init__  
self.find_dicom_series(self.paths)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 83, in find_dicom_series  
patients = self.dicom_patients(dpaths)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 99, in dicom_patients  
patient.studies_from_files(series)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 64, in
studies_from_files  
study.series_from_files(files)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 155, in
series_from_files  
s = Series(self.session, self, files)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 261, in __init__  
self.dicom_data.append(DicomData(self.session, self, file_list))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 463, in __init__  
self.value_type = self.numpy_value_type(bits, rep, self.rescale_slope,
self.rescale_intercept)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 848, 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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 848, in
numpy_value_type  
raise ValueError('Unsupported value type, bits_allocated = %d' %
bits_allocated)  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~  
  
See log for complete Python traceback.  
  

> volume #1.1.1 region 0,0,0,511,511,212 step 2

[Repeated 1 time(s)]

> hide #!1.1.3 models

> show #!1.1.3 models

> hide #!1.1.2 models

> hide #!1.1.3 models

> hide #!1.1.4 models

> hide #!1.1.5 models

> hide #!1.1.6 models

> hide #!1.1.7 models

> hide #!1.1.8 models

> hide #!1.1.9 models

> hide #!1.1.10 models

> hide #!1.1.11 models

> hide #!1.1.12 models

> hide #!1.1.13 models

> hide #!1.1.14 models

> hide #!1.1.15 models

> close #1

> open 1.2.276.0.7230010.3.1.3.1231426215.1108.1345549631.406 fromDatabase
> tcia format dicom

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 230, in <lambda>  
self.open_button.clicked.connect(lambda: self._on_open_button_clicked())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 373, in
_on_open_button_clicked  
self._on_series_table_double_clicked(self.series_entries.selected)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 377, in
_on_series_table_double_clicked  
run(self.session, f"open {item.seriesUid} fromDatabase tcia format dicom")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_fetcher.py", line 6, in fetch  
return TCIADatabase.getImages(session, ident, ignore_cache)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/databases/tcia.py", line 147, in getImages  
models, msg = DICOM.from_paths(session, final_download_dir).open()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 44, in from_paths  
return cls(path, session = session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 39, in __init__  
self.find_dicom_series(self.paths)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 83, in find_dicom_series  
patients = self.dicom_patients(dpaths)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 99, in dicom_patients  
patient.studies_from_files(series)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 64, in
studies_from_files  
study.series_from_files(files)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 155, in
series_from_files  
s = Series(self.session, self, files)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 261, in __init__  
self.dicom_data.append(DicomData(self.session, self, file_list))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 463, in __init__  
self.value_type = self.numpy_value_type(bits, rep, self.rescale_slope,
self.rescale_intercept)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 848, 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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 848, in
numpy_value_type  
raise ValueError('Unsupported value type, bits_allocated = %d' %
bits_allocated)  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~  
  
See log for complete Python traceback.  
  

> open 1.3.6.1.4.1.9328.50.1.19900204623473595432414037078138736948
> fromDatabase tcia format dicom

Summary of feedback from opening
1.3.6.1.4.1.9328.50.1.19900204623473595432414037078138736948 fetched from tcia  
---  
note | Opened 102 CT (No Description) as #1.1.1, grid size 512,512,270, pixel
0.877,0.877,1.26, shown at step 1, values int16  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.1031255639.896.1345990202.626 fromDatabase tcia
> format dicom

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 230, in <lambda>  
self.open_button.clicked.connect(lambda: self._on_open_button_clicked())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 373, in
_on_open_button_clicked  
self._on_series_table_double_clicked(self.series_entries.selected)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 377, in
_on_series_table_double_clicked  
run(self.session, f"open {item.seriesUid} fromDatabase tcia format dicom")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_fetcher.py", line 6, in fetch  
return TCIADatabase.getImages(session, ident, ignore_cache)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/databases/tcia.py", line 147, in getImages  
models, msg = DICOM.from_paths(session, final_download_dir).open()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 44, in from_paths  
return cls(path, session = session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 39, in __init__  
self.find_dicom_series(self.paths)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 83, in find_dicom_series  
patients = self.dicom_patients(dpaths)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 99, in dicom_patients  
patient.studies_from_files(series)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 64, in
studies_from_files  
study.series_from_files(files)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 155, in
series_from_files  
s = Series(self.session, self, files)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 261, in __init__  
self.dicom_data.append(DicomData(self.session, self, file_list))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 463, in __init__  
self.value_type = self.numpy_value_type(bits, rep, self.rescale_slope,
self.rescale_intercept)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 848, 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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 848, in
numpy_value_type  
raise ValueError('Unsupported value type, bits_allocated = %d' %
bits_allocated)  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~  
  
See log for complete Python traceback.  
  

> volume #1.1.1 region 0,0,0,511,511,269 step 2

[Repeated 1 time(s)]

> hide #1.1.1.1 models

> show #1.1.1.1 models

> close #1

> open 1.3.6.1.4.1.9328.50.1.232408293761209220974761841467324190361
> fromDatabase tcia format dicom

Summary of feedback from opening
1.3.6.1.4.1.9328.50.1.232408293761209220974761841467324190361 fetched from
tcia  
---  
note | Opened 100 CT (No Description) as #1.1.1, grid size 512,512,297, pixel
0.67,0.67,1.25, shown at step 1, values int16  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.246.352.71.2.494841863751.4253209.20190214212440 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.246.352.71.2.494841863751.4253209.20190214212440 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.8323329.9112.1554820506.221187 fromDatabase
> tcia format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.8323329.9112.1554820506.221187 fetched from tcia  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 300 SEG (RIDER-8509201188_20190220_TEST) as #1.1.3, grid size
512,512,594, pixel 0.67,0.67,0.623, shown at level 0.5, step 4, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.1231426215.2152.1345731988.147 fromDatabase
> tcia format dicom

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 230, in <lambda>  
self.open_button.clicked.connect(lambda: self._on_open_button_clicked())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 373, in
_on_open_button_clicked  
self._on_series_table_double_clicked(self.series_entries.selected)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 377, in
_on_series_table_double_clicked  
run(self.session, f"open {item.seriesUid} fromDatabase tcia format dicom")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_fetcher.py", line 6, in fetch  
return TCIADatabase.getImages(session, ident, ignore_cache)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/databases/tcia.py", line 147, in getImages  
models, msg = DICOM.from_paths(session, final_download_dir).open()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 44, in from_paths  
return cls(path, session = session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 39, in __init__  
self.find_dicom_series(self.paths)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 83, in find_dicom_series  
patients = self.dicom_patients(dpaths)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom.py", line 99, in dicom_patients  
patient.studies_from_files(series)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 64, in
studies_from_files  
study.series_from_files(files)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 155, in
series_from_files  
s = Series(self.session, self, files)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 261, in __init__  
self.dicom_data.append(DicomData(self.session, self, file_list))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 463, in __init__  
self.value_type = self.numpy_value_type(bits, rep, self.rescale_slope,
self.rescale_intercept)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 848, 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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_hierarchy.py", line 848, in
numpy_value_type  
raise ValueError('Unsupported value type, bits_allocated = %d' %
bits_allocated)  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.5.1, Qt 6.5.1
Qt runtime version: 6.5.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14W0010BLL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (c) (22F770820d)
      Kernel Version: Darwin 22.5.0
      Time since boot: 7 days, 11 hours, 3 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46.1
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202307220101
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.31.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.41.1
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.7
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.9.1
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.5.1
    PyQt6-Qt6: 6.5.1
    PyQt6-sip: 13.5.1
    PyQt6-WebEngine-commercial: 6.5.0
    PyQt6-WebEngine-Qt6: 6.5.1
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.4
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8

Change History (3)

comment:1 by pett, 2 years ago

Component: Unassigned → DICOM
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → DICOM: bits_allocated is None

comment:2 by Zach Pearson, 2 years ago

It's a bug that sometimes the RescaleSlope is a string and not an integer; that has been fixed. The bigger issue is the missing BitsAllocated attribute, which is required for all DICOM files. The modality of the tests image I tried to open, 1.2.276.0.7230010.3.1.3.505801377.2044.1345983847.24 and 1.2.276.0.7230010.3.1.3.1231426215.2152.1345731988.147, are both 'PR' for Presentation State. They probably don't have BitsAllocated because they exist to instruct compatible programs on how to display _other_ datasets. We might one day heed them, but we should ignore them for now.

comment:3 by Zach Pearson, 9 months ago

Resolution: → fixed
Status: assigned → closed

Should be fixed in tomorrow's build. Before, the test for whether to examine pixel data was whether or not the data represented a contour series. But now we make sure it is actually image data before we try the lines that throw that error. PR modality DICOMs should be able to be opened now, as in you can see a patient and study model in the model panel and look at the metadata.

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