Open dcm file: missing GDCM dependency

[stfuruie@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
report error to open dcm file.

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
> E:\\\trabalho\\\37647\\\745323\\\20250625154431381-2806-32625-3-7788.dcm

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\\__main__.py", line 1015, in init  
commands.run(sess, "open %s" % StringArg.unparse(arg))  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_opener.py", line 8, in open  
return dcm.open()  
^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom.py", line 58, in open  
patient.render()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 125, in render  
study.open_series_as_models()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 215, in
open_series_as_models  
models = s.to_models(all_opened_models, derived, sgrids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 330, in to_models  
grids = data.to_models(open_models, derived, sgrids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 649, in to_models  
models.extend(open_grids(self.session, originals, name=self.name)[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\map\volume.py", line 3727, in open_grids  
v.update_drawings()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\map\volume.py", line 821, in update_drawings  
self._keep_displayed_data = self.displayed_matrices()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\map\volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\map\volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\map\volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\map_data\griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_models.py", line 214, in read_matrix  
self.dicom_data.read_matrix(  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 921, in read_matrix  
a = self.read_frames(time, channel)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 963, in read_frames  
data = d.pixel_array  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 1145, in __getattr__  
return self.data.get(item)  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\pydicom\dataset.py",
line 829, in get  
return getattr(self, key)  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\pydicom\dataset.py",
line 1955, in pixel_array  
self.convert_pixel_data()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\pydicom\dataset.py",
line 1512, in convert_pixel_data  
self._convert_pixel_data_without_handler()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\pydicom\dataset.py",
line 1599, in _convert_pixel_data_without_handler  
raise RuntimeError(msg + ', '.join(pkg_msg))  
RuntimeError: The following handlers are available to decode the pixel data
however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg
(req. )  
  
RuntimeError: The following handlers are available to decode the pixel data
however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg
(req. )  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\pydicom\dataset.py",
line 1599, in _convert_pixel_data_without_handler  
raise RuntimeError(msg + ', '.join(pkg_msg))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 576.40
OpenGL renderer: NVIDIA GeForce RTX 4060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: pt_BR.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Gigabyte Technology Co., Ltd.
Model: B450M DS3H V2
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 51,457,974,272
MaxProcessMemory: 137,438,953,344
CPU: 24 AMD Ryzen 9 3900 12-Core Processor             
OSLanguage: pt-BR

Installed Packages:
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    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
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    beautifulsoup4: 4.12.3
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    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    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
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    ChimeraX-AxesPlanes: 2.4
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    WMI: 1.5.1

[pett]

Reported by Sergio Furuie