Veriton RDSR doesn't import correctly
Veriton SPECT-CT imports, but isn’t registered as CT.
Comments (22)
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reporter -
reporter DICOM TID_1020 details how the Person Participant should be implemented.
DICOM Table TID 10015. CT Dose Check Details shows that Person Participant is mandatory, conditional on the Accumulated DLP Forward Estimate exceeding DLP Alert Value or Accumulated CTDIvol Forward Estimate exceeding CTDIvol Alert Value. Which it didn’t in the example I have, but if it is there, it surely must conform!
This is the sequence from the Spectrum Dynamics RDSR:
(0040, a010) Relationship Type CS: 'CONTAINS' (0040, a040) Value Type CS: 'PERSON NAME' (0040, a043) Concept Name Code Sequence 1 item(s) ---- (0008, 0100) Code Value SH: '113870' (0008, 0102) Coding Scheme Designator SH: 'DCM' (0008, 0104) Code Meaning LO: 'Person Name' --------- (0040, a160) Text Value UT: '' --------- (0040, a010) Relationship Type CS: 'HAS PROPERTIES' (0040, a040) Value Type CS: 'CODE' (0040, a043) Concept Name Code Sequence 1 item(s) ---- (0008, 0100) Code Value SH: '113875' (0008, 0102) Coding Scheme Designator SH: 'DCM' (0008, 0104) Code Meaning LO: 'Person Role in Procedure' --------- (0040, a168) Concept Code Sequence 1 item(s) ---- (0008, 0100) Code Value SH: '113850' (0008, 0102) Coding Scheme Designator SH: 'DCM' (0008, 0104) Code Meaning LO: 'Irradiation Authorizing' --------- --------- (0040, a010) Relationship Type CS: 'HAS PROPERTIES' (0040, a040) Value Type CS: 'TEXT' (0040, a043) Concept Name Code Sequence 1 item(s) ---- (0008, 0100) Code Value SH: '113871' (0008, 0102) Coding Scheme Designator SH: 'DCM' (0008, 0104) Code Meaning LO: 'Person ID' --------- (0040, a160) Text Value UT: ''
This shows that instead of providing
(0040, a123) Person Name
in the Concept Name Code Sequence,(0040, a160) Text Value
has been provided.As that isn’t allowed or expected, the RDSR code fell over when it came across it.
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reporter @David Platten I’m getting nine errors like the following one when I run the tests locally on my machine, and I don’t understand where the 1.0.2 requirement comes from. Do you have any ideas?
====================================================================== ERROR: test_pulse_level_data (remapp.tests.test_export_rf_xlsx.ExportRFxlsx) Tests that RDSR with pulse level kVp, mA, pulse width data imports and exports with mean values ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/unittest/case.py", line 60, in testPartExecutor yield File "/usr/lib/python3.8/unittest/case.py", line 676, in run self._callTestMethod(testMethod) File "/usr/lib/python3.8/unittest/case.py", line 633, in _callTestMethod method() File "/home/mcdonaghe/research/bbOpenREM/openrem/remapp/tests/test_export_rf_xlsx.py", line 151, in test_pulse_level_data rfxlsx(filter_set, pid=pid, name=name, patid=patient_id, user=self.user) File "/home/mcdonaghe/research/vep38/lib/python3.8/site-packages/celery/local.py", line 191, in __call__ return self._get_current_object()(*a, **kw) File "/home/mcdonaghe/research/vep38/lib/python3.8/site-packages/celery/app/task.py", line 393, in __call__ return self.run(*args, **kwargs) File "/home/mcdonaghe/research/bbOpenREM/openrem/remapp/exports/rf_export.py", line 610, in rfxlsx create_summary_sheet(tsk, e, book, summarysheet, sheetlist) File "/home/mcdonaghe/research/bbOpenREM/openrem/remapp/exports/export_common.py", line 646, in create_summary_sheet vers = pkg_resources.require("openrem")[0].version File "/home/mcdonaghe/research/vep38/lib/python3.8/site-packages/pkg_resources/__init__.py", line 892, in require needed = self.resolve(parse_requirements(requirements)) File "/home/mcdonaghe/research/vep38/lib/python3.8/site-packages/pkg_resources/__init__.py", line 783, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (pandas 1.1.3 (/home/mcdonaghe/research/vep38/lib/python3.8/site-packages), Requirement.parse('pandas==1.0.2'), {'openrem'})
I’m also getting a lot of these:
/home/mcdonaghe/research/vep38/lib/python3.8/site-packages/plotly/express/_core.py:387: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version. Convert to a numpy array before indexing instead.
Have you seen this?
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reporter My virtenv has pandas 1.1.3 installed.
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reporter Found it - need to update the rtdrequirements file
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reporter Nope - it was a stale egg thing!
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reporter The plotly multi-dimensional indexing warning remains - you can see it in any of the pipeline builds - https://bitbucket.org/openrem/openrem/addon/pipelines/home#!/results/3440 for example.
Can I leave that with you to review @David Platten ?
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I’ve seen the plotly multi-dimensional indexing warning and have tried to identify exactly where in the code it is being used, but have been unable to track it down. I’ll have another look.
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reporter I was wondering if it was in the plotly code rather than yours, but the deprecation came into pandas for v1.0, and we are on v1.1.3 so it seems unlikely (there are several plotly releases between when pandas 1.0 was released and the version we are currently on)
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reporter Adding test Spectrum Dynamics RDSR and test script. Removed executable flag from Bigbore test file. Refs
#865→ <<cset cc1a8a63b9d8>>
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reporter Added ref
#865to changes.→ <<cset 1abde4ddee4f>>
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I’ve fixed the plotly multi-dimensional indexing warning - see the issue870improveDataFrameMemoryEfficiency branch and associated pull request.
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reporter Good, well done. I was thinking along the right lines then!
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reporter Consolidating imports to the top and relative for remapp. Sort of refs
#865→ <<cset 6893dc8e068e>>
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reporter Sorting out old_div and a few more imports. Sort of refs
#865→ <<cset a90902c2097e>>
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reporter Put Django setup after imports. Hope it still works when called... Sort of refs
#865→ <<cset 49ddc84a8176>>
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reporter Black. Refs
#865→ <<cset ca47d1a52421>>
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reporter Testing shows models need to be imported after django.setup(), and must be absolute imports from the APP name. Refs
#865→ <<cset a45c2f34c09c>>
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reporter Removing comment on placement. Refs
#865→ <<cset b2e748d5d940>>
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reporter Attempting to disable pylint warnings about importing the models not at the top. Refs
#865→ <<cset 13f15229631a>>
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reporter Missed =, still not sure if both will be respected. Refs
#865→ <<cset defa3d00a55f>>
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reporter - changed status to resolved
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Spectrum Dynamics Person name sequence appears to be malformed - will check against standard! Refs
#865→ <<cset 0fe0025fb32e>>