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Sk/doc dir sync #596

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Description

Fixes #{issue_number}: A few words or sentences describing the changes proposed in this pull request (PR).

Type of change

Please delete options accordingly to the description.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • This change requires a documentation update

Suggested Checklist

  • I have performed a self-review of my own code.
  • I have made corresponding changes to the documentation.
  • My changes generate no new warnings.
  • I have commented my code, particularly in hard-to-understand areas.
  • I have passed on my local host device. (see further details at the CONTRIBUTING document)
  • Make sure your branch is up-to-date with main branch. See CONTRIBUTING for a general example to syncronise your branch with the main branch.
  • I have requested review to this PR.
  • I have addressed and marked as resolved all the review comments in my PR.
  • Finally, I have selected squash and merge

skeating and others added 11 commits February 4, 2025 16:07
@skeating
synchronizing documentation from the-rolling-skeleton repository
a4f6358
@skeating
updating links and including references from the book of flower which…
f6c4940 
… is private
@p-j-smith @davecash75
Add configuration for DESPIAD project (#572)
28db049 
* Add initial anonymisation config for ct

* Add initial anonymisation config for pet

* Add config for despiad

* anonymnise all resources before notifying the export api

this is because resources sharing the same StudyInstanceUID in Orthanc Raw will be combined into a single resource in Orthanc Anon.
Previously, we would try to export each resource after anonymisation, but this meant other resources sharing the same StudyInstanceUID were not exported.

* remove despaid.yaml from project config

* generate label based on patient id and study count in xnat project

* Use pseudo-anonymised StudyInstanceUID for xnat experiment label

* Fix XNAT destination

* remove changes related to grouping resources before notifying export api

it's been addressed in another PR

* remove duplicated tags

* Add series_number_filters and allowed_manufacturers parameters to pixl project config

* clarify docstring of _import_study_from_raw

* Add min_instances_per_series parameter to project config

In orthanc anon plugin, skip series that have few than min_instances_per_series instances

* Keep study date and patient dob for despiad

* Changes after reviewing the PET data for DESPIAD (#592)

* Add Radiopharmaceutical Start DateTime to pet.yaml

* remove blank lines from ct.yaml

* remove tab from config file

* filter series number by manufacturer

also default to allowing no manufacturers

* Add allowed_manufacturers for all test configs

* Count number of instances skipped due to series having too few instances

* move get_series_to_skip to dcmd

* Add philips and carestream as allowed manufacturers for test project

* Update description of project config in readme

* Check _should_exclude_manufacurer before _should_exclude_series

in case the manufacturer doesn't exist

* filter out instance if manufacturer tag is missing

* allow all manufacturers for existing projects

* Add tests for PixlConfig.is_manufacturer_allowed and PixlConfig.is_series_number_excluded

* Add more tests for _should_exclude_series

* Add tests for test_should_exclude_manufacturer

* Add tests for get_series_to_skip

* Don't allow all manufacturers in the template config

* Set min_instances to 2 for despiad

* Only allow manufacturer GE MEDICAL SYSTEMS for DESPIAD

* Keep Number of Time Slices attribute for PET

* set 'pydicom.config.convert_wrong_length_to_UN = True' in dcmd

* Add series filters to despiad config

* Add series number and description filers for despiad

* Use ints for series numbers to exclude

* Update default config to exclude series with mip in their description

* Add ^company as an allowed manufacturer when testing anonymisation

* Use integers for series_number in tests

* set min_instances_per_series to 2 by default

* Set min_instances_per_series to 1 for testing

---------

Co-authored-by: davecash75 <[email protected]>
@tomaroberts @p-j-smith
Enables PIXL DB to operate as a service separate from Orthanc Raw (#593)
3f3419c 
* Adds environment variables to enable PIXL DB to be used on a db separate from Orthanc Raw

* Implements 'profiles' in docker-compose.yaml to control PIXL DB location

* Updates pixl dc up command to use profiles functionality

---------

Co-authored-by: Paul Smith <[email protected]>
@skeating
updating links
e819679
@skeating
Merge remote-tracking branch 'origin/main' into sk/doc_dir_sync
6972590
@skeating
updating links
160de83
@skeating
updating links
dc5cae0
@skeating
adding read mes
b92523e
@skeating
Merge remote-tracking branch 'origin/sk/doc_dir_sync' into sk/doc_dir…
629035d 
…_sync
@skeating
adding read mes
26b6e2d
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codecov bot commented Feb 11, 2025 •
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Codecov Report

Attention: Patch coverage is 93.93939% with 6 lines in your changes missing coverage. Please review.

Project coverage is 87.64%. Comparing base (4af6ed0) to head (26b6e2d).
Report is 25 commits behind head on sk/joss-publication.

Files with missing lines Patch % Lines
pixl_dcmd/src/pixl_dcmd/main.py 88.88% 4 Missing ⚠️
..._core/src/core/project_config/pixl_config_model.py 92.00% 2 Missing ⚠️
Additional details and impacted files 
@@                   Coverage Diff                   @@
##           sk/joss-publication     #596      +/-   ##
=======================================================
+ Coverage                87.51%   87.64%   +0.12%     
=======================================================
  Files                       76       76              
  Lines                     3437     3512      +75     
=======================================================
+ Hits                      3008     3078      +70     
- Misses                     429      434       +5

☔ View full report in Codecov by Sentry.
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@stefpiatek stefpiatek Awaiting requested review from stefpiatek

@tomaroberts tomaroberts Awaiting requested review from tomaroberts

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3 participants
@skeating @p-j-smith @tomaroberts