WIP: Volumetric Segmentations #277
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…ighdicom into feature/seg_volumes
* Enforce repo-review rule PP302 PP302: Sets a minimum pytest to at least 6 Must have a `minversion=`, and must be at least 6 (first version to support `pyproject.toml` configuration). * Enforce repo-review rule PP305 PP305: Specifies xfail_strict `xfail_strict` should be set. You can manually specify if a check should be strict when setting each xfail. * Enforce repo-review rule PP306 PP306: Specifies strict config `--strict-config` should be in `addopts = [...]`. This forces an error if a config setting is misspelled. * Enforce repo-review rule PP307 PP307: Specifies strict markers `--strict-markers` should be in `addopts = [...]`. This forces all markers to be specified in config, avoiding misspellings. * Enforce repo-review rule PP308 PP308: Specifies useful pytest summary An explicit summary flag like `-ra` should be in `addopts = [...]` (print summary of all fails/errors). * Enforce pytest ≥ 7.3.2 This is the first version to support Python 3.12: https://docs.pytest.org/en/stable/changelog.html#pytest-7-3-2-2023-06-10 * Enforce repo-review rule MY104 MY104: MyPy enables ignore-without-code Must have `"ignore-without-code"` in `enable_error_code = [...]`. This will force all skips in your project to include the error code, which makes them more readable, and avoids skipping something unintended. * Enforce repo-review rule MY105 MY105: MyPy enables redundant-expr Must have `"redundant-expr"` in `enable_error_code = [...]`. This helps catch useless lines of code, like checking the same condition twice. * Enforce repo-review rule MY106 MY106: MyPy enables truthy-bool Must have `"truthy-bool"` in `enable_error_code = []`. This catches mistakes in using a value as truthy if it cannot be falsy.
Preparation for 0.23.0 release
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Branch for NAMIC project week 40. Project page.
Goals
Add support for working with "volumetric": segmentations, i.e. regularly spaced frames in a 3D frame of reference. Specifically:
Details
In order to do this, I have generalized the existing
highdicom.seg.sop._SegDBManagerclass to create a generalhighdicom._multiframe.MultiFrameDBManagerclass to handle the logic of storing an in-memory sqlite database of per-frame information for general multiframe object. This simplifies the process of inspecting the geometry of subsets of frames and will also make it much easier to do similar things for other multiframe objects in the future (e.g. parametric maps, labelmap segmentations)