[Jules-GP]

Why

The three AREG engines read their two inputs as two folders, one per type: t1 and t2, or ios and cbct. Many cohorts are kept the other way round: one folder per patient holding both inputs (<patient>/T1/ and <patient>/T2/, or <patient>/IOS/ and <patient>/CBCT/). Running AREG on them meant reorganising the data by hand first.

Change

Choosing the layout

• Each engine takes a new input_layout: "One folder per type" (the default, today's behaviour) or "One folder per patient".
• It also takes patients, the folder of patient folders.
• t1/t2 and ios/cbct stop being required in the signature, since a per-patient request fills neither.

Sorting the per-patient layout (sadt_areg_common.patient_folders)

• Who a file belongs to: its patient folder, never its own name. <patient>/T1/scan.nii.gz is that patient's T1, whatever the file is called.
• The timepoint: read from a T1//T2/ folder or from _T1/_T2 in the name. A folder and a name that disagree give no timepoint: the file is left out, not guessed at.
• Intraoral vs CBCT: read from the file type alone, so IOS/ and CBCT/ sub-folders are optional.
• Left out: a segmentation kept beside its scan and anything the engine does not read.
• Where the files go: into the per-type layout, in a scratch folder beside the output folder, never inside it. The names carry the patient folder's name: <patient>_T1.nii.gz, <patient>_T1_U.vtk, <patient>_U.stl, <patient>_CBCT.nii.gz.
• No copies: files are hard-linked, with a copy only as fallback. The scratch folder is removed when the run ends, and also when sorting is refused.
• What follows is unchanged: pairing, the supervised tools and the output folders are exactly what a per-type request runs. Combined with FIX: name each AREG IOS-CBCT patient folder as its files do and hand back the oriented CBCT beside the meshes #88, each patient's results land in a folder named after its patient folder.
• Refusals with a clear message: two files that would be filed under one name, no patient sub-folder at all, and, for IOS to CBCT, a patient folder name with no number (that engine matches patients on digits).

Panel

• input_layout is drawn as two segments (ui: "segmented") above the inputs. Each segment's help shows the folder tree it expects (catalogs.LAYOUT_HELP).
• The per-type fields show only in their layout, and patients only in its own.
• Each is required_when its layout is chosen, so the panel does not label them "(optional)".

describe.py

• Publishes and checks required_when exactly like visible_when; the checker is shared.
• PAIRED axes need to be path arguments, no longer required ones, since t1/t2 are now optional.

Depends on

• FIX: name each AREG IOS-CBCT patient folder as its files do and hand back the oriented CBCT beside the meshes #88: this branch is built on it, and its diff here shrinks to this change once FIX: name each AREG IOS-CBCT patient folder as its files do and hand back the oriented CBCT beside the meshes #88 is merged.
• ADD: let a choice be drawn as segments and an input be required in one layout of the request only VISOR-serve#87: the server must be deployed first. It is what accepts ui: "segmented" on a choice and required_when; without it the three AREG tools are refused at load.
• ADD: draw a segmented choice, read required_when, and take AREG's patient folders as a folder only SlicerAutomatedDentalToolsRemote#53: the client draws the segments and reads required_when. Without it the panel still works, with a drop-down and "(optional)".

Still to do

The server publishes a paired batch plan on t1/t2; no client uses it today. A per-patient request fills neither axis, so a future client that splits cohorts would split nothing in that layout. Splitting by patient folder there is a follow-up.

Tests

• New tests:
  • common/tests/test_patient_folders.py (12): timepoint and jaw reading, sorting, refusals, the scratch folder.
  • test_patient_folders.py in each engine: IOS-CBCT registers a per-patient cohort end to end (side by side and with IOS//CBCT/), and the T1/T2 engines receive the patient's two timepoints.
  • The layout-condition test now checks every condition's values, not only automation's.
• AREG_CBCT 169, AREG_IOS 89, AREG_IOSCBCT 223, common 184 passed.
• scripts/tests: 100 passed. test_module_level_heavy_import_is_reported_as_such also fails on main.
• Checked by hand in Slicer against a local server serving this branch.

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