Contributing

Issues and pull requests are welcome on GitHub.

Development install

git clone git@github.com:Mo-Sc/OPTARI.git
cd OPTARI
pip install -e ".[test,docs,dev]"

Note: this pulls in a custom PATATO fork, not upstream BohndiekLab/patato.

Test data

The tests use two scans, recorded by the iThera MSOT Acuity Scanner, taken from doi.org/10.5281/zenodo.22044239. They can be downloaded here.

Study_19/
  Scan_2/          # iThera MSOT folder (Scan_2.msot, .bin, .us, ...)
  Scan_3.hdf5      # OPTARI HDF5

Running the tests

Unzip the archive, put the test folder under tests/testdata/ and run:

python -m pytest

Segmentation tests additionally need the ONNX weights of c_unet_gastrocnemius-transverse and skip when they are not in ~/.optari/models. Run segmentation once from the GUI to download them.

Tests overview

The tests are headless, so they dont cover publishing layers into the viewer, the Qt event loop, etc.

Module	Checks
test_roi_geometry.py	PATATO ↔ napari coordinate transforms, RoiGeometry round trips, FOV repositioning, ROI presets
test_roi_measurement.py	ROI statistics on synthetic images with known values, intensity clamping, layer translate, time series, spectra, ROI shapes from masks
test_roi_table.py	Saved Analysis table: stamping, autosave, XLSX export/import, de-duplication, rejected files
test_scan_loading.py	Study discovery, format detection, layer building from iThera and HDF5 scans, spectral and frame-to-frame motion scores and frame selection
test_processing.py	Backprojection, unmixing (THb, sO2), segmentation, automatic ROI placement, parameter resolution from presets
test_export.py	OPTARI HDF5 round trip with ROIs and derived images, IPASC export, batch report
test_batch.py	Batch preset → plan resolution, plan validation, the per-scan run loop, source and overlay layer selection