Add application test for pctpairprotons

.github/workflows/build-test-package.yml

@@ -50,7 +50,7 @@ jobs:
         echo "Installing wheel: $wheel"
         pip install $wheel
 
-        pip install pytest
+        pip install pytest uproot
 
         # Run tests with warning detection.
         # SWIG < 4.4 triggers the Py_LIMITED_API "builtin type swig…" warning when

documentation/docs/installation.md

@@ -80,6 +80,23 @@ export PATH=<path to ITK build folder>/Wrapping/Generators/Python/itk/:${PATH}
 ```
 in the user's `.bashrc` file. This allows to run PCT applications from anywhere on the computer.
 
+### Testing
+
+To run PCT Python tests with pytest, install the test dependencies from the directory containing `pyproject.toml`:
+
+```
+pip install --group test
+```
+
+This installs:
+* `pytest` - for running Python unit tests
+* `uproot` - for loading ROOT files
+
+After installing, run the tests with:
+```
+pytest test/*.py
+```
+
 ## Optional dependencies
 
 ### GATE
@@ -89,3 +106,10 @@ in the user's `.bashrc` file. This allows to run PCT applications from anywhere
 pip install opengate
 ```
 An example of proton CT GATE simulation can be found in [`gate/protonct.py`](https://github.com/RTKConsortium/PCT/blob/main/gate/protonct.py).
+
+### Uproot
+
+[Uproot](https://uproot.readthedocs.io/) is a library for reading and writing ROOT files in pure Python and NumPy. Some applications of PCT require Uproot, such as `pctpairprotons` and `pctweplfit`. The simplest way to install Uproot is by running
+```bash
+pip install uproot
+```

pyproject.toml

@@ -37,6 +37,8 @@ requires-python = ">=3.8"
 dependencies = [
     "itk-rtk == 2.7.*"
 ]
+[dependency-groups]
+test = ["pytest", "uproot"]
 
 [project.scripts]
 pctbinning = "itk.pctbinning:main"

test/pctapplicationtest.py

@@ -0,0 +1,45 @@
+import pytest
+import itk
+import urllib.request
+import numpy as np
+from itk import PCT as pct
+
+
+def download_file_fixture(file_key, filename):
+
+    @pytest.fixture(scope="session")
+    def fixture(tmp_path_factory):
+        path = tmp_path_factory.getbasetemp() / filename
+        url = f"https://data.kitware.com/api/v1/file/{file_key}/download"
+        with urllib.request.urlopen(url) as response, open(path, "wb") as out_file:
+            out_file.write(response.read())
+        return path
+
+    return fixture
+
+
+phasespacein_root = download_file_fixture(
+    "69cbef28303cec2e64feb78a", "PhaseSpaceIn.root"
+)
+phasespaceout_root = download_file_fixture(
+    "69cbef2a303cec2e64feb78d", "PhaseSpaceOut.root"
+)
+baseline_pairs_mhd = download_file_fixture("69cbefdf303cec2e64feb790", "pairs0000.mhd")
+baseline_pairs_raw = download_file_fixture("69cbefe0303cec2e64feb793", "pairs0000.raw")
+
+
+def test_pairprotons_application(
+    tmp_path,
+    phasespacein_root,
+    phasespaceout_root,
+    baseline_pairs_mhd,
+    baseline_pairs_raw,
+):
+    output = tmp_path / "pairs_test.mhd"
+    pct.pctpairprotons(
+        f"-i {phasespacein_root} -j {phasespaceout_root} -o {output} --plane-in -110 --plane-out 110 --psin PhaseSpaceIn --psout PhaseSpaceOut"
+    )
+    output0000 = tmp_path / "pairs_test0000.mhd"
+    pairs_test = itk.array_from_image(itk.imread(output0000))
+    pairs_baseline = itk.array_from_image(itk.imread(baseline_pairs_mhd))
+    assert np.array_equal(pairs_test, pairs_baseline)