test: Add unit tests for rolling ball options and background subtraction

Author: lguerard

tests/test_processing.py

@@ -0,0 +1,160 @@
+"""Unit tests for imcflibs.imagej.processing."""
+
+import importlib
+import sys
+import types
+
+import pytest
+
+
+def _import_processing():
+    """Import processing module in a runtime-independent way."""
+    """Load imcflibs.imagej.processing with a fake ij.IJ module for plain pytest."""
+    if "ij" not in sys.modules:
+        fake_ij = types.ModuleType("ij")
+        fake_ij.IJ = types.SimpleNamespace(run=lambda *args, **kwargs: None)
+        sys.modules["ij"] = fake_ij
+
+    import os
+    from importlib.util import module_from_spec, spec_from_file_location
+
+    pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+    processing_path = os.path.join(
+        pkg_root, "src", "imcflibs", "imagej", "processing.py"
+    )
+
+    spec = spec_from_file_location("imcflibs.imagej.processing", processing_path)
+    module = module_from_spec(spec)
+    sys.modules[spec.name] = module
+    spec.loader.exec_module(module)
+    return module
+
+
+def test_rolling_ball_options_combinations():
+    """rolling_ball_options should produce correct option strings."""
+    processing = _import_processing()
+
+    assert processing.rolling_ball_options(10) == "rolling=10"
+    assert processing.rolling_ball_options(10, sliding=True) == "rolling=10 sliding"
+    assert processing.rolling_ball_options(10, do_3d=True) == "rolling=10 stack"
+    assert (
+        processing.rolling_ball_options(10, sliding=True, do_3d=True)
+        == "rolling=10 sliding stack"
+    )
+    assert (
+        processing.rolling_ball_options(10, light_background=True, disable=True)
+        == "rolling=10 light disable"
+    )
+    assert (
+        processing.rolling_ball_options(
+            10, sliding=True, light_background=True, do_3d=True, disable=True
+        )
+        == "rolling=10 light sliding disable stack"
+    )
+
+
+def test_apply_rollingball_bg_subtraction_calls_IJ_run_with_expected_options():
+    """apply_rollingball_bg_subtraction should invoke ImageJ run with composed options."""
+    processing = _import_processing()
+
+    class DummyImagePlus:
+        def duplicate(self):
+            return self
+
+    image = DummyImagePlus()
+
+    executed = {}
+
+    def fake_run(arg_image, arg_command, arg_options):
+        executed["image"] = arg_image
+        executed["command"] = arg_command
+        executed["options"] = arg_options
+
+    processing.IJ = types.SimpleNamespace(run=fake_run)
+
+    output = processing.apply_rollingball_bg_subtraction(
+        image,
+        rolling_ball_radius=5,
+        light_background=True,
+        sliding=True,
+        disable=True,
+        do_3d=True,
+    )
+
+    assert output is image
+    assert executed["command"] == "Subtract Background..."
+    assert executed["options"] == "rolling=5 light sliding disable stack"
+
+
+def test_apply_filter_calls_IJ_run_with_expected_options():
+    """apply_filter should invoke ImageJ run with expected filter command and options."""
+    processing = _import_processing()
+
+    class DummyImagePlus:
+        def duplicate(self):
+            return self
+
+    image = DummyImagePlus()
+
+    executed = {}
+
+    def fake_run(arg_image, arg_command, arg_options):
+        executed["image"] = arg_image
+        executed["command"] = arg_command
+        executed["options"] = arg_options
+
+    processing.IJ = types.SimpleNamespace(run=fake_run)
+
+    output = processing.apply_filter(image, "Median", 3, do_3d=True)
+
+    assert output is image
+    assert executed["command"] == "Median 3D..."
+    assert executed["options"] == "radius=3 stack"
+
+
+def test_apply_filter_invalid_method_raises_value_error():
+    """apply_filter with unknown method raises ValueError."""
+    processing = _import_processing()
+
+    class DummyImagePlus:
+        def duplicate(self):
+            return self
+
+    image = DummyImagePlus()
+
+    with pytest.raises(ValueError):
+        processing.apply_filter(image, "BadFilter", 1)
+
+
+def test_apply_threshold_uses_IJ_setAutoThreshold_and_IJ_run():
+    """apply_threshold should call IJ.setAutoThreshold and IJ.run appropriately."""
+    processing = _import_processing()
+
+    class DummyImagePlus:
+        def duplicate(self):
+            return self
+
+    image = DummyImagePlus()
+
+    auto_threshold_called = {}
+    run_called = {}
+
+    def fake_set_auto_threshold(arg_image, arg_options):
+        auto_threshold_called["image"] = arg_image
+        auto_threshold_called["options"] = arg_options
+
+    def fake_run(arg_image, arg_command, arg_options):
+        run_called["image"] = arg_image
+        run_called["command"] = arg_command
+        run_called["options"] = arg_options
+
+    processing.IJ = types.SimpleNamespace(
+        setAutoThreshold=fake_set_auto_threshold, run=fake_run
+    )
+
+    output = processing.apply_threshold(image, "Default", do_3d=False)
+
+    assert output is image
+    assert auto_threshold_called["options"] == ""
+    assert run_called["command"] == "Convert to Mask"
+    assert run_called["options"] == "method=Default background=Dark black"