Added tests for big_stitcher_bridge

tests/test_unit/test_big_stitcher_bridge.py

@@ -0,0 +1,113 @@
+from importlib.resources import files
+from pathlib import Path
+
+import pytest
+
+from brainglobe_stitch.big_stitcher_bridge import run_big_stitcher
+
+IMAGEJ_PATH_WINDOWS = Path("C:/Fiji.app/ImageJ-win64.exe")
+XML_PATH_WINDOWS = Path("C:/stitching/Brain2/bdv.xml")
+TILE_CONFIG_PATH_WINDOWS = Path("C:/stitching/Brain2/bdv_tile_config.txt")
+
+IMAGEJ_PATH_MAC = Path("/Users/user/Fiji.app")
+IMAGEJ_PATH_MAC_CHECK = Path(
+    "/Users/user/Fiji.app/Contents/MacOS/ImageJ-macosx"
+)
+XML_PATH_MAC = Path("/Users/user/stitching/Brain2/bdv.xml")
+TILE_CONFIG_PATH_MAC = Path("/Users/user/stitching/Brain2/bdv_tile_config.txt")
+
+
+@pytest.mark.parametrize(
+    "test_platform, imagej_path, xml_path, tile_config_path",
+    [
+        (
+            "Windows",
+            IMAGEJ_PATH_WINDOWS,
+            XML_PATH_WINDOWS,
+            TILE_CONFIG_PATH_WINDOWS,
+        ),
+        ("Darwin", IMAGEJ_PATH_MAC, XML_PATH_MAC, TILE_CONFIG_PATH_MAC),
+    ],
+)
+def test_run_big_stitcher_defaults(
+    mocker, test_platform, imagej_path, xml_path, tile_config_path
+):
+    mock_subprocess_run = mocker.patch(
+        "brainglobe_stitch.big_stitcher_bridge.subprocess.run"
+    )
+    mocker.patch(
+        "brainglobe_stitch.big_stitcher_bridge.system",
+        return_value=test_platform,
+    )
+
+    run_big_stitcher(imagej_path, xml_path, tile_config_path)
+
+    macro_path = files("brainglobe_stitch").joinpath("bigstitcher_macro.ijm")
+
+    if test_platform == "Darwin":
+        imagej_path = IMAGEJ_PATH_MAC_CHECK
+
+    command = (
+        f"{imagej_path} --ij2"
+        f" --headless -macro {macro_path} "
+        f'"{xml_path} {tile_config_path} 0 488 4 4 4"'
+    )
+
+    mock_subprocess_run.assert_called_with(
+        command, capture_output=True, text=True, check=True, shell=True
+    )
+
+
+@pytest.mark.parametrize(
+    "all_channels, selected_channel, downsample_x, downsample_y, downsample_z",
+    [
+        (False, 488, 4, 4, 4),
+        (True, 488, 4, 4, 4),
+        (False, 488, 4, 8, 16),
+        (True, 576, 4, 8, 16),
+    ],
+)
+def test_run_big_stitcher(
+    mocker,
+    all_channels,
+    selected_channel,
+    downsample_x,
+    downsample_y,
+    downsample_z,
+):
+    mock_subprocess_run = mocker.patch(
+        "brainglobe_stitch.big_stitcher_bridge.subprocess.run"
+    )
+    mocker.patch(
+        "brainglobe_stitch.big_stitcher_bridge.system",
+        return_value="Windows",
+    )
+
+    imagej_path = IMAGEJ_PATH_WINDOWS
+    xml_path = XML_PATH_WINDOWS
+    tile_config_path = TILE_CONFIG_PATH_WINDOWS
+
+    run_big_stitcher(
+        imagej_path,
+        xml_path,
+        tile_config_path,
+        all_channels=all_channels,
+        selected_channel=selected_channel,
+        downsample_x=downsample_x,
+        downsample_y=downsample_y,
+        downsample_z=downsample_z,
+    )
+
+    macro_path = files("brainglobe_stitch").joinpath("bigstitcher_macro.ijm")
+
+    command = (
+        f"{imagej_path} --ij2"
+        f" --headless -macro {macro_path} "
+        f'"{xml_path} {tile_config_path} {int(all_channels)} '
+        f"{selected_channel} "
+        f'{downsample_x} {downsample_y} {downsample_z}"'
+    )
+
+    mock_subprocess_run.assert_called_with(
+        command, capture_output=True, text=True, check=True, shell=True
+    )