Added unit test for the 'atlas_jpg_from_mrc' function

Author: tieneupin

tests/workflows/spa/test_atlas_workflow.py

@@ -0,0 +1,39 @@
+from pathlib import Path
+from unittest.mock import MagicMock
+
+import numpy as np
+from pytest_mock import MockerFixture
+
+from murfey.workflows.spa.atlas import atlas_jpg_from_mrc
+
+
+def test_atlas_jpg_from_mrc(mocker: MockerFixture, tmp_path: Path):
+    visit_name = "test_visit"
+    instrument_name = "test"
+
+    # Create a 16-bit grayscale image
+    shape = (64, 64)
+    test_data = np.ones(shape).astype("uint16")
+
+    # Mock out the data returned from openning the file
+    mock_mrcfile = mocker.patch("murfey.workflows.spa.atlas.mrcfile")
+    mock_mrc = MagicMock()
+    mock_mrc.data = test_data
+    mock_mrcfile.open.return_value.__enter__.return_value = mock_mrc
+
+    # Mock the return result of 'get_machine_config()'
+    mock_machine_config = MagicMock()
+    mock_machine_config.processed_directory_name = "processed"
+    mocker.patch(
+        "murfey.workflows.spa.atlas.get_machine_config",
+        return_value={"test": mock_machine_config},
+    )
+
+    # Create a test file
+    test_dir = tmp_path / instrument_name / "data" / visit_name / "atlas"
+    test_dir.mkdir(parents=True, exist_ok=True)
+    test_file = test_dir / "Atlas1.mrc"
+    test_file.touch(exist_ok=True)
+
+    # Run the function
+    atlas_jpg_from_mrc(instrument_name, visit_name, test_file)