Add unit tests for generated stitching commands.

tests/test_stitching.py

@@ -0,0 +1,150 @@
+"""Test that the code that talks to the external stitching process acts as expected.
+
+This does not actually run stitching. Instead it checks that the expected commands are
+generated, and the subprocess calling works as expected.
+"""
+
+import logging
+from copy import copy
+
+import pytest
+
+from openflexure_microscope_server.stitching import (
+    BaseStitcher,
+    PreviewStitcher,
+    FinalStitcher,
+    STITCHING_RESOLUTION,
+)
+
+# A global logger pretending to be an Invocation Logger
+LOGGER = logging.getLogger("mock-invocation_logger")
+FAKE_DIR = "a/dir/that/is/fake"
+
+
+def test_base_stitcher():
+    """Test the logic in BaseStitcher.
+
+    Pretty much the only logic in base stitcher is forming a command, and calculating
+    the min_overlap from overlap.
+
+    The BaseStitcher can't start as the start method is explicitly NotImplemented.
+    """
+    # Overlaps and expected minimum overlap to be in command line argument.
+    overlaps = [(0.1, "0.09"), (0.4, "0.36"), (0.8, "0.72")]
+
+    for overlap, min_overlap in overlaps:
+        expected_command = [
+            "openflexure-stitch",
+            "--stitching_mode",
+            "all",
+            "--minimum_overlap",
+            min_overlap,
+            "--resize",
+            "0.5",
+            FAKE_DIR,
+        ]
+        stitcher = BaseStitcher(FAKE_DIR, overlap=overlap, correlation_resize=0.5)
+        assert stitcher.command == expected_command
+        # check that a BaseSticher can't start
+        with pytest.raises(NotImplementedError):
+            stitcher.start()
+
+
+def test_preview_stitcher_command():
+    """Check preview stitcher command for a specific example."""
+    expected_command = [
+        "openflexure-stitch",
+        "--stitching_mode",
+        "preview_stitch",
+        "--minimum_overlap",
+        "0.09",
+        "--resize",
+        "0.5",
+        FAKE_DIR,
+    ]
+    stitcher = PreviewStitcher(FAKE_DIR, overlap=0.1, correlation_resize=0.5)
+    assert stitcher.command == expected_command
+
+
+FINAL_EXPECTED_COMMAND = [
+    "openflexure-stitch",
+    "--stitching_mode",
+    "all",
+    "--stitch-dzi",
+    "--no-stitch_tiff",
+    "--minimum_overlap",
+    "0.09",
+    "--resize",
+    "0.5",
+    FAKE_DIR,
+]
+
+
+def test_final_stitcher_command_defaults(caplog):
+    """Check the FinalStitcher stitches with expected default values.
+
+    It should warn when default values are used as they are a fallback.
+    """
+    n_logs = 0
+    # Test with no dictionary data and with irrelevant dictionary data.
+    with caplog.at_level(logging.WARNING):
+        for data_dict in [None, {"irrelevant": "data"}]:
+            stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER, scan_data_dict=data_dict)
+            # Should log for overlap being None and correlation_resize being None
+            n_logs += 2
+            assert len(caplog.records) == n_logs
+        assert stitcher.command == FINAL_EXPECTED_COMMAND
+
+
+def test_final_stitcher_command_tiff(caplog):
+    """Check that the tiff can be requested."""
+    # Modify defaults
+    expected_command = copy(FINAL_EXPECTED_COMMAND)
+    expected_command[4] = "--stitch_tiff"
+    stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER, stitch_tiff=True)
+    # Should log for overlap being None and correlation_resize being None
+    assert len(caplog.records) == 2
+    assert stitcher.command == expected_command
+
+
+def test_final_stitcher_command_set_val_directly():
+    """Check that values are set as expected when directly input."""
+    # Modify defaults
+    expected_command = copy(FINAL_EXPECTED_COMMAND)
+    expected_command[6] = "0.36"
+    expected_command[8] = "0.25"
+    # Test with no data dictionary, irrelevant data, and also the wrong data
+    # When wrong data is submitted, it should take the directly input data.
+    dict_vals = [
+        None,
+        {"irrelevant": "data"},
+        {"overlap": 0.2, "save_resolution": [5, 5]},
+    ]
+    for data_dict in dict_vals:
+        stitcher = FinalStitcher(
+            FAKE_DIR,
+            logger=LOGGER,
+            overlap=0.4,
+            correlation_resize=0.25,
+            scan_data_dict=data_dict,
+        )
+        assert stitcher.command == expected_command
+
+
+def test_final_stitcher_command_set_with_dict():
+    """Check that values are set as expected when set from a ScanData dictionary."""
+    # Modify defaults
+    expected_command = copy(FINAL_EXPECTED_COMMAND)
+    expected_command[6] = "0.36"
+    expected_command[8] = "0.25"
+    # Check same thing works with a dictionary, resize is calculated from the saved image
+    # resolution. Make 4x bigger than STITCHING_RESOLUTION to get 0.25
+    resolution = [dim * 4 for dim in STITCHING_RESOLUTION]
+    # Check legacy key as well as current one:
+    for resolution_key in ["save_resolution", "capture resolution"]:
+        stitcher = FinalStitcher(
+            FAKE_DIR,
+            logger=LOGGER,
+            scan_data_dict={"overlap": 0.4, resolution_key: resolution},
+        )
+        assert stitcher.command == expected_command