Complete testing of HistoScanWorkflow

src/openflexure_microscope_server/things/scan_workflows.py

@@ -422,20 +422,22 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
         :return: A tuple of whether an image was taken, and the z-position for focus.
             If failed to find focus, returns for the focus z-position.
         """
-        # If skipping background, take an image to check if current field of view is background
         if settings.skip_background:
+            # If skipping background, take an image to check if current field of view
+            # is background
             image_array = self._cam.grab_as_array(stream_name="lores")
             capture_image, bg_message = self._background_detector.image_is_sample(
                 image_array
             )
             del image_array
 
-        if not capture_image:
-            msg = f"Skipping {xyz_pos} as it is {bg_message}."
-            self.logger.info(msg)
-            return False, None
+            if not capture_image:
+                # Return early if the image is background.
+                msg = f"Skipping {xyz_pos} as it is {bg_message}."
+                self.logger.info(msg)
+                return False, None
 
-        save_on_failure = settings.skip_background
+        save_on_failure = not settings.skip_background
 
         focus_height: Optional[int]
         focused, focus_height = self._autofocus.run_smart_stack(
@@ -445,6 +447,10 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
         # An image was captured if we are focussed or we are not skipping background.
         imaged = focused or save_on_failure
 
+        if not imaged:
+            msg = f"Stack failed at {xyz_pos} treating as background."
+            self.logger.info(msg)
+
         # run_smart_stage always returns a focus height for the sharpest image even
         # if it failed to find a good focus. Set to None if not focussed.
         if not focused:

tests/unit_tests/test_scan_workflows.py

@@ -9,6 +9,7 @@ from pydantic import BaseModel
 import labthings_fastapi as lt
 from labthings_fastapi.testing import create_thing_without_server
 
+from openflexure_microscope_server.scan_planners import SmartSpiral
 from openflexure_microscope_server.stitching import StitchingSettings
 from openflexure_microscope_server.things.autofocus import SmartStackParams
 from openflexure_microscope_server.things.camera_stage_mapping import csm_img_to_stage
@@ -190,6 +191,146 @@ def test_histo_calculate_overlap(csm_matrix, overlap, expected_steps, histo_work
     assert (dx, dy) == expected_steps
 
 
+def test_histo_pre_scan_routine(histo_workflow, mocker):
+    """Check the pre-scan routine does autofocusses."""
+    # Rather than create a whole Setting class, just create a mock with the value
+    # we need set
+    mock_settings = mocker.Mock()
+    mock_settings.smart_stack_params.autofocus_dz = 1234
+    # Run the function
+    histo_workflow.pre_scan_routine(mock_settings)
+    # Check the autofocus was run using the mocked slot.
+    assert histo_workflow._autofocus.looping_autofocus.call_count == 1
+    call_kwargs = histo_workflow._autofocus.looping_autofocus.call_args.kwargs
+    assert call_kwargs["dz"] == 1234
+    assert call_kwargs["start"] == "centre"
+
+
+def test_histo_new_scan_planner(histo_workflow, mocker):
+    """Check the pre-scan routine does autofocusses."""
+    # Rather than create a whole Setting class, just create a mock with the 3 values
+    # we need set
+    mock_settings = mocker.Mock()
+    mock_settings.dx = 666
+    mock_settings.dy = 999
+    mock_settings.max_dist = 54321
+
+    planner = histo_workflow.new_scan_planner(
+        mock_settings, position={"x": 1, "y": 2, "z": 3}
+    )
+    assert isinstance(planner, SmartSpiral)
+    # Check the settings were read
+    assert planner._dx == 666
+    assert planner._dy == 999
+    assert planner._max_dist == 54321
+
+
+def test_histo_acquisition_with_background_detected(histo_workflow, mocker, caplog):
+    """If background is detected it should return without a stack."""
+    # Mocking for settings as above
+    mock_settings = mocker.Mock()
+    mock_settings.skip_background = True
+
+    histo_workflow._background_detector.image_is_sample.return_value = (
+        False,
+        "totally empty",
+    )
+
+    with caplog.at_level(logging.INFO):
+        imaged, focus_height = histo_workflow.acquisition_routine(
+            mock_settings, xyz_pos=(1, 2, 3)
+        )
+
+    # Check returns
+    assert imaged is False
+    assert focus_height is None  # None meaning not focussed
+    # Check there is a log explaining what happened
+    assert len(caplog.records) == 1
+    assert caplog.records[0].message == "Skipping (1, 2, 3) as it is totally empty."
+    assert caplog.records[0].levelname == "INFO"
+
+    # And that smart stack never ran
+    assert histo_workflow._autofocus.run_smart_stack.call_count == 0
+
+
+def test_histo_acquisition_not_skipping_background(histo_workflow, mocker, caplog):
+    """Check when not skipping background an image is always saved."""
+    # Mocking for settings as above
+    mock_settings = mocker.Mock()
+    mock_settings.skip_background = False
+
+    # Set up background detector to say it is empty, this shouldn't stop stacking.
+    histo_workflow._background_detector.image_is_sample.return_value = (
+        False,
+        "totally empty",
+    )
+
+    with caplog.at_level(logging.INFO):
+        # First set smart stack to report failure
+        histo_workflow._autofocus.run_smart_stack.return_value = (False, 123)
+        imaged, focus_height = histo_workflow.acquisition_routine(
+            mock_settings, xyz_pos=(1, 2, 3)
+        )
+        # Check return
+        assert imaged is True  # Always images if not skipping background
+        assert focus_height is None  # None meaning didn't focus
+
+        # And again reporting a successful stack
+        histo_workflow._autofocus.run_smart_stack.return_value = (True, 123)
+        imaged, focus_height = histo_workflow.acquisition_routine(
+            mock_settings, xyz_pos=(1, 2, 3)
+        )
+        # Check return
+        assert imaged is True  # Always images if not skipping background
+        assert focus_height == 123
+
+    # Should never warn
+    assert len(caplog.records) == 0
+
+    # And that smart stack never ran
+    assert histo_workflow._autofocus.run_smart_stack.call_count == 2
+
+
+def test_histo_acquisition_on_sample(histo_workflow, mocker, caplog):
+    """Check when skipping background, but background not detected."""
+    # Mocking for settings as above
+    mock_settings = mocker.Mock()
+    mock_settings.skip_background = True
+
+    # Set up background detector to say there is sample.
+    histo_workflow._background_detector.image_is_sample.return_value = (True, None)
+
+    with caplog.at_level(logging.INFO):
+        # First set smart stack to report failure
+        histo_workflow._autofocus.run_smart_stack.return_value = (False, 123)
+        imaged, focus_height = histo_workflow.acquisition_routine(
+            mock_settings, xyz_pos=(1, 2, 3)
+        )
+        # Check return:
+        # Don't save failed stack when skipping background, assume it is actually
+        # background
+        assert imaged is False
+        assert focus_height is None  # None meaning didn't focus
+
+        # And again reporting a successful stack
+        histo_workflow._autofocus.run_smart_stack.return_value = (True, 123)
+        imaged, focus_height = histo_workflow.acquisition_routine(
+            mock_settings, xyz_pos=(1, 2, 3)
+        )
+        # Check return
+        assert imaged is True  # Always images if not skipping background
+        assert focus_height == 123
+
+    # Should never warn
+    assert len(caplog.records) == 1
+    expected_message = "Stack failed at (1, 2, 3) treating as background."
+    assert caplog.records[0].message == expected_message
+    assert caplog.records[0].levelname == "INFO"
+
+    # And that smart stack never ran
+    assert histo_workflow._autofocus.run_smart_stack.call_count == 2
+
+
 def test_histo_workflow_settings_ui(histo_workflow):
     """Check that the workflow specifies the expected controls."""
     ui = histo_workflow.settings_ui