Update unit tests for capture mode.

src/openflexure_microscope_server/things/__init__.py

@@ -82,6 +82,7 @@ class OFMThing(lt.Thing):
         return rel_data_path
 
 
+# TODO Write tests for this
 class RelativeDataPath(RootModel[str]):
     """A relative path that is validated, and can have a Thing assigned to it.
 

tests/unit_tests/test_camera_buffer.py

@@ -33,8 +33,8 @@ def test_add_and_get_image():
     """Check images can be captured and retrieved."""
     mem_buf = CameraMemoryBuffer()
     misc_image = random_image()
-    buffer_id = mem_buf.add_image(misc_image, random_metadata())
+    buffer_id = mem_buf.add_image(misc_image, random_metadata(), "standard")
-    returned_image, _ = mem_buf.get_image(buffer_id)
+    returned_image, _, _ = mem_buf.get_image(buffer_id)
     # It is the same image
     assert misc_image is returned_image
     # It is now removed from memory
@@ -46,12 +46,12 @@ def test_add_and_get_image_twice():
     """Check images can be retrieved twice if remove flag set false."""
     mem_buf = CameraMemoryBuffer()
     misc_image = random_image()
-    buffer_id = mem_buf.add_image(misc_image, random_metadata())
+    buffer_id = mem_buf.add_image(misc_image, random_metadata(), "standard")
-    returned_image, _ = mem_buf.get_image(buffer_id, remove=False)
+    returned_image, _, _ = mem_buf.get_image(buffer_id, remove=False)
     # It is the same image
     assert misc_image is returned_image
     # It is still in memory
-    returned_image, _ = mem_buf.get_image(buffer_id)
+    returned_image, _, _ = mem_buf.get_image(buffer_id)
     assert misc_image is returned_image
     # It is now removed from memory
     with pytest.raises(NoImageInMemoryError):
@@ -62,8 +62,8 @@ def test_get_without_id():
     """Check images can be captured and retrieved without ID."""
     mem_buf = CameraMemoryBuffer()
     misc_image = random_image()
-    mem_buf.add_image(misc_image, random_metadata())
+    mem_buf.add_image(misc_image, random_metadata(), "standard")
-    returned_image, _ = mem_buf.get_image()
+    returned_image, _, _ = mem_buf.get_image()
     # It is the same image
     assert misc_image is returned_image
     # It is now removed from memory
@@ -76,10 +76,20 @@ def test_get_two_images():
     mem_buf = CameraMemoryBuffer()
     misc_image1 = random_image()
     misc_image2 = random_image()
-    buffer_id1 = mem_buf.add_image(misc_image1, random_metadata(), buffer_max=2)
+    buffer_id1 = mem_buf.add_image(
-    buffer_id2 = mem_buf.add_image(misc_image2, random_metadata(), buffer_max=2)
+        misc_image1, random_metadata(), "standard", buffer_max=2
-    returned_image1, _ = mem_buf.get_image(buffer_id1)
+    )
-    returned_image2, _ = mem_buf.get_image(buffer_id2)
+    buffer_id1 = mem_buf.add_image(
+        misc_image1, random_metadata(), "standard", buffer_max=2
+    )
+    buffer_id1 = mem_buf.add_image(
+        misc_image1, random_metadata(), "standard", buffer_max=2
+    )
+    buffer_id2 = mem_buf.add_image(
+        misc_image2, random_metadata(), "standard", buffer_max=2
+    )
+    returned_image1, _, _ = mem_buf.get_image(buffer_id1)
+    returned_image2, _, _ = mem_buf.get_image(buffer_id2)
     # It they the same images
     assert misc_image1 is returned_image1
     assert misc_image2 is returned_image2
@@ -95,11 +105,11 @@ def test_get_two_images_without_setting_buffer_size():
     mem_buf = CameraMemoryBuffer()
     misc_image1 = random_image()
     misc_image2 = random_image()
-    buffer_id1 = mem_buf.add_image(misc_image1, random_metadata())
+    buffer_id1 = mem_buf.add_image(misc_image1, random_metadata(), "standard")
-    buffer_id2 = mem_buf.add_image(misc_image2, random_metadata())
+    buffer_id2 = mem_buf.add_image(misc_image2, random_metadata(), "standard")
     with pytest.raises(NoImageInMemoryError):
         mem_buf.get_image(buffer_id1)
-    returned_image2, _ = mem_buf.get_image(buffer_id2)
+    returned_image2, _, _ = mem_buf.get_image(buffer_id2)
     # Image 2 the expected image
     assert misc_image2 is returned_image2
 
@@ -110,16 +120,20 @@ def test_buffer_size_changing():
     misc_image1 = random_image()
     misc_image2 = random_image()
     misc_image3 = random_image()
-    buffer_id1 = mem_buf.add_image(misc_image1, random_metadata(), buffer_max=3)
+    buffer_id1 = mem_buf.add_image(
-    buffer_id2 = mem_buf.add_image(misc_image2, random_metadata(), buffer_max=3)
+        misc_image1, random_metadata(), "standard", buffer_max=3
+    )
+    buffer_id2 = mem_buf.add_image(
+        misc_image2, random_metadata(), "standard", buffer_max=3
+    )
     # Third capture doesn't set buffer size, so it will be reset
-    buffer_id3 = mem_buf.add_image(misc_image3, random_metadata())
+    buffer_id3 = mem_buf.add_image(misc_image3, random_metadata(), "standard")
     # As buffer size was reset, images 1 and 2 are deleted
     with pytest.raises(NoImageInMemoryError):
         mem_buf.get_image(buffer_id1)
     with pytest.raises(NoImageInMemoryError):
         mem_buf.get_image(buffer_id2)
-    returned_image3, _ = mem_buf.get_image(buffer_id3)
+    returned_image3, _, _ = mem_buf.get_image(buffer_id3)
     # Image 3 the expected image
     assert misc_image3 is returned_image3
 
@@ -129,9 +143,9 @@ def test_capture_two_images_get_without_id():
     mem_buf = CameraMemoryBuffer()
     misc_image1 = random_image()
     misc_image2 = random_image()
-    mem_buf.add_image(misc_image1, random_metadata(), buffer_max=2)
+    mem_buf.add_image(misc_image1, random_metadata(), "standard", buffer_max=2)
-    mem_buf.add_image(misc_image2, random_metadata(), buffer_max=2)
+    mem_buf.add_image(misc_image2, random_metadata(), "standard", buffer_max=2)
-    returned_image, _ = mem_buf.get_image()
+    returned_image, _, _ = mem_buf.get_image()
     # When buffer_id is not specified, the most recent image (image2) is expected to
     # be retrieved
     assert returned_image is misc_image2
@@ -148,7 +162,9 @@ def test_buffer_size_respected():
     buffer_ids = []
     for _i in range(10):
         image = random_image()
-        buffer_id = mem_buf.add_image(image, random_metadata(), buffer_max=5)
+        buffer_id = mem_buf.add_image(
+            image, random_metadata(), "standard", buffer_max=5
+        )
         images.append(image)
         buffer_ids.append(buffer_id)
 
@@ -157,7 +173,7 @@ def test_buffer_size_respected():
             with pytest.raises(NoImageInMemoryError):
                 mem_buf.get_image(buffer_id)
         else:
-            returned_image, _ = mem_buf.get_image(buffer_id)
+            returned_image, _, _ = mem_buf.get_image(buffer_id)
             assert image is returned_image
 
 
@@ -169,7 +185,9 @@ def test_clear_buffer():
     buffer_ids = []
     for _i in range(10):
         image = random_image()
-        buffer_id = mem_buf.add_image(image, random_metadata(), buffer_max=10)
+        buffer_id = mem_buf.add_image(
+            image, random_metadata(), "standard", buffer_max=10
+        )
         images.append(image)
         buffer_ids.append(buffer_id)
 
@@ -192,7 +210,7 @@ def test_get_metadata_too():
     for _i in range(10):
         image = random_image()
         metadata = random_metadata()
-        buffer_id = mem_buf.add_image(image, metadata, buffer_max=10)
+        buffer_id = mem_buf.add_image(image, metadata, "standard", buffer_max=10)
         images.append(image)
         metadatas.append(metadata)
         buffer_ids.append(buffer_id)
@@ -202,6 +220,19 @@ def test_get_metadata_too():
 
     # Check both image and metadata
     for image, metadata, buffer_id in zipped:
-        returned_image, returned_metadata = mem_buf.get_image(buffer_id)
+        returned_image, returned_metadata, _ = mem_buf.get_image(buffer_id)
         assert image is returned_image
         assert metadata is returned_metadata
+
+
+def test_mode_is_returned():
+    """Capture 10 images with metadata and check metadata is returned as expected."""
+    mem_buf = CameraMemoryBuffer()
+    misc_image = random_image()
+    buffer_id = mem_buf.add_image(misc_image, random_metadata(), "standard")
+    _, _, mode = mem_buf.get_image(buffer_id)
+    assert mode == "standard"
+
+    buffer_id = mem_buf.add_image(misc_image, random_metadata(), "foobar")
+    _, _, mode = mem_buf.get_image(buffer_id)
+    assert mode == "foobar"

tests/unit_tests/test_scan_workflows.py

@@ -4,6 +4,7 @@ import itertools
 import logging
 
 import pytest
+from PIL import Image
 from pydantic import BaseModel
 
 import labthings_fastapi as lt
@@ -11,6 +12,7 @@ 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 import RelativeDataPath
 from openflexure_microscope_server.things.autofocus import SmartStackParams
 from openflexure_microscope_server.things.camera_stage_mapping import csm_img_to_stage
 from openflexure_microscope_server.things.scan_workflows import (
@@ -44,8 +46,6 @@ def test_partial_base_classes():
     bad_workflow = create_thing_without_server(BadWorkflow)
 
     settings = MinimalSettings()
-    with pytest.raises(NotImplementedError):
-        bad_workflow.check_before_start(settings)
 
     with pytest.raises(NotImplementedError):
         bad_workflow.ready
@@ -69,7 +69,17 @@ def test_partial_base_classes():
 @pytest.fixture
 def histo_workflow():
     """Return a HistoScanWorkflow thing with slots mocked."""
-    return create_thing_without_server(HistoScanWorkflow, mock_all_slots=True)
+    workflow = create_thing_without_server(HistoScanWorkflow, mock_all_slots=True)
+    workflow._cam.capture_modes = {"standard": "Mock"}
+    workflow._cam._capture_image.return_value = Image.new("RGB", (1111, 1222))
+    return workflow
+
+
+def test_histo_workflow_save_resolution(histo_workflow):
+    """Check that the camera is used to get the save resolution."""
+    width, height = histo_workflow._get_save_resolution()
+    assert width == 1111
+    assert height == 1222
 
 
 # Use itertools to iterate over every true/false permutation
@@ -117,7 +127,12 @@ def test_histo_workflow_settings_generation(histo_workflow, mocker):
     mocker.patch.object(
         histo_workflow, "_calc_displacement_from_overlap", return_value=(123, 456)
     )
-    workflow_settings, stitching_settings = histo_workflow.all_settings("/this/img_dir")
+
+    img_dir = RelativeDataPath("this/img_dir")
+    workflow_settings, stitching_settings, save_res = histo_workflow.all_settings(
+        img_dir
+    )
+    assert save_res == (1111, 1222)
     ## Check type
     assert isinstance(workflow_settings, HistoScanSettingsModel)
     assert isinstance(stitching_settings, StitchingSettings)
@@ -137,7 +152,7 @@ def test_histo_workflow_settings_generation(histo_workflow, mocker):
     assert workflow_settings.dx == 123
     assert workflow_settings.dy == 456
     # And that the input image dir is passed to stack the stack parameter for saving
-    assert workflow_settings.capture_params.images_dir == "/this/img_dir"
+    assert workflow_settings.capture_params.images_dir.root == "this/img_dir"
 
 
 def test_histo_workflow_settings_generation_equal_overlap(histo_workflow, mocker):
@@ -148,8 +163,9 @@ def test_histo_workflow_settings_generation_equal_overlap(histo_workflow, mocker
 
     # Different when False
     histo_workflow.equal_distances = False
-    workflow_settings, _stitching_settings = histo_workflow.all_settings(
+    img_dir = RelativeDataPath("this/img_dir")
-        "/this/img_dir"
+    workflow_settings, _stitching_settings, _save_res = histo_workflow.all_settings(
+        img_dir
     )
 
     assert workflow_settings.dx == 123
@@ -157,8 +173,8 @@ def test_histo_workflow_settings_generation_equal_overlap(histo_workflow, mocker
 
     # Same when set True
     histo_workflow.equal_distances = True
-    workflow_settings, _stitching_settings = histo_workflow.all_settings(
+    workflow_settings, _stitching_settings, _save_res = histo_workflow.all_settings(
-        "/this/img_dir"
+        img_dir
     )
 
     assert workflow_settings.dx == 123
@@ -455,9 +471,8 @@ def test_correlation_resize(histo_workflow, save_res, expected_resize):
     target area, taking the square root, and rounding to the nearest integer N. Then
     correlation_resize = 1 / N.
     """
-    histo_workflow.save_resolution = save_res
     histo_workflow.overlap = 0.1
-    settings = histo_workflow._get_stitching_settings_model()
+    settings = histo_workflow._get_stitching_settings_model(save_res)
 
     assert isinstance(settings, StitchingSettings)
     assert settings.correlation_resize == expected_resize

tests/unit_tests/test_smart_scan.py

@@ -413,13 +413,14 @@ def scan_thing_mocked_for_scan_data(smart_scan_thing, mocker):
         smart_scan_thing._workflow.all_settings.return_value = (
             MockWorkflowSettingModel(),
             StitchingSettings(correlation_resize=0.5, overlap=0.45),
+            (1640, 1232),
         )
-        smart_scan_thing._workflow.save_resolution = (1640, 1232)
 
         mock_ongoing_scan = mocker.Mock()
         mock_ongoing_scan.name = MOCK_SCAN_NAME
         mock_ongoing_scan.images_dir = MOCK_SCAN_DIR
         smart_scan_thing._ongoing_scan = mock_ongoing_scan
+        smart_scan_thing._data_dir = "scans"
 
         yield smart_scan_thing
 

tests/unit_tests/test_stack.py

@@ -8,10 +8,13 @@ import numpy as np
 import pytest
 from hypothesis import given
 from hypothesis import strategies as st
+from PIL import Image
+from pydantic import ValidationError
 
 from labthings_fastapi.testing import create_thing_without_server
 
 from openflexure_microscope_server.scan_directories import IMAGE_REGEX
+from openflexure_microscope_server.things import RelativeDataPath
 from openflexure_microscope_server.things.autofocus import (
     EXTRA_STACK_CAPTURES,
     AutofocusThing,
@@ -262,6 +265,10 @@ def histo_scan_workflow():
     workflow._csm.calibration_required = False
     workflow._csm.convert_image_to_stage_coordinates = lambda x, y: {"x": x, "y": y}
 
+    # And set up camera
+    workflow._cam.capture_modes = {"standard": "Mock"}
+    workflow._cam._capture_image.return_value = Image.new("RGB", (1000, 1000))
+
     return workflow
 
 
@@ -341,7 +348,7 @@ def test_coercing_stack_save_ims(
 @pytest.mark.parametrize("pass_on", [1, 2, 3, 4])
 def test_run_smart_stack(pass_on, histo_scan_workflow, autofocus_thing, mocker):
     """Test Running smart stack with the stack passing on different attempts."""
-    scan_settings, _ = histo_scan_workflow.all_settings(images_dir="dummy")
+    scan_settings, _, _ = histo_scan_workflow.all_settings(RelativeDataPath("dummy"))
     assert scan_settings.smart_stack_params.max_attempts == 3
 
     # Set up returns from z-stack
@@ -878,37 +885,15 @@ def test_invalid_stack_settling_raises():
 
 
 @pytest.mark.parametrize(
-    ("bad_path", "match_err"),
+    ("bad_path", "error_type"),
     [
-        ("", "String should have at least 1 character"),
+        (None, TypeError),
-        (None, "Input should be a valid string"),
+        (67, TypeError),
-        (67, "Input should be a valid string"),
+        ("../dangerous", ValidationError),
+        ("/usr/bin/bash", ValidationError),
     ],
 )
-def test_invalid_capture_dir_raises(bad_path, match_err):
+def test_invalid_capture_dir_raises(bad_path, error_type):
     """Test basic stack raises expected error for bad image dir paths."""
-    with pytest.raises(ValueError, match=match_err):
+    with pytest.raises(error_type):
-        # TODO set images dir correctly as a RelDataPath
+        CaptureParams(images_dir=bad_path, capture_mode="foo")
-        CaptureParams(images_dir=bad_path, save_resolution=(20, 20))
-
-
-@pytest.mark.parametrize(
-    ("bad_res", "match_err"),
-    [
-        ((-100, 50), "Input should be greater than or equal to 1"),
-        ((20, 0), "Input should be greater than or equal to 1"),
-        ("", "Input should be a valid tuple"),
-        (None, "Input should be a valid tuple"),
-        (67, "Input should be a valid tuple"),
-        (
-            ["path"],
-            "Input should be a valid integer, unable to parse string as an integer",
-        ),
-        ((20, 20, 20), "Tuple should have at most 2 items"),
-    ],
-)
-def test_invalid_capture_res_raises(bad_res, match_err):
-    """Test basic stack raises expected error for invalid save resolutions."""
-    with pytest.raises(ValueError, match=match_err):
-        # TODO set images dir correctly as a RelDataPath
-        CaptureParams(images_dir="dummy", save_resolution=bad_res)