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Update unit tests for capture mode.

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This commit is contained in:
Julian Stirling 2026-06-02 17:22:38 +01:00
parent 9ed488e37d
commit c1915759b4
5 changed files with 102 additions and 69 deletions
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1
src/openflexure_microscope_server/things/__init__.py
View file

@ -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.

83
tests/unit_tests/test_camera_buffer.py
View file

@ -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())
returned_image, _ = mem_buf.get_image(buffer_id)
buffer_id = mem_buf.add_image(misc_image, random_metadata(), "standard")
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())
returned_image, _ = mem_buf.get_image(buffer_id, remove=False)
buffer_id = mem_buf.add_image(misc_image, random_metadata(), "standard")
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())
returned_image, _ = mem_buf.get_image()
mem_buf.add_image(misc_image, random_metadata(), "standard")
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_id2 = mem_buf.add_image(misc_image2, random_metadata(), 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_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_id2 = mem_buf.add_image(misc_image2, random_metadata())
buffer_id1 = mem_buf.add_image(misc_image1, random_metadata(), "standard")
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_id2 = mem_buf.add_image(misc_image2, random_metadata(), buffer_max=3)
buffer_id1 = mem_buf.add_image(
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_image2, random_metadata(), buffer_max=2)
returned_image, _ = mem_buf.get_image()
mem_buf.add_image(misc_image1, random_metadata(), "standard", buffer_max=2)
mem_buf.add_image(misc_image2, random_metadata(), "standard", buffer_max=2)
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"

37
tests/unit_tests/test_scan_workflows.py
View file

@ -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(
"/this/img_dir"
img_dir = RelativeDataPath("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(
"/this/img_dir"
workflow_settings, _stitching_settings, _save_res = histo_workflow.all_settings(
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

3
tests/unit_tests/test_smart_scan.py
View file

@ -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

47
tests/unit_tests/test_stack.py
View file

@ -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, "Input should be a valid string"),
(67, "Input should be a valid string"),
(None, TypeError),
(67, TypeError),
("../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):
# TODO set images dir correctly as a RelDataPath
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)
with pytest.raises(error_type):
CaptureParams(images_dir=bad_path, capture_mode="foo")