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Merge branch 'less-stack-coersion' into 'v3'

Browse source 
Do less coersion for stacks now labthings validates settings.

See merge request openflexure/openflexure-microscope-server!516
This commit is contained in:
Julian Stirling 2026-03-03 10:02:05 +00:00
commit ac9852a7ad
2 changed files with 10 additions and 32 deletions
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29
src/openflexure_microscope_server/things/scan_workflows.py
View file

@ -350,7 +350,9 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
Defaults to 1 unless you need to see either side of focus
"""
stack_min_images_to_test: int = lt.setting(default=9, ge=5, le=13)
stack_min_images_to_test: int = lt.setting(
default=9, ge=MIN_TEST_IMAGE_COUNT, le=MAX_TEST_IMAGE_COUNT
)
"""The minimum number of images to capture in a stack.
This many images are captures and tested for focus, if the focus is not central
@ -445,21 +447,7 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
"""
# Coerce min_images_to_test parameter
min_images_to_test = self.stack_min_images_to_test
if min_images_to_test < MIN_TEST_IMAGE_COUNT:
self.logger.warning(
f"Cannot test only {min_images_to_test} image(s) as this will fail. "
"Setting min images to test to lowest possible value of"
f"{MIN_TEST_IMAGE_COUNT}."
)
min_images_to_test = MIN_TEST_IMAGE_COUNT
elif min_images_to_test > MAX_TEST_IMAGE_COUNT:
self.logger.warning(
f"Testing {min_images_to_test} images will cause defocus. "
"Setting min images to test to highest possible value of "
f"{MAX_TEST_IMAGE_COUNT}."
)
min_images_to_test = MAX_TEST_IMAGE_COUNT
elif min_images_to_test % 2 == 0:
if min_images_to_test % 2 == 0:
min_images_to_test += 1
self.logger.warning(
"Minimum number of images to test should be odd, setting to "
@ -468,15 +456,10 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
# Set the Thing property to the coerced value
self.stack_min_images_to_test = min_images_to_test
# Coerce the images to save parameter to be positive, odd, and less than
# Coerce the images to save parameter to be odd, and less than
# min_images_to_save
images_to_save = self.stack_images_to_save
if images_to_save <= 0:
self.logger.warning(
"At least 1 images must be saved. Setting images to save to 1."
)
images_to_save = 1
elif images_to_save > min_images_to_test:
if images_to_save > min_images_to_test:
self.logger.warning(
f"Cannot save {images_to_save} images as this above the minimum "
f"number to test. Setting images to save to {MAX_TEST_IMAGE_COUNT}."

13
tests/unit_tests/test_stack.py
View file

@ -14,8 +14,6 @@ from labthings_fastapi.testing import create_thing_without_server
from openflexure_microscope_server.scan_directories import IMAGE_REGEX
from openflexure_microscope_server.things.autofocus import (
EXTRA_STACK_CAPTURES,
MAX_TEST_IMAGE_COUNT,
MIN_TEST_IMAGE_COUNT,
AutofocusThing,
CaptureInfo,
NotAPeakError,
@ -286,10 +284,7 @@ def test_create_stack(histo_scan_workflow, caplog):
@pytest.mark.parametrize(
("initial_test_ims", "coerced_test_ims", "expected_log_start"),
[
(0, MIN_TEST_IMAGE_COUNT, "Cannot test only 0"),
(-1, MIN_TEST_IMAGE_COUNT, "Cannot test only -1"),
(10, MAX_TEST_IMAGE_COUNT, "Testing 10 images will"),
(4, 5, "Minimum number of images to test should be odd"),
(6, 7, "Minimum number of images to test should be odd"),
],
)
def test_coercing_stack_test_ims(
@ -314,9 +309,7 @@ def test_coercing_stack_test_ims(
@pytest.mark.parametrize(
("initial_save_ims", "coerced_save_ims", "expected_log_start"),
[
(0, 1, "At least 1 images must be saved"),
(-1, 1, "At least 1 images must be saved"),
(10, 9, "Cannot save 10 images"),
(9, 7, "Cannot save 9 images"),
(4, 5, "Images to save should be odd, setting to 5"),
],
)
@ -324,6 +317,8 @@ def test_coercing_stack_save_ims(
initial_save_ims, coerced_save_ims, expected_log_start, histo_scan_workflow, caplog
):
"""Run create stack with images to save set to values requiring coercion, and check result."""
# First set the min images to test to 7
histo_scan_workflow.stack_min_images_to_test = 7
histo_scan_workflow.stack_images_to_save = initial_save_ims
with caplog.at_level(logging.WARNING):