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Merge branch 'openflexure-stitching-from-pip' into 'v3'

Browse source 
Import openflexure-stitching from pip

See merge request openflexure/openflexure-microscope-server!270
This commit is contained in:
Julian Stirling 2025-05-21 10:00:48 +00:00
commit 6332c8b647
5 changed files with 8 additions and 22 deletions
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7
ofm_config_full.json
View file

@ -7,12 +7,7 @@
"/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper", "/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
"/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing", "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing",
"/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager", "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager",
"/smart_scan/": { "/smart_scan/": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
"class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
"kwargs": {
"path_to_openflexure_stitch": "application/openflexure-stitching/.venv/bin/openflexure-stitch"
}
},
"/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing", "/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing",
"/capture/": "openflexure_microscope_server.things.capture:CaptureThing" "/capture/": "openflexure_microscope_server.things.capture:CaptureThing"
}, },

7
ofm_config_simulation.json
View file

@ -7,12 +7,7 @@
"/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper", "/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
"/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing", "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing",
"/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager", "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager",
"/smart_scan/": { "/smart_scan/": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
"class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
"kwargs": {
"path_to_openflexure_stitch": "application/openflexure-stitching/.venv/bin/openflexure-stitch"
}
},
"/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing", "/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing",
"/api_test/": "openflexure_microscope_server.things.test:APITestThing" "/api_test/": "openflexure_microscope_server.things.test:APITestThing"
}, },

7
ofm_config_stub.json
View file

@ -7,12 +7,7 @@
"/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper", "/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
"/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing", "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing",
"/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager", "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager",
"/smart_scan/": { "/smart_scan/": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
"class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
"kwargs": {
"path_to_openflexure_stitch": "application/openflexure-stitching/.venv/bin/openflexure-stitch"
}
},
"/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing", "/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing",
"/api_test/": "openflexure_microscope_server.things.test:APITestThing" "/api_test/": "openflexure_microscope_server.things.test:APITestThing"
}, },

1
pyproject.toml
View file

@ -19,6 +19,7 @@ dependencies = [
"labthings-sangaboard", "labthings-sangaboard",
"camera-stage-mapping ~= 0.1.10", "camera-stage-mapping ~= 0.1.10",
"opencv-python ~= 4.11.0", "opencv-python ~= 4.11.0",
"openflexure-stitching[libvips]==0.1.0",
"pillow ~= 10.4", "pillow ~= 10.4",
"anyio ~= 4.0", "anyio ~= 4.0",
"numpy ~= 2.2", "numpy ~= 2.2",

8
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -88,6 +88,7 @@ JPEGBlob = blob_type("image/jpeg")
ZipBlob = blob_type("application/zip") ZipBlob = blob_type("application/zip")
IMG_DIR_NAME = "images" IMG_DIR_NAME = "images"
SCAN_DATA_FILENAME = "scan_data.json" SCAN_DATA_FILENAME = "scan_data.json"
STITCHING_CMD = "openflexure-stitch"
SCAN_ZERO_PAD_DIGITS = 4 SCAN_ZERO_PAD_DIGITS = 4
@ -112,8 +113,7 @@ def _scan_running(method):
class SmartScanThing(Thing): class SmartScanThing(Thing):
def __init__(self, path_to_openflexure_stitch: str): def __init__(self):
self._stitching_script = path_to_openflexure_stitch
self._preview_stitch_popen = None self._preview_stitch_popen = None
self._preview_stitch_popen_lock = threading.Lock() self._preview_stitch_popen_lock = threading.Lock()
self._scan_lock = threading.Lock() self._scan_lock = threading.Lock()
@ -978,7 +978,7 @@ class SmartScanThing(Thing):
with self._preview_stitch_popen_lock: with self._preview_stitch_popen_lock:
self._preview_stitch_popen = Popen( self._preview_stitch_popen = Popen(
[ [
self._stitching_script, STITCHING_CMD,
"--stitching_mode", "--stitching_mode",
"only_stage_stitch", "only_stage_stitch",
"--minimum_overlap", "--minimum_overlap",
@ -1092,7 +1092,7 @@ class SmartScanThing(Thing):
self.run_subprocess( self.run_subprocess(
logger, logger,
[ [
self._stitching_script, STITCHING_CMD,
"--stitching_mode", "--stitching_mode",
"all", "all",
f"{tiff_arg}", f"{tiff_arg}",