diff --git a/ofm_config_full.json b/ofm_config_full.json index ecedc5a4..f182a774 100644 --- a/ofm_config_full.json +++ b/ofm_config_full.json @@ -7,12 +7,7 @@ "/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper", "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing", "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager", - "/smart_scan/": { - "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing", - "kwargs": { - "path_to_openflexure_stitch": "openflexure-stitch" - } - }, + "/smart_scan/": "openflexure_microscope_server.things.smart_scan:SmartScanThing", "/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing", "/capture/": "openflexure_microscope_server.things.capture:CaptureThing" }, diff --git a/ofm_config_simulation.json b/ofm_config_simulation.json index d06cf005..0d06ad87 100644 --- a/ofm_config_simulation.json +++ b/ofm_config_simulation.json @@ -7,12 +7,7 @@ "/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper", "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing", "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager", - "/smart_scan/": { - "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing", - "kwargs": { - "path_to_openflexure_stitch": "openflexure-stitch" - } - }, + "/smart_scan/": "openflexure_microscope_server.things.smart_scan:SmartScanThing", "/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing", "/api_test/": "openflexure_microscope_server.things.test:APITestThing" }, diff --git a/ofm_config_stub.json b/ofm_config_stub.json index b207287b..d312795e 100644 --- a/ofm_config_stub.json +++ b/ofm_config_stub.json @@ -7,12 +7,7 @@ "/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper", "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing", "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager", - "/smart_scan/": { - "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing", - "kwargs": { - "path_to_openflexure_stitch": "openflexure-stitch" - } - }, + "/smart_scan/": "openflexure_microscope_server.things.smart_scan:SmartScanThing", "/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing", "/api_test/": "openflexure_microscope_server.things.test:APITestThing" }, diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py index 962310fb..2b050294 100644 --- a/src/openflexure_microscope_server/things/smart_scan.py +++ b/src/openflexure_microscope_server/things/smart_scan.py @@ -88,6 +88,7 @@ JPEGBlob = blob_type("image/jpeg") ZipBlob = blob_type("application/zip") IMG_DIR_NAME = "images" SCAN_DATA_FILENAME = "scan_data.json" +STITCHING_CMD = "openflexure-stitch" SCAN_ZERO_PAD_DIGITS = 4 @@ -112,8 +113,7 @@ def _scan_running(method): class SmartScanThing(Thing): - def __init__(self, path_to_openflexure_stitch: str): - self._stitching_script = path_to_openflexure_stitch + def __init__(self): self._preview_stitch_popen = None self._preview_stitch_popen_lock = threading.Lock() self._scan_lock = threading.Lock() @@ -958,7 +958,7 @@ class SmartScanThing(Thing): with self._preview_stitch_popen_lock: self._preview_stitch_popen = Popen( [ - self._stitching_script, + STITCHING_CMD, "--stitching_mode", "only_stage_stitch", "--minimum_overlap", @@ -1072,7 +1072,7 @@ class SmartScanThing(Thing): self.run_subprocess( logger, [ - self._stitching_script, + STITCHING_CMD, "--stitching_mode", "all", f"{tiff_arg}",