Add scan directory to json config

ofm_config_full.json

@@ -7,7 +7,12 @@
         "/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/": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
+        "/smart_scan/": {
+            "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
+            "kwargs": {
+                "scans_folder": "/var/openflexure/scans/"
+            }
+        },
         "/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing",
         "/capture/": "openflexure_microscope_server.things.capture:CaptureThing"
     },

ofm_config_simulation.json

@@ -7,7 +7,12 @@
         "/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/": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
+        "/smart_scan/": {
+            "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
+            "kwargs": {
+                "scans_folder": "./openflexure/scans/"
+            }
+        },
         "/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing",
         "/capture/": "openflexure_microscope_server.things.capture:CaptureThing"
     },

ofm_config_stub.json

@@ -7,7 +7,12 @@
         "/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/": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
+        "/smart_scan/": {
+            "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
+            "kwargs": {
+                "scans_folder": "./openflexure/scans/"
+            }
+        },
         "/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing",
         "/capture/": "openflexure_microscope_server.things.capture:CaptureThing"
     },

src/openflexure_microscope_server/server/__init__.py

@@ -10,17 +10,33 @@ from .legacy_api import add_v2_endpoints
 from ..logging import configure_logging, retrieve_log, retrieve_log_from_file
 
 
-def customise_server(server: ThingServer, log_folder: str):
+def customise_server(server: ThingServer, log_folder: str, scans_folder: Optional[str]):
     """Customise the server with additional endpoints, etc."""
     configure_logging(log_folder)
     add_v2_endpoints(server)
-    add_static_files(server.app)
+    add_static_files(server.app, scans_folder)
 
     # Add an endpoint to get the logs - (directly calling the FastAPI decorator)
     server.app.get("/log/")(retrieve_log)
     server.app.get("/logfile/")(retrieve_log_from_file)
 
 
+def _get_scans_dir(config: dict) -> Optional[str]:
+    """
+    Read the config and return the scans directory.
+
+    Return is None if there is no /smart_scan/ thing loaded.
+    """
+
+    if "/smart_scan/" in config["things"]:
+        try:
+            return config["things"]["/smart_scan/"]["kwargs"]["scans_folder"]
+        except KeyError as e:
+            msg = "Configuration error smart scan should have scans_folder kwarg set"
+            raise RuntimeError(msg) from e
+    return None
+
+
 def serve_from_cli(argv: Optional[list[str]] = None):
     """Start the server from the command line"""
     args = cli.parse_args(argv)
@@ -32,8 +48,9 @@ def serve_from_cli(argv: Optional[list[str]] = None):
     try:
         config = cli.config_from_args(args)
         log_folder = config.get("log_folder", "./openflexure/logs")
+        scans_folder = _get_scans_dir(config)
         server = cli.server_from_config(config)
-        customise_server(server, log_folder)
+        customise_server(server, log_folder, scans_folder)
         uvicorn.run(
             server.app,
             host=args.host,

src/openflexure_microscope_server/server/serve_static_files.py

@@ -1,4 +1,5 @@
 import os
+from typing import Optional
 
 from fastapi.responses import FileResponse, RedirectResponse
 from fastapi.staticfiles import StaticFiles
@@ -22,7 +23,7 @@ def add_static_file(app: FastAPI, fname: str, folder: str) -> None:
     )
 
 
-def add_static_files(app: FastAPI) -> None:
+def add_static_files(app: FastAPI, scans_folder: Optional[str]) -> None:
     """Add the static files responsible for the webapp app to the FastAPI app
 
     app: The FastAPI app to add to, in this case the OpenFlexure server
@@ -45,9 +46,13 @@ def add_static_files(app: FastAPI) -> None:
                 name=f"static_{fname}",
             )
 
-    # Mount the scan directory to .../scans/, to allow dzi viewing
-    app.mount(
-        "/scans/",
-        StaticFiles(directory="/var/openflexure/scans/"),
-        name="scans",
-    )
+    # If scans folder is None, there is not smart scan thing. So nothing to mount.
+    if scans_folder is not None:
+        # Mount the scan directory to .../scans/, to allow dzi viewing
+        if not os.path.isdir(scans_folder):
+            os.makedirs(scans_folder)
+        app.mount(
+            "/scans/",
+            StaticFiles(directory=scans_folder),
+            name="scans",
+        )

src/openflexure_microscope_server/things/smart_scan.py

@@ -114,7 +114,8 @@ def _scan_running(method):
 
 
 class SmartScanThing(Thing):
-    def __init__(self):
+    def __init__(self, scans_folder):
+        self._scans_folder = scans_folder
         self._preview_stitch_popen = None
         self._preview_stitch_popen_lock = threading.Lock()
         self._scan_lock = threading.Lock()
@@ -270,11 +271,8 @@ class SmartScanThing(Thing):
 
     @property
     def base_scan_dir(self) -> str:
-        """This directory will hold all the scans we do."""
-        # TODO: This should be determined using sensible configuration.
-        # If the working directory is `/var/openflexure` this will result
-        # in scans being saved at `/var/openflexure/scans/`
-        return "scans"
+        """The path of the directory where the scans are saved."""
+        return self._scans_folder
 
     @thing_property
     def latest_scan_name(self) -> Optional[str]: