Added a Thing to run stitching as Actions

src/openflexure_microscope_server/server.py

@@ -11,6 +11,7 @@ from .things.system_control import SystemControlThing
 from .things.settings_manager import SettingsManager
 from .things.auto_recentre_stage import RecentringThing
 from .things.smart_scan import SmartScanThing, BackgroundDetectThing
+from .things.stitching import Stitcher
 from .things.test import APITestThing
 from .serve_static_files import add_static_files
 from .logging import configure_logging, retrieve_log
@@ -26,6 +27,7 @@ thing_server.add_thing(CameraStageMapper(), "/camera_stage_mapping/")
 thing_server.add_thing(SystemControlThing(), "/system_control/")
 thing_server.add_thing(SettingsManager(), "/settings/")
 thing_server.add_thing(SmartScanThing(), "/smart_scan/")
+thing_server.add_thing(Stitcher("application/openflexure-stitching/.venv/bin/openflexure-stitch"), "/stitching/")
 thing_server.add_thing(BackgroundDetectThing(), "/background_detect/")
 thing_server.add_thing(APITestThing(), "/api_test/")
 try:

src/openflexure_microscope_server/things/smart_scan.py

@@ -301,21 +301,30 @@ DOWNLOADABLE_SCAN_FILES = (
 
 class SmartScanThing(Thing):
     @property
-    def scan_folder_path(self) -> str:
+    def scans_folder_path(self) -> str:
         """This folder 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"
 
+    def scan_folder_path(self, scan_name: Optional[str]=None):
+        """The path to the scan folder with a given name"""
+        if not scan_name:
+            if not self.latest_scan_name:
+                raise IOError("There is no latest scan to return")
+            scan_name = self.latest_scan_name
+        return os.path.join(self.scans_folder_path, scan_name)
+    
     def new_scan_folder(self) -> str:
         """Create a new empty folder, into which we can save scan images"""
-        if not os.path.exists(self.scan_folder_path):
+        if not os.path.exists(self.scans_folder_path):
-            os.makedirs(self.scan_folder_path)
+            os.makedirs(self.scans_folder_path)
         for j in range(999999):
-            folder_path = os.path.join(self.scan_folder_path, f"scan_{j:06}")
+            folder_path = os.path.join(self.scans_folder_path, f"scan_{j:06}")
             if not os.path.exists(folder_path):
                 os.makedirs(folder_path)
+                self.latest_scan_name = os.path.basename(folder_path)
                 return folder_path
         raise FileExistsError("Could not create a new scan folder: all names in use!")
     
@@ -583,8 +592,8 @@ class SmartScanThing(Thing):
         in the `images` folder.
         """
         scans: list[ScanInfo] = []
-        for f in os.listdir(self.scan_folder_path):
+        for f in os.listdir(self.scans_folder_path):
-            path = os.path.join(self.scan_folder_path, f)
+            path = os.path.join(self.scans_folder_path, f)
             if os.path.isdir(path):
                 images_folder = os.path.join(path, "images")
                 if os.path.isdir(images_folder):
@@ -624,7 +633,7 @@ class SmartScanThing(Thing):
             raise HTTPException(
                 403, f"You may only download files named {DOWNLOADABLE_SCAN_FILES}"
             )
-        path = os.path.join(self.scan_folder_path, scan_name, file)
+        path = os.path.join(self.scans_folder_path, scan_name, file)
         if not os.path.isfile(path):
             raise HTTPException(404, "File not found")
         return FileResponse(path)
@@ -642,7 +651,7 @@ class SmartScanThing(Thing):
         
         This endpoint allows scans to be deleted from disk.
         """
-        path = os.path.join(self.scan_folder_path, scan_name)
+        path = os.path.join(self.scans_folder_path, scan_name)
         if not os.path.isdir(path):
             print(f"can't find {path}")
             raise HTTPException(404, "Scan not found")

src/openflexure_microscope_server/things/stitching.py

@@ -0,0 +1,72 @@
+import shutil
+from typing import Mapping, Optional
+import cv2
+from fastapi import HTTPException
+from fastapi.responses import FileResponse
+import numpy as np
+import os
+import time
+from PIL import Image
+from pydantic import BaseModel
+from scipy.stats import norm
+import logging
+from copy import deepcopy
+from datetime import datetime
+from subprocess import CompletedProcess, run, PIPE
+
+from labthings_fastapi.thing import Thing
+from labthings_fastapi.dependencies.raw_thing import raw_thing_dependency
+from labthings_fastapi.dependencies.invocation import CancelHook, InvocationLogger, InvocationCancelledError
+from labthings_fastapi.decorators import thing_action
+from labthings_fastapi.outputs.blob import BlobOutput
+from openflexure_microscope_server.things.autofocus import AutofocusThing
+from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
+from openflexure_microscope_server.things.auto_recentre_stage import RecentringThing
+
+from .smart_scan import SmartScanThing
+
+SmartScanDep = raw_thing_dependency(SmartScanThing)
+
+
+class JPEGBlob(BlobOutput):
+    media_type = "image/jpeg"
+
+
+class Stitcher(Thing):
+    def __init__(self, path_to_openflexure_stitch: str):
+        self._script = path_to_openflexure_stitch
+
+    def run_subprocess(
+            self, logger: InvocationLogger, cmd: list[str],
+        ) -> CompletedProcess:
+        """Run a  subprocess and log any output"""
+        logger.info(f"Running command in subprocess: `{' '.join(cmd)}")
+        output = run(cmd, stdout=PIPE, stderr=PIPE, universal_newlines=True)
+        for pipe in [output.stdout, output.stderr]:
+            if pipe:
+                logger.info(pipe)
+        output.check_returncode()
+        return output
+    
+    def images_folder(self, smart_scan: SmartScanDep, scan_name: Optional[str]=None) -> str:
+        scan_folder = smart_scan.scan_folder_path(scan_name=scan_name)
+        return os.path.join(scan_folder, "images")
+
+    @thing_action
+    def stitch_scan_from_stage(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None, downsample: float=1.0) -> JPEGBlob:
+        """Generate a stitched image based on stage position metadata"""
+        images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
+        self.run_subprocess(logger, [self._script, "--stitching_mode", "only_stage_stitch", images_folder])
+        return JPEGBlob.from_file(os.path.join(images_folder, "stitched_from_stage.jpg"))
+    
+    @thing_action
+    def update_scan_correlations(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None) -> None:
+        """Generate a stitched image based on stage position metadata"""
+        images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
+        self.run_subprocess(logger, [self._script, "--stitching_mode", "only_correlate", images_folder])
+
+    @thing_action
+    def stitch_scan(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None, downsample: float=1.0) -> None:
+        """Generate a stitched image based on stage position metadata"""
+        images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
+        self.run_subprocess(logger, [self._script, "--stitching_mode", "all", images_folder])