Remove all cancel hooks from smart scan and stitching

src/openflexure_microscope_server/stitching.py

@@ -6,6 +6,7 @@ CPU intensity of stitching causing scanning problems due to the Python Global
 Interpreter Lock (GIL). May be possible to shift to multiprocessing in the future.
 """
 
+import logging
 import os
 import shlex
 import signal
@@ -167,14 +168,17 @@ class PreviewStitcher(BaseStitcher):
                 return False
             return self._popen_obj.poll() is None
 
-    def wait(self, cancel: lt.deps.CancelHook) -> None:
+    def wait(self) -> None:
         """Wait for this preview stitch to return.
 
         :raises InvocationCancelledError: if the action is cancelled.
         """
         while self.running:
             try:
-                cancel.sleep(0.1)
+                # This should act exactly like sleep if not started in a LabThings
+                # action thread. In an action thread it will raise
+                # InvocationCancelledError if the action is cancelled.
+                lt.cancellable_sleep(0.2)
             except lt.exceptions.InvocationCancelledError as e:
                 with self._popen_lock:
                     if self._popen_obj is not None:
@@ -189,7 +193,7 @@ class FinalStitcher(BaseStitcher):
         self,
         images_dir: str,
         *,
-        logger: lt.deps.InvocationLogger,
+        logger: logging.Logger,
         overlap: Optional[float] = None,
         correlation_resize: Optional[float] = None,
         stitch_tiff: bool = False,
@@ -200,7 +204,7 @@ class FinalStitcher(BaseStitcher):
         All args except images_dir are positional only.
 
         :param images_dir: The images directory of the scan to stitch.
-        :param logger: The invocation logger for this stitch process.
+        :param logger: The logger from the Thing that created this stitcher.
         :param overlap: The scan overlap, if not known enter None. A value will be
             chosen from the scan_data_dict, or set to a default value if no value is
             available in the scan_data.
@@ -281,10 +285,7 @@ class FinalStitcher(BaseStitcher):
                 )
         return overlap, correlation_resize
 
-    def run(
-        self,
-        cancel: lt.deps.CancelHook,
-    ) -> None:
+    def run(self) -> None:
         """Run the final stitch logging any output.
 
         :raises ChildProcessError: if exit code is not zero
@@ -305,7 +306,7 @@ class FinalStitcher(BaseStitcher):
         # Stop opening pipe blocking writing to it
         os.set_blocking(process.stdout.fileno(), False)
 
-        self._log_ongoing(process, cancel=cancel)
+        self._log_ongoing(process)
 
         if process.poll() == 0:
             self.logger.info("Stitching complete")
@@ -319,11 +320,7 @@ class FinalStitcher(BaseStitcher):
                 f"Subprocess {STITCHING_CMD} errored with exit code {process.poll()}."
             )
 
-    def _log_ongoing(
-        self,
-        process: subprocess.Popen,
-        cancel: lt.deps.CancelHook,
-    ) -> None:
+    def _log_ongoing(self, process: subprocess.Popen) -> None:
         """Log the ongoing process unless it is cancelled."""
         # Poll returns None while running, will return the error code when finished
         while process.poll() is None:
@@ -331,9 +328,10 @@ class FinalStitcher(BaseStitcher):
             # Once buffer is clear sleep for 0.2s before trying again.
 
             try:
-                # Note that using cancel.sleep allows the InvocationCancelledError to
-                # be thrown
-                cancel.sleep(0.2)
+                # This should act exactly like sleep if not started in a LabThings
+                # action thread. In an action thread it will raise
+                # InvocationCancelledError if the action is cancelled.
+                lt.cancellable_sleep(0.2)
             except lt.exceptions.InvocationCancelledError as e:
                 self.logger.info("Stitching cancelled by user")
                 process.kill()

src/openflexure_microscope_server/things/smart_scan.py

@@ -126,7 +126,6 @@ class SmartScanThing(lt.Thing):
         # any method that calls these should be decorated with
         # @_scan_running
         self._scan_logger: Optional[lt.deps.InvocationLogger] = None
-        self._cancel: Optional[lt.deps.CancelHook] = None
         self._autofocus: Optional[AutofocusDep] = None
         self._stage: Optional[StageDep] = None
         self._cam: Optional[CameraClient] = None
@@ -139,7 +138,6 @@ class SmartScanThing(lt.Thing):
     @lt.action
     def sample_scan(
         self,
-        cancel: lt.deps.CancelHook,
         logger: lt.deps.InvocationLogger,
         autofocus: AutofocusDep,
         stage: StageDep,
@@ -158,7 +156,6 @@ class SmartScanThing(lt.Thing):
             raise RuntimeError("Trying to run scan while scan is already running!")
 
         # Set private variables for this scan
-        self._cancel = cancel
         self._scan_logger = logger
         self._autofocus = autofocus
         self._stage = stage
@@ -188,7 +185,6 @@ class SmartScanThing(lt.Thing):
             raise e
         finally:
             # However the scan finishes, unset all variables and release lock
-            self._cancel = None
             self._scan_logger = None
             self._autofocus = None
             self._stage = None
@@ -390,8 +386,6 @@ class SmartScanThing(lt.Thing):
             self._save_final_scan_data(scan_result="success")
 
         except lt.exceptions.InvocationCancelledError:
-            # Reset the cancel event so it can be thrown again
-            self._cancel.clear()
             self._scan_logger.info("Stopping scan because it was cancelled.")
             self._save_final_scan_data(scan_result="cancelled by user")
         except Exception as e:
@@ -513,13 +507,12 @@ class SmartScanThing(lt.Thing):
         self._scan_logger.info("Waiting for background processes to finish...")
 
         if self._preview_stitcher is not None:
-            self._preview_stitcher.wait(self._cancel)
+            self._preview_stitcher.wait()
 
         if self._scan_data.stitch_automatically:
             self._scan_logger.info("Stitching final image (may take some time)...")
             self.stitch_scan(
                 logger=self._scan_logger,
-                cancel=self._cancel,
                 scan_name=self._ongoing_scan.name,
                 correlation_resize=self._scan_data.correlation_resize,
                 overlap=self._scan_data.overlap,
@@ -731,7 +724,6 @@ class SmartScanThing(lt.Thing):
     def stitch_scan(
         self,
         logger: lt.deps.InvocationLogger,
-        cancel: lt.deps.CancelHook,
         scan_name: str,
         correlation_resize: Optional[float] = None,
         overlap: Optional[float] = None,
@@ -753,8 +745,7 @@ class SmartScanThing(lt.Thing):
             scan_data_dict=scan_data_dict,
         )
         try:
-            # start the final stitch, providing the cancel hook to allow aborting
-            final_stitcher.run(cancel)
+            final_stitcher.run()
         except lt.exceptions.InvocationCancelledError:
             # Sleep for 1 second just to allow invocation logs to pass to user.
             time.sleep(1)
@@ -774,9 +765,7 @@ class SmartScanThing(lt.Thing):
         return ZipBlob.from_file(zip_fname)
 
     @lt.action
-    def stitch_all_scans(
-        self, logger: lt.deps.InvocationLogger, cancel: lt.deps.CancelHook
-    ) -> None:
+    def stitch_all_scans(self, logger: lt.deps.InvocationLogger) -> None:
         """Check the list of scans, and stitch any that don't have a DZI associated with it.
 
         :raises RuntimeError: if the microscope is currently running a scan
@@ -786,4 +775,4 @@ class SmartScanThing(lt.Thing):
             raise RuntimeError("Can't stitch previous scans while a scan is ongoing")
         for scan in self._get_all_scan_info():
             if scan.dzi is None:
-                self.stitch_scan(logger=logger, cancel=cancel, scan_name=scan.name)
+                self.stitch_scan(logger=logger, scan_name=scan.name)