Merge branch 'let-preview-stitch-cancel' into 'v3'

Allow preview to cancel!

See merge request openflexure/openflexure-microscope-server!359

src/openflexure_microscope_server/stitching.py

@@ -9,6 +9,7 @@ Interpreter Lock (GIL). May be possible to shift to multiprocessing in the futur
 from typing import Optional, Any
 import threading
 import subprocess
+import signal
 import os
 from io import TextIOWrapper
 import shlex
@@ -160,11 +161,19 @@ class PreviewStitcher(BaseStitcher):
                 return True
             return False
 
-    def wait(self) -> None:
+    def wait(self, cancel: lt.deps.CancelHook) -> None:
-        """Wait for this preview stitch to return."""
+        """Wait for this preview stitch to return.
-        if self.running:
+
-            with self._popen_lock:
+        :raises InvocationCancelledError: if the action is cancelled.
-                self._popen_obj.wait()
+        """
+        while self.running:
+            try:
+                cancel.sleep(0.1)
+            except lt.exceptions.InvocationCancelledError as e:
+                with self._popen_lock:
+                    if self._popen_obj is not None:
+                        self._popen_obj.send_signal(signal.SIGKILL)
+                raise (e)
 
 
 class FinalStitcher(BaseStitcher):
@@ -272,10 +281,8 @@ class FinalStitcher(BaseStitcher):
     ) -> None:
         """Run the final stitch logging any output.
 
-        Raises:
+        :raises ChildProcessError: if exit code is not zero
-            ChildProcessError if exit code is not zero
+        :raises InvocationCancelledError: if the action is cancelled.
-            InvocationCancelledError if the action is cancelled.
-
         """
         cmd = self.command
         self.logger.debug(f"Running command in subprocess: `{' '.join(cmd)}`")

src/openflexure_microscope_server/things/smart_scan.py

@@ -466,7 +466,7 @@ 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._preview_stitcher.wait(self._cancel)
 
         if self._scan_data.stitch_automatically:
             self._scan_logger.info("Stitching final image (may take some time)...")

tests/mock_stitching/mock-stitch.py

@@ -11,6 +11,9 @@ def main():
         # This is used to check we catch errors correctly.
         if arg == "ERROR":
             raise RuntimeError("I was told to do this.")
+        if arg == "HANG":
+            # Rather than hang, just sleep for 10s:
+            time.sleep(10)
         print(arg, flush=True)
         time.sleep(0.2)
 

tests/test_stitching.py

@@ -9,7 +9,7 @@ import os
 from copy import copy
 import uuid
 import threading
-from time import sleep
+import time
 
 import pytest
 
@@ -200,6 +200,7 @@ def test_preview_stitching_command(caplog, mocker):
     mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
 
     with caplog.at_level(logging.INFO):
+        cancel_hook = lt.deps.CancelHook(id=uuid.uuid4())
         stitcher = PreviewStitcher(FAKE_DIR, overlap=0.1, correlation_resize=0.5)
         stitcher.start()
         # Should take a second or so to run so will still be running
@@ -208,12 +209,40 @@ def test_preview_stitching_command(caplog, mocker):
         with pytest.raises(RuntimeError):
             stitcher.start()
         # Wait for it to complete
-        stitcher.wait()
+        stitcher.wait(cancel_hook)
         # It is now not running
         assert not stitcher.running
         assert len(caplog.records) == 0
 
 
+def test_preview_stitching_cancelled(caplog, mocker):
+    """Check that preview stitch can be cancelled."""
+    mock_cmd = f"python {MOCK_STITCHER}"
+
+    mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
+
+    with caplog.at_level(logging.INFO):
+        stitcher = PreviewStitcher(FAKE_DIR, overlap=0.1, correlation_resize=0.5)
+        # Send in the argument HANG to mock-stitch and it just hang for 10s
+        stitcher._extra_args = ["HANG"]
+        cancel_hook = lt.deps.CancelHook(id=uuid.uuid4())
+        t_start = time.time()
+        # Start stitching
+        stitcher.start()
+        # Run wait() in a thread.
+        thread = threading.Thread(target=stitcher.wait, kwargs={"cancel": cancel_hook})
+        thread.start()
+        # Sleep long enough for at least 1 log.
+        time.sleep(0.5)
+        # use set() to cancel!
+        cancel_hook.set()
+        thread.join()
+        # If it wasn't cancelled it would hang for 10 s. Here we check the cancel killed
+        # it within 2s.
+        assert t_start - time.time() < 2
+        assert len(caplog.records) == 0
+
+
 def test_final_stitching_command(caplog, mocker):
     """Check the final stitch runs until completion, and print statements are logged."""
     mock_cmd = f"python {MOCK_STITCHER}"
@@ -252,7 +281,7 @@ def test_final_stitching_command_cancelled(caplog, mocker):
         thread = threading.Thread(target=stitcher.run, kwargs={"cancel": cancel_hook})
         thread.start()
         # Sleep long enough for at least 1 log.
-        sleep(0.5)
+        time.sleep(0.5)
         # use set() to cancel!
         cancel_hook.set()
         thread.join()