Merge branch 'stitch-all-logging' into 'v3'

Log during stitch all and handle errors

Closes #710

See merge request openflexure/openflexure-microscope-server!593

src/openflexure_microscope_server/things/smart_scan.py

@@ -11,7 +11,6 @@ import os
 import threading
 import time
 from datetime import datetime
-from subprocess import SubprocessError
 from types import TracebackType
 from typing import (
     Annotated,
@@ -717,7 +716,7 @@ class SmartScanThing(OFMThing):
         except lt.exceptions.InvocationCancelledError:
             # Sleep for 1 second just to allow invocation logs to pass to user.
             time.sleep(1)
-        except SubprocessError as e:
+        except ChildProcessError as e:
             self.logger.error(f"Stitching failed: {e}", exc_info=e)
 
     @lt.action(use_global_lock=False)
@@ -744,4 +743,5 @@ class SmartScanThing(OFMThing):
         # need stitching.
         for scan in self.get_data_for_gallery():
             if scan.dzi is None:
+                self.logger.info(f"Stitching {scan.name}")
                 self.stitch_scan(scan_name=scan.name)

tests/conftest.py

@@ -4,6 +4,7 @@ import json
 import logging
 import os
 import re
+import tempfile
 from collections.abc import Iterable
 from contextlib import contextmanager
 from typing import Optional
@@ -12,6 +13,10 @@ import pytest
 
 from labthings_fastapi.testing import create_thing_without_server
 
+from openflexure_microscope_server.things.smart_scan import (
+    SmartScanThing,
+)
+
 from .shared_utils.lt_test_utils import LabThingsTestEnv
 
 THIS_DIR = os.path.dirname(os.path.abspath(__file__))
@@ -105,3 +110,17 @@ def mock_picam_thing(mocker):
     from openflexure_microscope_server.things.camera.picamera import StreamingPiCamera2
 
     return create_thing_without_server(StreamingPiCamera2)
+
+
+@pytest.fixture
+def smart_scan_thing(mocker):
+    """Return a smart scan thing as a fixture."""
+    thing = create_thing_without_server(
+        SmartScanThing,
+        default_workflow="mock-_all_workflows",
+        mock_all_slots=True,
+    )
+    type(thing._thing_server_interface).application_config = mocker.PropertyMock(
+        return_value={"data_folder": tempfile.gettempdir()}
+    )
+    return thing

tests/unit_tests/test_smart_scan.py

@@ -50,20 +50,6 @@ def _clear_scan_dir() -> None:
         shutil.rmtree(SCAN_DIR)
 
 
-@pytest.fixture
-def smart_scan_thing(mocker):
-    """Return a smart scan thing as a fixture."""
-    thing = create_thing_without_server(
-        SmartScanThing,
-        default_workflow="mock-_all_workflows",
-        mock_all_slots=True,
-    )
-    type(thing._thing_server_interface).application_config = mocker.PropertyMock(
-        return_value={"data_folder": tempfile.gettempdir()}
-    )
-    return thing
-
-
 @pytest.fixture
 def entered_smart_scan_thing(smart_scan_thing):
     """Yield a smart scan thing as a fixture that has been entred.

tests/unit_tests/test_stitching.py

@@ -325,3 +325,57 @@ def test_final_stitching_command_error(mocker):
     stitcher._extra_args = ["ERROR"]
     with pytest.raises(ChildProcessError):
         stitcher.run()
+
+
+def test_stitch_all_scans_continues_after_error(mocker, caplog, smart_scan_thing):
+    """Test stitching all continues after an error and logs as expected."""
+    scans = [
+        mocker.Mock(name="scan1", dzi=None),
+        mocker.Mock(name="scan2", dzi=None),
+        mocker.Mock(name="scan3", dzi=None),
+    ]
+    scans[0].name = "scan1"
+    scans[1].name = "scan2"
+    scans[2].name = "scan3"
+
+    mocker.patch.object(
+        smart_scan_thing,
+        "get_data_for_gallery",
+        return_value=scans,
+    )
+
+    # ensure scan data exists for all scans
+    scan_data = mocker.Mock()
+    scan_data.stitching_settings = StitchingSettings(
+        overlap=0.45,
+        correlation_resize=0.5,
+    )
+
+    with smart_scan_thing:
+        mocker.patch.object(
+            smart_scan_thing._scan_dir_manager,
+            "get_scan_data",
+            return_value=scan_data,
+        )
+
+    def run_side_effect(self):
+        if "scan2" in str(self.images_dir):
+            raise ChildProcessError("test_message")
+
+    mocker.patch(
+        "openflexure_microscope_server.stitching.FinalStitcher.run",
+        autospec=True,
+        side_effect=run_side_effect,
+    )
+
+    with caplog.at_level("INFO"):
+        smart_scan_thing.stitch_all_scans()
+
+    messages = [r.message for r in caplog.records]
+
+    assert messages == [
+        "Stitching scan1",
+        "Stitching scan2",
+        "Stitching failed: test_message",
+        "Stitching scan3",
+    ]