Merge pull request #754 from henrypinkard/main

Clarify camera notifications
micro-manager · Apr 10, 2024 · 7587ed1 · 7587ed1
2 parents f97ce55 + 94c3c4c
commit 7587ed1
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Showing 6 changed files with 36 additions and 13 deletions.
diff --git a/java/pom.xml b/java/pom.xml
@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.pycro-manager</groupId>
     <artifactId>PycroManagerJava</artifactId>
-     <version>0.46.1</version>
+     <version>0.46.2</version>
     <packaging>jar</packaging>
     <name>Pycro-Manager Java</name>
     <description>The Java components of Pycro-Manager</description>
@@ -55,7 +55,7 @@
       <dependency>
          <groupId>org.micro-manager.acqengj</groupId>
          <artifactId>AcqEngJ</artifactId>
-     <version>0.35.1</version>
+     <version>0.36.0</version>
       </dependency>
       <dependency>
          <groupId>org.micro-manager.ndviewer</groupId>
@@ -112,11 +112,11 @@
           </goals>
 
                           <configuration>
-             	<gpgArguments>
-			<arg>--pinentry-mode</arg>
-			<arg>loopback</arg>
-		</gpgArguments>
-	     </configuration>
+                <gpgArguments>
+            <arg>--pinentry-mode</arg>
+            <arg>loopback</arg>
+        </gpgArguments>
+         </configuration>
 
          </execution>
         </executions>

diff --git a/pycromanager/_version.py b/pycromanager/_version.py
@@ -1,2 +1,2 @@
-version_info = (0, 31, 1)
+version_info = (0, 31, 2)
 __version__ = ".".join(map(str, version_info))
diff --git a/pycromanager/acq_future.py b/pycromanager/acq_future.py
@@ -31,7 +31,8 @@ def _add_notifications(self, axes_or_axes_list):
 
                 AcqNotification.Camera.PRE_SNAP: False,
                 AcqNotification.Camera.PRE_SEQUENCE_STARTED: False,
-                AcqNotification.Camera.POST_EXPOSURE: False,
+                AcqNotification.Camera.POST_SNAP: False,
+                AcqNotification.Camera.POST_SEQUENCE_STOPPED: False,
 
                 AcqNotification.Image.IMAGE_SAVED: False,
             }

diff --git a/pycromanager/acquisition/acq_eng_py/internal/engine.py b/pycromanager/acquisition/acq_eng_py/internal/engine.py
@@ -246,7 +246,7 @@ def acquire_images(self, event: AcquisitionEvent, hardware_sequences_in_progress
                 height = self.core.get_image_height()
                 self.core.snap_image()
             event.acquisition_.post_notification(AcqNotification(
-                AcqNotification.Camera, event.axisPositions_, AcqNotification.Camera.POST_EXPOSURE))
+                AcqNotification.Camera, event.axisPositions_, AcqNotification.Camera.POST_SNAP))
             for h in event.acquisition_.get_after_exposure_hooks():
                 h.run(event)
 
@@ -383,6 +383,12 @@ def acquire_images(self, event: AcquisitionEvent, hardware_sequences_in_progress
                 corresponding_event.acquisition_.add_to_image_metadata(ti.tags)
                 corresponding_event.acquisition_.add_to_output(ti)
 
+        self.stop_hardware_sequences(hardware_sequences_in_progress)
+
+        if event.get_sequence() is not None:
+            event.acquisition_.post_notification(AcqNotification(
+                AcqNotification.Camera, event.axisPositions_, AcqNotification.Camera.POST_SEQUENCE_STOPPED))
+
         if timeout:
             raise TimeoutError("Timeout waiting for images to arrive in circular buffer")
 

diff --git a/pycromanager/acquisition/acq_eng_py/main/acq_notification.py b/pycromanager/acquisition/acq_eng_py/main/acq_notification.py
@@ -20,8 +20,9 @@ def to_string():
 
     class Camera:
         PRE_SEQUENCE_STARTED = "pre_sequence_started"
+        POST_SEQUENCE_STOPPED = "post_sequence_stopped"
         PRE_SNAP = "pre_snap"
-        POST_EXPOSURE = "post_exposure"
+        POST_SNAP = "post_snap"
 
         @staticmethod
         def to_string():
@@ -45,8 +46,8 @@ def __init__(self, type, payload, milestone=None):
             self.type = AcqNotification.Image
             self.payload = payload
             self.milestone = milestone
-        elif milestone in [AcqNotification.Camera.PRE_SNAP, AcqNotification.Camera.POST_EXPOSURE,
-                     AcqNotification.Camera.PRE_SEQUENCE_STARTED]:
+        elif milestone in [AcqNotification.Camera.PRE_SNAP, AcqNotification.Camera.POST_SNAP,
+                     AcqNotification.Camera.PRE_SEQUENCE_STARTED, AcqNotification.Camera.POST_SEQUENCE_STOPPED]:
             self.type = AcqNotification.Camera
             self.payload = json.loads(payload) if isinstance(payload, str) else payload # convert from '{'time': 5}' to {'time': 5}
         elif milestone in [AcqNotification.Hardware.PRE_HARDWARE, AcqNotification.Hardware.POST_HARDWARE]:

diff --git a/pycromanager/test/test_acquisition.py b/pycromanager/test/test_acquisition.py
@@ -652,3 +652,18 @@ def test_multi_channel_parsing(launch_mm_headless, setup_data_folder):
         assert all([channel in dataset.get_channel_names() for channel in ["DAPI", "FITC"]])
     finally:
         dataset.close()
+
+
+def test_empty_axes(launch_mm_headless, setup_data_folder):
+    """
+    Test that images with empty axes are correctly saved
+    """
+
+    with Acquisition(setup_data_folder, 'acq', show_display=False) as acq:
+        acq.acquire({'axes': {}})
+
+    dataset = acq.get_dataset()
+    try:
+        assert dataset.read_image() is not None and dataset.read_image().max() > 0
+    finally:
+        dataset.close()