better error handling (but still havent fixed test)

pycromanager/acquisition/RAMStorage_java.py

@@ -54,10 +54,11 @@ def read_image(self, channel=None, z=None, time=None, position=None, row=None, c
         if key not in self._index_keys:
             return None
         java_hashmap = JavaObject('java.util.HashMap')
-        # raise Exception
         for k, v in axes.items():
             java_hashmap.put(k, v)
         tagged_image = self._java_RAM_data_storage.get_image(java_hashmap)
+        print('java ram storage class:', str(self._java_RAM_data_storage))
+        print('tagged image: ', str(tagged_image))
         pixels = tagged_image.pix
         metadata = tagged_image.tags
         return pixels.reshape(metadata['Height'], metadata['Width'])

pycromanager/acquisition/java_backend_acquisitions.py

@@ -190,10 +190,10 @@ def _notification_handler_fn(acquisition, notification_push_port, connected_even
     monitor_socket = PullSocket(notification_push_port)
     connected_event.set()
 
-    try:
-        events_finished = False
-        data_sink_finished = False
-        while True:
+    events_finished = False
+    data_sink_finished = False
+    while True:
+        try:
             message = monitor_socket.receive()
             notification = AcqNotification.from_json(message)
 
@@ -226,11 +226,12 @@ def _notification_handler_fn(acquisition, notification_push_port, connected_even
             if events_finished and data_sink_finished:
                 break
 
-    except Exception as e:
-        traceback.print_exc()
-        acquisition.abort(e)
-    finally:
-        monitor_socket.close()
+        except Exception as e:
+            traceback.print_exc()
+            acquisition.abort(e)
+            continue # perform an orderly shutdown
+
+    monitor_socket.close()
 
 
 class JavaBackendAcquisition(Acquisition, metaclass=NumpyDocstringInheritanceMeta):
@@ -319,6 +320,7 @@ def __init__(
         # while the acquisition is still running, and (optionally )so that a image_saved_fn can be called
         # when images are written to disk/RAM storage
         storage_java_class = data_sink.get_storage()
+        print(storage_java_class)
         summary_metadata = storage_java_class.get_summary_metadata()
         if directory is not None:
             # NDTiff dataset saved to disk on Java side
@@ -380,8 +382,12 @@ def await_completion(self):
                 self._remote_notification_handler = None
                 self._acq_notification_dispatcher_thread.join()
 
-            self._acq = None
-            self._finished = True
+            try:
+                # one final check for exceptions for stuff that may have happened during shutdown
+                self._check_for_exceptions()
+            finally:
+                self._acq = None
+                self._finished = True
 
 
     def get_viewer(self):

pycromanager/test/conftest.py

@@ -131,7 +131,9 @@ def install_mm():
 
 
 
-@pytest.fixture(scope="session",  params=['save_to_disk', 'RAM'])
+# @pytest.fixture(scope="session",  params=['save_to_disk', 'RAM'])
+@pytest.fixture(scope="session",  params=['RAM'])
+
 def setup_data_folder(request):
     if request.param != 'save_to_disk':
         yield None
@@ -145,7 +147,9 @@ def setup_data_folder(request):
         shutil.rmtree(data_folder_path)
 
 
-@pytest.fixture(scope="session", params=['python_backend', 'java_backend'])
+# @pytest.fixture(scope="session", params=['python_backend', 'java_backend'])
+@pytest.fixture(scope="session", params=['java_backend'])
+
 def launch_mm_headless(request, install_mm):
     python_backend = request.param == 'python_backend'
     mm_install_dir = install_mm

pycromanager/test/test_acquisition.py

@@ -77,6 +77,7 @@ def test_empty_mda_acq(launch_mm_headless, setup_data_folder):
     with Acquisition(setup_data_folder, 'acq', show_display=False) as acq:
         acq.acquire(events)
 
+
     dataset = acq.get_dataset()
     try:
         assert dataset.axes == {}