revert accidental changes

pycromanager/acquisition/RAMStorage_java.py

@@ -3,10 +3,10 @@
 
 class NDRAMDatasetJava(NDStorageBase):
     """
-    A python class that wraps a Java-backend RAM data storage_implementations.
+    A python class that wraps a Java-backend RAM data storage.
 
     This class maintains an index of which images have been saved, but otherwise routes all calls to the Java
-    implementation of the RAM data storage_implementations.
+    implementation of the RAM data storage.
     """
 
     def __init__(self, java_RAM_data_storage):
@@ -22,7 +22,7 @@ def close(self):
 
     def add_available_axes(self, image_coordinates):
         """
-        The Java RAM storage_implementations has received a execution_engine image with the given axes. Add these axes to the index.
+        The Java RAM storage has received a new image with the given axes. Add these axes to the index.
         """
         self._index_keys.add(frozenset(image_coordinates.items()))
         # update information about the available images

pycromanager/headless.py

@@ -6,7 +6,7 @@
 import types
 import os
 
-# from pycromanager.acquisition.acq_eng_py.kernel.engine import Engine
+from pycromanager.acquisition.acq_eng_py.internal.engine import Engine
 from pymmcore import CMMCore
 import pymmcore
 from pyjavaz import DEFAULT_BRIDGE_PORT, server_terminated
@@ -36,7 +36,7 @@ def _create_pymmcore_instance():
     2. add convenience methods to match the MMCoreJ API:
     """
 
-    # Create a execution_engine dictionary for the class attributes
+    # Create a new dictionary for the class attributes
     new_attributes = {}
 
     # Iterate through the original attributes
@@ -49,9 +49,42 @@ def _create_pymmcore_instance():
             new_attr_name = _camel_to_snake(attr_name)
             new_attributes[new_attr_name] = attr_value
 
-    # Create and return a execution_engine class that subclasses the original class and has the execution_engine attributes
+    # Create and return a new class that subclasses the original class and has the new attributes
     clz = type(CMMCore.__name__ + "SnakeCase", (CMMCore,), new_attributes)
+
     instance = clz()
+
+    def pop_next_tagged_image(self):
+        md = pymmcore.Metadata()
+        pix = self.pop_next_image_md(0, 0, md)
+        tags = {key: md.GetSingleTag(key).GetValue() for key in md.GetKeys()}
+        return TaggedImage(tags, pix)
+
+    def get_tagged_image(core, cam_index, camera, height, width, binning=None, pixel_type=None, roi_x_start=None,
+                         roi_y_start=None):
+        """
+        Different signature than the Java version because of difference in metadata handling in the swig layers
+        """
+        pix = core.get_image()
+        md = pymmcore.Metadata()
+        # most of the same tags from pop_next_tagged_image, which may not be the same as the MMCoreJ version of this function
+        tags = {'Camera': camera, 'Height': height, 'Width': width, 'PixelType': pixel_type,
+                'CameraChannelIndex': cam_index}
+        # Could optionally add these for completeness but there might be a performance hit
+        if binning is not None:
+            tags['Binning'] = binning
+        if roi_x_start is not None:
+            tags['ROI-X-start'] = roi_x_start
+        if roi_y_start is not None:
+            tags['ROI-Y-start'] = roi_y_start
+
+        return TaggedImage(tags, pix)
+
+    instance.get_tagged_image = types.MethodType(get_tagged_image, instance)
+    instance.pop_next_tagged_image = types.MethodType(pop_next_tagged_image, instance)
+
+    # attach TaggedImage class
+    instance.TaggedImage = TaggedImage
     return instance
 
 
@@ -79,9 +112,8 @@ def stop_headless(debug=False):
             logger.debug('Stopping pymmcore instance')
         c.unloadAllDevices()
         if debug:
-            logger.debug('Unloaded all device_implementations.py')
-        # TODO: shutdown execution_engine engine
-        # Engine.get_instance().shutdown()
+            logger.debug('Unloaded all devices')
+        Engine.get_instance().shutdown()
         if debug:
             logger.debug('Engine shut down')
     _PYMMCORES.clear()
@@ -137,8 +169,7 @@ def start_headless(
             mmc.load_system_configuration(config_file)
         mmc.set_circular_buffer_memory_footprint(buffer_size_mb)
         _PYMMCORES.append(mmc) # Store so it doesn't get garbage collected
-        # TODO: startup execution_engine engine
-        # Engine(mmc)
+        Engine(mmc)
     else:
         classpath = mm_app_path + '/plugins/Micro-Manager/*'
         if java_loc is None:

pycromanager/mm_java_classes.py

@@ -74,7 +74,7 @@ def __new__(
         port: int
             The port of the Bridge used to create the object
         new_socket: bool
-            If True, will create execution_engine java object on a execution_engine port so that blocking calls will not interfere
+            If True, will create new java object on a new port so that blocking calls will not interfere
             with the bridges main port
         debug:
             print debug messages
@@ -117,7 +117,7 @@ def __new__(
         port: int
             The port of the Bridge used to create the object
         new_socket: bool
-            If True, will create execution_engine java object on a execution_engine port so that blocking calls will not interfere
+            If True, will create new java object on a new port so that blocking calls will not interfere
             with the bridges main port
         debug: bool
             print debug messages
@@ -142,7 +142,7 @@ def __new__(
         port: int
             The port of the Bridge used to create the object
         new_socket: bool
-            If True, will create execution_engine java object on a execution_engine port so that blocking calls will not interfere
+            If True, will create new java object on a new port so that blocking calls will not interfere
             with the bridges main port
         debug: bool
             print debug messages

pycromanager/napari_util.py

@@ -8,7 +8,7 @@
 
 def start_napari_signalling(viewer, dataset):
     """
-    Start up a threadworker, which will check for execution_engine images arrived in the dataset
+    Start up a threadworker, which will check for new images arrived in the dataset
     and then signal to napari to update or refresh as needed
     :param viewer: the napari Viewer
     :param dataset: the Datatset being acquired
@@ -17,7 +17,7 @@ def start_napari_signalling(viewer, dataset):
 
     def update_layer(image):
         """
-        update the napari layer with the execution_engine image
+        update the napari layer with the new image
         """
         if image is not None:
             try:
@@ -29,7 +29,7 @@ def update_layer(image):
     @thread_worker(connect={'yielded': update_layer})
     def napari_signaller():
         """
-        Monitor for signals that Acquisition has a execution_engine image ready, and when that happens
+        Monitor for signals that Acquisition has a new image ready, and when that happens
         update napari appropriately
         """
         # don't update faster than the display can handle

pycromanager/test/conftest.py

@@ -72,7 +72,7 @@ def install_mm():
         # find pycro-manager/java path
         if os.path.isdir('java'):
             java_path = os.path.abspath('java')
-        # in case cwd is '/pycromanager/integration_tests'
+        # in case cwd is '/pycromanager/test'
         elif os.path.isdir('../../java'):
             java_path = os.path.abspath('../../java')
         else:
@@ -86,7 +86,7 @@ def install_mm():
                 print(f'Removed {file_path}')
 
             # Copy the pycromanagerjava.jar file that was compiled by the github action
-            # into the nightly build so that it will integration_tests with the latest code
+            # into the nightly build so that it will test with the latest code
             compiled_jar_path = os.path.join(java_path, 'target', 'PycromanagerJava-*.jar')
             destination_path = os.path.join(mm_install_dir, 'plugins', 'Micro-Manager', 'PycromanagerJava.jar')
 

pycromanager/test/test_callback_functions.py

@@ -90,7 +90,7 @@ def hook_fn(event):
         return None  # cancel the event
 
     with Acquisition(show_display=False, pre_hardware_hook_fn=hook_fn) as acq:
-        # copy list of event_implementations to avoid popping from original
+        # copy list of events to avoid popping from original
         events_copy = [e for e in events]
         for test_event in events:
             acq.acquire(test_event)

pycromanager/test/test_notifications.py

@@ -8,9 +8,9 @@
 # TODO: add tests for timing of blocking until different parts of the hardware sequence
 # def test_async_images_read(launch_mm_headless, setup_data_folder):
 #     start = time.time()
-#     event_implementations = multi_d_acquisition_events(num_time_points=10, time_interval_s=0.5)
+#     events = multi_d_acquisition_events(num_time_points=10, time_interval_s=0.5)
 #     with Acquisition(directory=setup_data_folder, show_display=False) as acq:
-#         future = acq.acquire(event_implementations)
+#         future = acq.acquire(events)
 #
 #         future.await_execution({'time': 5}, AcqNotification.Hardware.POST_HARDWARE)