Merge pull request #1 from micro-manager/main

Merging new updates from main fork

docs/requirements.txt

@@ -1,6 +1,6 @@
-Sphinx==2.1.0
+Sphinx
 nbsphinx
-pygments<3,>=2.4.1
+pygments
 ipykernel
 sphinx_rtd_theme
 docstring-inheritance

docs/source/apis.rst

@@ -85,10 +85,13 @@ Acquisition APIs
 
 Acquisition
 ==============
-.. currentmodule:: pycromanager
+.. currentmodule:: pycromanager.acquisition.acquisition_superclass
 .. autoclass:: Acquisition
 	:members:
 
+
+.. currentmodule:: pycromanager
+
 multi_d_acquisition_events
 ===========================
 .. autofunction:: multi_d_acquisition_events

java/pom.xml

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.pycro-manager</groupId>
     <artifactId>PycroManagerJava</artifactId>
-     <version>0.44.2</version>
+     <version>0.44.5</version>
     <packaging>jar</packaging>
     <name>Pycro-Manager Java</name>
     <description>The Java components of Pycro-Manager</description>
@@ -54,12 +54,12 @@
       <dependency>
          <groupId>org.micro-manager.acqengj</groupId>
          <artifactId>AcqEngJ</artifactId>
-     <version>0.33.0</version>
+     <version>0.34.0</version>
       </dependency>
       <dependency>
          <groupId>org.micro-manager.ndviewer</groupId>
          <artifactId>NDViewer</artifactId>
-     <version>0.10.0</version>
+     <version>0.10.2</version>
       </dependency>
       <dependency>
          <groupId>org.micro-manager.ndtiffstorage</groupId>
@@ -144,4 +144,4 @@
       </repository>
    </distributionManagement>
 
-</project>
+</project>

java/src/main/java/org/micromanager/internal/zmq/ZMQServer.java

@@ -37,7 +37,7 @@ public class ZMQServer extends ZMQSocketWrapper {
    //map of objects that exist in some client of the server
    protected final ConcurrentHashMap<String, Object> externalObjects_ = new ConcurrentHashMap<String, Object>();
 
-   public static final String VERSION = "5.0.0";
+   public static final String VERSION = "5.1.0";
 
    private static Function<Class, Object> classMapper_;
    private static ZMQServer mainServer_;

pycromanager/__init__.py

@@ -8,4 +8,5 @@
 from pycromanager.core import Core
 from pycromanager.zmq_bridge.wrappers import JavaObject, JavaClass, PullSocket, PushSocket
 from pycromanager.acquisition.acq_eng_py.main.acq_notification import AcqNotification
+from ndtiff import Dataset
 from ._version import __version__, version_info

pycromanager/_version.py

@@ -1,2 +1,2 @@
-version_info = (0, 29, 5)
+version_info = (0, 29, 9)
 __version__ = ".".join(map(str, version_info))

pycromanager/acq_future.py

@@ -3,7 +3,7 @@
 
 def _axes_to_key(axes):
     """ Turn axes into a hashable key """
-    return frozenset(axes.items())
+    return None if axes is None else frozenset(axes.items())
 
 class AcquisitionFuture:
 

pycromanager/acquisition/acq_eng_py/internal/engine.py

@@ -91,9 +91,18 @@ def submit_event_iterator_inner():
         return self.event_generator_executor.submit(submit_event_iterator_inner)
 
 
+    def check_for_default_devices(self, event: AcquisitionEvent):
+        xy_stage = self.core.get_xy_stage_device()
+        z_stage = self.core.get_focus_device()
+        if event.get_z_position() is not None and (z_stage is None or z_stage == ""):
+            raise Exception("Event requires a z position, but no Core-Focus device is set")
+        if event.get_x_position() is not None and (xy_stage is None or xy_stage == ""):
+            raise Exception("Event requires an x position, but no Core-XYStage device is set")
+
     def process_acquisition_event(self, event: AcquisitionEvent) -> Future:
         def process_acquisition_event_inner():
             try:
+                self.check_for_default_devices(event)
                 if event.acquisition_.is_debug_mode():
                     self.core.logMessage("Processing event: " + event.to_string())
                 if event.acquisition_.is_debug_mode():

pycromanager/acquisition/acq_eng_py/main/acq_notification.py

@@ -36,21 +36,22 @@ def to_string():
             return "image"
 
     def __init__(self, type, id, phase=None):
-        if type == AcqNotification.Acquisition.to_string():
+        if type == AcqNotification.Acquisition or type == AcqNotification.Acquisition.to_string():
             self.type = AcqNotification.Acquisition
             self.id = id
             self.phase = phase
-        elif type == AcqNotification.Image.to_string() and phase == AcqNotification.Image.DATA_SINK_FINISHED:
+        elif (type == AcqNotification.Image or type == AcqNotification.Image.to_string()) and \
+              phase == AcqNotification.Image.DATA_SINK_FINISHED:
             self.type = AcqNotification.Image
             self.id = id
             self.phase = phase
         elif phase in [AcqNotification.Camera.PRE_SNAP, AcqNotification.Camera.POST_EXPOSURE,
                      AcqNotification.Camera.PRE_SEQUENCE_STARTED]:
             self.type = AcqNotification.Camera
-            self.id = json.loads(id)
+            self.id = json.loads(id) if isinstance(id, str) else id # convert from '{'time': 5}' to {'time': 5}
         elif phase in [AcqNotification.Hardware.PRE_HARDWARE, AcqNotification.Hardware.POST_HARDWARE]:
             self.type = AcqNotification.Hardware
-            self.id = json.loads(id)
+            self.id = json.loads(id) if isinstance(id, str) else id # convert from '{'time': 5}' to {'time': 5}
         elif phase == AcqNotification.Image.IMAGE_SAVED:
             self.type = AcqNotification.Image
             self.id = id

pycromanager/acquisition/acq_eng_py/main/acquisition_event.py

@@ -69,6 +69,7 @@ def copy(self):
         e.stageDeviceNamesToAxisNames_ = self.stageDeviceNamesToAxisNames_.copy()
         e.xPosition_ = self.xPosition_
         e.yPosition_ = self.yPosition_
+        e.zPosition_ = self.zPosition_
         e.miniumumStartTime_ms_ = self.miniumumStartTime_ms_
         e.slmImage_ = self.slmImage_
         e.acquireImage_ = self.acquireImage_

pycromanager/acquisition/acquisition_superclass.py

@@ -47,6 +47,7 @@ def __init__(
         ----------
         directory : str
             saving directory for this acquisition. If it is not supplied, the image data will be stored in RAM
+            (Java backend only)
         name : str
             Name of the acquisition. This will be used to generate the folder where the data is saved.
         image_process_fn : Callable
@@ -76,7 +77,7 @@ def __init__(
             external timing device that synchronizes with other hardware. Accepts either one argument (the current
             acquisition event) or two arguments (current event, event_queue)
         notification_callback_fn : Callable
-            (Experimental) function that will be called whenever a notification is received from the acquisition engine. These
+            function that will be called whenever a notification is received from the acquisition engine. These
             include various stages of the control of hardware and the camera and saving of images. Notification
             callbacks will execute asynchronously with respect to the acquisition process. The supplied function
             should take a single argument, which will be an AcqNotification object. It should execute quickly,
@@ -91,6 +92,17 @@ def __init__(
             the user
         debug : bool
             whether to print debug messages
+        show_display : bool
+            If True, show the image viewer window. If False, show no viewer. (Java backend only)
+        saving_queue_size : int
+            The number of images to queue (in memory) while waiting to write to disk. Higher values should
+            in theory allow sequence acquisitions to go faster, but requires the RAM to hold images while
+            they are waiting to save (Java backend only)
+        timeout :
+            Timeout in ms for connecting to Java side (Java backend only)
+        port :
+            Allows overriding the default port for using Java backends on a different port. Use this
+            after calling start_headless with the same non-default port (Java backend only)
         """
         self._debug = debug
         self._dataset = None

pycromanager/acquisition/java_backend_acquisitions.py

@@ -234,25 +234,10 @@ def __init__(
         show_display: bool=True,
         napari_viewer=None,
         saving_queue_size: int=20,
-        timeout: int=2000,
+        timeout: int=2500,
         port: int=DEFAULT_PORT,
         debug: int=False
     ):
-        """
-        Parameters
-        ----------
-        show_display : bool
-            If True, show the image viewer window. If False, show no viewer.
-        saving_queue_size : int
-            The number of images to queue (in memory) while waiting to write to disk. Higher values should
-            in theory allow sequence acquisitions to go faster, but requires the RAM to hold images while
-            they are waiting to save
-        timeout :
-            Timeout in ms for connecting to Java side
-        port :
-            Allows overriding the default port for using Java backends on a different port. Use this
-            after calling start_headless with the same non-default port
-        """
         # Get a dict of all named argument values (or default values when nothing provided)
         arg_names = [k for k in signature(JavaBackendAcquisition.__init__).parameters.keys() if k != 'self']
         l = locals()
@@ -286,7 +271,8 @@ def __init__(
 
         try:
             self._remote_notification_handler = JavaObject('org.micromanager.remote.RemoteNotificationHandler',
-                                                           args=[self._acq], port=self._port, new_socket=False)
+                                                           args=[self._acq], port=self._port, new_socket=False,
+                                                           timeout=self._timeout)
             self._acq_notification_recieving_thread = self._start_receiving_notifications()
             self._acq_notification_dispatcher_thread = self._start_notification_dispatcher(notification_callback_fn)
         # TODO: can remove this after this feature has been present for a while
@@ -476,7 +462,7 @@ def _initialize_image_processor(self, **kwargs):
 
         if kwargs['image_process_fn'] is not None:
             java_processor = JavaObject(
-                "org.micromanager.remote.RemoteImageProcessor", port=self._port
+                "org.micromanager.remote.RemoteImageProcessor", port=self._port, timeout=self._timeout
             )
             self._acq.add_image_processor(java_processor)
             self._processor_thread = self._start_processor(
@@ -489,29 +475,29 @@ def _initialize_hooks(self, **kwargs):
         self._hook_threads = []
         if kwargs['event_generation_hook_fn'] is not None:
             hook = JavaObject(
-                "org.micromanager.remote.RemoteAcqHook", port=self._port, args=[self._acq]
+                "org.micromanager.remote.RemoteAcqHook", port=self._port, args=[self._acq], timeout=self._timeout
             )
             self._hook_threads.append(self._start_hook(hook, kwargs['event_generation_hook_fn'],
                                                        self._event_queue, process=False))
             self._acq.add_hook(hook, self._acq.EVENT_GENERATION_HOOK)
         if kwargs['pre_hardware_hook_fn'] is not None:
             hook = JavaObject(
-                "org.micromanager.remote.RemoteAcqHook", port=self._port, args=[self._acq]
+                "org.micromanager.remote.RemoteAcqHook", port=self._port, args=[self._acq], timeout=self._timeout
             )
             self._hook_threads.append(self._start_hook(hook,
                                             kwargs['pre_hardware_hook_fn'], self._event_queue,
                                                        process=False))
             self._acq.add_hook(hook, self._acq.BEFORE_HARDWARE_HOOK)
         if kwargs['post_hardware_hook_fn'] is not None:
             hook = JavaObject(
-                "org.micromanager.remote.RemoteAcqHook", port=self._port, args=[self._acq]
+                "org.micromanager.remote.RemoteAcqHook", port=self._port, args=[self._acq], timeout=self._timeout
             )
             self._hook_threads.append(self._start_hook(hook, kwargs['post_hardware_hook_fn'],
                                                        self._event_queue, process=False))
             self._acq.add_hook(hook, self._acq.AFTER_HARDWARE_HOOK)
         if kwargs['post_camera_hook_fn'] is not None:
             hook = JavaObject(
-                "org.micromanager.remote.RemoteAcqHook", port=self._port, args=[self._acq],
+                "org.micromanager.remote.RemoteAcqHook", port=self._port, args=[self._acq], timeout=self._timeout
             )
             self._hook_threads.append(self._start_hook(hook, kwargs['post_camera_hook_fn'],
                                                        self._event_queue, process=False))
@@ -523,7 +509,7 @@ def _create_remote_acquisition(self, **kwargs):
             # create a new socket for it to run on so that it can have blocking calls without interfering with
             # the main socket or other internal sockets
             new_socket=True,
-            port=self._port, args=[core], debug=self._debug)
+            port=self._port, args=[core], debug=self._debug, timeout=self._timeout)
         show_viewer = kwargs['show_display'] is True and kwargs['napari_viewer'] is None
         self._acq = acq_factory.create_acquisition(kwargs['directory'], kwargs['name'], show_viewer,
                                                    kwargs['saving_queue_size'], self._debug,)
@@ -665,9 +651,8 @@ def __init__(
 
     def _create_remote_acquisition(self, port, **kwargs):
         core = ZMQRemoteMMCoreJ(port=self._port, timeout=self._timeout)
-        acq_factory = JavaObject(
-            "org.micromanager.remote.RemoteAcquisitionFactory", port=self._port, args=[core]
-        )
+        acq_factory = JavaObject("org.micromanager.remote.RemoteAcquisitionFactory",
+                                 port=self._port, args=[core], timeout=self._timeout)
 
         show_viewer = kwargs['show_display'] is True and\
                       kwargs['napari_viewer'] is None and\
@@ -711,7 +696,7 @@ def __init__(
             show_display: bool=True,
             image_saved_fn: callable=None,
             saving_queue_size: int=20,
-            timeout: int=1000,
+            timeout: int=2500,
             port: int=DEFAULT_PORT,
             debug: bool=False,
     ):

pycromanager/acquisition/python_backend_acquisitions.py

@@ -19,7 +19,6 @@ class PythonBackendAcquisition(Acquisition, metaclass=NumpyDocstringInheritanceM
 
     def __init__(
         self,
-        directory: str=None,
         name: str='default_acq_name',
         image_process_fn: callable=None,
         event_generation_hook_fn: callable = None,
@@ -30,16 +29,20 @@ def __init__(
         napari_viewer=None,
         image_saved_fn: callable=None,
         debug: int=False,
+        # Specificly so the directory arg can be absorbed and ignored without error,
+        **kwargs
     ):
         # Get a dict of all named argument values (or default values when nothing provided)
         arg_names = [k for k in signature(PythonBackendAcquisition.__init__).parameters.keys() if k != 'self']
         l = locals()
         named_args = {arg_name: (l[arg_name] if arg_name in l else
                                      dict(signature(PythonBackendAcquisition.__init__).parameters.items())[arg_name].default)
                                      for arg_name in arg_names }
+        if 'kwargs' in named_args:
+            if 'directory' in named_args['kwargs'] and named_args['kwargs']['directory'] is not None:
+                raise Exception('The directory argument is not supported in Python backend acquisitions')
+            del named_args['kwargs']
         super().__init__(**named_args)
-        if directory is not None:
-            raise NotImplementedError('Saving to disk is not yet implemented for the python backend. ')
         self._dataset = RAMDataStorage()
         self._finished = False
         self._notifications_finished = False

pycromanager/zmq_bridge/bridge.py

@@ -223,7 +223,7 @@ class _Bridge:
 
     DEFAULT_PORT = 4827
     DEFAULT_TIMEOUT = 500
-    _EXPECTED_ZMQ_SERVER_VERSION = "5.0.0"
+    _EXPECTED_ZMQ_SERVER_VERSION = "5.1.0"
 
     _bridge_creation_lock = threading.Lock()
     _cached_bridges_by_port_and_thread = {}