Create CP5 special directory

- will eventually (on release) move current active_plugins to CP4 and
  move contents of CP5 to active_plugins, ditto for tests; but for now
  everything goes in CP5 directory since most people are on CP4

Author: gnodar01

CP5/active_plugins/calculatemoments.py

@@ -0,0 +1,4 @@
+# -*- coding: utf-8 -*-
+
+__author__ = "Mark Hiner, Alice Lucas, Beth Cimini"
+__all__ = ["bridge", "server"]

CP5/active_plugins/callbarcodes.py

@@ -0,0 +1,138 @@
+from multiprocessing.managers import SyncManager
+import multiprocessing as mp
+import atexit, cpij.server as ijserver
+from queue import Queue
+from threading import Lock
+
+
+class QueueManager(SyncManager):
+    pass
+
+
+QueueManager.register("input_queue")
+QueueManager.register("output_queue")
+QueueManager.register("get_lock")
+
+_init_method = None
+
+
+def init_method():
+    global _init_method
+    if not _init_method:
+        if ijserver.is_server_running():
+            l = lock()
+            l.acquire()
+            to_imagej().put(
+                {ijserver.PYIMAGEJ_KEY_COMMAND: ijserver.PYIMAGEJ_CMD_GET_INIT_METHOD}
+            )
+            _init_method = from_imagej().get()[ijserver.PYIMAGEJ_KEY_OUTPUT]
+            l.release()
+
+    return _init_method
+
+
+def lock() -> Lock:
+    """
+    Helper method to synchronzie requests with the ImageJ server.
+
+    A lock should be acquired before sending data to the server, and released after
+    receiving the result.
+
+    Returns
+    ---------
+    A Lock connected to the ImageJ server.
+    """
+    return _manager().get_lock()
+
+
+def to_imagej() -> Queue:
+    """
+    Helper method to send data to the ImageJ server
+
+    Returns
+    ---------
+    A Queue connected to the ImageJ server. Only its put method should be called.
+    """
+    return _manager().input_queue()
+
+
+def from_imagej() -> Queue:
+    """
+    Helper method to retrieve data from the ImageJ server
+
+    Returns
+    ---------
+    A Queue connected to the ImageJ server. Only its get method should be called.
+    """
+    return _manager().output_queue()
+
+
+def init_pyimagej(init_string):
+    """
+    Start the pyimagej daemon thread if it isn't already running.
+
+    Parameters
+    ----------
+    init_string : str, optional
+        This can be a path to a local ImageJ installation, or an initialization string per imagej.init(),
+        e.g. sc.fiji:fiji:2.1.0
+    """
+    to_imagej().put(
+        {
+            ijserver.PYIMAGEJ_KEY_COMMAND: ijserver.PYIMAGEJ_CMD_START,
+            ijserver.PYIMAGEJ_KEY_INPUT: init_string,
+        }
+    )
+    result = from_imagej().get()
+    if result == ijserver.PYIMAGEJ_STATUS_STARTUP_FAILED:
+        _shutdown_imagej()
+        # Wait for the server to shut down
+        while ijserver.is_server_running():
+            pass
+        return False
+
+    global _init_method
+    _init_method = init_string
+    return True
+
+
+def _manager() -> QueueManager:
+    """
+    Helper method to return a QueueManager connected to the ImageJ server
+    """
+    if not ijserver.is_server_running():
+        raise RuntimeError("No ImageJ server instance available")
+
+    manager = QueueManager(
+        address=("127.0.0.1", ijserver.SERVER_PORT), authkey=ijserver._SERVER_KEY
+    )
+    manager.connect()
+    return manager
+
+
+def _shutdown_imagej():
+    """
+    Helper method to send the shutdown signal to ImageJ. Intended to be called
+    at process exit.
+    """
+    if ijserver.is_server_running():
+        to_imagej().put({ijserver.PYIMAGEJ_KEY_COMMAND: ijserver.PYIMAGEJ_CMD_EXIT})
+
+
+def start_imagej_server():
+    """
+    If the ImageJ server is not already running, spawns the server in a new
+    Process. Blocks until the server is up and running.
+    """
+    if ijserver.is_server_running():
+        return
+
+    ctx = mp.get_context("spawn")
+    p = ctx.Process(target=ijserver.main)
+    p.start()
+
+    # wait for the server to start up
+    ijserver.wait_for_server_startup()
+
+    # Ensure server shuts down when main app closes
+    atexit.register(_shutdown_imagej)