Merge pull request #301 from imagej/global-gateway

Add callback mechanism for GUI mode

conftest.py

@@ -34,7 +34,7 @@ def pytest_addoption(parser):
 
 
 @pytest.fixture(scope="session")
-def ij_fixture(request):
+def ij(request):
     """
     Create an ImageJ instance to be used by the whole testing environment
     :param request: Pytest variable passed in to fixtures
@@ -43,12 +43,14 @@ def ij_fixture(request):
     legacy = request.config.getoption("--legacy")
     headless = request.config.getoption("--headless")
 
+    imagej.when_imagej_starts(lambda ij: setattr(ij, "_testing", True))
+
     mode = "headless" if headless else "interactive"
-    ij_wrapper = imagej.init(ij_dir, mode=mode, add_legacy=legacy)
+    ij = imagej.init(ij_dir, mode=mode, add_legacy=legacy)
 
-    yield ij_wrapper
+    yield ij
 
-    ij_wrapper.dispose()
+    ij.dispose()
 
 
 def str2bool(v):

doc/05-Convenience-methods-of-PyImageJ.ipynb

@@ -129,6 +129,31 @@
    "source": [
     "Note the warnings! We're currently in headless mode. The many legacy ImageJ functions operate limitedly or not at all in headless mode. For example the `RoiManager` is not functional in a true headless enviornment."
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 5.2 Register functions to start with ImageJ\n",
+    "\n",
+    "Functions can be executed during ImageJ's initialization routine by registering the functions with PyImageJ's callback mechanism `when_imagej_starts()`. This is particularly useful for macOS users in `gui` mode, allowing functions to be called before the Python [REPL/interpreter](https://docs.python.org/3/tutorial/interpreter.html) is [blocked](Initialization.md/#gui-mode).\n",
+    "\n",
+    "The following example uses `when_imagej_starts()` callback display a to `uint16` 2D NumPy array it with ImageJ's viewer, print it's dimensions (_i.e._ shape) and open the `RoiManager` while ImageJ initializes.\n",
+    "\n",
+    "```python\n",
+    "import imagej\n",
+    "import numpy as np\n",
+    "\n",
+    "# register functions\n",
+    "arr = np.random.randint(0, 2**16, size=(256, 256), dtype=np.uint16) # create random 16-bit array\n",
+    "imagej.when_imagej_starts(lambda ij: ij.RoiManager.getRoiManager()) # open the RoiManager\n",
+    "imagej.when_imagej_starts(lambda ij: ij.ui().show(ij.py.to_dataset(arr))) # convert and display the array\n",
+    "imagej.when_imagej_starts(lambda _: print(f\"array shape: {arr.shape}\"))\n",
+    "\n",
+    "# initialize imagej\n",
+    "ij = imagej.init(mode='interactive')\n",
+    "```"
+   ]
   }
  ],
  "metadata": {

src/imagej/__init__.py

@@ -38,6 +38,7 @@
 import sys
 import threading
 import time
+from ctypes import cdll
 from enum import Enum
 from functools import lru_cache
 from pathlib import Path
@@ -60,7 +61,8 @@
 __version__ = sj.get_version("pyimagej")
 
 _logger = logging.getLogger(__name__)
-rai_lock = threading.Lock()
+_init_callbacks = []
+_rai_lock = threading.Lock()
 
 # Enable debug logging if DEBUG environment variable is set.
 try:
@@ -1007,14 +1009,14 @@ def _op(self):
     def _ra(self):
         threadLocal = getattr(self, "_threadLocal", None)
         if threadLocal is None:
-            with rai_lock:
+            with _rai_lock:
                 threadLocal = getattr(self, "_threadLocal", None)
                 if threadLocal is None:
                     threadLocal = threading.local()
                     self._threadLocal = threadLocal
         ra = getattr(threadLocal, "ra", None)
         if ra is None:
-            with rai_lock:
+            with _rai_lock:
                 ra = getattr(threadLocal, "ra", None)
                 if ra is None:
                     ra = self.randomAccess()
@@ -1205,19 +1207,39 @@ def init(
     macos = sys.platform == "darwin"
 
     if macos and mode == Mode.INTERACTIVE:
-        raise EnvironmentError("Sorry, the interactive mode is not available on macOS.")
+        # check for main thread only on macOS
+        if _macos_is_main_thread():
+            raise EnvironmentError(
+                "Sorry, the interactive mode is not available on macOS."
+            )
 
     if not sj.jvm_started():
         success = _create_jvm(ij_dir_or_version_or_endpoint, mode, add_legacy)
         if not success:
             raise RuntimeError("Failed to create a JVM with the requested environment.")
 
+    def run_callbacks(ij):
+        # invoke registered callback functions
+        for callback in _init_callbacks:
+            callback(ij)
+        return ij
+
     if mode == Mode.GUI:
         # Show the GUI and block.
+        global gateway
+        gateway = None
+
+        def show_gui_and_run_callbacks():
+            global gateway
+            gateway = _create_gateway()
+            gateway.ui().showUI()
+            run_callbacks(gateway)
+            return gateway
+
         if macos:
             # NB: This will block the calling (main) thread forever!
             try:
-                setupGuiEnvironment(lambda: _create_gateway().ui().showUI())
+                setupGuiEnvironment(show_gui_and_run_callbacks)
             except ModuleNotFoundError as e:
                 if e.msg == "No module named 'PyObjCTools'":
                     advice = (
@@ -1237,16 +1259,34 @@ def init(
                     raise
         else:
             # Create and show the application.
-            gateway = _create_gateway()
-            gateway.ui().showUI()
+            gateway = show_gui_and_run_callbacks()
             # We are responsible for our own blocking.
             # TODO: Poll using something better than ui().isVisible().
-            while gateway.ui().isVisible():
+            while sj.jvm_started() and gateway.ui().isVisible():
                 time.sleep(1)
-            return None
-    else:
-        # HEADLESS or INTERACTIVE mode: create the gateway and return it.
-        return _create_gateway()
+
+        del gateway
+        return None
+
+    # HEADLESS or INTERACTIVE mode: create the gateway and return it.
+    return run_callbacks(_create_gateway())
+
+
+def when_imagej_starts(f) -> None:
+    """
+    Registers a function to be called immediately after ImageJ2 starts.
+    This is useful especially with GUI mode, to perform additional
+    configuration and operations following initialization of ImageJ2,
+    because the use of GUI mode blocks the calling thread indefinitely.
+
+    :param f: Single-argument function to invoke during imagej.init().
+        The function will be passed the newly created ImageJ2 Gateway
+        as its sole argument, and called as the final action of the
+        init function before it returns or blocks.
+    """
+    # Add function to the list of callbacks to invoke upon start_jvm().
+    global _init_callbacks
+    _init_callbacks.append(f)
 
 
 def imagej_main():
@@ -1484,6 +1524,27 @@ def _includes_imagej_legacy(items: list):
     return any(item.startswith("net.imagej:imagej-legacy") for item in items)
 
 
+def _macos_is_main_thread():
+    """Detect if the current thread is the main thread on macOS.
+
+    :return: Boolean indicating if the current thread is the main thread.
+    """
+    # try to load the pthread library
+    try:
+        pthread = cdll.LoadLibrary("libpthread.dylib")
+    except OSError as exc:
+        _log_exception(_logger, exc)
+        print("No pthread library found.")
+        # assume the current thread is the main thread
+        return True
+
+    # detect if the current thread is the main thread
+    if pthread.pthread_main_np() == 1:
+        return True
+    else:
+        return False
+
+
 def _set_ij_env(ij_dir):
     """
     Create a list of required jars and add to the java classpath.

tests/test_callbacks.py

@@ -0,0 +1,7 @@
+def test_when_imagej_starts(ij):
+    """
+    The ImageJ2 gateway test fixture registers a callback function via
+    when_imagej_starts, which injects a small piece of data into the gateway
+    object. We check for that data here to make sure the callback happened.
+    """
+    assert True is getattr(ij, "_testing", None)

tests/test_ctypes.py

@@ -29,14 +29,14 @@
 
 
 @pytest.mark.parametrize(argnames="ctype,jtype_str,value", argvalues=parameters)
-def test_ctype_to_realtype(ij_fixture, ctype, jtype_str, value):
+def test_ctype_to_realtype(ij, ctype, jtype_str, value):
     py_type = ctype(value)
     # Convert the ctype into a RealType
-    converted = ij_fixture.py.to_java(py_type)
+    converted = ij.py.to_java(py_type)
     jtype = sj.jimport(jtype_str)
     assert isinstance(converted, jtype)
     assert converted.get() == value
     # Convert the RealType back into a ctype
-    converted_back = ij_fixture.py.from_java(converted)
+    converted_back = ij.py.from_java(converted)
     assert isinstance(converted_back, ctype)
     assert converted_back.value == value

tests/test_fiji.py

@@ -4,23 +4,23 @@
 # -- Tests --
 
 
-def test_plugins_load_using_pairwise_stitching(ij_fixture):
+def test_plugins_load_using_pairwise_stitching(ij):
     try:
         sj.jimport("plugin.Stitching_Pairwise")
     except TypeError:
         pytest.skip("No Pairwise Stitching plugin available. Skipping test.")
 
-    if not ij_fixture.legacy:
+    if not ij.legacy:
         pytest.skip("No original ImageJ. Skipping test.")
-    if ij_fixture.ui().isHeadless():
+    if ij.ui().isHeadless():
         pytest.skip("No GUI. Skipping test.")
 
-    tile1 = ij_fixture.IJ.createImage("Tile1", "8-bit random", 512, 512, 1)
-    tile2 = ij_fixture.IJ.createImage("Tile2", "8-bit random", 512, 512, 1)
+    tile1 = ij.IJ.createImage("Tile1", "8-bit random", 512, 512, 1)
+    tile2 = ij.IJ.createImage("Tile2", "8-bit random", 512, 512, 1)
     args = {"first_image": tile1.getTitle(), "second_image": tile2.getTitle()}
-    ij_fixture.py.run_plugin("Pairwise stitching", args)
-    result_name = ij_fixture.WindowManager.getCurrentImage().getTitle()
+    ij.py.run_plugin("Pairwise stitching", args)
+    result_name = ij.WindowManager.getCurrentImage().getTitle()
 
-    ij_fixture.IJ.run("Close All", "")
+    ij.IJ.run("Close All", "")
 
     assert result_name == "Tile1<->Tile2"