Setup apposednepari

- create appose/napari env
- launch nepari and transfer image on run

Author: gnodar01

CP5/active_plugins/appose_demo.py

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+import os
+from time import sleep
+
+import appose
+from appose.service import ResponseType
+import numpy as np
+
+from cellprofiler_core.module._module import Module
+from cellprofiler_core.setting.do_something import DoSomething
+from cellprofiler_core.setting.subscriber import ImageSubscriber
+from cellprofiler_core.setting.text import Text
+
+__doc__ = """\
+ApposeDemo
+============
+
+**ApposeDemo** is a demo of runnin napari through Appose.
+
+
+TODO: more docs
+
+|
+
+============ ============ ===============
+Supports 2D? Supports 3D? Respects masks?
+============ ============ ===============
+YES          YES          YES
+============ ============ ===============
+
+"""
+
+cite_paper_link = "https://doi.org/10.1016/1047-3203(90)90014-M"
+
+qt_setup = """
+# CRITICAL: Qt must run on main thread on macOS.
+
+from qtpy.QtWidgets import QApplication
+from qtpy.QtCore import Qt, QTimer
+import threading
+import sys
+
+# Configure Qt for macOS before any QApplication creation
+QApplication.setAttribute(Qt.AA_MacPluginApplication, True)
+QApplication.setAttribute(Qt.AA_PluginApplication, True)
+QApplication.setAttribute(Qt.AA_DisableSessionManager, True)
+
+# Create QApplication on main thread.
+qt_app = QApplication(sys.argv)
+
+# Prevent Qt from quitting when last Qt window closes; we want napari to stay running.
+qt_app.setQuitOnLastWindowClosed(False)
+
+task.export(qt_app=qt_app)
+task.update()
+
+# Run Qt event loop on main thread.
+qt_app.exec()
+"""
+
+qt_shutdown = """
+# Signal main thread to quit.
+qt_app.quit()
+"""
+
+napari_show = """
+import napari
+import numpy as np
+
+from superqt import ensure_main_thread
+
+@ensure_main_thread
+def show(narr):
+    napari.imshow(narr)
+
+show(ndarr.ndarray())
+task.outputs["shape"] = ndarr.shape
+"""
+
+READY = False
+
+class ApposeDemo(Module):
+    category = "Image Processing"
+
+    module_name = "ApposeDemo"
+
+    variable_revision_number = 1
+
+    def create_settings(self):
+        super().create_settings()
+
+        self.x_name = ImageSubscriber(
+            "Select the input image", doc="Select the image you want to use."
+        )
+        
+        self.package_path = Text(
+            "Path to apposednapari environment",
+            f"{os.path.dirname(__file__)}/apposednapari/.pixi/envs/default",
+        )
+        self.doit = DoSomething(
+            "Do the thing",
+            "Do it",
+            lambda: self.send_to_napari(),
+            doc=f"""\
+Press this button to do the job.
+""",
+        )
+
+    def settings(self):
+        return super().settings() + [self.x_name, self.package_path, self.doit]
+    
+    def visible_settings(self):
+        return self.settings()
+    
+    def volumetric(self):
+        return True
+
+    def run(self, workspace):
+        x_name = self.x_name.value
+
+        images = workspace.image_set
+
+        x = images.get_image(x_name)
+
+        x_data = x.pixel_data
+
+        self.send_to_napari(x_data)
+
+        if self.show_window:
+            ...
+
+    # credit to Curtis Rueden:
+    # https://github.com/ctrueden/appose-napari-demo/blob/a803e50347a023578afdd9ddc2c287567d5445fc/napari-show.py
+    def send_to_napari(self, img_data=None):
+        env = appose.base(str(self.package_path)).build()
+        with env.python() as python:
+            # Print Appose events verbosely, for debugging purposes.
+            python.debug(print)
+
+            # Start the Qt application event loop in the worker process.
+            print("Starting Qt app event loop")
+            setup = python.task(qt_setup, queue="main")
+            def check_ready(event):
+                if event.response_type == ResponseType.UPDATE:
+                    print("Got update event! Marking Qt as ready")
+                    global READY
+                    READY = True
+                    print("Ready...", READY)
+            print("attempting to start to listen")
+            setup.listen(check_ready)
+            print("attempting start setup")
+            setup.start()
+            print("Waiting for Qt startup...")
+            global READY
+            while not READY:
+                #print("sleeping", READY)
+                sleep(0.1)
+            print("Qt is ready!")
+
+            if img_data is None:
+                img_data = np.random.random([512, 384]).astype("float64")
+
+            # Create a test image in shared memory.
+            ndarr = appose.NDArray(dtype=str(img_data.dtype), shape=img_data.shape)
+            # There's probably a slicker way without needing to slice/copy...
+            ndarr.ndarray()[:] = img_data[:]
+
+            # Actually do a real thing with napari: create and show an image.
+            print("Showing image with napari...")
+            task = python.task(napari_show, inputs={"ndarr": ndarr})
+
+            task.wait_for()
+            shape = task.outputs["shape"]
+            print(f"Task complete! Got shape: {shape}")

CP5/active_plugins/apposednapari/.gitattributes

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+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

CP5/active_plugins/apposednapari/.gitignore

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+# pixi environments
+.pixi