diff --git a/CP5/active_plugins/appose_demo.py b/CP5/active_plugins/appose_demo.py new file mode 100644 index 00000000..0b94c821 --- /dev/null +++ b/CP5/active_plugins/appose_demo.py @@ -0,0 +1,173 @@ +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}") diff --git a/CP5/active_plugins/apposednapari/.gitattributes b/CP5/active_plugins/apposednapari/.gitattributes new file mode 100644 index 00000000..887a2c18 --- /dev/null +++ b/CP5/active_plugins/apposednapari/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/CP5/active_plugins/apposednapari/.gitignore b/CP5/active_plugins/apposednapari/.gitignore new file mode 100644 index 00000000..c9314b7c --- /dev/null +++ b/CP5/active_plugins/apposednapari/.gitignore @@ -0,0 +1,2 @@ +# pixi environments +.pixi diff --git a/CP5/active_plugins/apposednapari/pixi.lock b/CP5/active_plugins/apposednapari/pixi.lock new file mode 100644 index 00000000..e519c738 --- /dev/null +++ b/CP5/active_plugins/apposednapari/pixi.lock @@ -0,0 +1,3351 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + packages: + osx-64: + - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda + - 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