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@marcelmaatkamp
marcelmaatkamp committed Feb 25, 2023
1 parent 49af8fc commit 7a022f5
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Showing 3 changed files with 111 additions and 4 deletions.
25 changes: 21 additions & 4 deletions docs/jupyter/PyImageJ/PyImageJ.ipynb
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Expand Up @@ -178,11 +178,28 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 9,
"id": "049bb67e-f969-49ff-974f-f465c6ec5b97",
"metadata": {},
"outputs": [],
"source": []
"metadata": {
"tags": []
},
"outputs": [
{
"ename": "ModuleNotFoundError",
"evalue": "No module named 'itkwidgets'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[9], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mitkwidgets\u001b[39;00m\n\u001b[1;32m 2\u001b[0m itkwidgets\u001b[38;5;241m.\u001b[39mview(ij\u001b[38;5;241m.\u001b[39mpy\u001b[38;5;241m.\u001b[39mfrom_java(web_image))\n",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'itkwidgets'"
]
}
],
"source": [
"import itkwidgets\n",
"itkwidgets.view(ij.py.from_java(web_image))"
]
}
],
"metadata": {
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88 changes: 88 additions & 0 deletions docs/jupyter/napari/napari.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"id": "2ee026a3-6483-4027-b39a-6b1d844d475d",
"metadata": {
"tags": []
},
"outputs": [
{
"ename": "TypeError",
"evalue": "QtBindingsNotFoundError.__init__() takes 1 positional argument but 2 were given",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"File \u001b[0;32m/opt/conda/lib/python3.10/site-packages/qtpy/__init__.py:252\u001b[0m\n\u001b[1;32m 251\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 252\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mPySide6\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m __version__ \u001b[38;5;28;01mas\u001b[39;00m PYSIDE_VERSION \u001b[38;5;66;03m# analysis:ignore\u001b[39;00m\n\u001b[1;32m 253\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mPySide6\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mQtCore\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m __version__ \u001b[38;5;28;01mas\u001b[39;00m QT_VERSION \u001b[38;5;66;03m# analysis:ignore\u001b[39;00m\n",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'PySide6'",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mQtBindingsNotFoundError\u001b[0m Traceback (most recent call last)",
"File \u001b[0;32m/opt/conda/lib/python3.10/site-packages/napari/_qt/__init__.py:9\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m----> 9\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mqtpy\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m API_NAME, QtCore\n\u001b[1;32m 10\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n",
"File \u001b[0;32m/opt/conda/lib/python3.10/site-packages/qtpy/__init__.py:259\u001b[0m\n\u001b[1;32m 258\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mImportError\u001b[39;00m:\n\u001b[0;32m--> 259\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m QtBindingsNotFoundError()\n\u001b[1;32m 260\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
"\u001b[0;31mQtBindingsNotFoundError\u001b[0m: No Qt bindings could be found",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[2], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mnapari\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mnapari\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mqt\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mthreading\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m thread_worker\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mjupyter_rfb\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m RemoteFrameBuffer\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mskimage\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m data\n",
"File \u001b[0;32m/opt/conda/lib/python3.10/site-packages/napari/qt/__init__.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m_qt\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mqt_event_loop\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m get_app, run\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m_qt\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mqt_main_window\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Window\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m_qt\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mqt_resources\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m get_current_stylesheet, get_stylesheet\n",
"File \u001b[0;32m/opt/conda/lib/python3.10/site-packages/napari/_qt/__init__.py:12\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 11\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mNo Qt bindings could be found\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e):\n\u001b[0;32m---> 12\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28;43mtype\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43me\u001b[49m\u001b[43m)\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 13\u001b[0m \u001b[43m \u001b[49m\u001b[43mtrans\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 14\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mNo Qt bindings could be found.\u001b[39;49m\u001b[38;5;130;43;01m\\n\u001b[39;49;00m\u001b[38;5;130;43;01m\\n\u001b[39;49;00m\u001b[38;5;124;43mnapari requires either PyQt5 or PySide2 to be installed in the environment.\u001b[39;49m\u001b[38;5;130;43;01m\\n\u001b[39;49;00m\u001b[38;5;124;43mTo install the default backend (currently PyQt5), run \u001b[39;49m\u001b[38;5;130;43;01m\\\"\u001b[39;49;00m\u001b[38;5;124;43mpip install napari[all]\u001b[39;49m\u001b[38;5;130;43;01m\\\"\u001b[39;49;00m\u001b[38;5;124;43m \u001b[39;49m\u001b[38;5;130;43;01m\\n\u001b[39;49;00m\u001b[38;5;124;43mYou may also use \u001b[39;49m\u001b[38;5;130;43;01m\\\"\u001b[39;49;00m\u001b[38;5;124;43mpip install napari[pyside2]\u001b[39;49m\u001b[38;5;130;43;01m\\\"\u001b[39;49;00m\u001b[38;5;124;43mfor Pyside2, or \u001b[39;49m\u001b[38;5;130;43;01m\\\"\u001b[39;49;00m\u001b[38;5;124;43mpip install napari[pyqt5]\u001b[39;49m\u001b[38;5;130;43;01m\\\"\u001b[39;49;00m\u001b[38;5;124;43m for PyQt5\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 15\u001b[0m \u001b[43m \u001b[49m\u001b[43mdeferred\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 16\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 17\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01me\u001b[39;00m\n\u001b[1;32m 18\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m\n\u001b[1;32m 21\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m API_NAME \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPySide2\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 22\u001b[0m \u001b[38;5;66;03m# Set plugin path appropriately if using PySide2. This is a bug fix\u001b[39;00m\n\u001b[1;32m 23\u001b[0m \u001b[38;5;66;03m# for when both PyQt5 and Pyside2 are installed\u001b[39;00m\n",
"\u001b[0;31mTypeError\u001b[0m: QtBindingsNotFoundError.__init__() takes 1 positional argument but 2 were given"
]
}
],
"source": [
"import napari\n",
"from napari.qt.threading import thread_worker\n",
"from jupyter_rfb import RemoteFrameBuffer\n",
"from skimage import data\n",
"a = data.astronaut()\n",
"viewer = napari.Viewer()\n",
"viewer.add_image(a)\n",
"\n",
"class LiveViewer(RemoteFrameBuffer):\n",
" def __init__(self, viewer: napari.Viewer):\n",
" super().__init__()\n",
" self.viewer = viewer\n",
" \n",
" def get_frame(self):\n",
" return self.viewer.screenshot(canvas_only=False, flash=False)\n",
" \n",
" def handle_event(self, event):\n",
" self.request_draw()\n",
" \n",
"live_viewer = LiveViewer(viewer)\n",
"live_viewer"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "edaeda7a-cbc2-4e52-b6c7-07fbf3df77d2",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.9"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
2 changes: 2 additions & 0 deletions requirements.in
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Expand Up @@ -40,3 +40,5 @@ gravis
pyimagej
itkwidgets
napari
PySide6
jupyter-rfb

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