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Merge pull request #34 from haesleinhuepf/extend_bia-bob
Extend bia bob
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‎docs/generate_bia_bob_connector.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "906a254e-5fc2-41de-894e-91ace6a2756b",
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"metadata": {},
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"source": [
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"# Bia-bob\n",
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"This notebook is used to generate a python-file that serves as interoperability connector to [bia-bob](https://github.com/haesleinhuepf/bia-bob). You need an OpenAI account to run this notebook. Note: It uses chatGPT in a loop and executing this notebook costs some cents."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "f77d1470-7f46-47e8-8ac4-5db660a52586",
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"metadata": {},
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"outputs": [],
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"source": [
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"import stackview\n",
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"import openai"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "45bea0e2-3e26-4723-a529-1bf3340679b9",
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"metadata": {},
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"outputs": [],
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"source": [
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"def prompt(message:str, model=\"gpt-3.5-turbo\"):\n",
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" \"\"\"A prompt helper function that sends a message to openAI\n",
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" and returns only the text response.\n",
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" \"\"\"\n",
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" client = openai.OpenAI()\n",
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" response = client.chat.completions.create(\n",
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" model=model,\n",
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" messages=[{\"role\": \"user\", \"content\": message}]\n",
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" )\n",
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" return response.choices[0].message.content"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "e24d6116-d19b-42d0-8387-b71202a364e7",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"dict_keys(['annotate', 'assist', 'create_colormap', 'crop', 'curtain', 'insight', 'interact', 'jupyter_displayable_output', 'merge_rgb', 'nop', 'orthogonal', 'picker', 'side_by_side', 'slice', 'switch'])"
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]
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},
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"execution_count": 3,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"all = {}\n",
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"for n in dir(stackview):\n",
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" if not n.startswith('_'):\n",
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" all[n] = getattr(stackview, n)\n",
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"\n",
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"all.keys()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "6fda77e3-718f-4317-9afc-3e22958abb79",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"{'annotate': <function stackview._annotate.annotate(image, labels, slice_number: int = None, alpha: float = 0.5, axis: int = 0, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)>,\n",
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" 'crop': <function stackview._crop.crop(image, slice_number: int = None, axis: int = 0, continuous_update: bool = True, slider_text: str = 'Slice', axis_names=None, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)>,\n",
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" 'curtain': <function stackview._curtain.curtain(image, image_curtain, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, alpha: float = 1, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, curtain_colormap: str = None, curtain_display_min: float = None, curtain_display_max: float = None)>,\n",
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" 'insight': <function stackview._static_view.insight(image, library_name=None, help_url=None)>,\n",
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" 'interact': <function stackview._interact.interact(func, image=None, *args, continuous_update: bool = True, context: dict = None, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, viewer: stackview._slice_viewer._SliceViewer = None, **kwargs)>,\n",
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" 'orthogonal': <function stackview._orthogonal.orthogonal(image, display_width: int = None, display_height: int = None, continuous_update: bool = True, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)>,\n",
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" 'picker': <function stackview._picker.picker(image, slice_number: int = None, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)>,\n",
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" 'side_by_side': <function stackview._side_by_side.side_by_side(image1, image2, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)>,\n",
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" 'slice': <function stackview._slice.slice(image, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)>,\n",
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" 'switch': <function stackview._switch.switch(images, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, toggleable: bool = False)>}"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"all.pop('jupyter_displayable_output')\n",
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"all.pop('create_colormap')\n",
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"all.pop('merge_rgb')\n",
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"all.pop('nop')\n",
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"all.pop('assist')\n",
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"\n",
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"all"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "dc8af4de-826b-4f2c-8630-f6ad96665ffc",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Displays an image with a slider and label showing mouse position and intensity.\n",
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"stackview.annotate(image, labels, slice_number: int = None, alpha: float = 0.5, axis: int = 0, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\n",
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"\n",
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"\n",
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"Allows cropping an image along all axes.\n",
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"stackview.crop(image, slice_number: int = None, axis: int = 0, continuous_update: bool = True, slider_text: str = 'Slice', axis_names=None, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\n",
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"\n",
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"\n",
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"- Display two images and use a slider to switch between them.\n",
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"stackview.curtain(image, image_curtain, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, alpha: float = 1, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, curtain_colormap: str = None, curtain_display_min: float = None, curtain_display_max: float = None)\n",
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"\n",
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"\n",
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"- Convert numpy-array-like image to numpy-compatible array with convenient display in Jupyter notebooks\n",
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"stackview.insight(image, library_name=None, help_url=None)\n",
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"\n",
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"\n",
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"Build a user interface with sliders for numeric and \"footprint\" or \"selem\" parameters\n",
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"stackview.interact(func, image=None, *args, continuous_update: bool = True, context: dict = None, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, viewer: stackview._slice_viewer._SliceViewer = None, **kwargs)\n",
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"\n",
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"\n",
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"- Display an image and allows slicing in three dimensions (Z, Y, and X) with optional zooming and colormap settings.\n",
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"stackview.orthogonal(image, display_width: int = None, display_height: int = None, continuous_update: bool = True, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\n",
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"\n",
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"\n",
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"* Display an image with a slider and label showing the mouse position and intensity.\n",
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"stackview.picker(image, slice_number: int = None, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\n",
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"\n",
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"\n",
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"* Display two images side by side, with an additional overlay view of their colocalization, and a slider to navigate through a stack.\n",
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"stackview.side_by_side(image1, image2, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\n",
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"\n",
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"\n",
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"* Display an image with a slider to navigate through a stack.\n",
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"stackview.slice(image, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\n",
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"\n",
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"\n",
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"- Allows switching between multiple images and displaying them with a slider.\n",
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"stackview.switch(images, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, toggleable: bool = False)\n",
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"\n",
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"\n",
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"[\"Displays an image with a slider and label showing mouse position and intensity.\\nstackview.annotate(image, labels, slice_number: int = None, alpha: float = 0.5, axis: int = 0, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\\n\\n\", \"Allows cropping an image along all axes.\\nstackview.crop(image, slice_number: int = None, axis: int = 0, continuous_update: bool = True, slider_text: str = 'Slice', axis_names=None, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\\n\\n\", '- Display two images and use a slider to switch between them.\\nstackview.curtain(image, image_curtain, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, alpha: float = 1, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, curtain_colormap: str = None, curtain_display_min: float = None, curtain_display_max: float = None)\\n\\n', '- Convert numpy-array-like image to numpy-compatible array with convenient display in Jupyter notebooks\\nstackview.insight(image, library_name=None, help_url=None)\\n\\n', 'Build a user interface with sliders for numeric and \"footprint\" or \"selem\" parameters\\nstackview.interact(func, image=None, *args, continuous_update: bool = True, context: dict = None, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, viewer: stackview._slice_viewer._SliceViewer = None, **kwargs)\\n\\n', '- Display an image and allows slicing in three dimensions (Z, Y, and X) with optional zooming and colormap settings.\\nstackview.orthogonal(image, display_width: int = None, display_height: int = None, continuous_update: bool = True, zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\\n\\n', \"* Display an image with a slider and label showing the mouse position and intensity.\\nstackview.picker(image, slice_number: int = None, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\\n\\n\", \"* Display two images side by side, with an additional overlay view of their colocalization, and a slider to navigate through a stack.\\nstackview.side_by_side(image1, image2, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\\n\\n\", \"* Display an image with a slider to navigate through a stack.\\nstackview.slice(image, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None)\\n\\n\", \"- Allows switching between multiple images and displaying them with a slider.\\nstackview.switch(images, slice_number: int = None, axis: int = 0, display_width: int = None, display_height: int = None, continuous_update: bool = True, slider_text: str = 'Slice', zoom_factor: float = 1.0, zoom_spline_order: int = 0, colormap: str = None, display_min: float = None, display_max: float = None, toggleable: bool = False)\\n\\n\"]\n"
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]
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}
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],
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"source": [
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"def get_function_signature(func):\n",
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" import inspect\n",
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" \n",
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" function_object = func\n",
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" signature_object = inspect.signature(function_object)\n",
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" signature_string = \"stackview.\" + func.__name__ + str(signature_object)\n",
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" return signature_string\n",
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"\n",
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"all_descriptions = []\n",
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"for name, func in all.items():\n",
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" \n",
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" description = prompt(f\"\"\"Shorten the following docstring into a single bullet point:\n",
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"\n",
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" ```\n",
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" {func.__doc__}\n",
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" ```\n",
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" \n",
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" Shorten it to a single bullet point explaining what the function does without mentioning the function name and without phrases such as `use this function`. Do not mention and explain all parameters. Keep it short.\n",
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"\n",
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" Examples:\n",
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"\n",
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" * compute the absolute value of every individual pixel in an image\n",
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" cle.absolute(source: ndarray, destination: ndarray = None) -> ndarray\n",
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"\n",
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" * determine the absolute difference pixel by pixel between two images\n",
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" cle.absolute_difference(source1: ndarray, source2: ndarray, destination: ndarray = None) -> ndarray\n",
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" \n",
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" * add a scalar value to all pixels of an image\n",
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" cle.add_image_and_scalar(source: ndarray, destination: ndarray = None, scalar: float = 1) -> ndarray\n",
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" \n",
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" \"\"\").replace(\"If you want to \", \"* \")\n",
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" description = description + \"\\n\" + get_function_signature(func) + \"\\n\\n\"\n",
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" print(description)\n",
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" \n",
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" all_descriptions.append(description)\n",
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"\n",
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"print(all_descriptions[:1000])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "754b2914-3556-4f2b-8361-5bcd8f3286bf",
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"metadata": {},
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"outputs": [],
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"source": [
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"descriptions = []\n",
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"for bullet_point in all_descriptions:\n",
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" if bullet_point[0:2] in ['- ', '* ']:\n",
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" bullet_point = bullet_point[2:]\n",
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"\n",
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" descriptions.append(\"* \" + bullet_point)\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"id": "99adee01-0847-43e8-9ef3-df511805f7cd",
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"metadata": {},
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"outputs": [],
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"source": [
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"text = \"\".join(descriptions).replace('\"', \"'\")\n",
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"text = \" \" + text.replace(\"\\n\", \"\\n \")\n",
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"text = f'''\n",
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"def list_bia_bob_plugins():\n",
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" \"\"\"List of function hints for bia_bob\"\"\"\n",
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" return \"\"\"{text}\"\"\"\n",
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"'''\n",
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"\n",
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"with open(\"../stackview/_bia_bob_plugins.py\", 'w') as file:\n",
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" file.write(text)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "003174bb-9c47-48f7-8e2b-361f7d7a4359",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.13"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎setup.py‎

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setuptools.setup(
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name="stackview",
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version="0.7.3",
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version="0.7.4",
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author="Robert Haase",
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author_email="robert.haase@tu-dresden.de",
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description="Interactive image stack viewing in jupyter notebooks",
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"Intended Audience :: Science/Research",
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"Development Status :: 3 - Alpha",
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],
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entry_points={
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'bia_bob_plugins': [
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'stackview_plugins = stackview._bia_bob_plugins:list_bia_bob_plugins',
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]
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}
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)

‎stackview/__init__.py‎

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__version__ = "0.7.3"
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__version__ = "0.7.4"
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from ._static_view import jupyter_displayable_output, insight
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from ._utilities import merge_rgb

‎stackview/_bia_bob_plugins.py‎

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def list_bia_bob_plugins():
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"""List of function hints for bia_bob"""
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return """ * Displays an image with a slider and label showing mouse position and intensity.
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stackview.annotate(image, labels)
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* Allows cropping an image along all axes.
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stackview.crop(image)
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* Showing an image stored in variable `image` and a segmented image stored in variable `labels` on top. Also works with two images or two label images.
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stackview.curtain(image, labels, alpha: float = 1)
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* Display an image stored in a variable `image` (this also works with label images). Prefer stackview.insight over matplotlib.pyplot.imshow!
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stackview.insight(image)
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* Build a user interface with sliders for numeric parameters
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stackview.interact(func, image)
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* Display an image and allows slicing in three dimensions (Z, Y, and X).
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stackview.orthogonal(image)
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* Display an image with a slider and label showing the mouse position and intensity.
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stackview.picker(image)
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* Display two images side by side, with an additional overlay view of their overlap
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stackview.side_by_side(image1, image2)
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* Display an image with a slider to navigate through a stack.
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stackview.slice(image)
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* Allows switching between multiple images and displaying them with a slider.
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stackview.switch(images:list)
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"""

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