docs/generate_bia_bob_connector.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "906a254e-5fc2-41de-894e-91ace6a2756b",
   "metadata": {},
   "source": [
    "# Bia-bob\n",
    "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."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "f77d1470-7f46-47e8-8ac4-5db660a52586",
   "metadata": {},
   "outputs": [],
   "source": [
    "import stackview\n",
    "import openai"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "45bea0e2-3e26-4723-a529-1bf3340679b9",
   "metadata": {},
   "outputs": [],
   "source": [
    "def prompt(message:str, model=\"gpt-3.5-turbo\"):\n",
    "    \"\"\"A prompt helper function that sends a message to openAI\n",
    "    and returns only the text response.\n",
    "    \"\"\"\n",
    "    client = openai.OpenAI()\n",
    "    response = client.chat.completions.create(\n",
    "        model=model,\n",
    "        messages=[{\"role\": \"user\", \"content\": message}]\n",
    "    )\n",
    "    return response.choices[0].message.content"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "e24d6116-d19b-42d0-8387-b71202a364e7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['annotate', 'assist', 'create_colormap', 'crop', 'curtain', 'insight', 'interact', 'jupyter_displayable_output', 'merge_rgb', 'nop', 'orthogonal', 'picker', 'side_by_side', 'slice', 'switch'])"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all = {}\n",
    "for n in dir(stackview):\n",
    "    if not n.startswith('_'):\n",
    "        all[n] = getattr(stackview, n)\n",
    "\n",
    "all.keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "6fda77e3-718f-4317-9afc-3e22958abb79",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'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",
       " '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",
       " '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",
       " 'insight': <function stackview._static_view.insight(image, library_name=None, help_url=None)>,\n",
       " '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",
       " '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",
       " '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",
       " '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",
       " '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",
       " '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)>}"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all.pop('jupyter_displayable_output')\n",
    "all.pop('create_colormap')\n",
    "all.pop('merge_rgb')\n",
    "all.pop('nop')\n",
    "all.pop('assist')\n",
    "\n",
    "all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "dc8af4de-826b-4f2c-8630-f6ad96665ffc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Displays an image with a slider and label showing mouse position and intensity.\n",
      "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",
      "\n",
      "\n",
      "Allows cropping an image along all axes.\n",
      "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",
      "\n",
      "\n",
      "- Display two images and use a slider to switch between them.\n",
      "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",
      "\n",
      "\n",
      "- Convert numpy-array-like image to numpy-compatible array with convenient display in Jupyter notebooks\n",
      "stackview.insight(image, library_name=None, help_url=None)\n",
      "\n",
      "\n",
      "Build a user interface with sliders for numeric and \"footprint\" or \"selem\" parameters\n",
      "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",
      "\n",
      "\n",
      "- Display an image and allows slicing in three dimensions (Z, Y, and X) with optional zooming and colormap settings.\n",
      "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",
      "\n",
      "\n",
      "* Display an image with a slider and label showing the mouse position and intensity.\n",
      "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",
      "\n",
      "\n",
      "* Display two images side by side, with an additional overlay view of their colocalization, and a slider to navigate through a stack.\n",
      "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",
      "\n",
      "\n",
      "* Display an image with a slider to navigate through a stack.\n",
      "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",
      "\n",
      "\n",
      "- Allows switching between multiple images and displaying them with a slider.\n",
      "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",
      "\n",
      "\n",
      "[\"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"
     ]
    }
   ],
   "source": [
    "def get_function_signature(func):\n",
    "    import inspect\n",
    "    \n",
    "    function_object = func\n",
    "    signature_object = inspect.signature(function_object)\n",
    "    signature_string = \"stackview.\" + func.__name__ + str(signature_object)\n",
    "    return signature_string\n",
    "\n",
    "all_descriptions = []\n",
    "for name, func in all.items():\n",
    "    \n",
    "    description = prompt(f\"\"\"Shorten the following docstring into a single bullet point:\n",
    "\n",
    "    ```\n",
    "    {func.__doc__}\n",
    "    ```\n",
    "    \n",
    "    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",
    "\n",
    "    Examples:\n",
    "\n",
    "    * compute the absolute value of every individual pixel in an image\n",
    "    cle.absolute(source: ndarray, destination: ndarray = None) -> ndarray\n",
    "\n",
    "    * determine the absolute difference pixel by pixel between two images\n",
    "    cle.absolute_difference(source1: ndarray, source2: ndarray, destination: ndarray = None) -> ndarray\n",
    "    \n",
    "    * add a scalar value to all pixels of an image\n",
    "    cle.add_image_and_scalar(source: ndarray, destination: ndarray = None, scalar: float = 1) -> ndarray\n",
    "    \n",
    "    \"\"\").replace(\"If you want to \", \"* \")\n",
    "    description = description + \"\\n\" + get_function_signature(func) + \"\\n\\n\"\n",
    "    print(description)\n",
    "    \n",
    "    all_descriptions.append(description)\n",
    "\n",
    "print(all_descriptions[:1000])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "754b2914-3556-4f2b-8361-5bcd8f3286bf",
   "metadata": {},
   "outputs": [],
   "source": [
    "descriptions = []\n",
    "for bullet_point in all_descriptions:\n",
    "    if bullet_point[0:2] in ['- ', '* ']:\n",
    "        bullet_point = bullet_point[2:]\n",
    "\n",
    "    descriptions.append(\"* \" + bullet_point)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "99adee01-0847-43e8-9ef3-df511805f7cd",
   "metadata": {},
   "outputs": [],
   "source": [
    "text = \"\".join(descriptions).replace('\"', \"'\")\n",
    "text = \"    \" + text.replace(\"\\n\", \"\\n    \")\n",
    "text = f'''\n",
    "def list_bia_bob_plugins():\n",
    "    \"\"\"List of function hints for bia_bob\"\"\"\n",
    "    return \"\"\"{text}\"\"\"\n",
    "'''\n",
    "\n",
    "with open(\"../stackview/_bia_bob_plugins.py\", 'w') as file:\n",
    "    file.write(text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "003174bb-9c47-48f7-8e2b-361f7d7a4359",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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