app.py

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Ralstonia Annotation Tool"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "from io import StringIO\n",
    "\n",
    "import pandas as pd\n",
    "import panel as pn\n",
    "\n",
    "import scripts.tap_const as tc"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pn.extension(\"plotly\", \"tabulator\")\n",
    "\n",
    "template = pn.template.BootstrapTemplate(title=\"Ralstonia Annotation Tool\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Constants"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "EXPERIMENT = \"72AC_PhD_2404\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Setup Paths\n",
    "if tc.phenopsis.joinpath(EXPERIMENT).is_dir() is True:\n",
    "    pt_data = tc.data\n",
    "    pt_images = tc.phenopsis.joinpath(EXPERIMENT)\n",
    "    pt_rotations = tc.dataout.joinpath(\"rotation_angles\").joinpath(f\"{EXPERIMENT}\")\n",
    "else:\n",
    "    here = Path(\".\").parent\n",
    "    pt_data = here.joinpath(\"data\")\n",
    "    pt_images = here.joinpath(\"images\").joinpath(EXPERIMENT)\n",
    "    pt_rotations = here.joinpath(\"rotation_angles\").joinpath(f\"{EXPERIMENT}\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def to_dataframe(value):\n",
    "    if not value or not isinstance(value, bytes):\n",
    "        return pd.DataFrame()\n",
    "\n",
    "    string_io = StringIO(value.decode(\"utf8\"))\n",
    "    return pd.read_csv(string_io, sep=\";\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Source Selection"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download Template"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "template_download = pn.widgets.FileDownload(\n",
    "    file=pt_data.joinpath(f\"{EXPERIMENT}_raw.csv\"),\n",
    "    filename=f\"{EXPERIMENT}_raw.csv\",\n",
    "    button_type=\"success\",\n",
    "    label=\"Download template annotation file\",\n",
    ")\n",
    "template_download"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Upload existing file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "file_input = pn.widgets.FileInput(accept=\".csv,.json\")\n",
    "table = pn.widgets.Tabulator(\n",
    "    pn.bind(to_dataframe, file_input),\n",
    "    pagination=\"local\",\n",
    "    page_size=20,\n",
    "    sizing_mode=\"stretch_width\",\n",
    ")\n",
    "layout = pn.Column(file_input, table)\n",
    "layout"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Annotation Tools"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sl_plant = pn.widgets.Select(name=\"Plant\", options=[])\n",
    "@pn.depends(table.param.value, watch=True)\n",
    "def on_file_loaded(file):\n",
    "    sl_plant.options = list(table.value.plant.unique())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Render"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "template.sidebar.append(\n",
    "    pn.Card(pn.Column(template_download, file_input), title=\"File Manager\"),\n",
    ")\n",
    "template.sidebar.append(sl_plant)\n",
    "\n",
    "template.main.append(table)\n",
    "\n",
    "template.servable()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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