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app.py

@@ -1,23 +1,239 @@
-from pathlib import Path
-
-import panel as pn
-
-import scripts.tap_const as tc
-
-EXPERIMENT = "72AC_PhD_2404"
-
-# Setup Paths
-if tc.phenopsis.joinpath(EXPERIMENT).is_dir() is True:
-    pt_data = tc.data
-    pt_images = tc.phenopsis.joinpath(EXPERIMENT)
-    pt_rotations = tc.dataout.joinpath("rotation_angles").joinpath(f"{EXPERIMENT}")
-else:
-    here = Path(".").parent
-    pt_data = here.joinpath("data")
-    pt_images = here.joinpath("images").joinpath(EXPERIMENT)
-    pt_rotations = here.joinpath("rotation_angles").joinpath(f"{EXPERIMENT}")
-
-
-pn.extension("plotly", "tabulator")
-
-template = pn.template.BootstrapTemplate(title="Raltonia Annotation Tool")
+{
+ "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": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "env",
+   "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": "3.11.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}