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app.ipynb

@@ -32,11 +32,14 @@
    "source": [
     "from pathlib import Path\n",
     "from io import StringIO\n",
+    "import json\n",
+    "from datetime import datetime as dt\n",
     "\n",
     "import pandas as pd\n",
     "import panel as pn\n",
     "\n",
-    "import scripts.tap_const as tc"
+    "import scripts.tap_const as tc\n",
+    "import scripts.tap_image as ti"
    ]
   },
   {
@@ -52,11 +55,23 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pn.extension(\"plotly\", \"tabulator\")\n",
+    "pn.extension(\"tabulator\", design=\"bootstrap\")\n",
     "\n",
     "template = pn.template.BootstrapTemplate(title=\"Ralstonia Annotation Tool\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pd.set_option(\"display.max_colwidth\", 500)\n",
+    "pd.set_option(\"display.max_columns\", 500)\n",
+    "pd.set_option(\"display.width\", 1000)\n",
+    "pd.set_option(\"display.max_rows\", 20)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -95,35 +110,21 @@
    "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=\";\")"
+    "## User Interface"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Source Selection"
+    "### Source Selection"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Download Template"
+    "#### Download Template"
    ]
   },
   {
@@ -132,20 +133,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "template_download = pn.widgets.FileDownload(\n",
+    "dwn_template = 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"
+    "#### Upload existing file"
    ]
   },
   {
@@ -156,20 +156,47 @@
    "source": [
     "file_input = pn.widgets.FileInput(accept=\".csv,.json\")\n",
     "table = pn.widgets.Tabulator(\n",
-    "    pn.bind(to_dataframe, file_input),\n",
+    "    value=pd.DataFrame(),\n",
     "    pagination=\"local\",\n",
     "    page_size=20,\n",
     "    sizing_mode=\"stretch_width\",\n",
     ")\n",
-    "layout = pn.Column(file_input, table)\n",
-    "layout"
+    "\n",
+    "ck_show_finished = pn.widgets.ToggleIcon(\n",
+    "    icon=\"eye-x\", size=\"4em\", active_icon=\"eye\", value=False\n",
+    ")\n",
+    "mk_show_finished = pn.pane.Markdown(\"Hide complete plants\")\n",
+    "\n",
+    "@pn.depends(file_input.param.value, watch=True)\n",
+    "def on_file_loaded(value):\n",
+    "    if not value or not isinstance(value, bytes):\n",
+    "        return pd.DataFrame()\n",
+    "\n",
+    "    string_io = StringIO(value.decode(\"utf8\"))\n",
+    "    ret = pd.read_csv(string_io, sep=\";\").assign(\n",
+    "        file_name=lambda x: x.filepath.str.replace(\".tif\", \".jpg\")\n",
+    "    )\n",
+    "    ret = ret[ret.treatment == \"RS\"]\n",
+    "    if \"di\" not in ret:\n",
+    "        ret[\"di\"] = 0\n",
+    "    if \"done\" not in ret:\n",
+    "        ret[\"done\"] = False\n",
+    "\n",
+    "    table.value = ret"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Annotation Tools"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Annotation Tools"
+    "#### Plant Selection"
    ]
   },
   {
@@ -179,16 +206,24 @@
    "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())"
+    "\n",
+    "@pn.depends(table.param.value, ck_show_finished.param.value, watch=True)\n",
+    "def on_table_changed(file: str, show_done: bool):\n",
+    "    df = table.value\n",
+    "    if \"done\" in df:\n",
+    "        sl_plant.options = list(\n",
+    "            df.plant.unique() if show_done is True else df[df.done == False].plant.unique()\n",
+    "        )\n",
+    "        mk_show_finished.object = (\n",
+    "            \"Show complete plants\" if show_done is True else \"Hide complete plants\"\n",
+    "        )"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Render"
+    "#### Main Annotation UI"
    ]
   },
   {
@@ -197,14 +232,165 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "template.sidebar.append(\n",
-    "    pn.Card(pn.Column(template_download, file_input), title=\"File Manager\"),\n",
+    "im_current = pn.pane.Image(max_width=800, max_height=800, sizing_mode=\"stretch_width\")\n",
+    "discrete_player = pn.widgets.DiscretePlayer(\n",
+    "    name=\"Discrete Player\", options=[0], value=0, loop_policy=\"loop\"\n",
+    ")\n",
+    "discrete_player.interval = 1000\n",
+    "ii_disease_index = pn.widgets.IntInput(\n",
+    "    name=\"Disease Index\",\n",
+    "    start=0,\n",
+    "    end=4,\n",
+    "    step=1,\n",
+    "    value=0,\n",
+    "    max_width=80,\n",
+    "    sizing_mode=\"stretch_width\",\n",
+    ")\n",
+    "\n",
+    "dwn_annotations = pn.widgets.FileDownload(\n",
+    "    file=pt_data.joinpath(f\"{EXPERIMENT}_raw.csv\"),\n",
+    "    filename=f\"{EXPERIMENT}_raw.csv\",\n",
+    "    label=\" \",\n",
+    "    name=\"Download Annotations\",\n",
+    "    sizing_mode=\"stretch_width\",\n",
+    "    icon=\"file-download\",\n",
+    "    button_type=\"primary\",\n",
     ")\n",
-    "template.sidebar.append(sl_plant)\n",
     "\n",
-    "template.main.append(table)\n",
+    "updating: bool = False\n",
     "\n",
-    "template.servable()"
+    "\n",
+    "@pn.cache(max_items=10, policy=\"LRU\")\n",
+    "def get_plant_data(df, plant_name) -> pd.DataFrame:\n",
+    "    file_names, rotations = [], []\n",
+    "    for k, v in json.load(\n",
+    "        open(pt_rotations.joinpath(sl_plant.value).with_suffix(\".json\"), \"r\")\n",
+    "    ).items():\n",
+    "        file_names.append(k + \".jpg\")\n",
+    "        rotations.append(v)\n",
+    "\n",
+    "    return df[df.plant == plant_name].merge(\n",
+    "        pd.DataFrame(data={\"file_name\": file_names, \"rotation\": rotations}),\n",
+    "        on=\"file_name\",\n",
+    "        how=\"left\",\n",
+    "    )\n",
+    "\n",
+    "\n",
+    "def update_image():\n",
+    "    global updating\n",
+    "    updating = True\n",
+    "    try:\n",
+    "        row = (\n",
+    "            get_plant_data(df=table.value, plant_name=sl_plant.value)\n",
+    "            .set_index(\"job_id\")\n",
+    "            .loc[discrete_player.value]\n",
+    "        )\n",
+    "        if pt_images.joinpath(row.file_name).is_file() is True:\n",
+    "            im_current.object = ti.to_pil(\n",
+    "                ti.rotate_image(\n",
+    "                    image=ti.load_image(file_name=row.file_name, file_path=pt_images),\n",
+    "                    angle=row.rotation,\n",
+    "                )\n",
+    "            )\n",
+    "            ii_disease_index.value = row.di\n",
+    "        else:\n",
+    "            im_current.object = None\n",
+    "    finally:\n",
+    "        updating = False\n",
+    "\n",
+    "\n",
+    "@pn.depends(sl_plant.param.value, watch=True)\n",
+    "def on_plant_changed(plant_name):\n",
+    "    discrete_player.options = get_plant_data(\n",
+    "        df=table.value, plant_name=plant_name\n",
+    "    ).job_id.to_list()\n",
+    "    discrete_player.value = discrete_player.options[0]\n",
+    "    update_image()\n",
+    "\n",
+    "\n",
+    "@pn.depends(discrete_player.param.value, watch=True)\n",
+    "def on_index_changed(index):\n",
+    "    update_image()\n",
+    "\n",
+    "\n",
+    "@pn.depends(ii_disease_index.param.value, watch=True)\n",
+    "def on_di_changed(di):\n",
+    "    if updating is True:\n",
+    "        return\n",
+    "    table.value.loc[\n",
+    "        (table.value.plant == sl_plant.value)\n",
+    "        & (table.value.job_id >= discrete_player.value),\n",
+    "        \"di\",\n",
+    "    ] = di\n",
+    "    table.value.loc[(table.value.plant == sl_plant.value), \"done\"] = True\n",
+    "\n",
+    "    s_buf = StringIO()\n",
+    "    table.value.to_csv(s_buf, sep=\";\")\n",
+    "    s_buf.seek(0)\n",
+    "    dwn_annotations.filename = f\"{EXPERIMENT}_{dt.now().strftime('%Y%d%m_%H%M%S')}.csv\"\n",
+    "    dwn_annotations.label = \"Download\"\n",
+    "    dwn_annotations.file = s_buf\n",
+    "    dwn_annotations.icon = \"file-download\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Build Components"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sidebar = pn.Column(\n",
+    "    pn.Card(pn.Column(dwn_template, file_input), title=\"File Manager\"),\n",
+    "    sl_plant,\n",
+    "    pn.Row(\n",
+    "        ck_show_finished,\n",
+    "        pn.Column(pn.layout.VSpacer(), mk_show_finished, pn.layout.VSpacer()),\n",
+    "        height=50,\n",
+    "    ),\n",
+    ")\n",
+    "main = pn.Column(\n",
+    "    im_current,\n",
+    "    pn.Row(\n",
+    "        # pn.layout.HSpacer(),\n",
+    "        discrete_player,\n",
+    "        ii_disease_index,\n",
+    "        dwn_annotations,\n",
+    "        # pn.layout.HSpacer(),\n",
+    "    ),\n",
+    "    max_width=800,\n",
+    "    max_height=800,\n",
+    "    sizing_mode=\"stretch_width\",\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Test"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pn.Row(sidebar, main)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Render"
    ]
   },
   {
@@ -212,7 +398,11 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "template.sidebar.append(sidebar)\n",
+    "template.main.append(main)\n",
+    "template.servable()"
+   ]
   }
  ],
  "metadata": {