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app.ipynb

@@ -55,7 +55,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pn.extension(\"tabulator\", design=\"bootstrap\")\n",
+    "pn.extension(\"tabulator\")\n",
     "\n",
     "template = pn.template.BootstrapTemplate(title=\"Ralstonia Annotation Tool\")"
    ]
@@ -107,24 +107,31 @@
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "## User Interface"
+    "treatments = {\n",
+    "    \"Ralstonia\": \"RS\",\n",
+    "    \"Control\": \"CT\",\n",
+    "    \"Hydric Stress\": \"HS\",\n",
+    "    \"DC3000\": \"DC\",\n",
+    "}"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Source Selection"
+    "## User Interface"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Download Template"
+    "### Widgets"
    ]
   },
   {
@@ -138,14 +145,56 @@
     "    filename=f\"{EXPERIMENT}_raw.csv\",\n",
     "    button_type=\"success\",\n",
     "    label=\"Download template annotation file\",\n",
-    ")"
+    "    sizing_mode=\"stretch_width\",\n",
+    ")\n",
+    "\n",
+    "file_input = pn.widgets.FileInput(accept=\".csv,.json\", sizing_mode=\"stretch_width\")\n",
+    "table = pn.widgets.Tabulator(\n",
+    "    value=pd.DataFrame(),\n",
+    "    pagination=\"local\",\n",
+    "    page_size=20,\n",
+    "    sizing_mode=\"stretch_width\",\n",
+    ")\n",
+    "\n",
+    "\n",
+    "sl_treatment = pn.widgets.Select(\n",
+    "    name=\"Treatment\", options=list(treatments.keys()), value=\"Ralstonia\"\n",
+    ")\n",
+    "sl_plant = pn.widgets.Select(name=\"Plant\", options=[])\n",
+    "ck_show_finished = pn.widgets.Checkbox(name=\"Show completed plants\", value=False)\n",
+    "\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 = 500\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=\"Download\",\n",
+    "    name=\"Download Annotations\",\n",
+    "    sizing_mode=\"stretch_width\",\n",
+    "    icon=\"file-download\",\n",
+    "    button_type=\"primary\",\n",
+    ")\n",
+    "pg_completion = pn.indicators.Progress(name=\"Annotation progress\", value=0)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Upload existing file"
+    "### Callbacks"
    ]
   },
   {
@@ -154,18 +203,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "file_input = pn.widgets.FileInput(accept=\".csv,.json\")\n",
-    "table = pn.widgets.Tabulator(\n",
-    "    value=pd.DataFrame(),\n",
-    "    pagination=\"local\",\n",
-    "    page_size=20,\n",
-    "    sizing_mode=\"stretch_width\",\n",
-    ")\n",
+    "updating: bool = False\n",
     "\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",
@@ -176,88 +215,29 @@
     "    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": [
-    "#### Plant Selection"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "sl_plant = pn.widgets.Select(name=\"Plant\", options=[])\n",
+    "    table.value = ret\n",
+    "\n",
     "\n",
-    "@pn.depends(table.param.value, ck_show_finished.param.value, watch=True)\n",
-    "def on_table_changed(file: str, show_done: bool):\n",
+    "@pn.depends(\n",
+    "    table.param.value,\n",
+    "    ck_show_finished.param.value,\n",
+    "    sl_treatment.param.value,\n",
+    "    watch=True,\n",
+    ")\n",
+    "def on_table_changed(file: str, show_done: bool, treatment):\n",
     "    df = table.value\n",
-    "    if \"done\" in df:\n",
+    "    if \"done\" in df and \"treatment\" in df:\n",
+    "        df = df[df.treatment == treatments[treatment]]\n",
     "        sl_plant.options = list(\n",
-    "            df.plant.unique() if show_done is True else df[df.done == False].plant.unique()\n",
+    "            df.plant.unique()\n",
+    "            if show_done is True\n",
+    "            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": [
-    "#### Main Annotation UI"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "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",
-    "\n",
-    "updating: bool = False\n",
     "\n",
     "\n",
     "@pn.cache(max_items=10, policy=\"LRU\")\n",
@@ -328,9 +308,11 @@
     "    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\""
+    "    dwn_annotations.visible = True\n",
+    "\n",
+    "    pg_completion.max = len(table.value.plant.unique())\n",
+    "    pg_completion.value = len(table.value[table.value.done == True].plant.unique())"
    ]
   },
   {
@@ -347,23 +329,41 @@
    "outputs": [],
    "source": [
     "sidebar = pn.Column(\n",
-    "    pn.Card(pn.Column(dwn_template, file_input), title=\"File Manager\"),\n",
-    "    sl_plant,\n",
-    "    pn.Row(\n",
+    "    pn.Card(\n",
+    "        pn.Column(\n",
+    "            pn.pane.Markdown(\"**Step 1:** Doawload the annaotation template file.\"),\n",
+    "            pn.pane.Alert(\n",
+    "                \"\"\"Only download the template the first time, changes are stored on your computer only.\"\"\",\n",
+    "                alert_type=\"danger\",\n",
+    "            ),\n",
+    "            dwn_template,\n",
+    "            pn.pane.Markdown(\"**Step 2:** Uplaod the downloaded template file.\"),\n",
+    "            file_input,\n",
+    "            pn.pane.Markdown(\n",
+    "                \"\"\"**Step 3:** Annotate images. \n",
+    "                Uppon finishing or before closing the app us the download button next to the disease index selector to download the annotations.\"\"\"\n",
+    "            ),\n",
+    "            pn.pane.Alert(\n",
+    "                \"If you want to resume an existing annotation session, upload your latest download.\",\n",
+    "                alert_type=\"info\",\n",
+    "            ),\n",
+    "        ),\n",
+    "        title=\"File Manager\",\n",
+    "    ),\n",
+    "    pn.WidgetBox(\n",
+    "        \"#### Plant selection\",\n",
+    "        sl_treatment,\n",
+    "        sl_plant,\n",
     "        ck_show_finished,\n",
-    "        pn.Column(pn.layout.VSpacer(), mk_show_finished, pn.layout.VSpacer()),\n",
-    "        height=50,\n",
+    "        sizing_mode=\"stretch_width\",\n",
+    "    ),\n",
+    "    pn.WidgetBox(\n",
+    "        \"#### Annotation progress\", pg_completion, sizing_mode=\"stretch_width\"\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",
+    "    pn.Row(discrete_player, ii_disease_index, dwn_annotations),\n",
     "    max_width=800,\n",
     "    max_height=800,\n",
     "    sizing_mode=\"stretch_width\",\n",