{
"cells": [
{
"cell_type": "raw",
"metadata": {},
"source": [
"---\n",
"title: stoer\n",
"show-code: False\n",
"---"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import plotly.express as px\n",
"import plotly.graph_objects as go\n",
"import pandas as pd\n",
"\n",
"pd.options.plotting.backend = \"plotly\"\n",
"from urllib.request import urlopen\n",
"import json\n",
"import numpy as np\n",
"import geopandas"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import mercury as mr\n",
"\n",
"# checkbox to control code visibility\n",
"#show_code = mr.Checkbox(label=\"Show code\", value=False)\n",
"# App object to set `show_code` attribute\n",
"app = mr.App(title=\"Störe\", description=\"Zeige den Weg der Störe.\", show_code=False)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"def adjust_coordinates(row):\n",
" row.lat += np.random.normal(0, 1e-4)\n",
" row.lon += np.random.normal(0, 1e-4)\n",
" return row\n",
"\n",
"def load_data():\n",
" df_receiver = pd.read_csv(\"./data/receiver.csv\", encoding=\"latin-1\", delimiter=\";\")\n",
"\n",
" df_fishes = pd.read_excel(\"./data/20230310_Receiver_Polen.xlsx\")\n",
" df_stoer_ids = pd.read_excel(\"./data/20230310_Receiver_Polen.xlsx\",\n",
" sheet_name = \"eingesetzte Akustik-Tags\")\n",
"\n",
" df_fishes_vemco = pd.read_excel(\"./data/Daten Vemco Receiver.xlsx\", decimal=',').copy()\n",
" #df_stoer_ids_vemco = pd.read_excel(\"Daten Vemco Receiver.xlsx\",)\n",
" #sheet_name = \"eingesetzte Akustik-Tags\")\n",
" df_fishes_vemco = df_fishes_vemco.drop(columns=[\"Longitude\", \"Latitude\"])\n",
"\n",
" df_receiver_vemco = pd.read_csv(\"./data/Sturgeons.txt\",\n",
" delimiter=\",\").copy()\n",
"\n",
" df_fishes_vemco_m = pd.merge(left=df_fishes_vemco, right=df_receiver_vemco, how=\"left\", on=\"Receiver\", suffixes=(\"\", \"_y\"))\n",
"\n",
" receiver = df_receiver.copy()\n",
" receiver_vemco = df_receiver_vemco.copy()\n",
"\n",
" receiver_formatted = receiver_vemco.rename(columns={\n",
" \"Receiver\" : \"receiver_sn\",\n",
" \"Latitude\": \"lat\",\n",
" \"Longitude\": \"lon\",\n",
" \"Station.name\" : \"station_name\"})[[\"receiver_sn\",\n",
" \"lat\", \"lon\",\n",
" \"station_name\"]]\n",
" all_receivers = pd.concat([receiver, receiver_formatted])\n",
"\n",
" fishes = df_fishes.copy()\n",
" fishes = fishes.loc[fishes[\" ID\"].isin(df_stoer_ids[\"ID\"])]\n",
" fishes = fishes.rename(columns={\" Receiver\":\"receiver_sn\"})\n",
" fishes = pd.merge(fishes, all_receivers[[\"lon\", \"lat\", \"receiver_sn\"]],\n",
" on=\"receiver_sn\", how=\"left\")\n",
"\n",
"\n",
" df_fishes_vemco_form = df_fishes_vemco_m.drop(columns=\"ID\")\n",
" df_fishes_vemco_form = df_fishes_vemco_form.rename(columns={\"Date.and.Time.nocor\": \"Date and Time (UTC)\",\n",
" \"Longitude\" : \"lon\",\n",
" \"Latitude\": \"lat\",\n",
" \"Transmitter\": \" ID\",\n",
" \"Receiver\" : \"receiver_sn\"\n",
" })\n",
"\n",
" all_fishes = pd.concat([fishes, df_fishes_vemco_form])\n",
"\n",
"\n",
" all_fishes = all_fishes.drop_duplicates([\" ID\", \"receiver_sn\"]).reset_index().drop(columns=\"index\")\n",
" all_fishes.index = list(all_fishes.index)\n",
"\n",
"\n",
"\n",
" all_fishes = all_fishes.apply(adjust_coordinates, axis=1)\n",
"\n",
" gdf_fishes = geopandas.GeoDataFrame(\n",
" all_fishes, geometry=geopandas.points_from_xy(\n",
" all_fishes.lon, all_fishes.lat), crs = 4326)\n",
"\n",
" receiver_vemco = df_receiver_vemco.copy()\n",
"\n",
" df_wm = gdf_fishes.to_crs(epsg=3857)\n",
"\n",
" gdf_receiver = geopandas.GeoDataFrame(\n",
" all_receivers,\n",
" geometry=geopandas.points_from_xy(all_receivers.lon, all_receivers.lat),\n",
" crs = 4326)\n",
"\n",
" gdf_receiver['coords'] = gdf_receiver.to_crs(epsg=3857)['geometry'].apply(\n",
" lambda x: x.representative_point().coords[:])\n",
"\n",
" gdf_receiver['coords'] = [coords[0] for coords in gdf_receiver['coords']]\n",
"\n",
" return gdf_receiver, df_wm"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
"#gdf_receiver, df_wm = load_data()\n",
"gdf_receiver = pd.read_csv(\"gdf_receiver.csv\", index_col=0)\n",
"df_wm = pd.read_csv(\"df_wm.csv\", index_col=0)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"unique_ids = [str(element) for element in df_wm[\" ID\"].unique().tolist()]"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"application/mercury+json": {
"choices": [
"6702",
"6710",
"6712",
"6685",
"6664",
"6672",
"6692",
"6691",
"6695",
"6705",
"6654",
"6698",
"6667",
"6655",
"6680",
"6699",
"6706",
"6658",
"6666",
"6674",
"6689",
"6683",
"6682",
"6661",
"6676",
"6659",
"6688",
"6673",
"6678",
"6707",
"6693",
"6694"
],
"code_uid": "MultiSelect.0.40.16.2-rand73a38024",
"disabled": false,
"hidden": false,
"label": "Wähle die Störe aus anhand Ihrer ID",
"model_id": "170c0cb9372542ab8e51eaeadacba941",
"url_key": "",
"value": [
"6702",
"6710",
"6712",
"6685",
"6664",
"6672",
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"6695",
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"widget": "MultiSelect"
},
"application/vnd.jupyter.widget-view+json": {
"model_id": "170c0cb9372542ab8e51eaeadacba941",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"mercury.MultiSelect"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# add select widget\n",
"selected = mr.MultiSelect(label=\"Wähle die Störe aus anhand Ihrer ID\",\n",
" choices=unique_ids,\n",
" value=unique_ids\n",
" )"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"a = pd.to_datetime(df_wm.iloc[:45][\"Date and Time (UTC)\"])\n",
"b = pd.to_datetime(df_wm.iloc[:45][\"Date and Time (UTC)\"])"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"a = pd.to_datetime(df_wm.iloc[:45][\"Date and Time (UTC)\"]).dt.strftime(\"%Y-%m-%d %H:%M:%S\")\n",
"b = pd.to_datetime(df_wm.iloc[45:][\"Date and Time (UTC)\"]).dt.strftime(\"%Y-%m-%d %H:%M:%S\")"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"df_wm[\"Date\"] = pd.to_datetime(pd.concat([a,b]))"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"# df_one_fish = df_wm.loc[df_wm[\" ID\"] == 6689]\n",
"if len(selected.value) < 1:\n",
" selected_value = df_wm[\" ID\"].unique()[0]\n",
" df_one_fish = df_wm.loc[df_wm[\" ID\"] == selected_value ].sort_values(\"Date\")\n",
"else:\n",
" df_one_fish = df_wm.loc[df_wm[\" ID\"].astype(str).isin(selected.value)].sort_values(\"Date\")"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"dfs = []\n",
"for ID in df_one_fish[\" ID\"].values.tolist():\n",
" _df = df_one_fish.loc[df_one_fish[\" ID\"] == ID].sort_values(by=\"Date\")\n",
" _df[\"Date\"] = _df[\"Date\"].dt.round(\"1d\")\n",
" idx = pd.date_range( _df.iloc[0][\"Date\"].strftime(\"%m-%d-%Y\"), df_one_fish.iloc[-1][\"Date\"].strftime(\"%m-%d-%Y\"), freq=\"d\")\n",
" _df = pd.DataFrame(idx, columns=[\"Date\"]).set_index(\"Date\").merge(_df, how=\"outer\", on=\"Date\")\n",
"\n",
" _df = _df.set_index(\"Date\")\n",
"\n",
" _df[\"lat\"] = _df[[\"lat\"]].interpolate(method=\"time\")\n",
" _df[\"lon\"] = _df[[\"lon\"]].interpolate(method=\"time\")\n",
" _df[\" ID\"] = ID\n",
" dfs.append(_df)\n",
"\n",
"dfs = pd.concat(dfs)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"dfs = dfs.rename(columns={\" ID\": \"ID\"})\n",
"dfs = dfs.sort_index()\n",
"\n",
"dfs[\"lat\"] = dfs[[\"lat\"]].interpolate(method=\"time\")\n",
"dfs[\"lon\"] = dfs[[\"lon\"]].interpolate(method=\"time\")\n",
"dfs = dfs.loc[dfs[\"lon\"].notna()]\n",
"dfs = dfs.reset_index().rename(columns={\"index\": \"Date\"})\n"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
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"source": [
"fig = px.scatter_mapbox(\n",
" dfs.loc[dfs.Date > \"2022-11-27\"],\n",
" lat=\"lat\", lon=\"lon\",\n",
" hover_name=\"ID\",\n",
" mapbox_style=\"open-street-map\",\n",
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