mirror of
https://github.com/JHUAPL/SIMoN.git
synced 2026-01-08 22:37:56 -05:00
update notebook
Former-commit-id: e3e56624943670abf758a0d86414e7251610ed9c
This commit is contained in:
Michael T. Kelbaugh
223
viz/Plot.ipynb
223
viz/Plot.ipynb
@@ -13,11 +13,11 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"json_file = \"path/to/mongo_doc.json\" # path to the Mongo document to plot\n",
|
||||
"shapefile_dir = \"path/to/shapefiles/\" # path to the directory of shapefiles\n",
|
||||
"json_file = \"demo/gfdl_cm3.json\" # path to the Mongo document to plot\n",
|
||||
"shapefile_dir = \"../graphs/shapefiles/\" # path to the directory of shapefiles\n",
|
||||
"plot_width = 1200 # pixel width of the plot\n",
|
||||
"plot_height = 800 # pixel height of the plot\n",
|
||||
"projection = 4326 # coordinate reference system to use for plotting"
|
||||
"projection = 4326 # coordinate reference system to use for plotting (also try 3085)"
|
||||
]
|
||||
},
|
||||
{
|
||||
@@ -33,18 +33,65 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import os\n",
|
||||
"import numpy as np\n",
|
||||
"from shapely.geometry.polygon import Polygon\n",
|
||||
"from shapely.geometry.multipolygon import MultiPolygon\n",
|
||||
"from geopandas import read_file\n",
|
||||
"import pandas as pd\n",
|
||||
"import json\n",
|
||||
"\n",
|
||||
"from bokeh.io import show\n",
|
||||
"from bokeh.models import LogColorMapper\n",
|
||||
"from bokeh.palettes import Blues256 as palette\n",
|
||||
"palette.reverse()\n",
|
||||
"from bokeh.plotting import figure, output_file, save"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# color palettes\n",
|
||||
"\n",
|
||||
"from bokeh.palettes import Purples256\n",
|
||||
"from bokeh.palettes import Blues256\n",
|
||||
"from bokeh.palettes import Greens256\n",
|
||||
"from bokeh.palettes import Oranges256\n",
|
||||
"from bokeh.palettes import Reds256\n",
|
||||
"from bokeh.palettes import Greys256\n",
|
||||
"from bokeh.palettes import Blues256\n",
|
||||
"from bokeh.palettes import Inferno256\n",
|
||||
"from bokeh.palettes import Magma256\n",
|
||||
"from bokeh.palettes import Plasma256\n",
|
||||
"from bokeh.palettes import Viridis256\n",
|
||||
"from bokeh.palettes import Cividis256\n",
|
||||
"from bokeh.palettes import Turbo256\n",
|
||||
"\n",
|
||||
"from bokeh.palettes import PuOr11\n",
|
||||
"from bokeh.palettes import BrBG11\n",
|
||||
"from bokeh.palettes import PRGn11\n",
|
||||
"from bokeh.palettes import PiYG11\n",
|
||||
"from bokeh.palettes import RdBu11\n",
|
||||
"from bokeh.palettes import RdGy11\n",
|
||||
"from bokeh.palettes import RdYlBu11\n",
|
||||
"from bokeh.palettes import Spectral11\n",
|
||||
"from bokeh.palettes import RdYlGn11\n",
|
||||
"\n",
|
||||
"from bokeh.palettes import YlGn9\n",
|
||||
"from bokeh.palettes import YlGnBu9\n",
|
||||
"from bokeh.palettes import GnBu9\n",
|
||||
"from bokeh.palettes import BuGn9\n",
|
||||
"from bokeh.palettes import PuBuGn9\n",
|
||||
"from bokeh.palettes import PuBu9\n",
|
||||
"from bokeh.palettes import BuPu9\n",
|
||||
"from bokeh.palettes import RdPu9\n",
|
||||
"from bokeh.palettes import PuRd9\n",
|
||||
"from bokeh.palettes import OrRd9\n",
|
||||
"from bokeh.palettes import YlOrRd9\n",
|
||||
"from bokeh.palettes import YlOrBr9"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
@@ -63,62 +110,55 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"def getXYCoords(geometry, coord_type):\n",
|
||||
" # Returns either x or y coordinates from geometry coordinate sequence. Used with LineString and Polygon geometries.\"\"\"\n",
|
||||
"def get_xy_coords(geometry, coord_type):\n",
|
||||
" \"\"\"\n",
|
||||
" Returns either x or y coordinates from geometry coordinate sequence. Used with Polygon geometries.\n",
|
||||
" \"\"\"\n",
|
||||
" if coord_type == 'x':\n",
|
||||
" return list(geometry.coords.xy[0])\n",
|
||||
" elif coord_type == 'y':\n",
|
||||
" return list(geometry.coords.xy[1])\n",
|
||||
"\n",
|
||||
"def getPolyCoords(geometry, coord_type):\n",
|
||||
" # Returns Coordinates of Polygon using the Exterior of the Polygon.\"\"\"\n",
|
||||
" ext = geometry.exterior\n",
|
||||
" return getXYCoords(ext, coord_type)\n",
|
||||
"\n",
|
||||
"def multiGeomHandler(multi_geometry, coord_type, geom_type):\n",
|
||||
"def get_poly_coords(geometry, coord_type):\n",
|
||||
" \"\"\"\n",
|
||||
" Function for handling multi-geometries. Can be MultiPoint, MultiLineString or MultiPolygon.\n",
|
||||
" Returns Coordinates of Polygon using the Exterior of the Polygon\n",
|
||||
" \"\"\"\n",
|
||||
" return get_xy_coords(geometry.exterior, coord_type)\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"def multi_geom_handler(multi_geometry, coord_type):\n",
|
||||
" \"\"\"\n",
|
||||
" Function for handling MultiPolygon geometries.\n",
|
||||
" Returns a list of coordinates where all parts of Multi-geometries are merged into a single list.\n",
|
||||
" Individual geometries are separated with np.nan which is how Bokeh wants them.\n",
|
||||
" # Bokeh documentation regarding the Multi-geometry issues can be found here (it is an open issue)\n",
|
||||
" # https://github.com/bokeh/bokeh/issues/2321\n",
|
||||
" Bokeh documentation regarding the Multi-geometry issues can be found here (it is an open issue).\n",
|
||||
" https://github.com/bokeh/bokeh/issues/2321\n",
|
||||
" \"\"\"\n",
|
||||
"\n",
|
||||
" for i, part in enumerate(multi_geometry):\n",
|
||||
" # On the first part of the Multi-geometry initialize the coord_array (np.array)\n",
|
||||
" if i == 0:\n",
|
||||
" if geom_type == \"MultiPoint\":\n",
|
||||
" coord_arrays = np.append(getPointCoords(part, coord_type), np.nan)\n",
|
||||
" elif geom_type == \"MultiLineString\":\n",
|
||||
" coord_arrays = np.append(getLineCoords(part, coord_type), np.nan)\n",
|
||||
" elif geom_type == \"MultiPolygon\":\n",
|
||||
" coord_arrays = np.append(getPolyCoords(part, coord_type), np.nan)\n",
|
||||
" else:\n",
|
||||
" if geom_type == \"MultiPoint\":\n",
|
||||
" coord_arrays = np.concatenate([coord_arrays, np.append(getPointCoords(part, coord_type), np.nan)])\n",
|
||||
" elif geom_type == \"MultiLineString\":\n",
|
||||
" coord_arrays = np.concatenate([coord_arrays, np.append(getLineCoords(part, coord_type), np.nan)])\n",
|
||||
" elif geom_type == \"MultiPolygon\":\n",
|
||||
" coord_arrays = np.concatenate([coord_arrays, np.append(getPolyCoords(part, coord_type), np.nan)])\n",
|
||||
"\n",
|
||||
" # Return the coordinates\n",
|
||||
" all_poly_coords = [np.append(get_poly_coords(part, coord_type), np.nan) for part in multi_geometry]\n",
|
||||
" coord_arrays = np.concatenate(all_poly_coords)\n",
|
||||
" return coord_arrays\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"def get_coords(row, coord_type):\n",
|
||||
" \"\"\"Returns the coordinates ('x' or 'y') of edges of a Polygon exterior\"\"\"\n",
|
||||
" try:\n",
|
||||
" # plot a single polygon\n",
|
||||
" return getPolyCoords(row['geometry'], coord_type)\n",
|
||||
" except Exception as e:\n",
|
||||
" # plot multiple polygons\n",
|
||||
" return multiGeomHandler(row['geometry'], coord_type, 'MultiPolygon')"
|
||||
" \"\"\"\n",
|
||||
" Returns the coordinates ('x' or 'y') of edges of a Polygon exterior\n",
|
||||
" \"\"\"\n",
|
||||
" poly_type = type(row['geometry'])\n",
|
||||
"\n",
|
||||
" # get coords from a single polygon\n",
|
||||
" if poly_type == Polygon:\n",
|
||||
" return get_poly_coords(row['geometry'], coord_type)\n",
|
||||
" # get coords from multiple polygons\n",
|
||||
" elif poly_type == MultiPolygon:\n",
|
||||
" return multi_geom_handler(row['geometry'], coord_type)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## plot data on the shapefile\n",
|
||||
"## merge data with the shapefile\n",
|
||||
"### references:\n",
|
||||
"\n",
|
||||
"https://docs.bokeh.org/en/latest/docs/gallery/texas.html"
|
||||
@@ -130,54 +170,94 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"def plot_mongo_doc(data, projection=4326, save_fig=True, show_fig=True):\n",
|
||||
" \n",
|
||||
"def plot_mongo_doc(data, shapefile_dir=\".\", palette=Blues256.reverse(), projection=4326, plot_width=1200, plot_height=800, show_fig=False, save_fig=True):\n",
|
||||
"\n",
|
||||
" df = {}\n",
|
||||
" geographies = {}\n",
|
||||
" datasets = data['payload'].keys()\n",
|
||||
" \n",
|
||||
"\n",
|
||||
" for dataset in datasets:\n",
|
||||
"\n",
|
||||
" # get data\n",
|
||||
" \n",
|
||||
" granularity = data['payload'][dataset]['granularity']\n",
|
||||
" print(f\"dataset: {dataset}, granularity: {granularity}\")\n",
|
||||
" if not granularity:\n",
|
||||
" print(f\"skipping {dataset} (does not have a granularity specified)\")\n",
|
||||
" continue\n",
|
||||
" else:\n",
|
||||
" print(f\"plotting {dataset} (granularity: {granularity})\")\n",
|
||||
" instance_col_name = 'ID'\n",
|
||||
" year = data['year']\n",
|
||||
"\n",
|
||||
" df[dataset] = pd.DataFrame.from_dict(data['payload'][dataset]['data'], orient='index', columns=[f\"{dataset}_value\"])\n",
|
||||
" df[dataset] = pd.DataFrame.from_dict(\n",
|
||||
" data['payload'][dataset]['data'],\n",
|
||||
" orient='index',\n",
|
||||
" columns=[f\"{dataset}_value\"],\n",
|
||||
" )\n",
|
||||
" df[dataset][instance_col_name] = df[dataset].index\n",
|
||||
"\n",
|
||||
" geographies[dataset] = read_file(f\"{shapefile_dir}/{granularity}.shp\").to_crs(epsg=projection)\n",
|
||||
" geographies[dataset] = geographies[dataset].merge(df[dataset], on=instance_col_name)\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" # merge data with the shapefile\n",
|
||||
" \n",
|
||||
" shapefile_path = f\"{shapefile_dir}/{granularity}.shp\"\n",
|
||||
" if os.path.exists(shapefile_path):\n",
|
||||
" geographies[dataset] = read_file(shapefile_path).to_crs(epsg=projection)\n",
|
||||
" else:\n",
|
||||
" print(f\"{shapefile_path} not found, skipping\")\n",
|
||||
" continue\n",
|
||||
" geographies[dataset] = geographies[dataset].merge(\n",
|
||||
" df[dataset], on=instance_col_name\n",
|
||||
" )\n",
|
||||
" geographies[dataset]['x'] = geographies[dataset].apply(\n",
|
||||
" get_coords, coord_type='x', axis=1\n",
|
||||
" )\n",
|
||||
" geographies[dataset]['y'] = geographies[dataset].apply(\n",
|
||||
" get_coords, coord_type='y', axis=1\n",
|
||||
" )\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" # create figure\n",
|
||||
"\n",
|
||||
" # reset the color palette\n",
|
||||
" color_mapper = LogColorMapper(palette=palette)\n",
|
||||
"\n",
|
||||
" geographies[dataset]['x'] = geographies[dataset].apply(get_coords, coord_type='x', axis=1)\n",
|
||||
" geographies[dataset]['y'] = geographies[dataset].apply(get_coords, coord_type='y', axis=1)\n",
|
||||
"\n",
|
||||
" plot_data=dict(\n",
|
||||
" plot_data = dict(\n",
|
||||
" x=geographies[dataset]['x'].tolist(),\n",
|
||||
" y=geographies[dataset]['y'].tolist(),\n",
|
||||
" name=geographies[dataset]['ID'].tolist(),\n",
|
||||
" value=geographies[dataset][f\"{dataset}_value\"].tolist()\n",
|
||||
" value=geographies[dataset][f\"{dataset}_value\"].tolist(),\n",
|
||||
" )\n",
|
||||
"\n",
|
||||
" TOOLS = \"pan,wheel_zoom,reset,hover,save,box_zoom\"\n",
|
||||
"\n",
|
||||
" coords_tuple = (\"(Lat, Lon)\", \"($y, $x)\") if projection == 4326 else (\"(x, y)\", \"($x, $y)\")\n",
|
||||
" \n",
|
||||
" coords_tuple = (\n",
|
||||
" (\"(Lat, Lon)\", \"($y, $x)\")\n",
|
||||
" if projection == 4326\n",
|
||||
" else (\"(x, y)\", \"($x, $y)\")\n",
|
||||
" )\n",
|
||||
" \n",
|
||||
" fig = figure(\n",
|
||||
" title=f\"USA {dataset} ({year})\", tools=TOOLS,\n",
|
||||
" plot_width=plot_width, plot_height=plot_height,\n",
|
||||
" x_axis_location=None, y_axis_location=None,\n",
|
||||
" tooltips=[\n",
|
||||
" (\"Name\", \"@name\"), (\"Value\", \"@value\"), coords_tuple\n",
|
||||
" ])\n",
|
||||
" title=f\"USA {dataset} ({year})\",\n",
|
||||
" tools=TOOLS,\n",
|
||||
" plot_width=plot_width,\n",
|
||||
" plot_height=plot_height,\n",
|
||||
" x_axis_location=None,\n",
|
||||
" y_axis_location=None,\n",
|
||||
" tooltips=[(\"Name\", \"@name\"), (\"Value\", \"@value\"), coords_tuple],\n",
|
||||
" )\n",
|
||||
" fig.grid.grid_line_color = None\n",
|
||||
" fig.hover.point_policy = \"follow_mouse\"\n",
|
||||
"\n",
|
||||
" fig.patches('x', 'y', source=plot_data,\n",
|
||||
" fill_color={'field': 'value', 'transform': color_mapper},\n",
|
||||
" fill_alpha=0.7, line_color=\"white\", line_width=0.5)\n",
|
||||
" # reset the color palette\n",
|
||||
" color_mapper = LogColorMapper(palette=palette)\n",
|
||||
" \n",
|
||||
" fig.patches(\n",
|
||||
" 'x',\n",
|
||||
" 'y',\n",
|
||||
" source=plot_data,\n",
|
||||
" fill_color={'field': 'value', 'transform': color_mapper},\n",
|
||||
" fill_alpha=0.7,\n",
|
||||
" line_color=\"white\",\n",
|
||||
" line_width=0.5,\n",
|
||||
" )\n",
|
||||
"\n",
|
||||
" if save_fig:\n",
|
||||
" output_file(f\"{year}_{dataset}.html\")\n",
|
||||
@@ -202,7 +282,10 @@
|
||||
"with open(json_file) as f:\n",
|
||||
" data = json.load(f)\n",
|
||||
"\n",
|
||||
"plot_mongo_doc(data, projection=projection, show_fig=False)"
|
||||
"palette = PuBu9\n",
|
||||
"palette.reverse()\n",
|
||||
" \n",
|
||||
"plot_mongo_doc(data, palette=palette, shapefile_dir=shapefile_dir, projection=projection, show_fig=True)"
|
||||
]
|
||||
}
|
||||
],
|
||||
@@ -222,7 +305,7 @@
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.6.7"
|
||||
"version": "3.6.9"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
|
||||
Reference in New Issue
Block a user