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eo_utils.py
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eo_utils.py
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# Import necessary libraries
from time import time
import rasterio
import numpy as np
# import openeo
# from openeo.rest.datacube import PGNode, THIS
# from openeo.processes import *
import math
import xarray as xr
import rioxarray
from ipyleaflet import (
Map,
Marker,
TileLayer, ImageOverlay,
Polygon, Rectangle,
GeoJSON,
DrawControl,
LayersControl,
WidgetControl,
basemaps,
basemap_to_tiles,
WMSLayer,
FullScreenControl
)
import ipywidgets as widgets
from ipywidgets import Output, FloatSlider
from traitlets import link
import shapely.geometry
import os
import xarray_leaflet
from xarray_leaflet.transform import passthrough
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
from bqplot import Lines, Figure, LinearScale, DateScale, Axis, Scatter
import bqplot.pyplot as bqplt
from datetime import datetime
import json
import hvplot.xarray
import PIL
from base64 import b64encode
from io import StringIO, BytesIO
import warnings
warnings.filterwarnings("ignore")
class openeoMap:
def __init__(self,center,zoom):
self.map = Map(center=center, zoom=zoom, scroll_wheel_zoom=True, interpolation='nearest')
self.bbox = []
self.point_coords = []
self.figure = None
self.figure_widget = None
self.feature_collection = {
'type': 'FeatureCollection',
'features': []
}
draw = DrawControl(
circlemarker={}, polyline={},
marker= {"shapeOptions": {
"original": {},
"editing": {},
}},
rectangle = {"shapeOptions": {
"original": {},
"editing": {},
}},
polygon = {"shapeOptions": {
"original": {},
"editing": {},
}})
self.map.add_control(draw)
def handle_draw(target, action, geo_json):
self.feature_collection['features'].append(geo_json)
if self.feature_collection['features'][0]['geometry']['type'] == 'Point':
self.point_coords = self.feature_collection['features'][0]['geometry']['coordinates']
else:
coords = self.feature_collection['features'][0]['geometry']['coordinates'][0]
polygon = shapely.geometry.Polygon(coords)
self.bbox = polygon.bounds
layers_control = LayersControl(position='topright')
self.map.add_control(layers_control)
self.map.add_control(FullScreenControl())
self.map.add_layer(basemap_to_tiles(basemaps.Esri.WorldImagery));
draw.on_draw(handle_draw)
def getBbox(self):
if(len(self.bbox) == 0):
mapBox = self.map.bounds
return [ mapBox[0][1],mapBox[0][0],mapBox[1][1],mapBox[1][0]]
else:
return self.bbox
def addImageLayer(inMap,filename,spatial_extent,name):
im = PIL.Image.open(filename)
f = BytesIO()
im.save(f, 'png')
data = b64encode(f.getvalue())
data = data.decode('ascii')
imgurl = 'data:image/png;base64,' + data
image = ImageOverlay(
url=imgurl,
bounds=((spatial_extent['south'], spatial_extent['east']), (spatial_extent['north'], spatial_extent['west'])),
name=name
)
layers_control = LayersControl(position='topright')
inMap.map.add_layer(image)
return
def addLayer(inMap,path,name,clip=[0,0.8],bands=None):
#Check the filetype: netcdf or geotiff
if isinstance(path,str):
if path.split('.')[-1] == 'nc':
da = xr.open_dataset(path)
if 't' in da.dims:
da = da.drop('t').squeeze('t').to_array().astype(np.float32)
elif 'time' in da.dims:
da = da.drop('time').squeeze('time').to_array().astype(np.float32)
else:
da = da.to_array().astype(np.float32)
if 'variable' in da.dims and 'bands' in da.dims:
da = da.drop('variable').squeeze('variable').rename({'bands':'variable'})
else:
da = xr.open_rasterio(path)
if 't' in da.dims:
da = da.rename({'band':'variable'}).drop('t').squeeze('t').astype(np.float32)
else:
da = da.rename({'band':'variable'}).astype(np.float32)
else:
da = path
if 't' in da.dims:
da = da.max('t').to_array().astype(np.float32)
elif 'time' in da.dims:
da = da.max('time').to_array().astype(np.float32)
else:
da = da.to_array().astype(np.float32)
if 'variable' in da.dims and 'bands' in da.dims:
da = da.drop('variable').squeeze('variable').rename({'bands':'variable'})
rds4326 = da.rio.reproject("epsg:4326")
rds4326.name = name
rds4326 = rds4326.rio.write_crs(4326) # WGS 84
if bands is not None:
rds4326 = rds4326.loc[dict(variable=bands)]
opacity_slider = FloatSlider(description=name + ' opacity:', min=0, max=1, value=1)
def set_opacity(change):
l.opacity = change['new']
if(len(rds4326.variable)==3):
rds4326 = rds4326.where(rds4326>clip[0])
rds4326 = rds4326.where(rds4326<clip[1])
rds4326 = rds4326.rio.write_nodata(np.nan)
rds4326 = rds4326/clip[1]*255
rds4326 = rds4326.chunk((1000, 1000))
l = rds4326.leaflet.plot(inMap.map, rgb_dim='variable')
opacity_slider.observe(set_opacity, names='value')
slider_control = WidgetControl(widget=opacity_slider, position='bottomleft')
inMap.map.add_control(slider_control)
elif(len(rds4326.variable)==1):
rds4326 = rds4326[0]
rds4326 = rds4326.where(rds4326>clip[0])
rds4326 = rds4326.where(rds4326<clip[1])
rds4326 = rds4326.rio.write_nodata(np.nan)
rds4326 = rds4326.chunk((1000, 1000))
cmap = plt.cm.get_cmap('Greys_r')
l = rds4326.leaflet.plot(inMap.map,colormap=cmap)
def set_opacity(change):
l.opacity = change['new']
opacity_slider.observe(set_opacity, names='value')
slider_control = WidgetControl(widget=opacity_slider, position='bottomleft')
inMap.map.add_control(slider_control)
else:
rds4326 = rds4326[0]
rds4326 = rds4326.chunk((1000, 1000))
rds4326 = rds4326.where(rds4326>clip[0])
rds4326 = rds4326.where(rds4326<clip[1])
rds4326 = rds4326.rio.write_nodata(np.nan)
cmap = plt.cm.get_cmap('Greys_r')
l = rds4326.leaflet.plot(inMap.map,colormap=cmap)
def set_opacity(change):
l.opacity = change['new']
opacity_slider.observe(set_opacity, names='value')
slider_control = WidgetControl(widget=opacity_slider, position='bottomleft')
inMap.map.add_control(slider_control)
return
def addS2Tiles(inMap):
with open('./Europe.geojson') as f:
data = json.load(f)
for feature in data['features']:
feature['properties']['style'] = {
'color': 'grey',
'weight': 1,
'fillColor': None,
'fillOpacity': 0.1 }
s2_tiles_layer = GeoJSON(data=data,name='S2_tiles')
inMap.map.add_layer(s2_tiles_layer)
return
def addTimeseries(inMap,path,bands,new_plot):
px_series = xr.open_dataarray(path)
if 't' in px_series.dims:
date_start = px_series.t.min().values
date_end = px_series.t.max().values
color = ['blue','red','green','yellow']
for i,b in enumerate(bands):
x_data = px_series.t.values
y_data = px_series.to_array().loc[dict(variable=b)][:,0,0].values
x_data = x_data[~np.isnan(y_data)]
y_data = y_data[~np.isnan(y_data)]
x_data = x_data[y_data!=0]
y_data = y_data[y_data!=0]
axes_options = {'x': {'label':'Time', 'side':'bottom', 'num_ticks':8, 'tick_format':'%b %y'}, 'y': {'orientation':'vertical', 'side':'left', 'num_ticks':10}}
if i==0:
title = ''
for x in bands:
title += (x + ' ')
title += ' timeseries'
if new_plot:
inMap.figure = bqplt.figure(title=title,layout={'max_height': '250px', 'width': '600px'})
else:
if inMap.figure is not None:
pass
else:
inMap.figure = bqplt.figure(title=title,layout={'max_height': '250px', 'width': '600px'})
scatt = bqplt.scatter(x_data, y_data, labels=[b], display_legend=True, colors=[color[i]], default_size=10, axes_options=axes_options)
widget_control = WidgetControl(widget=inMap.figure, position='bottomright')
else:
date_start = px_series.time.min().values
date_end = px_series.time.max().values
color = ['blue','red','green','yellow']
for i,b in enumerate(bands):
x_data = px_series.time.values
y_data = px_series.loc[dict(variable=b)][:,0,0].values
x_data = x_data[~np.isnan(y_data)]
y_data = y_data[~np.isnan(y_data)]
x_data = x_data[y_data!=0]
y_data = y_data[y_data!=0]
axes_options = {'x': {'label':'Time', 'side':'bottom', 'num_ticks':8, 'tick_format':'%b %y'}, 'y': {'orientation':'vertical', 'side':'left', 'num_ticks':10}}
if i==0:
title = ''
for x in bands:
title += (x + ' ')
title += ' timeseries'
if new_plot:
inMap.figure = bqplt.figure(title=title,layout={'max_height': '250px', 'width': '600px'})
else:
if inMap.figure is not None:
pass
else:
inMap.figure = bqplt.figure(title=title,layout={'max_height': '250px', 'width': '600px'})
scatt = bqplt.scatter(x_data, y_data, labels=[b], display_legend=True, colors=[color[i]], default_size=10, axes_options=axes_options)
widget_control = WidgetControl(widget=inMap.figure, position='bottomright')
if inMap.figure_widget is not None:
inMap.map.remove_control(inMap.figure_widget)
inMap.figure_widget = widget_control
inMap.map.add_control(inMap.figure_widget)
return
def tone_mapping(B04,B03,B02):
red = B04.values
green = B03.values
blue = B02.values
red = (red+1)/1733*255
green = (green+1)/1630*255
blue = (blue+1)/1347*255
red = np.clip(red,0,255).astype(np.uint8)
green = np.clip(green,0,255).astype(np.uint8)
blue = np.clip(blue,0,255).astype(np.uint8)
brg = np.zeros((red.shape[0],red.shape[1],3),dtype=np.uint8)
brg[:,:,0] = red
brg[:,:,1] = green
brg[:,:,2] = blue
return brg