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first commit
This commit is contained in:
nghiadang
@@ -0,0 +1,505 @@
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"""
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Digital Earth Africa Coastline widget, which can be used to
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interactively extract shoreline data using transects.
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"""
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# Import required packages
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# Force GeoPandas to use Shapely instead of PyGEOS
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# In a future release, GeoPandas will switch to using Shapely by default.
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import os
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os.environ['USE_PYGEOS'] = '0'
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import fiona
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import sys
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import datacube
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import warnings
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import matplotlib.pyplot as plt
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from datacube.utils.geometry import CRS
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from ipyleaflet import (
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WMSLayer,
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basemaps,
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basemap_to_tiles,
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Map,
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DrawControl,
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WidgetControl,
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LayerGroup,
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LayersControl,
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GeoData,
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)
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from traitlets import Unicode
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from ipywidgets import (
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GridspecLayout,
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Button,
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Layout,
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HBox,
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VBox,
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HTML,
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Output,
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)
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import json
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import geopandas as gpd
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from io import BytesIO
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import ipywidgets as widgets
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import deafrica_tools.app.widgetconstructors as deawidgets
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from deafrica_tools.coastal import get_coastlines, transect_distances
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from owslib.wms import WebMapService
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def make_box_layout():
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return Layout(
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# border='solid 1px black',
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margin='0px 10px 10px 0px',
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padding='5px 5px 5px 5px',
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width='100%',
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height='100%',
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)
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def create_expanded_button(description, button_style):
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return Button(
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description=description,
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button_style=button_style,
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layout=Layout(width="auto", height="auto"),
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)
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class transect_app(HBox):
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def __init__(self):
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super().__init__()
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######################
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# INITIAL ATTRIBUTES #
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######################
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self.output_name = "example_output"
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self.export_csv = False
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self.export_plot = False
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self.product_list = [
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("ESRI World Imagery", "none"),
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("Open Street Map", "open_street_map"),
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]
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self.product = self.product_list[0][1]
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self.mode_list = [('Distance', 'distance'), ('Width', 'width')]
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self.mode = self.mode_list[0][1]
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self.target = None
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self.action = None
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self.gdf_drawn = None
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self.gdf_uploaded = None
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##################
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# HEADER FOR APP #
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##################
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# Create the Header widget
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header_title_text = "<h3>Digital Earth Africa Coastlines shoreline transect extraction</h3>"
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instruction_text = "Select parameters and draw a transect on the map to extract shoreline data. <b>In distance mode</b>, draw a transect line starting from land that crosses multiple shorelines. <br><b>In width mode</b>, draw a transect line that intersects shorelines at least twice. Alternatively, <b>upload an vector file</b> to extract shoreline data for multiple existing transects."
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self.header = deawidgets.create_html(
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f"{header_title_text}<p>{instruction_text}</p>")
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self.header.layout = make_box_layout()
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#####################################
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# HANDLER FUNCTION FOR DRAW CONTROL #
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#####################################
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# Define the action to take once something is drawn on the map
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def update_geojson(target, action, geo_json):
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# Remove previously uploaded data if present
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self.gdf_uploaded = None
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fileupload_transects._counter = 0
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# Get data from action
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self.action = action
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# Convert data to geopandas
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json_data = json.dumps(geo_json)
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binary_data = json_data.encode()
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io = BytesIO(binary_data)
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io.seek(0)
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gdf = gpd.read_file(io)
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gdf.crs = "EPSG:4326"
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# Convert to WGS 84 / NSIDC EASE-Grid 2.0 Global and compute area
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gdf_drawn_nsidc = gdf.copy().to_crs("EPSG:6933")
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m2_per_km2 = 10**6
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area = gdf_drawn_nsidc.envelope.area.values[0] / m2_per_km2
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polyarea_label = 'Total area of DE Africa Coastlines data to extract'
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polyarea_text = f"<b>{polyarea_label}</b>: {area:.2f} km<sup>2</sup>"
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# Test area size
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if area <= 50000:
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confirmation_text = '<span style="color: #33cc33"> <b>(Area to extract falls within recommended limit; click "Extract shoreline data" to continue)</b></span>'
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self.header.value = header_title_text + polyarea_text + confirmation_text
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self.gdf_drawn = gdf
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else:
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warning_text = '<span style="color: #ff5050"> <b>(Area to extract is too large, please select a smaller transect)</b></span>'
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self.header.value = header_title_text + polyarea_text + warning_text
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self.gdf_drawn = None
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###########################
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# WIDGETS FOR APP OUTPUTS #
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###########################
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self.status_info = Output(layout=make_box_layout())
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self.output_plot = Output(layout=make_box_layout())
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#########################################
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# MAP WIDGET, DRAWING TOOLS, WMS LAYERS #
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#########################################
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# Create drawing tools
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desired_drawtools = ['polyline']
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draw_control = deawidgets.create_drawcontrol(desired_drawtools)
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# Load DEACoastLines WMS
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deacl_url = "https://geoserver.digitalearth.africa/geoserver/wms"
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deacl_layer = "coastlines:DEAfrica_Coastlines"
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deacoastlines = WMSLayer(
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url=deacl_url,
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layers=deacl_layer,
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format='image/png',
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transparent=True,
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attribution='DE Africa Coastlines © 2022 Digital Earth Africa')
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# Begin by displaying an empty layer group, and update the group with desired WMS on interaction.
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self.map_layers = LayerGroup(layers=(deacoastlines,))
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self.map_layers.name = 'Map Overlays'
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# Create map widget
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self.m = deawidgets.create_map(map_center=(0.5273, 25.1367),
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zoom_level=3,
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basemap=basemaps.Esri.WorldImagery)
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self.m.layout = make_box_layout()
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# Add tools to map widget
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self.m.add_control(draw_control)
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self.m.add_layer(self.map_layers)
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# Store current basemap for future use
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self.basemap = self.m.basemap
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############################
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# WIDGETS FOR APP CONTROLS #
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############################
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# Create parameter widgets
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text_output_name = deawidgets.create_inputtext(self.output_name,
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self.output_name)
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checkbox_csv = deawidgets.create_checkbox(self.export_csv,
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'Distance table (.csv)')
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checkbox_plot = deawidgets.create_checkbox(self.export_plot,
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'Figure (.png)')
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deaoverlay_dropdown = deawidgets.create_dropdown(
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self.product_list, self.product_list[0][1])
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mode_dropdown = deawidgets.create_dropdown(self.mode_list,
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self.mode_list[0][1])
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run_button = create_expanded_button("Extract shoreline data", "info")
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fileupload_transects = widgets.FileUpload(accept='', multiple=True)
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####################################
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# UPDATE FUNCTIONS FOR EACH WIDGET #
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####################################
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# Run update functions whenever various widgets are changed.
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text_output_name.observe(self.update_text_output_name, "value")
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checkbox_csv.observe(self.update_checkbox_csv, "value")
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checkbox_plot.observe(self.update_checkbox_plot, "value")
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deaoverlay_dropdown.observe(self.update_deaoverlay, "value")
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mode_dropdown.observe(self.update_mode, "value")
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run_button.on_click(self.run_app)
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draw_control.on_draw(update_geojson)
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fileupload_transects.observe(self.update_fileupload_transects, "value")
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##################################
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# COLLECTION OF ALL APP CONTROLS #
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##################################
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parameter_selection = VBox([
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HTML("<b>Output name:</b>"), text_output_name,
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HTML(
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'<b>Transect extraction mode:</b><br><img src="https://i.imgur.com/9fdTH9C.png">'
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),
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mode_dropdown,
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HTML("<b></br>Output files:</b>"),
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checkbox_plot,
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checkbox_csv,
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HTML(
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"</br><i><b>Advanced</b></br>Upload a GeoJSON or ESRI "
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"Shapefile (<5 mb) containing one or more transect lines.</i>"),
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fileupload_transects
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])
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map_selection = VBox([
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HTML("</br><b>Map overlay:</b>"),
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deaoverlay_dropdown,
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])
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parameter_selection.layout = make_box_layout()
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map_selection.layout = make_box_layout()
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###############################
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# SPECIFICATION OF APP LAYOUT #
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###############################
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# 0 1 2 3 4 5 6 7 8 9
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# ---------------------------------------------
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# 0 | Header | Map sel. |
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# ---------------------------------------------
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# 1 | Params | |
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# 2 | | |
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# 3 | | |
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# 4 | | Map |
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# 5 | | |
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# ---------- |
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# 6 | Run | |
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# ---------------------------------------------
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# 7 | Status info |
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# ---------------------------------------------
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# 8 | |
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# 9 | Output/figure |
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# 10 | |
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# 11 | ------------------------------------------|
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# Create the layout #[rowspan, colspan]
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grid = GridspecLayout(12, 10, height="1350px", width="auto")
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# Header and controls
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grid[0, :8] = self.header
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grid[0, 8:] = map_selection
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grid[1:6, 0:2] = parameter_selection
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grid[6, 0:2] = run_button
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# Status info, map and plot
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grid[1:7, 2:] = self.m # map
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grid[7:8, :] = self.status_info
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grid[8:, :] = self.output_plot
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# Display using HBox children attribute
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self.children = [grid]
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######################################
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# DEFINITION OF ALL UPDATE FUNCTIONS #
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######################################
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# Set the output csv
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def update_fileupload_transects(self, change):
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# Clear any drawn data if present
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self.gdf_drawn = None
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# Save to file
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for uploaded_filename in change.new.keys():
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with open(uploaded_filename, "wb") as output_file:
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content = change.new[uploaded_filename]['content']
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output_file.write(content)
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with self.status_info:
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try:
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print('Loading vector data...', end='\r')
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valid_files = [
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file for file in change.new.keys()
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if file.lower().endswith(('.shp', '.geojson'))
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]
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valid_file = valid_files[0]
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transect_gdf = (gpd.read_file(valid_file).to_crs(
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"EPSG:4326").explode().reset_index(drop=True))
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# Use ID column if it exists
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if 'id' in transect_gdf:
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transect_gdf = transect_gdf.set_index('id')
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print(f"Uploaded '{valid_file}'; automatically labelling "
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"transects using column 'id'.")
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else:
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print(
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f"Uploaded '{valid_file}'; no 'id' column detected, "
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f"labelling transects from 0 to {len(transect_gdf.index) - 1}."
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)
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# Create a geodata
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geodata = GeoData(geo_dataframe=transect_gdf,
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style={
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'color': 'black',
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'weight': 3
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})
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# Add to map
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xmin, ymin, xmax, ymax = transect_gdf.total_bounds
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self.m.fit_bounds([[ymin, xmin], [ymax, xmax]])
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self.m.add_layer(geodata)
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# If completed, add to attribute
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self.gdf_uploaded = transect_gdf
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except IndexError:
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print(
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"Cannot read uploaded files. Please ensure that data is "
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"in either GeoJSON or ESRI Shapefile format.",
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end='\r')
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self.gdf_uploaded = None
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except fiona.errors.DriverError:
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print(
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"Shapefile is invalid. Please ensure that all shapefile "
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"components (e.g. .shp, .shx, .dbf, .prj) are uploaded.",
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end='\r')
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self.gdf_uploaded = None
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# Set output name
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def update_text_output_name(self, change):
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self.output_name = change.new
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# Output CSV
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def update_checkbox_csv(self, change):
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self.export_csv = change.new
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# Output plot
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def update_checkbox_plot(self, change):
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self.export_plot = change.new
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# Set mode
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def update_mode(self, change):
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self.mode = change.new
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# Update product
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def update_deaoverlay(self, change):
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self.product = change.new
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# Load DE Africa CoastLines WMS
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deacl_url = "https://geoserver.digitalearth.africa/geoserver/wms"
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deacl_layer = "coastlines:DEAfrica_Coastlines"
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deacoastlines = WMSLayer(
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url=deacl_url,
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layers=deacl_layer,
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format="image/png",
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transparent=True,
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attribution="DE Africa Coastlines © 2022 Digital Earth Africa")
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if self.product == "none":
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self.map_layers.clear_layers()
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self.map_layers.add_layer(deacoastlines)
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elif self.product == "open_street_map":
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self.map_layers.clear_layers()
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layer = basemap_to_tiles(basemaps.OpenStreetMap.Mapnik)
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self.map_layers.add_layer(layer)
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self.map_layers.add_layer(deacoastlines)
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def run_app(self, change):
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# Clear progress bar and output areas before running
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self.status_info.clear_output()
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self.output_plot.clear_output()
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# Run DE Africa Coastlines analysis
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with self.status_info:
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warnings.filterwarnings("ignore")
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# Load transects from either map or uploaded files
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if self.gdf_uploaded is not None:
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transect_gdf = self.gdf_uploaded
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run_text = 'uploaded file'
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elif self.gdf_drawn is not None:
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transect_gdf = self.gdf_drawn
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transect_gdf.index = [self.output_name]
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run_text = 'selected transect'
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else:
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print(f'No transect drawn or uploaded. Please select a transect on the map, or upload a GeoJSON or ESRI Shapefile.',
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end='\r')
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transect_gdf = None
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# If valid data was returned, load DEA Coastlines data
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if transect_gdf is not None:
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# Load Coastlines data from WFS
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deacl_gdf = get_coastlines(bbox=transect_gdf)
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# Test that data was correctly returned
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if len(deacl_gdf.index) > 0:
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# Dissolve by year to remove duplicates, then sort by date
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deacl_gdf = deacl_gdf.dissolve(by='year', as_index=False)
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deacl_gdf['year'] = deacl_gdf.year.astype(int)
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deacl_gdf = deacl_gdf.sort_values('year')
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deacl_gdf = deacl_gdf.set_index('year')
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else:
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print(
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"No annual shoreline data was found near the "
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"supplied transect. Please draw or select a new "
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"transect.",
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end='\r')
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deacl_gdf = None
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# If valid DEA Coastlines data returned, calculate distances
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if deacl_gdf is not None:
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print(f'Analysing transect distances using "{self.mode}" mode...',
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end='\r')
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dist_df = transect_distances(
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transect_gdf.to_crs("EPSG:6933"),
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deacl_gdf.to_crs("EPSG:6933"),
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mode=self.mode)
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# If valid data was produced:
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if dist_df.any(axis=None):
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# Successful output
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print(f'DE Africa Coastlines data successfully extracted for {run_text}.')
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# Export distance data
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if self.export_csv:
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# Create folder if required and set path
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out_dir = 'deacoastlines_outputs'
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os.makedirs(out_dir, exist_ok=True)
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csv_filename = f"{out_dir}/{self.output_name}.csv"
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# Export to file
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dist_df.to_csv(csv_filename, index_label="Transect")
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print(f'Distance data exported to "{csv_filename}".')
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# Generate plot
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with self.output_plot:
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fig, ax = plt.subplots(constrained_layout=True,
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figsize=(15, 5.5))
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dist_df.T.plot(ax=ax, linewidth=3)
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ax.legend(frameon=False, ncol=3, title='Transect')
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ax.set_title(f"Digital Earth Africa Coastlines transect extraction - {self.output_name}")
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ax.set_ylabel(f"Along-transect {self.mode} (m)")
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ax.set_xlim(dist_df.T.index[0], dist_df.T.index[-1])
|
||||
|
||||
# Hide the right and top spines
|
||||
ax.spines['right'].set_visible(False)
|
||||
ax.spines['top'].set_visible(False)
|
||||
|
||||
# Only show ticks on the left and bottom spines
|
||||
ax.yaxis.set_ticks_position('left')
|
||||
ax.xaxis.set_ticks_position('bottom')
|
||||
plt.show()
|
||||
|
||||
# Export plot
|
||||
with self.status_info:
|
||||
if self.export_plot:
|
||||
|
||||
# Create folder if required and set path
|
||||
out_dir = 'deacoastlines_outputs'
|
||||
os.makedirs(out_dir, exist_ok=True)
|
||||
figure_filename = f"{out_dir}/{self.output_name}.png"
|
||||
|
||||
# Export to file
|
||||
fig.savefig(figure_filename)
|
||||
print(f'Figure exported to "{figure_filename}".')
|
||||
|
||||
else:
|
||||
print(
|
||||
"No valid shoreline data intersects with the "
|
||||
"supplied transect. This can occur if:\n\n"
|
||||
" - the transect does not intersect with any shorelines\n"
|
||||
" - the transect intersects with shorelines more than once in 'distance' mode\n"
|
||||
" - the transect intersects with shorelines only once in 'width' mode\n\n"
|
||||
"Please draw or upload a new transect.",
|
||||
end='\r')
|
||||
Reference in New Issue
Block a user