import gradio as gr import plotly.graph_objects as go import os import duckdb import pandas as pd import datetime import ee # import geemap import yaml import numpy as np import json import geojson # Define constants MD_SERVICE_TOKEN = 'md_service_token.txt' # to-do: set-up with papermill parameters DATE='2020-01-01' YEAR = 2020 LOCATION=[-74.653370, 5.845328] ROI_RADIUS = 20000 GEE_SERVICE_ACCOUNT = 'climatebase-july-2023@ee-geospatialml-aquarry.iam.gserviceaccount.com' GEE_SERVICE_ACCOUNT_CREDENTIALS_FILE = 'ee_service_account.json' INDICES_FILE = 'indices.yaml' START_YEAR = 2015 END_YEAR = 2022 class IndexGenerator: """ A class to generate indices and compute zonal means. Args: centroid (tuple): The centroid coordinates (latitude, longitude) of the region of interest. year (int): The year for which indices are generated. roi_radius (int, optional): The radius (in meters) for creating a buffer around the centroid as the region of interest. Defaults to 20000. project_name (str, optional): The name of the project. Defaults to "". map (geemap.Map, optional): Map object for mapping. Defaults to None (i.e. no map created) """ def __init__(self, centroid, roi_radius, year, indices_file, project_name="", map = None, ): self.indices = self._load_indices(indices_file) self.centroid = centroid self.roi = ee.Geometry.Point(*centroid).buffer(roi_radius) self.year = year self.start_date = str(datetime.date(self.year, 1, 1)) self.end_date = str(datetime.date(self.year, 12, 31)) self.daterange=[self.start_date, self.end_date] self.project_name=project_name self.map = map if self.map is not None: self.show = True else: self.show = False def _cloudfree(self, gee_path): """ Internal method to generate a cloud-free composite. Args: gee_path (str): The path to the Google Earth Engine (GEE) image or image collection. Returns: ee.Image: The cloud-free composite clipped to the region of interest. """ # Load a raw Landsat ImageCollection for a single year. collection = ( ee.ImageCollection(gee_path) .filterDate(*self.daterange) .filterBounds(self.roi) ) # Create a cloud-free composite with custom parameters for cloud score threshold and percentile. composite_cloudfree = ee.Algorithms.Landsat.simpleComposite(**{ 'collection': collection, 'percentile': 75, 'cloudScoreRange': 5 }) return composite_cloudfree.clip(self.roi) def _load_indices(self, indices_file): # Read index configurations with open(indices_file, 'r') as stream: try: return yaml.safe_load(stream) except yaml.YAMLError as e: print(e) return None def show_map(self, map=None): if map is not None: self.map = map self.show = True def disable_map(self): self.show = False def generate_index(self, index_config): """ Generates an index based on the provided index configuration. Args: index_config (dict): Configuration for generating the index. Returns: ee.Image: The generated index clipped to the region of interest. """ match index_config["gee_type"]: case 'image': dataset = ee.Image(index_config['gee_path']).clip(self.roi) if index_config.get('select'): dataset = dataset.select(index_config['select']) case 'image_collection': dataset = ee.ImageCollection(index_config['gee_path']).filterBounds(self.roi).map(lambda image: image.clip(self.roi)).mean() if index_config.get('select'): dataset = dataset.select(index_config['select']) case 'feature_collection': dataset = ee.Image().float().paint(ee.FeatureCollection(index_config['gee_path']), index_config['select']).clip(self.roi) case 'algebraic': image = self._cloudfree(index_config['gee_path']) dataset = image.normalizedDifference(['B4', 'B3']) case _: dataset=None if not dataset: raise Exception("Failed to generate dataset.") if self.show and index_config.get('show'): map.addLayer(dataset, index_config['viz'], index_config['name']) print(f"Generated index: {index_config['name']}") return dataset def zonal_mean_index(self, index_key): index_config = self.indices[index_key] dataset = self.generate_index(index_config) # zm = self._zonal_mean(single, index_config.get('bandname') or 'constant') out = dataset.reduceRegion(**{ 'reducer': ee.Reducer.mean(), 'geometry': self.roi, 'scale': 200 # map scale }).getInfo() if index_config.get('bandname'): return out[index_config.get('bandname')] return out def generate_composite_index_df(self, indices=[]): data={ "metric": indices, "year":self.year, "centroid": str(self.centroid), "project_name": self.project_name, "value": list(map(self.zonal_mean_index, indices)), "area": self.roi.area().getInfo(), # m^2 "geojson": str(self.roi.getInfo()), } print('data', data) df = pd.DataFrame(data) return df def set_up_duckdb(service_token_file=None): print('setting up duckdb') # use `climatebase` db if service_token_file is not None: with open(service_token_file, 'r') as f: md_service_token=f.read() os.environ['motherduck_token'] = md_service_token con = duckdb.connect('md:climatebase') else: con = duckdb.connect(':climatebase:') con.sql("USE climatebase;") # load extensions con.sql("""INSTALL spatial; LOAD spatial;""") return con def authenticate_gee(gee_service_account, gee_service_account_credentials_file): print('authenticate_gee') # to-do: alert if dataset filter date nan credentials = ee.ServiceAccountCredentials(gee_service_account, gee_service_account_credentials_file) ee.Initialize(credentials) def load_indices(indices_file): # Read index configurations with open(indices_file, 'r') as stream: try: return yaml.safe_load(stream) except yaml.YAMLError as e: print(e) return None def create_dataframe(years, project_name): dfs=[] print(years) indices = load_indices(INDICES_FILE) for year in years: print(year) ig = IndexGenerator(centroid=LOCATION, roi_radius=ROI_RADIUS, year=year, indices_file=INDICES_FILE, project_name=project_name) df = ig.generate_composite_index_df(list(indices.keys())) dfs.append(df) return pd.concat(dfs) def filter_map(): prepared_statement = \ con.execute("SELECT geometry FROM project WHERE name = ? LIMIT 1", ["My project name"]).fetchall() features = \ json.loads(prepared_statement[0][0].replace("\'", "\""))['features'] geometry = features[0]['geometry'] x_centroid = np.mean(np.array(geometry["coordinates"])[0, :, 0]) y_centroid = np.mean(np.array(geometry["coordinates"])[0, :, 1]) fig = go.Figure(go.Scattermapbox( mode = "markers", lon = [x_centroid], lat = [y_centroid], marker = {'size': 20, 'color': ["cyan"]})) fig.update_layout( mapbox = { 'style': "stamen-terrain", 'center': { 'lon': x_centroid, 'lat': y_centroid}, 'zoom': 12, 'layers': [{ 'source': { 'type': "FeatureCollection", 'features': [{ 'type': "Feature", 'geometry': geometry }] }, 'type': "fill", 'below': "traces", 'color': "royalblue"}]}, margin = {'l':0, 'r':0, 'b':0, 't':0}) return fig def calculate_biodiversity_score(start_year, end_year, project_name): years = [] for year in range(start_year, end_year): row_exists = \ con.execute("SELECT COUNT(1) FROM bioindicator WHERE (year = ? AND project_name = '?')", [year, project_name]).fetchall()[0][0] if not row_exists: years.append(year) if len(years)>0: df = create_dataframe(years, project_name) # Write score table to `_temptable` con.sql('CREATE OR REPLACE TABLE _temptable AS SELECT *, (value * area) AS score FROM (SELECT year, project_name, AVG(value) AS value, area FROM df GROUP BY year, project_name, area ORDER BY project_name)') # Create `bioindicator` table IF NOT EXISTS. con.sql(""" USE climatebase; CREATE TABLE IF NOT EXISTS bioindicator (year BIGINT, project_name VARCHAR(255), value DOUBLE, area DOUBLE, score DOUBLE, CONSTRAINT unique_year_project_name UNIQUE (year, project_name)); """) scores = \ con.execute("SELECT * FROM bioindicator WHERE (year > ? AND year <= ? AND project_name = '?')", [start_year, end_year, project_name]).fetchall().df() return scores def view_all(): print('view_all') return con.sql("SELECT * FROM bioindicator").df() def push_to_md(): # UPSERT project record con.sql(""" INSERT INTO bioindicator FROM _temptable ON CONFLICT (year, project_name) DO UPDATE SET value = excluded.value; """) print('Saved records') with gr.Blocks() as demo: con = set_up_duckdb(MD_SERVICE_TOKEN) authenticate_gee(GEE_SERVICE_ACCOUNT, GEE_SERVICE_ACCOUNT_CREDENTIALS_FILE) with gr.Column(): m1 = gr.Plot() with gr.Row(): start_year = gr.Number(value=2017, label="Start Year", precision=0) end_year = gr.Number(value=2022, label="End Year", precision=0) project_name = gr.Textbox(label='Project Name') with gr.Row(): calc_btn = gr.Button(value="Calculate!") view_btn = gr.Button(value="View all") save_btn = gr.Button(value="Save") results_df = gr.Dataframe( headers=["Year", "Project Name", "Score"], datatype=["number", "str", "number"], label="Biodiversity scores by year", ) demo.load(filter_map, outputs=[m1]) calc_btn.click(calculate_biodiversity_score, inputs=[start_year, end_year, project_name], outputs=[results_df]) view_btn.click(view_all, outputs=[results_df]) save_btn.click(push_to_md) demo.launch()