import streamlit as st import ibis from ibis import _ import pydeck as pdk from utilities import * import leafmap.maplibregl as leafmap import requests import geopandas as gpd st.set_page_config(page_title="Redlining & GBIF", layout="wide") st.title("Redlining & GBIF") con = ibis.duckdb.connect(extensions=['httpfs', 'spatial', 'h3']) set_secrets(con) # s3 credentials #set_aws_secrets(con) #set_source_secrets(con) distinct_taxa = "" # default col1, col2, col3, col4 = st.columns([1,3,3,3]) # placed outside the form so that toggling this immediately updates the form options available with col1: st.markdown("#### Start πŸ‘‡") area_source = st.radio("Area types", ["City", "All"]) nunique = st.toggle("unique taxa only", False) # config with different default settings by area config = { "City": { "names": con.read_parquet("s3://public-gbif/app/city_names.parquet").select("name").execute(), "index": 183, "zoom": 10, "vertical": 0.1, "rank_index": 2, "taxa": "Aves", "unique_rank_index": 6, }, "All": { "names": ["All"], "index": 0, "zoom": 9, "vertical": 1.0, "rank_index": 2, "taxa": "Aves", "unique_rank_index": 6, } } with st.form("my_form"): taxonomic_ranks = ["kingdom", "phylum", "class", "order", "family","genus", "species"] default = config[area_source] with col2: ## Add additional layer toggles here, e.g. SVI? st.markdown("#### πŸ—ΊοΈ Select map layers") gdf_name = st.selectbox("Area", default["names"], index=default["index"]) with col3: st.markdown("#### 🐦 Select taxonomic groups") ## add support for multiple taxa! rank = st.selectbox("Taxonomic Rank", options=taxonomic_ranks, index = default["rank_index"]) taxa = st.text_input("taxa", default["taxa"]) if nunique: distinct_taxa = st.selectbox("Count only unique occurrences by:", options=taxonomic_ranks, index = default["unique_rank_index"]) with col4: st.markdown(''' #### πŸ”Ž Set spatial resolution See [H3 cell size by zoom level](https://h3geo.org/docs/core-library/restable/#cell-areas) ''') zoom = st.slider("H3 zoom", min_value=1, max_value=11, value = default["zoom"]) v_scale = st.number_input("vertical scale", min_value = 0.0, value = default["vertical"]) submitted = st.form_submit_button("Go") @st.cache_data def compute_hexes(_gdf, gdf_name, rank, taxa, zoom, distinct_taxa = ""): # FIXME check if dest exists in cache dest = unique_path(gdf_name, rank, taxa, zoom, distinct_taxa) bucket = "public-gbif" url = base_url + f"/{bucket}/" + dest response = requests.head(url) if response.status_code != 404: return url sel = con.read_parquet("s3://public-gbif/app/redlined_cities_gbif.parquet") sel = (sel .rename(hex = "h" + str(zoom)) # h3 == 41,150 hexes. h5 == 2,016,830 hexes .group_by(_.hex) ) if distinct_taxa != "": # count n unique taxa sel = sel.agg(n = _[distinct_taxa].nunique()) else: # count occurrences sel = sel.agg(n = _.count()) sel = (sel .filter(_.n > 0) .mutate(logn = _.n.log()) .mutate(value = (255 * _.logn / _.logn.max()).cast("int")) # normalized color-scale ) # .to_json() doesn't exist in ibis, use SQL query = ibis.to_sql(sel) con.raw_sql(f"COPY ({query}) TO 's3://{bucket}/{dest}' (FORMAT JSON, ARRAY true);") return url import altair as alt @st.cache_data def bar_chart(gdf_name, rank, taxa, zoom, distinct_taxa = ""): sel = con.read_parquet("s3://public-gbif/app/redlined_cities_gbif.parquet") sel = sel.filter(_[rank] == taxa) if gdf_name != "All": sel = sel.filter(_.city == gdf_name) sel = sel.group_by(_.city, _.grade) if distinct_taxa: # count n unique taxa sel = sel.agg(n = _[distinct_taxa].nunique(), area = _.area.sum()) else: sel = sel.agg(n = _.count(), area = _.area.sum()) sel = (sel .mutate(density = _.n /_.area) .group_by(_.grade) .agg(mean = _.density.mean(),sd = _.density.std()) .order_by(_.mean.desc()) ) plt = alt.Chart(sel.execute()).mark_bar().encode(x = "grade", y = "mean") return st.altair_chart(plt) mappinginequality = 'https://data.source.coop/cboettig/us-boundaries/mappinginequality.pmtiles' redlines = {'version': 8, 'sources': {'source': {'type': 'vector', 'url': 'pmtiles://' + mappinginequality, 'attribution': 'PMTiles'}}, 'layers': [{'id': 'mappinginequality_fill', 'source': 'source', 'source-layer': 'mappinginequality', 'type': 'fill', 'paint': {'fill-color': ["get", "fill"], 'fill-opacity': 0.9},} ]} count = "occurrences" if nunique: count = "unique " + distinct_taxa mapcol, chartcol = st.columns([4,1]) if submitted: gdf = get_polygon(gdf_name, area_source, con) url = compute_hexes(gdf, gdf_name, rank, taxa, zoom, distinct_taxa = distinct_taxa) layer = HexagonLayer(url, v_scale) m = leafmap.Map(style=terrain_styling(), center=[-120, 37.6], zoom=2, pitch=35, bearing=10) if gdf is not None: m.add_gdf(gdf[[gdf.geometry.name]], "fill", paint = {"fill-opacity": 0.2}) # adds area of interest & zooms in m.add_pmtiles(mappinginequality, style=redlines, visible=True, opacity = 0.9, fit_bounds=False) m.add_deck_layers([layer]) m.add_layer_control() with mapcol: m.to_streamlit() with chartcol: st.markdown("Mean number of " + count + " by redline grade") bar_chart(gdf_name, rank, taxa, zoom, distinct_taxa = distinct_taxa) st.divider() ''' ## Overview Select an individual city or choose "All" to show all 319 cities in the Mapping Inequality Project. You can set arbitrary taxonomic filters on what GBIF data is displayed -- e.g. show all of Aves or just show _Canis latrans_. Toggle `unique taxa only` to show either all occurrences or just unique species (or other rank) counts. The map will show all counts at the selected 'H3 cell' resolution, while the chart on the left shows aggregate counts by redlining grade. Note that only GBIF data inside graded sectors of the Mapping Inequality maps are shown, occurrences outside these areas have been cropped. You may need to adjust the vertical scale of map hexes. After making your selections, hit **Go**! Map layers may take a while to load on slower networks. ## Credits App developed by Carl Boettiger & Diego Soto, UC Berkeley (2024). ### Data Sources - Global Biodiversity Information Facility (GBIF) Species Occurrences snapshot on 2024-10-01. Copyright: Public Domain. Visualization based on pre-computed H3 cell values for all of GBIF, hosted on Source.Coop, as GeoParquet and PMTiles. - Historical Redlining Data from the Mapping Inequality Project, . ### Software - All open-source software implementation, hosted on HuggingFace Spaces. - Built with `duckdb`, `maplibre`, `leafmap`, and `streamlit`. - Source code at '''