app.py

# -*- coding: utf-8 -*-
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#    http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.



"""An example of showing species richness from GBIF data."""
import pydeck as pdk
import streamlit as st
import ibis
from ibis import _

# SETTING PAGE CONFIG TO WIDE MODE AND ADDING A TITLE AND FAVICON
st.set_page_config(layout="wide", page_title="GBIF Biodiversity Demo", page_icon=":globe:")


# +

@st.cache_data
def load_data(zoom=7):
    con = ibis.duckdb.connect()
    path = "gbif-vert-gb-h3z" + str(zoom) + ".csv"
    df_all = (
        con.
        read_csv(path).
        group_by(_.h3).
        aggregate(n = _.n.sum()).
        mutate(color = 255 * _.n / _.n.max()).
        to_pandas()
        )
    return df_all

@st.cache_data
def load_class(taxa, zoom=7):
    con = ibis.duckdb.connect()
    path = "gbif-vert-gb-h3z" + str(zoom) + ".csv"
    df = (con.
      read_csv(path).
      filter(_['class']==taxa).
      mutate(color = 255 * _.n / _.n.max()).
      to_pandas()
     )
    return df



# -

def map(data, lat, lon, zoom):
    st.write(
        pdk.Deck(
            map_style="mapbox://styles/mapbox/light-v9",
            initial_view_state={
                "latitude": lat,
                "longitude": lon,
                "zoom": zoom,
                "pitch": 50,
            },
            layers=[
                pdk.Layer(
                    "H3HexagonLayer",
                    data,
                    pickable=True,
                    stroked=True,
                    filled=True,
                    extruded=True,
                    elevation_scale=200,
                    get_elevation='color',
                    get_hexagon="h3", # set by zoom
                    get_fill_color="[color, 30, 255 - color, 160]",
                    get_line_color=[255, 255, 255],
                    line_width_min_pixels=2,
                ),
            ],
        )
    )


# LAYING OUT THE TOP SECTION OF THE APP
row1_1, row1_2 = st.columns((2, 3))

## Interactive elements, see https://docs.streamlit.io/library/api-reference/widgets
with row1_1:
    st.title("GBIF Species Richness")
    taxa = st.text_input('taxonomic class (Chordates only)', value = "Amphibia")

    zoom = st.slider("Select hex resolution", 4, 7, key="zoom", value = 5)


with row1_2:
    st.write(
    """
    ## GBIF Streamlit demo

    This shows a simple interactive demonstration using a series of [pydeck maps](https://deckgl.readthedocs.io/) overlaid with
    [h3 hexagons](https://h3geo.org/) whose height and color indicate species richness of the group.  

    Adjust the [h3 hexagon size](https://h3geo.org/docs/core-library/restable/) to increase the geographic area over which richness coordinates are aggregated. Select a focal taxonomic group to compare, zoom in and out of maps. 

    Data derived from GBIF 2024-02-01 and h3 aggregations are pre-computed for cell sizes 1-7 across the UK using [duckdb-hs](https://github.com/isaacbrodsky/h3-duckdb)
    """
    )

# +
# LAYING OUT THE MIDDLE SECTION OF THE APP WITH THE MAPS
# -

# SETTING THE ZOOM LOCATIONS
midpoint =  (52.0, -1.0)  #mpoint(data["lat"], data["lon"])

# STREAMLIT APP LAYOUT
# +
row2_1, row2_2, row2_3, row2_4 = st.columns((2, 1, 1, 1))

with row2_1:
    st.write(
        f"""**All**"""
    )
    map(load_data(zoom=zoom), midpoint[0], midpoint[1], 3)

with row2_2:
    st.write(f"Selected class is {taxa}")
    map(load_class(taxa=taxa, zoom=zoom),  midpoint[0], midpoint[1], 3)

with row2_3:
    st.write("**Mammals**")
    map(load_class("Mammalia", zoom=zoom),  midpoint[0], midpoint[1], 4)

with row2_4:
    st.write("**Birds**")
    map(load_class("Aves", zoom=zoom), midpoint[0], midpoint[1], 4)