def add_spatial_joins(df):
"""Add spatial joins of data provided by API, but not needed for network analysis.
Parameters
----------
df : GeoDataFrame
Returns
-------
GeoDataFrame
has fields added by spatial joins to other datasets
"""
### Protected lands
print("Joining to protected areas")
protected = from_geofeather(boundaries_dir / "protected_areas.feather")
df = spatial_join(df, protected)
df.OwnerType = df.OwnerType.fillna(-1).astype("int8")
df.ProtectedLand = df.ProtectedLand.fillna(False).astype("bool")
### Priority layers
print("Joining to priority watersheds")
priorities = (
deserialize_df(boundaries_dir / "priorities.feather")
.set_index("HUC8")
.rename(columns={"usfs": "HUC8_USFS", "coa": "HUC8_COA", "sgcn": "HUC8_SGCN"})
)
df = df.join(priorities, on="HUC8")
df[priorities.columns] = df[priorities.columns].fillna(0).astype("uint8")
return df
def test_points_geofeather_wkt(tmpdir, points_albers_conus_wkt):
"""Confirm that we can round-trip points to / from feather file with a wkt defined CRS"""
filename = tmpdir / "points_albers_conus.feather"
to_geofeather(points_albers_conus_wkt, filename)
df = from_geofeather(filename)
assert_frame_equal(df, points_albers_conus_wkt)
assert df.crs == points_albers_conus_wkt.crs
def main(tile, input_pt_feather):
# Data Directories
source_dir = '/Users/arbailey/natcap/idb/data/source/'
data_dir = '/Users/arbailey/natcap/idb/data/work/mangroves'
work_dir = os.path.join(data_dir, 'yucatan')
pt_data_source = os.path.join(work_dir, input_pt_feather)
out_feather_path = os.path.join(work_dir,
"gliht_srtm_{}.feather".format(tile))
#--- Load the G-LiHT points
print("Loading data from: {}".format(pt_data_source))
start_time = time.time()
gliht_pts = from_geofeather(os.path.join(work_dir, pt_data_source))
print("Load time for {0}: {1}".format(pt_data_source,
time_elapsed(start_time)))
print(gliht_pts.dtypes)
print(gliht_pts)
#--- SRTM elevation data
srtm_source = os.path.join(source_dir, 'srtm/nasa', ".".join(
(tile, 'SRTMGL1', 'hgt', 'zip')))
# Clip the points to SRTM raster extent (1 degree tile)
# gliht_pts_clip = clip_pts_with_raster(gliht_pts[1:100], srtm_source) # subset for testing
gliht_pts_clip = clip_pts_with_raster(gliht_pts, srtm_source)
# Sample the SRTM raster
gliht_pts_clip = sample_raster(gliht_pts_clip, srtm_source, 'srtm_m')
print(gliht_pts_clip.dtypes)
print(gliht_pts_clip)
# Create unique index value for SRTM raster
srtm_unique_source = os.path.join(
work_dir, "{}_{}_{}.{}".format(tile, 'srtm', 'uniqueid', 'tif'))
make_unique_raster(srtm_source, srtm_unique_source)
# Sample Unique ID SRTM raster
gliht_pts_clip = sample_raster(gliht_pts_clip, srtm_unique_source,
'srtm_idx')
gliht_pts_clip.reset_index(inplace=True)
print(gliht_pts_clip.dtypes)
print(gliht_pts_clip)
# Add columns to show the tile and unique index plus tile
gliht_pts_clip['tile'] = tile
gliht_pts_clip['tile_srtmidx'] = gliht_pts_clip[
'tile'] + '_' + gliht_pts_clip['srtm_idx'].astype(str)
print(gliht_pts_clip.dtypes)
print(gliht_pts_clip)
# Export to Feather format
print("Exporting to Geofeather format")
start_time = time.time()
to_geofeather(gliht_pts_clip, out_feather_path)
print("Export execution time for {0}: {1}".format(
out_feather_path, time_elapsed(start_time)))
def test_polygons_geofeather(tmpdir, polygons_wgs84):
"""Confirm that we can round-trip polygons to / from feather file"""
filename = tmpdir / "polygons_wgs84.feather"
to_geofeather(polygons_wgs84, filename)
assert os.path.exists(filename)
df = from_geofeather(filename)
assert_frame_equal(df, polygons_wgs84)
assert df.crs == polygons_wgs84.crs
def cut_flowlines_at_barriers(region, barriers):
"""Read in flowlines and joins between segments, cut flowlines at barriers, and return updated
flowlines, joins, and joins at each of the barriers
NOTE: loops are dropped from the analysis.
Parameters
----------
region : str
ID of region group
barriers : GeoDataFrame
Barriers to cut the network
Returns
-------
(GeoDataFrame, DataFrame, DataFrame)
cut flowlines, updated joins, barrier joins
"""
### Read NHD flowlines and joins
print("Reading flowlines...")
flowline_start = time()
flowlines = (from_geofeather(
nhd_dir / region / "flowlines.feather").set_index(
"lineID", drop=False).drop(columns=["HUC2"], errors="ignore"))
joins = deserialize_df(nhd_dir / region / "flowline_joins.feather")
# Fix data issue; remove on next full run of prepare_flowlines_waterbodies.py
ix = flowlines.loc[flowlines.loop].index
joins.loc[joins.upstream_id.isin(ix) | joins.downstream_id.isin(ix),
"loop"] = True
joins.loop = joins.loop.fillna(False)
ix = flowlines.loop == True
print("Found {:,} loops, dropping...".format(ix.sum()))
flowlines = flowlines.loc[~ix].copy()
joins = joins.loc[~joins.loop].copy()
print("Read {:,} flowlines in {:.2f}s".format(len(flowlines),
time() - flowline_start))
### Cut flowlines at barriers
cut_start = time()
# since all other lineIDs use HUC4 prefixes, this should be unique
# Use the first HUC2 for the region group
next_segment_id = int(REGION_GROUPS[region][0]) * 1000000 + 1
flowlines, joins, barrier_joins = cut_flowlines(
flowlines, barriers, joins, next_segment_id=next_segment_id)
print("Done cutting flowlines in {:.2f}".format(time() - cut_start))
return flowlines, joins, barrier_joins
def test_missing_crs_warning(tmpdir, points_wgs84):
"""Confirm that a warning is raised if the crs file is missing"""
filename = tmpdir / "points_wgs84.feather"
to_geofeather(points_wgs84, filename)
os.remove("{}.crs".format(filename))
with pytest.warns(UserWarning) as warning:
df = from_geofeather(filename)
assert ("coordinate reference system file is missing"
in warning[0].message.args[0])
assert df.crs is None
def test_points_geofeather_proj4(tmpdir, points_albers_conus_proj4):
"""Confirm that we can round-trip points to / from feather file with a proj4 defined CRS"""
filename = tmpdir / "points_albers_conus.feather"
to_geofeather(points_albers_conus_proj4, filename)
df = from_geofeather(filename)
assert_frame_equal(df, points_albers_conus_proj4)
# equality comparision fails for CRS object constructed from proj4, even though they are still the same
if hasattr(df.crs, "to_proj4"):
assert df.crs.to_proj4() == points_albers_conus_proj4.crs.to_proj4()
else:
assert df.crs == points_albers_conus_proj4.crs
def main(raster_source, uniqueid_file, work_dir, input_pt_feather,
out_feather):
pt_data_source = os.path.join(work_dir, input_pt_feather)
out_feather_path = os.path.join(work_dir, out_feather)
#--- Load the points
print("Loading data from: {}".format(pt_data_source))
start_time = time.time()
in_pts = from_geofeather(os.path.join(work_dir, pt_data_source))
print("Load time for {0}: {1}".format(pt_data_source,
time_elapsed(start_time)))
print(in_pts.dtypes)
print(in_pts)
# Clip the points to raster extent
# in_pts_clip = clip_pts_with_raster(in_pts[1:100], raster_source) # subset for testing
in_pts_clip = clip_pts_with_raster(in_pts, raster_source)
# Sample the raster
in_pts_clip = sample_raster(in_pts_clip, raster_source, 'tncdep_m')
print(in_pts_clip.dtypes)
print(in_pts_clip)
# Create unique index value for SRTM raster
raster_unique_source = os.path.join(work_dir, uniqueid_file)
make_unique_raster(raster_source, raster_unique_source)
# Sample Unique ID SRTM raster
in_pts_clip = sample_raster(in_pts_clip, raster_unique_source,
'tncdep_idx')
in_pts_clip.reset_index(inplace=True)
print(in_pts_clip.dtypes)
print(in_pts_clip)
# Export to Feather format
print("Exporting to Geofeather format")
start_time = time.time()
to_geofeather(in_pts_clip, out_feather_path)
print("Export execution time for {0}: {1}".format(
out_feather_path, time_elapsed(start_time)))
columns=["miles", "free_miles"])
serialize_df(barrier_networks.reset_index(drop=False),
out_dir / "barriers_network.feather")
### Update network geometries and barrier networks
# Cut networks from upstream regions and paste them into downstream regions
cut_networks = None
for region in cross_region.from_region.unique():
out_dir = data_dir / "networks" / region / network_type
### Update network geometries
print(
"Cutting downstream network from upstream region {}...".format(region))
network = from_geofeather(data_dir / "networks" / region / network_type /
"raw/network.feather")
# select the affected networks
idx = network.networkID.isin(cross_region.upstream_network)
cut = network.loc[idx].copy()
if cut_networks is None:
cut_networks = cut
else:
cut_networks = cut_networks.append(cut, ignore_index=True, sort=False)
# write the updated network back out
network = network.loc[~idx].copy()
print("Serializing updated network...")
### Read in master
print("Reading master...")
df = (
from_geofeather(barriers_dir / "small_barriers.feather")
.set_index("id")
.drop(
columns=[
"level_0",
"index",
"dup_group",
"dup_count",
"dup_log",
"snap_dist",
"snap_tolerance",
"snap_ref_id",
"snap_log",
"snapped",
"ProtectedLand",
"log",
"lineID",
"wbID",
],
errors="ignore",
)
.rename(columns={"streamorder": "StreamOrder", "excluded": "Excluded"})
)
# drop any that should be DROPPED (dropped or duplicate) from the analysis
# NOTE: excluded ones are retained but don't have networks
def main(tile, input_pt_feather):
# Data Directories
data_dir = '/Users/arbailey/natcap/idb/data/work/mangroves'
work_dir = os.path.join(data_dir, 'yucatan')
pt_data_source = os.path.join(work_dir, input_pt_feather)
out_feather_path = os.path.join(work_dir, "gliht_srtm_mangroves_{}.feather".format(tile))
# --- Mangrove Max Height raster
hmax_source = os.path.join(data_dir, 'gmc_hmax95_bahamas_MAR.tif')
hba_source = os.path.join(data_dir, 'gmc_hba95_bahamas_MAR.tif')
#--- Load the G-LiHT/SRTM points
print("Loading data from: {}".format(pt_data_source))
start_time = time.time()
gliht_pts = from_geofeather(os.path.join(work_dir, pt_data_source))
print("Load time for {0}: {1}".format(pt_data_source, time_elapsed(start_time)))
gliht_pts.drop(columns=['index'], inplace=True)
print(gliht_pts.dtypes)
print(gliht_pts)
# Sample the Canopy Height rasters
# Max Height - hmax95
# gliht_pts = sample_raster(gliht_pts[0:100], hmax_source, 'hmax95')
gliht_pts = sample_raster(gliht_pts, hmax_source, 'hmax95')
print(gliht_pts.dtypes)
print(gliht_pts)
# Weighted Average Height - hba95
gliht_pts = sample_raster(gliht_pts, hba_source, 'hba95')
print(gliht_pts.dtypes)
print(gliht_pts)
# # Create unique index value for Canopy raster
gmc_unique_source = os.path.join(work_dir, "gmc_uniqueid.tif")
# make_unique_raster(hmax_source, gmc_unique_source) # Takes 1:55:14.79
#
# Sample Unique ID raster
gliht_pts = sample_raster(gliht_pts, gmc_unique_source, 'hmax_idx')
# gliht_pts.reset_index(inplace=True)
# gliht_pts.drop(columns=['index'], inplace=True)
print(gliht_pts.dtypes)
print(gliht_pts)
# Add columns to show the tile and unique index plus tile
gliht_pts['tile'] = tile
gliht_pts['tile_hmaxidx'] = gliht_pts['tile'] + '_' + gliht_pts['hmax_idx'].astype(str)
print(gliht_pts.dtypes)
print(gliht_pts)
# Mangrove Extent Vector shapefile paths to join to Points
#-- World Atlas of Mangroves
wam_path = os.path.join(data_dir, 'wam_Bahamas_MAR.shp')
wam_att = 'wam'
wam = mangrove_poly_to_gdf(wam_path, wam_att)
print(wam)
gliht_pts = mangrove_join(gliht_pts, wam)
print(gliht_pts)
#-- Global Mangrove Watch
gmw2016_path = os.path.join(data_dir, 'gmw2016_Bahamas_MAR.shp')
gmw2016_att = 'gmw2016'
gmw2016 = mangrove_poly_to_gdf(gmw2016_path, gmw2016_att)
print(gmw2016)
gliht_pts = mangrove_join(gliht_pts, gmw2016)
print(gliht_pts)
# Global Mangrove Forests
gmf_path = os.path.join(data_dir, 'gmf_bahamas_MAR.shp')
gmf_att = 'gmf'
gmf = mangrove_poly_to_gdf(gmf_path, gmf_att)
print(gmf)
gliht_pts = mangrove_join(gliht_pts, gmf)
print(gliht_pts)
# NAtCap Mangrove compilation for MAR region (Mex, Belize, Guatemala, Honduras)
ncmar_path = os.path.join(data_dir, 'natcap_mangrovesV4_MAR.shp')
ncmar_att = 'ncMAR'
ncmar = mangrove_poly_to_gdf(ncmar_path, ncmar_att)
print(ncmar)
gliht_pts = mangrove_join(gliht_pts, ncmar)
print(gliht_pts)
print(gliht_pts.dtypes)
print(gliht_pts.describe())
# Export to GeoFeather format
gliht_pts.reset_index(inplace=True) # get an error from feather export if don't do this
# ValueError: feather does not support serializing a non-default index for the index; you can .reset_index() to make the index into column(s)
print(gliht_pts.dtypes)
print("Exporting to Geofeather format")
start_time = time.time()
to_geofeather(gliht_pts, out_feather_path)
print("Export execution time for {0}: {1}".format(out_feather_path, time_elapsed(start_time)))
from dash.dependencies import Input, Output, State
import dash_core_components as dcc
import dash_html_components as html
import dash_table
import plotly
import plotly.express as px
from flask import Flask
# API keys and datasets
mb_token = 'pk.eyJ1IjoiamF2aS1hbGZhcm8iLCJhIjoiY2tiMnR0cm5zMDBoejJ4cWNxb3Bzcno5aiJ9.Zh0OEJmyiH27YG4Yw_KLyg'
map_shape = gpd.read_file('./data/slv_adm2/SLV_adm2.shp')
map_shape.columns = map(str.lower, map_shape.columns)
map_shape['codigomunic'] = map_shape.name_2
map_shape['depto'] = map_shape.name_1
gdf = gf.from_geofeather('./data/ehpm19_merged_sample.feather')
gdf.crs = "EPSG:4326"
map_data = gdf.copy()
map_data["lon"] = gdf.centroid.x
map_data["lat"] = gdf.centroid.y
del gdf
# Preparing geojson
map_shape.to_file("./data/esa.json", driver="GeoJSON")
with open('./data/esa.json') as response:
esa_geoj = json.load(response)
px.set_mapbox_access_token(mb_token)
### Read in master
print("Reading master...")
df = (from_geofeather(barriers_dir / "dams.feather").set_index("id").drop(
columns=[
"level_0",
"index",
"dup_group",
"dup_count",
"dup_sort",
"dup_log",
"snap_dist",
"snap_tolerance",
"snap_ref_id",
"snap_log",
"snapped",
"ProtectedLand",
"NHDPlusID",
"SourceState",
"lineID",
"wbID",
"waterbody",
"src",
"kind",
"log",
],
errors="ignore",
).rename(columns={
"streamorder": "StreamOrder",
"excluded": "Excluded"
}))
# drop any that should be DROPPED (dropped or duplicate) from the analysis
print("{:,} duplicate road crossings".format(len(df) - len(keep_ids)))
df = df.loc[keep_ids].copy()
### Remove crossings that are very close
print("Removing nearby road crossings...")
# consider 5 m nearby
df = mark_duplicates(df, 5)
print("{:,} very close road crossings dropped".format(len(
df.loc[df.duplicate])))
df = df.loc[~df.duplicate].drop(
columns=["duplicate", "dup_count", "dup_group"])
### Remove those that otherwise duplicate existing small barriers
print("Removing crossings that duplicate existing barriers")
barriers = from_geofeather(barriers_dir / "master/small_barriers.feather")
barriers = barriers.loc[~barriers.duplicate]
barriers["kind"] = "barrier"
df["joinID"] = (df.index * 1e6).astype("uint32")
df["kind"] = "crossing"
merged = barriers[["kind",
"geometry"]].append(df[["joinID", "kind", "geometry"]],
sort=False,
ignore_index=True)
merged = mark_duplicates(merged, tolerance=DUPLICATE_TOLERANCE)
dup_groups = merged.loc[(merged.dup_count > 1)
& (merged.kind == "barrier")].dup_group.unique()
remove_ids = merged.loc[merged.dup_group.isin(dup_groups)
def read_barriers(region, mode):
"""Read files created by prep_dams.py, prep_waterfalls.py, prep_small_barriers.py
Merge together and assign uniqueID for internal use in network analysis
NOTE: barriers on loops are dropped
Parameters
----------
region : str
region group identifier, e.g., "02"
mode : str
One of "natural", "dams", "small_barriers"
Returns
-------
GeoDataFrame
Merged barriers file
"""
start = time()
print("Reading waterfalls")
wf = from_geofeather(barriers_dir / "waterfalls.feather")
wf = wf.loc[wf.HUC2.isin(REGION_GROUPS[region])].copy()
print("Selected {:,} waterfalls".format(len(wf)))
wf["barrierID"] = WATERFALLS_ID + wf.id
wf["kind"] = "waterfall"
barriers = wf
if mode != "natural":
print("Reading dams")
dams = from_geofeather(barriers_dir / "dams.feather")
dams = dams.loc[dams.HUC2.isin(REGION_GROUPS[region])].copy()
print("Selected {:,} dams".format(len(dams)))
dams["barrierID"] = DAMS_ID + dams.id
dams["kind"] = "dam"
if len(dams):
barriers = barriers.append(dams, ignore_index=True, sort=False)
if mode == "small_barriers":
print("Reading small barriers")
sb = from_geofeather(barriers_dir / "small_barriers.feather")
sb = sb.loc[sb.HUC2.isin(REGION_GROUPS[region])].copy()
print("Selected {:,} small barriers".format(len(sb)))
sb["barrierID"] = SB_ID + sb.id
sb["kind"] = "small_barrier"
if len(sb):
barriers = barriers.append(sb, ignore_index=True, sort=False)
# Update dtypes
# TODO: not neeed after rerun of prep_*.py scripts
barriers.id = barriers.id.astype("uint32")
barriers.lineID = barriers.lineID.astype("uint32")
barriers.NHDPlusID = barriers.NHDPlusID.astype("uint64")
barriers.barrierID = barriers.barrierID.astype("uint64")
ix = barriers.loop == True
print("Found {:,} barriers on loops, dropping".format(ix.sum()))
barriers = barriers.loc[~ix].copy()
print("Extracted {:,} barriers in {:.2f}s".format(len(barriers), time() - start))
return barriers[
["geometry", "id", "lineID", "NHDPlusID", "barrierID", "kind"]
].set_index("barrierID", drop=False)
os.makedirs(tile_dir)
### Read in master
print("Reading master...")
df = (from_geofeather(barriers_dir /
"waterfalls.feather").set_index("id").drop(
columns=[
"level_0",
"index",
"dup_group",
"dup_count",
"dup_log",
"snap_dist",
"snap_tolerance",
"snap_log",
"snapped",
"log",
"lineID",
"wbID",
],
errors="ignore",
).rename(
columns={
"streamorder": "StreamOrder",
"name": "Name",
"watercours": "Stream",
"gnis_name_": "GNIS_Name",
}))
### Fix data type issues
# TODO: move to prep script
df.Name = df.Name.fillna("").str.strip()
parallel_runner, enumerate(chunks)),
total=chunk_count):
partial_results[index] = chunk
df_join = pd.concat(partial_results)
return df_join
if __name__ == "__main__":
with open(PROCESSED_DATA_SOURCES + TEMP + "TEMP_2019.pkl", 'rb') as f:
data_TEMP = pickle.load(f)
crs = {'init': 'EPSG:4326'}
geometry = [Point(xy) for xy in zip(data_TEMP['x'], data_TEMP['y'])]
df_points = gpd.GeoDataFrame(data_TEMP, crs=crs, geometry=geometry)
df_zones = from_geofeather(PROCESSED_DATA_SOURCES + 'Shape_Joined.feather')
df_joined = run(df_zones, df_points, use_parallel=True, processes=10)
df_joined = df_joined.reset_index(drop=True)
aggregations = {
'NAME_0': 'first',
'value': 'mean',
'TYPE_1': 'first',
'ENGTYPE_1': 'first',
'GID_0': 'first',
'GID_1': 'first'
}
temp_grouped = df_joined.groupby(['date_range',
'NAME_1']).agg(aggregations)
temp_grouped.to_csv(PROCESSED_DATA_SOURCES + 'temp_19.csv')