def close_gaps(df, tolerance):
"""Close gaps in LineString geometry where it should be contiguous.
Snaps both lines to a centroid of a gap in between.
"""
geom = df.geometry.values.data
coords = pygeos.get_coordinates(geom)
indices = pygeos.get_num_coordinates(geom)
# generate a list of start and end coordinates and create point geometries
edges = [0]
i = 0
for ind in indices:
ix = i + ind
edges.append(ix - 1)
edges.append(ix)
i = ix
edges = edges[:-1]
points = pygeos.points(np.unique(coords[edges], axis=0))
buffered = pygeos.buffer(points, tolerance)
dissolved = pygeos.union_all(buffered)
exploded = [
pygeos.get_geometry(dissolved, i)
for i in range(pygeos.get_num_geometries(dissolved))
]
centroids = pygeos.centroid(exploded)
snapped = pygeos.snap(geom, pygeos.union_all(centroids), tolerance)
return snapped
def close_gaps(gdf, tolerance):
"""Close gaps in LineString geometry where it should be contiguous.
Snaps both lines to a centroid of a gap in between.
Parameters
----------
gdf : GeoDataFrame, GeoSeries
GeoDataFrame or GeoSeries containing LineString representation of a network.
tolerance : float
nodes within a tolerance will be snapped together
Returns
-------
GeoSeries
See also
--------
momepy.extend_lines
momepy.remove_false_nodes
"""
geom = gdf.geometry.values.data
coords = pygeos.get_coordinates(geom)
indices = pygeos.get_num_coordinates(geom)
# generate a list of start and end coordinates and create point geometries
edges = [0]
i = 0
for ind in indices:
ix = i + ind
edges.append(ix - 1)
edges.append(ix)
i = ix
edges = edges[:-1]
points = pygeos.points(np.unique(coords[edges], axis=0))
buffered = pygeos.buffer(points, tolerance / 2)
dissolved = pygeos.union_all(buffered)
exploded = [
pygeos.get_geometry(dissolved, i)
for i in range(pygeos.get_num_geometries(dissolved))
]
centroids = pygeos.centroid(exploded)
snapped = pygeos.snap(geom, pygeos.union_all(centroids), tolerance)
return gpd.GeoSeries(snapped, crs=gdf.crs)
def get_input_area_boundary(input_area):
"""Extract and union polygons associated with input area into a single
boundary (Multi)Polygon.
Parameters
----------
input_area : str
id of input area
Returns
-------
(Multi)Polygon
"""
# have to make valid or we get errors during union for FL
values = [
e["value"] for e in INPUT_AREA_VALUES
if input_area in set(e["id"].split(","))
]
inputs_df = gp.read_feather(bnd_dir / "input_areas.feather")
bnd = pg.union_all(
pg.make_valid(
inputs_df.loc[inputs_df.value.isin(values)].geometry.values.data))
return bnd
def setup(self):
# create irregular polygons by merging overlapping point buffers
self.left = pygeos.union_all(
pygeos.buffer(pygeos.points(np.random.random((500, 2)) * 500), 15)
)
# shift this up and right
self.right = pygeos.apply(self.left, lambda x: x + 50)
def unary_union(data):
if compat.USE_PYGEOS:
return _pygeos_to_shapely(pygeos.union_all(data))
else:
data = [g for g in data if g is not None]
if data:
return shapely.ops.unary_union(data)
else:
return None
def setup(self):
# create irregular polygons by merging overlapping point buffers
self.polygon = pygeos.union_all(
pygeos.buffer(pygeos.points(np.random.random((1000, 2)) * 500),
10))
xmin = np.random.random(100) * 100
xmax = xmin + 100
ymin = np.random.random(100) * 100
ymax = ymin + 100
self.bounds = np.array([xmin, ymin, xmax, ymax]).T
self.boxes = pygeos.box(xmin, ymin, xmax, ymax)
def _pandas(cls, column, **kwargs):
shape = kwargs.get("shape")
shape_format = kwargs.get("shape_format")
column_shape_format = kwargs.get("column_shape_format")
# Check that shape is given and given in the correct format
if shape is not None:
try:
if shape_format == "wkt":
shape_ref = geos.from_wkt(shape)
elif shape_format == "wkb":
shape_ref = geos.from_wkb(shape)
elif shape_format == "geojson":
shape_ref = geos.from_geojson(shape)
else:
raise NotImplementedError(
"Shape constructor method not implemented. Must be in WKT, WKB, or GeoJSON format."
)
except:
raise Exception("A valid reference shape was not given.")
else:
raise Exception("A shape must be provided for this method.")
# Load the column into a pygeos Geometry vector from numpy array (Series not supported).
if column_shape_format == "wkt":
shape_test = geos.from_wkt(column.to_numpy(), on_invalid="ignore")
elif column_shape_format == "wkb":
shape_test = geos.from_wkb(column.to_numpy(), on_invalid="ignore")
else:
raise NotImplementedError(
"Column values shape format not implemented.")
# Allow for an array of reference shapes to be provided. Return a union of all the shapes in the array (Polygon or Multipolygon)
shape_ref = geos.union_all(shape_ref)
# Prepare the geometries
geos.prepare(shape_ref)
geos.prepare(shape_test)
column_centroids = geos.centroid(shape_test)
print(column_centroids)
return pd.Series(geos.within(column_centroids, shape_ref))
def _pandas(cls, column, **kwargs):
column_shape_format = kwargs.get("column_shape_format")
# Load the column into a pygeos Geometry vector from numpy array (Series not supported).
if column_shape_format == "wkt":
shape_test = geos.from_wkt(column.to_numpy(), on_invalid="ignore")
elif column_shape_format == "wkb":
shape_test = geos.from_wkb(column.to_numpy(), on_invalid="ignore")
elif column_shape_format == "xy":
shape_df = pd.DataFrame(column.to_list(), columns=("x", "y"))
shape_test = geos.points(shape_df.lon, y=shape_df.lat)
else:
raise NotImplementedError(
"Column values shape format not implemented.")
shape_test = geos.union_all(shape_test)
radius = geos.minimum_bounding_radius(shape_test)
return radius
def setup(self):
# create irregular polygons my merging overlapping point buffers
self.polygons = pygeos.get_parts(
pygeos.union_all(
pygeos.buffer(pygeos.points(np.random.random((2000, 2)) * 500),
5)))
self.tree = pygeos.STRtree(self.polygons)
# initialize the tree by making a tiny query first
self.tree.query(pygeos.points(0, 0))
# create points that extend beyond the domain of the above polygons to ensure
# some don't overlap
self.points = pygeos.points((np.random.random((2000, 2)) * 750) - 125)
self.point_tree = pygeos.STRtree(
pygeos.points(np.random.random((2000, 2)) * 750))
self.point_tree.query(pygeos.points(0, 0))
# create points on a grid for testing equidistant nearest neighbors
# creates 2025 points
grid_coords = np.mgrid[:45, :45].T.reshape(-1, 2)
self.grid_point_tree = pygeos.STRtree(pygeos.points(grid_coords))
self.grid_points = pygeos.points(grid_coords + 0.5)
async def create_custom_report(ctx, zip_filename, dataset, layer, name=""):
"""Create a Blueprint report for a user-uploaded GIS file contained in a zip.
Zip must contain either a shapefile or a file geodatabase.
Parameters
----------
ctx : job context
zip_filename : str
full path to zip filename
dataset : str
full path to dataset within zip file
layer : str
name of layer within dataset
name : str, optional (default: "")
Name of area of interest (included in output report)
Returns
-------
str
path to output file
Raises
------
DataError
Raised if bounds are too large or if area of interest doesn't overalap SA region
"""
errors = []
await set_progress(ctx["job_id"], 0, "Loading data")
path = f"/vsizip/{zip_filename}/{dataset}"
df = read_dataframe(path, layer=layer)
geometry = pg.make_valid(df.geometry.values.data)
await set_progress(ctx["job_id"], 5, "Preparing area of interest")
# dissolve
geometry = np.asarray([pg.union_all(geometry)])
geo_geometry = to_crs(geometry, df.crs, GEO_CRS)
bounds = pg.total_bounds(geo_geometry)
# estimate area
extent_area = (
pg.area(pg.box(*pg.total_bounds(to_crs(geometry, df.crs, DATA_CRS)))) *
M2_ACRES)
if extent_area >= CUSTOM_REPORT_MAX_ACRES:
raise DataError(
f"The bounding box of your area of interest is too large ({extent_area:,.0f} acres), it must be < {CUSTOM_REPORT_MAX_ACRES:,.0f} acres."
)
await set_progress(ctx["job_id"], 10,
"Calculating results (this might take a while)")
# calculate results, data must be in DATA_CRS
print("Calculating results...")
results = CustomArea(geometry, df.crs, name).get_results()
if results is None:
raise DataError(
"area of interest does not overlap Southeast Blueprint")
if name:
results["name"] = name
has_urban = "proj_urban" in results and results["proj_urban"][4] > 0
has_slr = "slr" in results
has_ownership = "ownership" in results
has_protection = "protection" in results
# compile indicator IDs across all inputs
indicators = []
for input_area in results["inputs"]:
for ecosystem in input_area.get("ecosystems", []):
indicators.extend([i["id"] for i in ecosystem["indicators"]])
await set_progress(ctx["job_id"], 25,
"Creating maps (this might take a while)")
print("Rendering maps...")
maps, scale, map_errors = await render_maps(
bounds,
geometry=geo_geometry[0],
input_ids=results["input_ids"],
indicators=indicators,
urban=has_urban,
slr=has_slr,
ownership=has_ownership,
protection=has_protection,
)
if map_errors:
log.error(f"Map rendering errors: {map_errors}")
if "basemap" in map_errors:
errors.append("Error creating basemap for all maps")
if "aoi" in map_errors:
errors.append("Error rendering area of interest on maps")
if set(map_errors.keys()).difference(["basemap", "aoi"]):
errors.append("Error creating one or more maps")
await set_progress(ctx["job_id"],
75,
"Creating PDF (this might take a while)",
errors=errors)
results["scale"] = scale
pdf = create_report(maps=maps, results=results)
await set_progress(ctx["job_id"], 95, "Nearly done", errors=errors)
fp, name = tempfile.mkstemp(suffix=".pdf", dir=TEMP_DIR)
with open(fp, "wb") as out:
out.write(pdf)
await set_progress(ctx["job_id"], 100, "All done!", errors=errors)
log.debug(f"Created PDF at: {name}")
return name, errors
import rasterio
import geopandas as gp
import pygeos as pg
from analysis.constants import DATA_CRS
from analysis.lib.raster import add_overviews
data_dir = Path("data/inputs")
src_dir = data_dir / "threats/slr"
boxes = []
for filename in (src_dir).glob("*.tif"):
with rasterio.open(filename) as src:
boxes.append(pg.box(*src.bounds))
# union them together into a single polygon
bnd = pg.union_all(boxes)
df = gp.GeoDataFrame({"geometry": [bnd], "index": [0]}, crs=DATA_CRS)
df.to_feather(src_dir / "slr_bounds.feather")
# For debugging
# write_dataframe(df, "/tmp/slr_bounds.gpkg", driver="GPKG")
# Create overviews for each individual file in the VRT
# Note: these have varying resolution, but this creates lower resolutions for each
print("Adding overviews to SLR files...")
for filename in src_dir.glob("*.tif"):
print(f"Processing {filename}...")
add_overviews(filename)
message=".*initial implementation of Parquet.*")
from analysis.constants import DATA_CRS, GEO_CRS, M2_ACRES
src_dir = Path("source_data")
data_dir = Path("data")
analysis_dir = data_dir / "inputs/summary_units"
bnd_dir = data_dir / "boundaries" # GPKGs output for reference
tile_dir = data_dir / "for_tiles"
### Extract the boundary
sa_df = read_dataframe(src_dir /
"boundaries/SABlueprint2020_Extent.shp")[["geometry"]]
# boundary has self-intersections and 4 geometries, need to clean up
bnd = pg.union_all(pg.make_valid(sa_df.geometry.values.data))
### Extract HUC12 within boundary
print("Reading source HUC12s...")
merged = None
for huc2 in [2, 3, 5, 6]:
df = read_dataframe(
src_dir / f"summary_units/WBD_0{huc2}_HU2_GDB/WBD_0{huc2}_HU2_GDB.gdb",
layer="WBDHU12",
)[["huc12", "name", "geometry"]].rename(columns={"huc12": "id"})
if merged is None:
merged = df
else:
merged = merged.append(df, ignore_index=True)
connectors_outfilename = out_dir / "ns_connectors.tif"
tnc_outfilename = out_dir / "tnc_resilient_connected.tif"
ns_outfilename = out_dir / "ns_priority.tif"
if not out_dir.exists():
os.makedirs(out_dir)
### Get input area mask
print("Extracting NatureScape input area mask...")
mask, transform, window = get_input_area_mask("app")
inputs_df = gp.read_feather(data_dir / "boundaries/input_areas.feather")
values = [
e["value"] for e in INPUT_AREA_VALUES if "app" in set(e["id"].split(","))
]
bnd = pg.union_all(
inputs_df.loc[inputs_df.value.isin(values)].geometry.values.data)
### Warp TNC resilient and connected landscapes to match Blueprint input area
print("Reading and warping TNC resilient and connected landscapes...")
with rasterio.open(src_dir / "Resilient_and_Connected20180308.tif") as rc:
vrt = WarpedVRT(
rc,
width=window.width,
height=window.height,
nodata=int(rc.nodata),
transform=transform,
crs=DATA_CRS,
resampling=Resampling.nearest,
)
data = vrt.read()[0]
def union_or_combine(geometries, grid_size=None, op="union"):
"""First does a check for overlap of geometries according to STRtree
intersects. If any overlap, then will use union_all on all of them;
otherwise will return as a multipolygon.
If only one polygon is present, it will be returned in a MultiPolygon.
If coverage_union op is provided, geometries must be polygons and
topologically related or this will produce bad output or fail outright.
See docs for coverage_union in GEOS.
Parameters
----------
geometries : ndarray of single part polygons
grid_size : [type], optional (default: None)
provided to union_all; otherwise no effect
op : str, one of {'union', 'coverage_union'}
Returns
-------
MultiPolygon
"""
if not (pg.get_type_id(geometries) == 3).all():
print("Inputs to union or combine must be single-part geometries")
if len(geometries) == 1:
return pg.multipolygons(geometries)
tree = pg.STRtree(geometries)
left, right = tree.query_bulk(geometries, predicate="intersects")
# drop self intersections
ix = left != right
left = left[ix]
right = right[ix]
# no intersections, just combine parts
if len(left) == 0:
return pg.multipolygons(geometries)
# find groups of contiguous geometries and union them together individually
contiguous = np.sort(np.unique(np.concatenate([left, right])))
discontiguous = np.setdiff1d(np.arange(len(geometries), dtype="uint"),
contiguous)
groups = find_adjacent_groups(left, right)
parts = []
if op == "coverage_union":
for group in groups:
parts.extend(
pg.get_parts(pg.coverage_union_all(geometries[list(group)])))
else:
for group in groups:
parts.extend(
pg.get_parts(
pg.union_all(geometries[list(group)],
grid_size=grid_size)))
parts.extend(pg.get_parts(geometries[discontiguous]))
return pg.multipolygons(parts)
columns=["ls_cond"]).rename(columns=field_map).rename(
columns={"chat_rank": "chatrank"}))
for col in chat_fields:
df[col] = df[col].astype("uint8")
df = df.drop(columns=["hexagon_id"])
### Find the CHAT units that intersect with OK / TX input areas
# Use centerpoints, since input area roughly follows edges of hexes
points = pg.centroid(df.geometry.values.data)
tree = pg.STRtree(points)
for state in ["ok", "tx"]:
print(f"Processing {state} CHAT...")
input_area = pg.union_all(
inputs_df.loc[inputs_df.inputs == f"{state}chat"].geometry.values.data)
ix = tree.query(input_area, predicate="intersects")
state_df = df.iloc[ix].reset_index(drop=True)
# lcon not present for TX
if state == "tx":
state_df = state_df.drop(columns=["lcon"])
# Reclassify chatrank to match blueprint integration rules.
# First shift other values up one
ix = state_df.chatrank >= 2
state_df.loc[ix, "chatrank"] = state_df.chatrank + 1
# for any that were previously a chatrank of 2 but with higher values of aquatic or
# terrestrial, map them back to 2
ix = ((state_df.chatrank == 3)
& state_df.arank.isin([2, 3])
# {"name": "Cave Spring, VA area", "path": "CaveSpring"},
# {"name": "South Atlantic Offshore", "path": "SAOffshore"},
# {"name": "Florida Offshore", "path": "FLOffshore"}
]
for aoi in aois:
name = aoi["name"]
path = aoi["path"]
print(f"Creating report for {name}...")
start = time()
df = read_dataframe(f"examples/{path}.shp", columns=[])
geometry = pg.make_valid(df.geometry.values.data)
# dissolve
geometry = np.asarray([pg.union_all(geometry)])
extent_area = (
pg.area(pg.box(*pg.total_bounds(to_crs(geometry, df.crs, DATA_CRS)))) *
M2_ACRES)
print("Area of extent", extent_area.round())
### calculate results, data must be in DATA_CRS
print("Calculating results...")
results = CustomArea(geometry, df.crs, name=name).get_results()
if results is None:
print(f"AOI: {path} does not overlap Blueprint")
continue
out_dir = Path("/tmp/aoi") / path
def find_nhd_waterbody_breaks(geometries, nhd_lines):
"""Some large waterbody complexes are divided by dams; these breaks
need to be preserved. This is done by finding the shared edges between
adjacent waterbodies that fall near NHD lines (which include dams) and
buffering them by 10 meters (arbitrary, from trial and error).
This should be skipped if nhd_lines is empty.
Parameters
----------
df : GeoDataFrame
nhd_lines : GeoDataFrame
Returns
-------
MultiPolygon containing all buffered lines between waterbodies that are near
NHD lines. Returns None if no adjacent waterbodies meet these criteria
"""
# find all nhd lines that intersect waterbodies
# first, buffer them slightly
nhd_lines = pg.get_parts(pg.union_all(pg.buffer(nhd_lines, 0.1)))
tree = pg.STRtree(geometries)
left, right = tree.query_bulk(nhd_lines, predicate="intersects")
# add these to the return
keep_nhd_lines = nhd_lines[np.unique(left)]
# find connected boundaries
boundaries = pg.polygons(pg.get_exterior_ring(geometries))
tree = pg.STRtree(boundaries)
left, right = tree.query_bulk(boundaries, predicate="intersects")
# drop self intersections
ix = left != right
left = left[ix]
right = right[ix]
# extract unique pairs (dedup symmetric pairs)
pairs = np.array([left, right]).T
pairs = (
pd.DataFrame({"left": pairs.min(axis=1), "right": pairs.max(axis=1)})
.groupby(["left", "right"])
.first()
.reset_index()
)
# calculate geometric intersection
i = pg.intersection(
geometries.take(pairs.left.values), geometries.take(pairs.right.values)
)
# extract individual parts (may be geom collections)
parts = pg.get_parts(pg.get_parts(pg.get_parts(i)))
# extract only the lines or polygons
t = pg.get_type_id(parts)
parts = parts[((t == 1) | (t == 3)) & (~pg.is_empty(parts))].copy()
# buffer and merge
split_lines = pg.get_parts(pg.union_all(pg.buffer(parts, 10)))
# now find the ones that are within 100m of nhd lines
nhd_lines = pg.get_parts(nhd_lines)
tree = pg.STRtree(nhd_lines)
left, right = tree.nearest_all(split_lines, max_distance=100)
split_lines = split_lines[np.unique(left)]
if len(split_lines) or len(keep_nhd_lines):
return pg.union_all(np.append(split_lines, keep_nhd_lines))
return None
from analysis.lib.pygeos_util import explode
src_dir = Path("source_data")
data_dir = Path("data")
out_dir = data_dir / "inputs/boundaries" # used as inputs for other steps
tile_dir = data_dir / "for_tiles"
sa_df = read_dataframe(src_dir / "boundaries/SABlueprint2020_Extent.shp")
### Create mask by cutting SA bounds out of world bounds
print("Creating mask...")
world = pg.box(-180, -85, 180, 85)
# boundary has self-intersections and 4 geometries, need to clean up
bnd = pg.union_all(pg.make_valid(sa_df.geometry.values.data))
bnd_geo = pg.union_all(
pg.make_valid(sa_df.to_crs(GEO_CRS).geometry.values.data))
mask = pg.normalize(pg.difference(world, bnd_geo))
gp.GeoDataFrame(geometry=[bnd],
crs=DATA_CRS).to_feather(out_dir / "sa_boundary.feather")
write_dataframe(
gp.GeoDataFrame({"geometry": bnd_geo}, index=[0], crs=GEO_CRS),
tile_dir / "sa_boundary.geojson",
driver="GeoJSONSeq",
)
write_dataframe(
gp.GeoDataFrame({"geometry": mask}, index=[0], crs=GEO_CRS),
def test_union_all_prec(geom, grid_size, expected):
actual = pygeos.union_all(geom, grid_size=grid_size)
assert pygeos.equals(actual, expected)
def time_union_all_prec2(self):
pygeos.union_all([self.left, self.right], grid_size=2)
def unary_union(data):
if compat.USE_PYGEOS:
return _pygeos_to_shapely(pygeos.union_all(data))
else:
return shapely.ops.unary_union(data)
def convex_hull_all(arr):
if isinstance(arr, LazyObj):
arr = arr.values()
points = pg.union_all(pg.extract_unique_points(pg.from_wkb(arr)))
return pg.to_wkb(pg.convex_hull(points))
def union_all(arr):
if isinstance(arr, LazyObj):
arr = arr.values()
return pg.union_all(from_wkb(arr))
def time_union_all(self):
pygeos.union_all([self.left, self.right])
tile_dir = data_dir / "for_tiles"
if not out_dir.exists():
os.makedirs(out_dir)
if not tile_dir.exists():
os.makedirs(tile_dir)
### Extract the boundary
bnd_df = read_dataframe(
src_dir / "blueprint/SE_Blueprint_2021_Vectors.gdb",
layer="SECAS_Boundary_2021_20211117",
)[["geometry"]]
# boundary has multiple geometries, union together and cleanup
bnd_df = gp.GeoDataFrame(
geometry=[pg.union_all(pg.make_valid(bnd_df.geometry.values.data))],
index=[0],
crs=bnd_df.crs,
)
bnd_df.to_feather(out_dir / "se_boundary.feather")
write_dataframe(bnd_df, data_dir / "boundaries/se_boundary.fgb")
# create GeoJSON for tiling
bnd_geo = bnd_df.to_crs(GEO_CRS)
write_dataframe(bnd_geo, tile_dir / "se_boundary.geojson", driver="GeoJSONSeq")
### Create mask by cutting SA bounds out of world bounds
print("Creating mask...")
world = pg.box(-180, -85, 180, 85)
mask = pg.normalize(pg.difference(world, bnd_geo.geometry.values.data))
# save all states for spatial joins
state_df.to_feather(out_dir / "states.feather")
state_df = state_df.loc[state_df.id.isin(STATES.keys())].copy()
state_df.to_feather(out_dir / "region_states.feather")
write_dataframe(
state_df[["State", "geometry"]].rename(columns={"State": "id"}),
out_dir / "region_states.gpkg",
)
# dissolve to create outer state boundary for total analysis area and regions
bnd_df = gp.GeoDataFrame(
[
{
"geometry": pg.union_all(state_df.geometry.values.data),
"id": "total"
},
] + [{
"geometry":
pg.union_all(state_df.loc[state_df.id.isin(
REGION_STATES[region])].geometry.values.data),
"id":
region,
} for region in REGION_STATES],
crs=CRS,
)
write_dataframe(bnd_df, out_dir / "region_boundary.gpkg")
bnd_df.to_feather(out_dir / "region_boundary.feather")
bnd = bnd_df.geometry.values.data[0]
def remove_false_nodes(gdf):
"""
Clean topology of existing LineString geometry by removal of nodes of degree 2.
Parameters
----------
gdf : GeoDataFrame, GeoSeries, array of pygeos geometries
(Multi)LineString data of street network
Returns
-------
gdf : GeoDataFrame, GeoSeries
See also
--------
momepy.extend_lines
momepy.close_gaps
"""
if isinstance(gdf, (gpd.GeoDataFrame, gpd.GeoSeries)):
# explode to avoid MultiLineStrings
# double reset index due to the bug in GeoPandas explode
df = gdf.reset_index(drop=True).explode().reset_index(drop=True)
# get underlying pygeos geometry
geom = df.geometry.values.data
else:
geom = gdf
# extract array of coordinates and number per geometry
coords = pygeos.get_coordinates(geom)
indices = pygeos.get_num_coordinates(geom)
# generate a list of start and end coordinates and create point geometries
edges = [0]
i = 0
for ind in indices:
ix = i + ind
edges.append(ix - 1)
edges.append(ix)
i = ix
edges = edges[:-1]
points = pygeos.points(np.unique(coords[edges], axis=0))
# query LineString geometry to identify points intersecting 2 geometries
tree = pygeos.STRtree(geom)
inp, res = tree.query_bulk(points, predicate="intersects")
unique, counts = np.unique(inp, return_counts=True)
merge = res[np.isin(inp, unique[counts == 2])]
if len(merge) > 0:
# filter duplications and create a dictionary with indication of components to
# be merged together
dups = [
item for item, count in collections.Counter(merge).items()
if count > 1
]
split = np.split(merge, len(merge) / 2)
components = {}
for i, a in enumerate(split):
if a[0] in dups or a[1] in dups:
if a[0] in components.keys():
i = components[a[0]]
elif a[1] in components.keys():
i = components[a[1]]
components[a[0]] = i
components[a[1]] = i
# iterate through components and create new geometries
new = []
for c in set(components.values()):
keys = []
for item in components.items():
if item[1] == c:
keys.append(item[0])
new.append(pygeos.line_merge(pygeos.union_all(geom[keys])))
# remove incorrect geometries and append fixed versions
df = df.drop(merge)
final = gpd.GeoSeries(new).explode().reset_index(drop=True)
if isinstance(gdf, gpd.GeoDataFrame):
return df.append(
gpd.GeoDataFrame({df.geometry.name: final},
geometry=df.geometry.name),
ignore_index=True,
)
return df.append(final, ignore_index=True)
def enclosures(primary_barriers,
limit=None,
additional_barriers=None,
enclosure_id="eID"):
"""
Generate enclosures based on passed barriers.
Enclosures are areas enclosed from all sides by at least one type of
a barrier. Barriers are typically roads, railways, natural features
like rivers and other water bodies or coastline. Enclosures are a
result of polygonization of the ``primary_barrier`` and ``limit`` and its
subdivision based on additional_barriers.
Parameters
----------
primary_barriers : GeoDataFrame, GeoSeries
GeoDataFrame or GeoSeries containing primary barriers.
(Multi)LineString geometry is expected.
limit : GeoDataFrame, GeoSeries (default None)
GeoDataFrame or GeoSeries containing external limit of enclosures,
i.e. the area which gets partitioned. If None is passed,
the internal area of ``primary_barriers`` will be used.
additional_barriers : GeoDataFrame
GeoDataFrame or GeoSeries containing additional barriers.
(Multi)LineString geometry is expected.
enclosure_id : str (default 'eID')
name of the enclosure_id (to be created).
Returns
-------
enclosures : GeoDataFrame
GeoDataFrame containing enclosure geometries and enclosure_id
Examples
--------
>>> enclosures = mm.enclosures(streets, admin_boundary, [railway, rivers])
"""
if limit is not None:
if limit.geom_type.isin(["Polygon", "MultiPolygon"]).any():
limit = limit.boundary
barriers = pd.concat([primary_barriers.geometry, limit.geometry])
else:
barriers = primary_barriers
unioned = barriers.unary_union
polygons = polygonize(unioned)
enclosures = gpd.GeoSeries(list(polygons), crs=primary_barriers.crs)
if additional_barriers is not None:
if not isinstance(additional_barriers, list):
raise TypeError(
"`additional_barriers` expects a list of GeoDataFrames or GeoSeries."
f"Got {type(additional_barriers)}.")
additional = pd.concat([gdf.geometry for gdf in additional_barriers])
inp, res = enclosures.sindex.query_bulk(additional.geometry,
predicate="intersects")
unique = np.unique(res)
new = []
for i in unique:
poly = enclosures.values.data[i] # get enclosure polygon
crossing = inp[res == i] # get relevant additional barriers
buf = pygeos.buffer(poly, 0.01) # to avoid floating point errors
crossing_ins = pygeos.intersection(
buf, additional.values.data[crossing]
) # keeping only parts of additional barriers within polygon
union = pygeos.union_all(
np.append(crossing_ins, pygeos.boundary(poly))) # union
polygons = np.array(list(polygonize(
_pygeos_to_shapely(union)))) # polygonize
within = pygeos.covered_by(
pygeos.from_shapely(polygons),
buf) # keep only those within original polygon
new += list(polygons[within])
final_enclosures = (gpd.GeoSeries(enclosures).drop(unique).append(
gpd.GeoSeries(new)).reset_index(drop=True)).set_crs(
primary_barriers.crs)
return gpd.GeoDataFrame({enclosure_id: range(len(final_enclosures))},
geometry=final_enclosures)
return gpd.GeoDataFrame({enclosure_id: range(len(enclosures))},
geometry=enclosures)
marine = atl.append(gulf, ignore_index=True)
marine["id"] = marine.PROT_NUMBE.str.strip() + "-" + marine.BLOCK_NUMB.str.strip()
marine["name"] = (
marine.PROT_NUMBE.str.strip() + ": Block " + marine.BLOCK_NUMB.str.strip()
)
# there are a couple blocks without proper names and 0 area; drop them
marine = marine[["id", "name", "geometry"]].dropna().to_crs(DATA_CRS)
# some blocks have multiple parts, merge them
grouped = marine.groupby("id")
# save as DataFrame instead of GeoDataFrame for easier processing
marine = pd.DataFrame(
grouped.geometry.apply(lambda g: g.values.data).apply(
lambda g: pg.union_all(g) if len(g) > 1 else g[0]
)
).join(grouped.name.first())
# coerce all to MultiPolygons
ix = pg.get_type_id(marine.geometry.values) == 3
marine.loc[ix, "geometry"] = marine.loc[ix].geometry.apply(
lambda g: pg.multipolygons([g])
)
marine = (
gp.GeoDataFrame(marine, geometry="geometry", crs=DATA_CRS)
.reset_index()
.rename(columns={"index": "id"})
)
