# -*- coding: utf-8 -*-
# Copyright 2022, SERTIT-ICube - France, https://sertit.unistra.fr/
# This file is part of sertit-utils project
# https://github.com/sertit/sertit-utils
#
# 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.
"""
Vectors tools
You can use this only if you have installed sertit[full] or sertit[vectors]
"""
import logging
import os
import re
import shutil
import tarfile
import tempfile
import zipfile
from pathlib import Path
from typing import Any, Generator, Union
import numpy as np
import pandas as pd
from cloudpathlib import AnyPath, CloudPath
from cloudpathlib.exceptions import AnyPathTypeError
from fiona._err import CPLE_AppDefinedError
from fiona.errors import UnsupportedGeometryTypeError
from sertit import files, misc, strings
try:
import geopandas as gpd
from shapely import wkt
from shapely.geometry import MultiPolygon, Polygon, box
except ModuleNotFoundError as ex:
raise ModuleNotFoundError(
"Please install 'geopandas' to use the rasters package."
) from ex
from sertit.logs import SU_NAME
LOGGER = logging.getLogger(SU_NAME)
WGS84 = "EPSG:4326"
[docs]def corresponding_utm_projection(lon: float, lat: float) -> str:
"""
Find the EPSG code of the UTM projection from a lon/lat in WGS84.
.. code-block:: python
>>> corresponding_utm_projection(lon=7.8, lat=48.6) # Strasbourg
'EPSG:32632'
Args:
lon (float): Longitude (WGS84)
lat (float): Latitude (WGS84)
Returns:
str: EPSG string
"""
# EPSG code begins with 32
# Then 6 if north, 7 if south -> (np.sign(lat) + 1) / 2 * 100 == 1 if lat > 0 (north), 0 if lat < 0 (south)
# Then EPSG code with usual formula np.floor((180 + lon) / 6) + 1)
epsg = int(32700 - (np.sign(lat) + 1) / 2 * 100 + np.floor((180 + lon) / 6) + 1)
return f"EPSG:{epsg}"
[docs]def from_polygon_to_bounds(
polygon: Union[Polygon, MultiPolygon]
) -> (float, float, float, float):
"""
Convert a :code:`shapely.polygon` to its bounds, sorted as :code:`left, bottom, right, top`.
.. code-block:: python
>>> poly = Polygon(((0., 0.), (0., 1.), (1., 1.), (1., 0.), (0., 0.)))
>>> from_polygon_to_bounds(poly)
(0.0, 0.0, 1.0, 1.0)
Args:
polygon (MultiPolygon): polygon to convert
Returns:
(float, float, float, float): left, bottom, right, top
"""
left = polygon.bounds[0] # xmin
bottom = polygon.bounds[1] # ymin
right = polygon.bounds[2] # xmax
top = polygon.bounds[3] # ymax
assert left < right
assert bottom < top
return left, bottom, right, top
[docs]def from_bounds_to_polygon(
left: float, bottom: float, right: float, top: float
) -> Polygon:
"""
Convert the bounds to a :code:`shapely.polygon`.
.. code-block:: python
>>> poly = from_bounds_to_polygon(0.0, 0.0, 1.0, 1.0)
>>> print(poly)
'POLYGON ((1 0, 1 1, 0 1, 0 0, 1 0))'
Args:
left (float): Left coordinates
bottom (float): Bottom coordinates
right (float): Right coordinates
top (float): Top coordinates
Returns:
Polygon: Polygon corresponding to the bounds
"""
return box(min(left, right), min(top, bottom), max(left, right), max(top, bottom))
[docs]def get_geodf(
geometry: Union[Polygon, list, gpd.GeoSeries], crs: str
) -> gpd.GeoDataFrame:
"""
Get a GeoDataFrame from a geometry and a crs
.. code-block:: python
>>> poly = Polygon(((0., 0.), (0., 1.), (1., 1.), (1., 0.), (0., 0.)))
>>> geodf = get_geodf(poly, crs=WGS84)
>>> print(geodf)
geometry
0 POLYGON ((0.00000 0.00000, 0.00000 1.00000, 1....
Args:
geometry (Union[Polygon, list]): List of Polygons, or Polygon or bounds
crs (str): CRS of the polygon
Returns:
gpd.GeoDataFrame: Geometry as a geodataframe
"""
if isinstance(geometry, list):
if isinstance(geometry[0], Polygon):
pass
else:
try:
geometry = [from_bounds_to_polygon(*geometry)]
except TypeError as ex:
raise TypeError(
"Give the extent as 'left', 'bottom', 'right', and 'top'"
) from ex
elif isinstance(geometry, Polygon):
geometry = [geometry]
elif isinstance(geometry, gpd.GeoSeries):
geometry = geometry.geometry
else:
raise TypeError("geometry should be a list or a Polygon.")
return gpd.GeoDataFrame(geometry=geometry, crs=crs)
[docs]def set_kml_driver() -> None:
"""
Set KML driver for Fiona data (use it at your own risks !)
.. code-block:: python
>>> path = "path/to/kml.kml"
>>> gpd.read_file(path)
fiona.errors.DriverError: unsupported driver: 'LIBKML'
>>> set_kml_driver()
>>> gpd.read_file(path)
Name ... geometry
0 CC679_new_AOI2_3 ... POLYGON Z ((45.03532 32.49765 0.00000, 46.1947...
[1 rows x 12 columns]
"""
import fiona
drivers = fiona.drvsupport.supported_drivers
if "LIBKML" not in drivers:
drivers["LIBKML"] = "rw"
if "KML" not in drivers: # Just in case
drivers["KML"] = "rw"
[docs]def get_aoi_wkt(
aoi_path: Union[str, CloudPath, Path], as_str: bool = True
) -> Union[str, Polygon]:
"""
Get AOI formatted as a WKT from files that can be read by Fiona (like shapefiles, ...)
or directly from a WKT file. The use of KML has been forced (use it at your own risks !).
See: https://fiona.readthedocs.io/en/latest/fiona.html#fiona.open
It is assessed that:
- only **one** polygon composes the AOI (as only the first one is read)
- it should be specified in lat/lon (WGS84) if a WKT file is provided
.. code-block:: python
>>> path = "path/to/vec.geojson" # OK with ESRI Shapefile, geojson, WKT, KML...
>>> get_aoi_wkt(path)
'POLYGON Z ((46.1947755465253067 32.4973553439109324 0.0000000000000000, 45.0353174370802520 32.4976496856158974
0.0000000000000000, 45.0355748149750283 34.1139970085580018 0.0000000000000000, 46.1956059695554089
34.1144793800670882 0.0000000000000000, 46.1947755465253067 32.4973553439109324 0.0000000000000000))'
Args:
aoi_path (Union[str, CloudPath, Path]): Absolute or relative path to an AOI.
Its format should be WKT or any format read by Fiona, like shapefiles.
as_str (bool): If True, return WKT as a str, otherwise as a shapely geometry
Returns:
Union[str, Polygon]: AOI formatted as a WKT stored in lat/lon
"""
aoi_path = AnyPath(aoi_path)
if not aoi_path.is_file():
raise FileNotFoundError(f"AOI file {aoi_path} does not exist.")
if aoi_path.suffix == ".wkt":
try:
with open(aoi_path, "r") as aoi_f:
aoi = wkt.load(aoi_f)
except Exception as ex:
raise ValueError("AOI WKT cannot be read") from ex
else:
try:
# Open file
aoi_file = read(aoi_path, crs=WGS84)
# Get envelope polygon
geom = aoi_file["geometry"]
if len(geom) > 1:
LOGGER.warning(
"Your AOI contains several polygons. Only the first will be treated !"
)
polygon = geom[0].convex_hull
# Convert to WKT
aoi = wkt.loads(str(polygon))
except Exception as ex:
raise ValueError("AOI cannot be read by Fiona") from ex
# Convert to string if needed
if as_str:
aoi = wkt.dumps(aoi)
LOGGER.debug("Specified AOI in WKT: %s", aoi)
return aoi
[docs]def get_wider_exterior(vector: gpd.GeoDataFrame) -> gpd.GeoDataFrame:
"""
Get the wider exterior of a MultiPolygon as a Polygon
Args:
vector (gpd.GeoDataFrame): Polygon to simplify
Returns:
vector: gpd.GeoDataFrame: Wider exterior
"""
# Get the footprint max (discard small holes stored in other polygons)
wider = vector[vector.area == np.max(vector.area)]
# Only select the exterior of this footprint(sometimes some holes persist)
if not wider.empty:
poly = Polygon(list(wider.exterior.iat[0].coords))
wider = gpd.GeoDataFrame(geometry=[poly], crs=wider.crs)
# Resets index as we only got one polygon left which should have index 0
wider.reset_index(inplace=True)
return wider
def _to_polygons(val: Any) -> Polygon:
"""
Convert to polygon (to be used in pandas) -> convert the geometry column
Args:
val (Any): Pandas value that has a "coordinates" field
Returns:
Polygon: Pandas value as a Polygon
"""
# Donut cases
if len(val["coordinates"]) > 1:
poly = Polygon(val["coordinates"][0], val["coordinates"][1:])
else:
poly = Polygon(val["coordinates"][0])
pass
return poly
[docs]def shapes_to_gdf(shapes: Generator, crs: str) -> gpd.GeoDataFrame:
"""
Convert rasterio shapes to geodataframe
Args:
shapes (Generator): Shapes from rasterio
crs: Wanted CRS of the vector. If None, using naive or origin CRS.
Returns:
gpd.GeoDataFrame: Shapes as a GeoDataFrame
"""
# Convert results to pandas (because of invalid geometries) and save it
pd_results = pd.DataFrame(shapes, columns=["geometry", "raster_val"])
if not pd_results.empty:
# Convert to proper polygons(correct geometries)
pd_results.geometry = pd_results.geometry.apply(_to_polygons)
# Convert to geodataframe with correct geometry
gdf = gpd.GeoDataFrame(pd_results, geometry=pd_results.geometry, crs=crs)
# Return valid geometries
gdf = make_valid(gdf)
return gdf
[docs]def read(
path: Union[str, CloudPath, Path], crs: Any = None, archive_regex: str = None
) -> gpd.GeoDataFrame:
"""
Read any vector:
- if KML: sets correctly the drivers and open layered KML (you may need :code:`ogr2ogr` to make it work !)
- if archive (only zip or tar), use a regex to look for the vector inside the archive.
You can use this `site <https://regexr.com/>`_ to build your regex.
- if GML: manages the empty errors
.. code-block:: python
>>> # Usual
>>> path = 'D:/path/to/vector.geojson'
>>> vectors.read(path, crs=WGS84)
Name ... geometry
0 Sentinel-1 Image Overlay ... POLYGON ((0.85336 42.24660, -2.32032 42.65493,...
>>> # Archive
>>> arch_path = 'D:/path/to/zip.zip'
>>> vectors.read(arch_path, archive_regex=r".*map-overlay.kml")
Name ... geometry
0 Sentinel-1 Image Overlay ... POLYGON ((0.85336 42.24660, -2.32032 42.65493,...
Args:
path (Union[str, CloudPath, Path]): Path to vector to read. In case of archive, path to the archive.
crs: Wanted CRS of the vector. If None, using naive or origin CRS.
archive_regex (str): [Archive only] Regex for the wanted vector inside the archive
Returns:
gpd.GeoDataFrame: Read vector as a GeoDataFrame
"""
tmp_dir = None
arch_vect_path = None
try:
path = AnyPath(path)
# Load vector in cache if needed (geopandas do not use correctly S3 paths for now)
if isinstance(path, CloudPath):
tmp_dir = tempfile.TemporaryDirectory()
if path.suffix == ".shp":
# Download everything to disk
for shp_file in path.parent.glob(path.with_suffix(".*").name):
cached_path = shp_file.download_to(tmp_dir.name)
if cached_path.suffix == ".shp":
path = cached_path
else:
path = AnyPath(path.fspath)
# Manage archive case
if path.suffix in [".tar", ".zip"]:
prefix = path.suffix[-3:]
file_list = files.get_archived_file_list(path)
try:
regex = re.compile(archive_regex)
arch_vect_path = list(filter(regex.match, file_list))[0]
if isinstance(path, CloudPath):
vect_path = f"{prefix}+{path}!{arch_vect_path}"
else:
vect_path = f"{prefix}://{path}!{arch_vect_path}"
except IndexError:
raise FileNotFoundError(
f"Impossible to find vector {archive_regex} in {files.get_filename(path)}"
)
elif path.suffixes == [".tar", ".gz"]:
raise TypeError(
".tar.gz files are too slow to read from inside the archive. Please extract them instead."
)
else:
vect_path = str(path)
except AnyPathTypeError:
vect_path = str(path)
if not os.path.isfile(path):
raise FileNotFoundError(f"Non existing file: {path}")
# Open vector
try:
# Discard some weird error concerning a NULL pointer that outputs a ValueError (as we already except it)
fiona_logger = logging.getLogger("fiona")
fiona_logger.setLevel(logging.CRITICAL)
# Read mask
# Manage KML driver
if vect_path.endswith(".kml"):
set_kml_driver()
vect = gpd.GeoDataFrame()
# Document tags in KML file are separate layers for GeoPandas.
# When you try to get the KML content, you actually get the first layer.
# So you need for loop for iterating over layers.
# https://gis.stackexchange.com/questions/328525/geopandas-read-file-only-reading-first-part-of-kml/328554
import fiona
for layer in fiona.listlayers(vect_path):
try:
vect_layer = gpd.read_file(vect_path, driver="KML", layer=layer)
if not vect_layer.empty:
# KML files are always in WGS84 (and does not contain this information)
vect_layer.crs = WGS84
vect = pd.concat([vect, vect_layer])
except ValueError:
pass # Except Null Layer
# Workaround for archived KML -> they may be empty
# Convert KML to GeoJSON
# Needs ogr2ogr here
if vect.empty and shutil.which("ogr2ogr"):
# Open the geojson
if not tmp_dir:
tmp_dir = tempfile.TemporaryDirectory()
vect_path_gj = ogr2geojson(path, tmp_dir.name, arch_vect_path)
vect = gpd.read_file(vect_path_gj)
else:
vect.crs = WGS84 # Force set CRS to whole vector
else:
vect = gpd.read_file(vect_path)
# Manage naive geometries
if vect.crs and crs:
vect = vect.to_crs(crs)
# Set fiona logger back to what it was
fiona_logger.setLevel(logging.INFO)
except (ValueError, UnsupportedGeometryTypeError) as ex:
# Do not print warning for null layer
if "Null layer" not in str(ex):
LOGGER.warning(ex)
vect = gpd.GeoDataFrame(geometry=[], crs=crs)
except CPLE_AppDefinedError as ex:
# Needs ogr2ogr here
if shutil.which("ogr2ogr"):
# Open as geojson
if not tmp_dir:
tmp_dir = tempfile.TemporaryDirectory()
vect_path_gj = ogr2geojson(path, tmp_dir.name, arch_vect_path)
vect = gpd.read_file(vect_path_gj)
vect.crs = None
else:
# Do not print warning for null layer
if "Null layer" not in str(ex):
LOGGER.warning(ex)
vect = gpd.GeoDataFrame(geometry=[], crs=crs)
# Clean
if tmp_dir:
tmp_dir.cleanup()
return vect
[docs]def ogr2geojson(
path: Union[str, CloudPath, Path],
out_dir: Union[str, CloudPath, Path],
arch_vect_path: str = None,
) -> str:
"""
Wrapper of ogr2ogr function, converting the input vector to GeoJSON.
Args:
path (Union[str, CloudPath, Path]): Path to vector to read. In case of archive, path to the archive.
out_dir (Union[str, CloudPath, Path]): Output directory
arch_vect_path: If archived vector, archive path
Returns:
str: Converted file
"""
assert shutil.which("ogr2ogr") # Needs ogr2ogr here
out_dir = str(out_dir)
if path.suffix == ".zip":
with zipfile.ZipFile(path, "r") as zip_ds:
vect_path = zip_ds.extract(arch_vect_path, out_dir)
elif path.suffix == ".tar":
with tarfile.open(path, "r") as tar_ds:
tar_ds.extract(arch_vect_path, out_dir)
vect_path = os.path.join(out_dir, arch_vect_path)
else:
vect_path = str(path)
vect_path_gj = os.path.join(
out_dir,
os.path.basename(vect_path).replace(files.get_ext(vect_path), "geojson"),
)
cmd_line = [
"ogr2ogr",
"-fieldTypeToString DateTime", # Disable warning
"-f GeoJSON",
strings.to_cmd_string(vect_path_gj), # dst
strings.to_cmd_string(vect_path), # src
]
try:
misc.run_cli(cmd_line)
except RuntimeError as ex:
raise RuntimeError(f"Something went wrong with ogr2ogr: {ex}") from ex
return vect_path_gj
[docs]def make_valid(gdf: gpd.GeoDataFrame, verbose=False) -> gpd.GeoDataFrame:
try:
geos_logger = logging.getLogger("shapely.geos")
previous_level = geos_logger.level
if verbose:
logging.debug("Invalid geometries:\n" f"\t{gdf[~gdf.is_valid]}")
else:
geos_logger.setLevel(logging.CRITICAL)
# Discard self-intersection and null geometries
from shapely.validation import make_valid
gdf.geometry = gdf.geometry.apply(make_valid)
if not verbose:
geos_logger.setLevel(previous_level)
except ImportError:
import shapely
LOGGER.warning(
f"make_valid not available in shapely (version {shapely.__version__} < 1.8). "
f"The obtained vector may be broken !"
)
return gdf
