def check_crs(crs):
"""
Checks a CRS instance
Args:
crs (``CRS`` | int | dict | str): The CRS instance.
Returns:
``rasterio.crs.CRS``
"""
if isinstance(crs, pyproj.crs.crs.CRS):
dst_crs = CRS.from_proj4(crs.to_proj4())
elif isinstance(crs, CRS):
dst_crs = crs
elif isinstance(crs, int):
dst_crs = CRS.from_epsg(crs)
elif isinstance(crs, dict):
dst_crs = CRS.from_dict(crs)
elif isinstance(crs, str):
if crs.startswith('+proj'):
dst_crs = CRS.from_proj4(crs)
else:
dst_crs = CRS.from_string(crs)
else:
logger.exception(' The CRS was not understood.')
raise TypeError
return dst_crs
def make_geotiff(grid_x, grid_y, points, data_to_grid,name,epsg_data,no_data):
#grid the data. The linear grid help id nan's.
nan_grid = griddata(points, data_to_grid, (grid_x, grid_y), method='linear')
data_grid = griddata(points, data_to_grid, (grid_x, grid_y), method='nearest')
sum_data = np.sum([nan_grid*0,data_grid], axis=0)
#set areas without data and with very large displacements to the no_data value
a = np.isnan(sum_data)*no_data
x_list = np.arange(0,sum_data.flatten().size,1)
b1 = x_list[abs(sum_data.flatten()) > np.median(abs(data_to_grid))*5];
b2 = x_list[a.flatten()==no_data];
data_grid_flatten= data_grid.flatten()
data_grid_flatten[b1]=no_data
data_grid_flatten[b2]=no_data
#reshape, as expected for geotiffs
data_grid1= data_grid_flatten.reshape( data_grid.shape)
data_grid1_ta=np.rot90(data_grid1)
#create the affine transform
aff=Affine.translation(min(x)-window_compare/2, max(y)+window_compare/2)*Affine.scale(window_compare,-window_compare)
#coordinate system for geotiffs
a,b=data_grid1.shape
epsg_code = 'epsg:'+str(epsg_data)
c=CRS.from_dict(init=epsg_code)
d = {'driver' : 'GTiff','dtype' : 'float64','nodata': no_data, 'width': a+1, 'height' : b+1,'count':1,'crs':c,'transform':aff}
with rio.open(name, 'w', **d) as outf:
outf.write(data_grid1_ta, 1)
return
def _reproject_polygon(self, dst_crs):
"""
Reproject polygon objects to destination projection.
fiona transform geom object does not handle shapely objects but
"GeoJSON-like" dictionaries instead.
"""
# get epsg
src_crs = self.src_crs
if isinstance(src_crs, int):
# assume epsg number
epsg = src_crs
src_crs = CRS.from_epsg(epsg)
elif isinstance(src_crs, dict):
src_crs = CRS.from_dict(**src_crs)
epsg = src_crs.to_epsg()
elif isinstance(src_crs, CRS):
epsg = src_crs.to_epsg()
else:
src_crs = CRS.from_string(src_crs)
epsg = src_crs.to_epsg()
if dst_crs.to_epsg() != epsg:
if isinstance(self.polygon, MultiPolygon):
coords = [
list(geom.exterior.coords) for geom in self.polygon.geoms
]
type_str = 'MultiPolygon'
transformed_poly = transform_geom(src_crs, dst_crs, {
'type': type_str,
'coordinates': coords
})
# convert all polygon features back to shapely polygons
polygons = [
Polygon(transformed_poly[i]["coordinates"][0])
for i in range(len(transformed_poly))
]
# join all shapely polygons to a single layer
self.polygon = unary_union(MultiPolygon(polygons))
else:
coords = [list(self.polygon.exterior.coords)]
type_str = 'Polygon'
transformed_poly = transform_geom(src_crs, dst_crs, {
'type': type_str,
'coordinates': coords
})
self.polygon = Polygon(transformed_poly['coordinates'][0])
def test_areas_rasterio(self):
"""Test all areas have valid projections with rasterio."""
try:
from rasterio.crs import CRS
except ImportError:
return unittest.skip("Missing rasterio dependency")
if not hasattr(CRS, 'from_dict'):
return unittest.skip("RasterIO 1.0+ required")
from pyresample import parse_area_file
from satpy.resample import get_area_file
all_areas = parse_area_file(get_area_file())
for area_obj in all_areas:
if getattr(area_obj, 'optimize_projection', False):
# the PROJ.4 is known to not be valid on this DynamicAreaDef
continue
proj_dict = area_obj.proj_dict
_ = CRS.from_dict(proj_dict)
def get_profile(lon, lat, crs, size=SIZE):
x, y = transform(Proj(init='epsg:4326'), Proj(init=crs), lon, lat)
x, y = int(round(x)), int(round(y))
xmin = x - HALF_SIZE
ymin = y - HALF_SIZE
return {
'compress': 'lzw',
'count': len(INPUT_BANDS),
'crs': CRS.from_dict(init=crs),
'driver': 'GTiff',
'dtype': 'uint16',
'height': SIZE,
'interleave': 'pixel',
'nodata': None,
'tiled': False,
'transform': Affine(RES, 0, xmin, 0, -RES, ymin),
'width': SIZE
}
def check_crs(crs):
"""
Checks a CRS instance
Args:
crs (``CRS`` | int | dict | str): The CRS instance.
Returns:
``rasterio.crs.CRS``
"""
import warnings
with rio.Env():
with warnings.catch_warnings():
warnings.simplefilter('ignore', UserWarning)
if isinstance(crs, pyproj.crs.crs.CRS):
dst_crs = CRS.from_proj4(crs.to_proj4())
elif isinstance(crs, CRS):
dst_crs = crs
elif isinstance(crs, int):
dst_crs = CRS.from_epsg(crs)
elif isinstance(crs, dict):
dst_crs = CRS.from_dict(crs)
elif isinstance(crs, str):
if crs.startswith('+proj'):
dst_crs = CRS.from_proj4(crs)
else:
dst_crs = CRS.from_string(crs.replace('+init=', ''))
else:
logger.exception(' The CRS was not understood.')
raise TypeError
return dst_crs
def test_areas_rasterio(self):
"""Test all areas have valid projections with rasterio."""
try:
from rasterio.crs import CRS
except ImportError:
return unittest.skip("Missing rasterio dependency")
if not hasattr(CRS, 'from_dict'):
return unittest.skip("RasterIO 1.0+ required")
import numpy as np
import xarray as xr
from pyresample import parse_area_file
from pyresample.geometry import SwathDefinition
from satpy.resample import get_area_file
lons = np.array([[0, 0.1, 0.2], [0.05, 0.15, 0.25]])
lats = np.array([[0, 0.1, 0.2], [0.05, 0.15, 0.25]])
lons = xr.DataArray(lons)
lats = xr.DataArray(lats)
swath_def = SwathDefinition(lons, lats)
all_areas = parse_area_file(get_area_file())
for area_obj in all_areas:
if hasattr(area_obj, 'freeze'):
try:
area_obj = area_obj.freeze(lonslats=swath_def)
except RuntimeError:
# we didn't provide enough info to freeze, hard to guess
# in a generic test so just skip this area
continue
proj_dict = area_obj.proj_dict
if proj_dict.get('proj') in ('ob_tran', 'nsper') and \
'wktext' not in proj_dict:
# FIXME: rasterio doesn't understand ob_tran unless +wktext
# See: https://github.com/pyproj4/pyproj/issues/357
# pyproj 2.0+ seems to drop wktext from PROJ dict
continue
_ = CRS.from_dict(proj_dict)
def test_meta_of_rasterio(self):
expected_general = {
'driver': 'GTiff',
'dtype': 'uint16',
'nodata': None,
'width': 9,
'height': 8,
'count': 7,
'crs': CRS.from_dict(init='epsg:32618'),
}
self.assertEqual(expected_general['driver'],
self.landsat5.meta['driver'])
self.assertEqual(expected_general['dtype'],
self.landsat5.meta['dtype'])
self.assertEqual(expected_general['nodata'],
self.landsat5.meta['nodata'])
self.assertEqual(expected_general['width'],
self.landsat5.meta['width'])
self.assertEqual(expected_general["height"],
self.landsat5.meta["height"])
self.assertEqual(expected_general["count"],
self.landsat5.meta["count"])
self.assertEqual(expected_general["crs"], self.landsat5.meta["crs"])
def main():
#-- Read the system arguments listed after the program
long_options = ['DIR=', 'FILTER=', 'DX=', 'DY=']
optlist, arglist = getopt.getopt(sys.argv[1:], 'D:F:X:Y:', long_options)
#-- Set default settings
ddir = os.path.join(os.path.expanduser('~'),'GL_learning_data',\
'geocoded_v1','stitched.dir',\
'atrous_32init_drop0.2_customLossR727.dir','shapefiles.dir')
FILTER = 6000
dx = 100.
dy = 100.
for opt, arg in optlist:
if opt in ("-D", "--DIR"):
ddir = os.path.expanduser(arg)
elif opt in ("-F", "--FILTER"):
if arg not in ['NONE', 'none', 'None', 'N', 'n', 0]:
FILTER = float(arg)
elif opt in ('-X', '--DX'):
dx = float(arg)
elif opt in ('-Y', '--DY'):
dy = float(arg)
flt_str = '_%.1fkm' % (FILTER / 1000)
#-- Get list of files
fileList = os.listdir(ddir)
pred_list = [
f for f in fileList
if (f.endswith('%s.shp' % flt_str) and ('ERR' not in f))
]
print(pred_list)
print(ddir)
#-- read one error scene to get projection
gdf = gpd.read_file(os.path.join(ddir, pred_list[0]))
crs_wkt = CRS.from_dict(gdf.crs).to_wkt()
#-- go through shapefiles and shift them by half a pixel
for f in pred_list:
gdf = gpd.read_file(os.path.join(ddir, f))
for g in range(len(gdf['geometry'])):
#-- get coordinates
x, y = gdf['geometry'][g].coords.xy
#-- convert to numpy array
x = np.array(x)
y = np.array(y)
#-- add offset
x -= dx / 2
y += dy / 2
#-- make new linestring
ll = LineString(zip(x, y))
#-- replace original geometry
gdf['geometry'][g] = ll
try:
#-- save update geodataframe to file
gdf.to_file(os.path.join(ddir, f),
driver='ESRI Shapefile',
crs_wkt=crs_wkt)
except:
print('empty file.')
print(f)
pass
# ROI information
dir_location = os.path.join(dir_data, location)
if not os.path.exists(dir_location):
os.mkdir(dir_location)
x_min, y_min, x_max, y_max = df_communities.loc[df_communities["NAAM"] == location, "geometry"].to_numpy()[0].bounds
x_min, y_min = np.floor([x_min, y_min])
x_max, y_max = np.ceil([x_max, y_max])
x_max += (s1_resolution - ((x_max - x_min) % s1_resolution))
y_max += (s1_resolution - ((y_max - y_min) % s1_resolution))
roi_extent = (x_min, y_min, x_max, y_max)
roi_extent_wgs = transformer_utm_wgs.transform(x_min, y_min) + transformer_utm_wgs.transform(x_max, y_max)
roi_shape = (int((x_max - x_min) / s1_resolution), int((y_max - y_min) / s1_resolution)) # width, height
roi_transform = rasterio.transform.from_bounds(*roi_extent, *roi_shape)
roi_metadata = {
"crs": CRS.from_dict(init=utm),
"transform": roi_transform,
"width": roi_shape[0],
"height": roi_shape[1]
}
pixel_resolution_x = roi_transform[0]
pixel_resolution_y = -roi_transform[4]
# Tree & PW presence data
print("{} - Gathering LC data...".format(dt.now()))
trees_filename = os.path.join(dir_location, "Trees.tif")
if not os.path.exists(trees_filename):
trees = caf.mosaic_tiles(dir_lc, *roi_extent, roi_transform, *roi_shape, utm, "int8", nd_pres, query_string="Trees",
kbl_dir=dir_kbl, kbl_scale=0, resampling="max", fill_nodata=False,
mosaic_filename=trees_filename)
else:
def _parse_parameter_file(self):
self.num_particles = {}
with rasterio.open(self.parameter_filename, "r") as f:
for key in f.meta.keys():
v = f.meta[key]
self.parameters[key] = v
self.parameters["res"] = f.res
self.parameters["profile"] = f.profile
self.current_time = 0
# overwrite crs if one is provided by user
if not (self.crs is None):
# make sure user provided CRS is valid CRS object
if not isinstance(self.crs, CRS):
if isinstance(self.crs, int):
# assume epsg number
self.crs = CRS.from_epsg(self.crs)
elif isinstance(self.crs, dict):
self.crs = CRS.from_dict(**self.crs)
else:
self.crs = CRS.from_string(self.crs)
# get reprojected transform
left_edge = self.parameters["transform"] * (0, 0)
right_edge = self.parameters["transform"] * (
self.parameters["width"], self.parameters["height"])
transform, width, height = warp.calculate_default_transform(
self.parameters["crs"],
self.crs,
self.parameters["width"],
self.parameters["height"],
left=left_edge[0],
bottom=left_edge[1],
right=right_edge[0],
top=right_edge[1],
# resolution=self.parameters["transform"][0]
dst_width=self.parameters["width"],
dst_height=self.parameters["height"]
) # current solution can create rectangular pixels
# xs, ys = warp.transform(
# self.parameters["crs"],
# dst_crs,
# [left_edge[0], right_edge[0]],
# [left_edge[1], right_edge[1]],
# zs=None
# )
# update parameters
self.parameters["res"] = (transform[0], -transform[4])
self.parameters["crs"] = self.crs
self.parameters["transform"] = transform
self.parameters["width"] = width
self.parameters["height"] = height
else:
# if no crs has be provided replace None with base image CRS
self.crs = self.parameters["crs"]
# get units and conversion factor to metres
self.parameters["units"] = self.parameters["crs"].linear_units
# for non-projected crs this is unknown
if self.parameters["units"] == 'unknown':
mylog.warning(f"Dataset CRS {self.parameters['crs']} "
"units are 'unknown'. Using meters.")
self.parameters["units"] = 'm' # just a place holder
else:
mylog.info(f"Dataset CRS {self.parameters['crs']} "
f"units are '{self.parameters['units']}'. ")
# set domain
width = self.parameters["width"]
height = self.parameters["height"]
transform = self.parameters["transform"]
self.dimensionality = 3
self.domain_dimensions = np.array([width, height, 1], dtype=np.int32)
rast_left = np.concatenate([transform * (0, 0), [0]])
rast_right = np.concatenate([transform * (width, height), [1]])
# save dimensions that need to be flipped
self._flip_axes = np.where(rast_left > rast_right)[0]
self.domain_left_edge = self.arr(
np.min([rast_left, rast_right], axis=0), self.parameters["units"])
self.domain_right_edge = self.arr(
np.max([rast_left, rast_right], axis=0), self.parameters["units"])
self.resolution = self.arr(self.parameters["res"],
self.parameters["units"])
def read_raster(file_name, band=[1], src_crs=None, window=False, geometry=False,
dst_crs=False, transform=None, width=None, height=None,
resampling=Resampling.nearest):
""" Read raster of bands and set 0 values to the masked ones. Each
band is an event. Select region using window or geometry. Reproject
input by proving dst_crs and/or (transform, width, height). Returns matrix
in 2d: band x coordinates in 1d (evtl. reshape to band x height x width)
Parameters:
file_name (str): name of the file
band (list(int), optional): band number to read. Default: 1
window (rasterio.windows.Window, optional): window to read
geometry (shapely.geometry, optional): consider pixels only in shape
dst_crs (crs, optional): reproject to given crs
transform (rasterio.Affine): affine transformation to apply
wdith (float): number of lons for transform
height (float): number of lats for transform
resampling (rasterio.warp,.Resampling optional): resampling
function used for reprojection to dst_crs
Returns:
dict (meta), np.array (band x coordinates_in_1d)
"""
LOGGER.info('Reading %s', file_name)
if os.path.splitext(file_name)[1] == '.gz':
file_name = '/vsigzip/' + file_name
with rasterio.Env():
with rasterio.open(file_name, 'r') as src:
if src_crs is None:
src_meta = CRS.from_dict(DEF_CRS) if not src.crs else src.crs
else:
src_meta = src_crs
if dst_crs or transform:
LOGGER.debug('Reprojecting ...')
if not dst_crs:
dst_crs = src_meta
if not transform:
transform, width, height = calculate_default_transform(\
src_meta, dst_crs, src.width, src.height, *src.bounds)
dst_meta = src.meta.copy()
dst_meta.update({'crs': dst_crs,
'transform': transform,
'width': width,
'height': height
})
kwargs = {}
if src.meta['nodata']:
kwargs['src_nodata'] = src.meta['nodata']
kwargs['dst_nodata'] = src.meta['nodata']
intensity = np.zeros((len(band), height, width))
for idx_band, i_band in enumerate(band):
reproject(source=src.read(i_band),
destination=intensity[idx_band, :],
src_transform=src.transform,
src_crs=src_meta,
dst_transform=transform,
dst_crs=dst_crs,
resampling=resampling,
**kwargs)
if dst_meta['nodata'] and np.isnan(dst_meta['nodata']):
intensity[idx_band, :][np.isnan(intensity[idx_band, :])] = 0
else:
intensity[idx_band, :][intensity[idx_band, :] == dst_meta['nodata']] = 0
meta = dst_meta
return meta, intensity.reshape((len(band), meta['height']*meta['width']))
meta = src.meta.copy()
if geometry:
inten, mask_trans = mask(src, geometry, crop=True, indexes=band)
if meta['nodata'] and np.isnan(meta['nodata']):
inten[np.isnan(inten)] = 0
else:
inten[inten == meta['nodata']] = 0
meta.update({"height": inten.shape[1],
"width": inten.shape[2],
"transform": mask_trans})
else:
masked_array = src.read(band, window=window, masked=True)
inten = masked_array.data
inten[masked_array.mask] = 0
if window:
meta.update({"height": window.height, \
"width": window.width, \
"transform": rasterio.windows.transform(window, src.transform)})
if not meta['crs']:
meta['crs'] = CRS.from_dict(DEF_CRS)
intensity = inten[range(len(band)), :]
return meta, intensity.reshape((len(band), meta['height']*meta['width']))
def test_issue1620():
"""Different forms of EPSG:3857 are equal"""
assert CRS.from_wkt(
'PROJCS["WGS 84 / Pseudo-Mercator",GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]],PROJECTION["Mercator_1SP"],PARAMETER["central_meridian",0],PARAMETER["scale_factor",1],PARAMETER["false_easting",0],PARAMETER["false_northing",0],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AXIS["X",EAST],AXIS["Y",NORTH],EXTENSION["PROJ4","+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +wktext +no_defs"],AUTHORITY["EPSG","3857"]]'
) == CRS.from_dict(init='epsg:3857')
def test_issue1620():
"""Different forms of EPSG:3857 are equal"""
assert CRS.from_wkt('PROJCS["WGS 84 / Pseudo-Mercator",GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]],PROJECTION["Mercator_1SP"],PARAMETER["central_meridian",0],PARAMETER["scale_factor",1],PARAMETER["false_easting",0],PARAMETER["false_northing",0],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AXIS["X",EAST],AXIS["Y",NORTH],EXTENSION["PROJ4","+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +wktext +no_defs"],AUTHORITY["EPSG","3857"]]') == CRS.from_dict(init='epsg:3857')
len(col_dan_1km_ind), len(row_dan_1km_ind))
kwargs_1km_sub = {
'driver':
'GTiff',
'dtype':
'float32',
'nodata':
0.0,
'width':
len(lon_world_ease_1km),
'height':
len(lat_world_ease_1km),
'count':
1,
'crs':
CRS.from_dict(init='epsg:6933'),
'transform':
Affine(1000.89502334956, 0.0, -17367530.44516138, 0.0, -1000.89502334956,
7314540.79258289)
}
smap_sm_dan_1km_output = sub_n_reproj(smap_sm_dan_1km_sub, kwargs_1km_sub,
sub_window_dan_1km, output_crs)
masked_ds_dan_1km, mask_transform_ds_dan_1km = mask(
dataset=smap_sm_dan_1km_output, shapes=crop_shape, crop=True)
masked_ds_dan_1km[np.where(masked_ds_dan_1km == 0)] = np.nan
sub_window_dan_9km = Window(col_dan_9km_ind[0], row_dan_9km_ind[0],
len(col_dan_9km_ind), len(row_dan_9km_ind))
kwargs_9km_sub = {
'driver':
import re
import torch
from torch.autograd import Variable
import torch.backends.cudnn as cudnn
import torch.nn as nn
from util.visualizer import Visualizer
import networks.networks as networks
from .mtl_test import MTL_Test as GenericTestModel
from rasterio.crs import CRS
from rasterio.transform import Affine
GEN_META = {'driver': 'GTiff', 'dtype': 'float32', 'nodata': None, 'width': 3816, 'height': 2550, 'count': 1, 'transform': Affine(1.0, 0.0, 0.0, 0.0, 1.0, 0.0), 'crs': CRS.from_dict(init='epsg:26915')}
class TestModel(GenericTestModel):
def initialize(self, opt):
GenericTestModel.initialize(self, opt)
self.get_color_palette()
def name(self):
return 'Raster Test Model'
def get_color_palette(self):
if self.opt.dataset_name == 'dfc':
self.opt.color_palette = [
[0, 0, 0], [0, 205, 0], [127, 255, 0], [46, 139, 87], [0, 139, 0], [0, 70, 0], [160, 82, 45], [0, 255, 255], [255, 255, 255], [216, 191, 216], [255, 0, 0], [170, 160, 150], [128, 128, 128], [160, 0, 0], [80, 0, 0], [232, 161, 24], [255, 255, 0], [238, 154, 0], [255, 0, 255], [0, 0, 255], [176, 196, 222]
]
from util.visualizer import Visualizer
import networks.networks as networks
from .mtl_test import MTL_Test as GenericTestModel
from rasterio.crs import CRS
from rasterio.transform import Affine
OUT_META_SEM = [{
'driver': 'GTiff',
'dtype': 'uint8',
'nodata': None,
'width': 1192,
'height': 1202,
'count': 1,
'crs': CRS.from_dict(init='epsg:26915'),
'transform': Affine(0.5, 0.0, 271460.0, 0.0, -0.5, 3290290.0)
}, {
'driver': 'GTiff',
'dtype': 'uint8',
'nodata': None,
'width': 1192,
'height': 1202,
'count': 1,
'crs': CRS.from_dict(init='epsg:26915'),
'transform': Affine(0.5, 0.0, 271460.0, 0.0, -0.5, 3290891.0)
}, {
'driver': 'GTiff',
'dtype': 'uint8',
'nodata': None,
'width': 1192,
def warp(filename,
resampling='nearest',
bounds=None,
crs=None,
res=None,
nodata=0,
warp_mem_limit=512,
num_threads=1,
tap=False):
"""
Warps an image to a VRT object
Args:
filename (str): The input file name.
resampling (Optional[str]): The resampling method. Choices are ['average', 'bilinear', 'cubic',
'cubic_spline', 'gauss', 'lanczos', 'max', 'med', 'min', 'mode', 'nearest'].
bounds (Optional[tuple]): The extent bounds to warp to.
crs (Optional[object]): The CRS to warp to.
res (Optional[tuple]): The cell resolution to warp to.
nodata (Optional[int or float]): The 'no data' value.
warp_mem_limit (Optional[int]): The memory limit (in MB) for the ``rasterio.vrt.WarpedVRT`` function.
num_threads (Optional[int]): The number of warp worker threads.
tap (Optional[bool]): Whether to target align pixels.
Returns:
``rasterio.vrt.WarpedVRT``
"""
with rio.open(filename) as src:
if res:
dst_res = res
else:
dst_res = src.res
if crs:
if isinstance(crs, CRS):
dst_crs = crs
elif isinstance(crs, int):
dst_crs = CRS.from_epsg(crs)
elif isinstance(crs, dict):
dst_crs = CRS.from_dict(crs)
elif isinstance(crs, str):
if crs.startswith('+proj'):
dst_crs = CRS.from_proj4(crs)
else:
dst_crs = CRS.from_string(crs)
else:
logger.exception(' The CRS was not understood.')
else:
dst_crs = src.crs
dst_transform, dst_width, dst_height = calculate_default_transform(
src.crs,
dst_crs,
src.width,
src.height,
left=src.bounds.left,
bottom=src.bounds.bottom,
right=src.bounds.right,
top=src.bounds.top,
resolution=dst_res)
# Check if the data need to be subset
if bounds and (bounds != src.bounds):
if isinstance(bounds, str):
if bounds.startswith('BoundingBox'):
bounds_str = bounds.replace('BoundingBox(', '').split(',')
for str_ in bounds_str:
if str_.strip().startswith('left='):
left_coord = float(
str_.strip().split('=')[1].replace(')', ''))
elif str_.strip().startswith('bottom='):
bottom_coord = float(
str_.strip().split('=')[1].replace(')', ''))
elif str_.strip().startswith('right='):
right_coord = float(
str_.strip().split('=')[1].replace(')', ''))
elif str_.strip().startswith('top='):
top_coord = float(
str_.strip().split('=')[1].replace(')', ''))
bounds = BoundingBox(left=left_coord,
bottom=bottom_coord,
right=right_coord,
top=top_coord)
else:
logger.exception(' The bounds were not accepted.')
left, bottom, right, top = bounds
# Keep the CRS but subset the data
dst_transform, dst_width, dst_height = calculate_default_transform(
dst_crs,
dst_crs,
dst_width,
dst_height,
left=left,
bottom=bottom,
right=right,
top=top,
resolution=dst_res)
dst_width = int((right - left) / dst_res[0])
dst_height = int((top - bottom) / dst_res[1])
else:
bounds = src.bounds
# Do not warp if all the key metadata match the reference information
if (src.bounds == bounds) and (src.res == dst_res) and (
src.crs == dst_crs) and (src.width
== dst_width) and (src.height
== dst_height):
output = filename
else:
if tap:
# Align the cells
dst_transform, dst_width, dst_height = aligned_target(
dst_transform, dst_width, dst_height, dst_res)
vrt_options = {
'resampling': getattr(Resampling, resampling),
'crs': dst_crs,
'transform': dst_transform,
'height': dst_height,
'width': dst_width,
'nodata': nodata,
'warp_mem_limit': warp_mem_limit,
'warp_extras': {
'multi': True,
'warp_option': 'NUM_THREADS={:d}'.format(num_threads)
}
}
with WarpedVRT(src, **vrt_options) as vrt:
output = vrt
return output
def write_raster(
self,
output_filename: PathLike,
variable: str,
time: datetime,
fill_value=LEAFLET_NODATA_VALUE,
driver: str = 'GTiff',
crop: bool = True,
):
"""
Writes interpolated raster of given variable to output path.
:param output_filename: path of raster file to create
:param variable: name of variable
:param time: time from which to retrieve data
:param fill_value: desired fill value of output
:param driver: strings of valid GDAL driver (currently one of 'GTiff', 'GPKG', or 'AAIGrid')
:param crop: whether to crop to study area extent
"""
if not isinstance(output_filename, Path):
output_filename = Path(output_filename)
output_data = self.data(variable, time, crop).values
if output_data is not None:
if crop:
transform = self.study_area_transform
else:
transform = self.global_grid_transform
gdal_args = {
'transform':
transform,
'height':
output_data.shape[0],
'width':
output_data.shape[1],
'count':
1,
'dtype':
rasterio.float32,
'crs':
CRS.from_dict(OUTPUT_CRS),
'nodata':
numpy.array([fill_value]).astype(output_data.dtype).item(),
}
if driver == 'AAIGrid':
file_extension = 'asc'
gdal_args.update({'FORCE_CELLSIZE': 'YES'})
elif driver == 'GPKG':
file_extension = 'gpkg'
else:
file_extension = 'tiff'
gdal_args.update(TIFF_CREATION_OPTIONS)
output_filename = f'{output_filename.stem}.{file_extension}'
LOGGER.info(f'Writing {output_filename}')
with rasterio.open(output_filename, 'w', driver,
**gdal_args) as output_raster:
output_raster.write(output_data, 1)
if driver == 'GTiff':
output_raster.build_overviews(
PyOFS.overview_levels(output_data.shape),
Resampling['average'])
output_raster.update_tags(ns='rio_overview',
resampling='average')
def write_rasters(
self,
output_dir: PathLike,
variables: list,
time: datetime,
filename_prefix: str = None,
filename_suffix: str = None,
fill_value=LEAFLET_NODATA_VALUE,
driver: str = 'GTiff',
crop: bool = True,
):
"""
Write averaged raster data of given variables to given output directory.
:param output_dir: path to directory
:param variables: variable names to use
:param time: time from which to retrieve data
:param filename_prefix: prefix for filenames
:param filename_suffix: suffix for filenames
:param fill_value: desired fill value of output
:param driver: strings of valid GDAL driver (currently one of 'GTiff', 'GPKG', or 'AAIGrid')
:param crop: whether to crop to study area extent
"""
if not isinstance(output_dir, Path):
output_dir = Path(output_dir)
if variables is None:
variables = DATA_VARIABLES[self.source]
if filename_prefix is None:
filename_prefix = 'rtofs'
filename_suffix = f'_{filename_suffix}' if filename_suffix is not None else ''
if self.time_interval == 'daily':
time = time.replace(hour=0, minute=0, second=0, microsecond=0)
time_delta = int((time - self.model_time) / timedelta(days=1))
direction = 'forecast' if time_delta >= 0 else 'nowcast'
time_delta_string = f'{direction[0]}{abs(time_delta) + 1 if direction == "forecast" else abs(time_delta):03}'
variable_means = {}
for variable in variables:
if variable not in ['dir', 'mag']:
try:
variable_means[variable] = self.data(variable, time, crop)
except KeyError:
LOGGER.warning(
f'variable "{variable}" not found in RTOFS dataset')
except Exception as error:
LOGGER.warning(error)
variable_means = {
variable: variable_mean.values
for variable, variable_mean in variable_means.items()
if variable_mean is not None
}
if 'dir' in variables or 'mag' in variables:
u_name = 'ssu'
v_name = 'ssv'
if u_name not in variable_means:
u_data = self.data(u_name, time, crop)
u_data = u_data.values if u_data is not None else None
else:
u_data = variable_means[u_name]
if v_name not in variable_means:
v_data = self.data(v_name, time, crop)
v_data = v_data.values if v_data is not None else None
else:
v_data = variable_means[v_name]
if 'anim' in filename_suffix:
variable_means['dir'] = u_data
variable_means['mag'] = v_data
else:
# calculate direction and magnitude of vector in degrees (0-360) and in metres per second
variable_means['dir'] = (numpy.arctan2(u_data, v_data) +
numpy.pi) * (180 / numpy.pi)
variable_means['mag'] = numpy.sqrt(u_data**2 + v_data**2)
# write interpolated grids to raster files
for variable, variable_mean in variable_means.items():
if variable_mean is not None and variable_mean.size > 0:
if crop:
transform = self.study_area_transform
else:
transform = self.global_grid_transform
if fill_value is not None:
variable_mean[numpy.isnan(variable_mean)] = fill_value
gdal_args = {
'transform':
transform,
'height':
variable_mean.shape[0],
'width':
variable_mean.shape[1],
'count':
1,
'dtype':
rasterio.float32,
'crs':
CRS.from_dict(OUTPUT_CRS),
'nodata':
numpy.array([fill_value
]).astype(variable_mean.dtype).item(),
}
if driver == 'AAIGrid':
file_extension = 'asc'
gdal_args.update({'FORCE_CELLSIZE': 'YES'})
elif driver == 'GPKG':
file_extension = 'gpkg'
else:
file_extension = 'tiff'
gdal_args.update(TIFF_CREATION_OPTIONS)
output_filename = f'{filename_prefix}_{variable}_{self.model_time:%Y%m%d}_{time_delta_string}{filename_suffix}.{file_extension}'
output_filename = output_dir / output_filename
LOGGER.info(f'Writing {output_filename}')
with rasterio.open(output_filename, 'w', driver,
**gdal_args) as output_raster:
output_raster.write(variable_mean, 1)
if driver == 'GTiff':
output_raster.build_overviews(
PyOFS.overview_levels(variable_mean.shape),
Resampling['average'])
output_raster.update_tags(ns='rio_overview',
resampling='average')
def test_crs_from_json_dict():
aeqd_crs = CRS(proj="aeqd", lon_0=-80, lat_0=40.5)
assert CRS.from_dict(aeqd_crs.to_dict(projjson=True)) == aeqd_crs
def __init__(self, filename, ds=None, field_parameters=None, crs=None):
validate_object(ds, Dataset)
validate_object(field_parameters, dict)
self.src_crs = crs
if isinstance(filename, str):
self.filename = filename
# read shapefile with fiona
with fiona.open(filename, "r") as shapefile:
shapes_from_file = [
feature["geometry"] for feature in shapefile
]
self.src_crs = CRS.from_dict(**shapefile.crs) # shapefile crs
# save number of polygons
self._number_features = len(shapes_from_file)
# reproject to datasets crs
for i in range(self._number_features):
shapes_from_file[i] = transform_geom(
f'EPSG:{self.src_crs.to_epsg()}',
f'EPSG:{ds.parameters["crs"].to_epsg()}',
shapes_from_file[i])
# convert all polygon features in shapefile to list of shapely polygons
polygons = [
Polygon(shapes_from_file[i]["coordinates"][0])
for i in range(self._number_features)
]
# fix invalid MultiPolygons
m = MultiPolygon(polygons)
# join all shapely polygons to a single layer
self.polygon = unary_union(m)
elif isinstance(filename, Polygon):
# only one polygon
self._number_features = 1
self.polygon = filename
if not (self.src_crs is None):
self._reproject_polygon(ds.parameters['crs'])
elif isinstance(filename, MultiPolygon):
# only one polygon
self._number_features = len(filename.geoms)
self.polygon = unary_union(filename)
if not (self.src_crs is None):
self._reproject_polygon(ds.parameters['crs'])
elif isinstance(filename, list):
# assume list of shapely polygons
self._number_features = len(filename)
# fix invalid MultiPolygons
m = MultiPolygon(filename)
# join all shapely polygons to a single layer
self.polygon = unary_union(m)
if not (self.src_crs is None):
self._reproject_polygon(ds.parameters['crs'])
mylog.info(
f"Number of features in poly object: {self._number_features}")
# define coordinates of center
self.center = [
self.polygon.centroid.coords.xy[0][0],
self.polygon.centroid.coords.xy[1][0],
]
data_source = None
super().__init__(self.center, ds, field_parameters, data_source)
def prepare_points(self,
data,
aoi,
frac=1.0,
all_touched=False,
id_column='id',
mask=None,
n_jobs=8,
verbose=0):
if isinstance(aoi, gpd.GeoDataFrame):
df = aoi
else:
if isinstance(aoi, str):
if not os.path.isfile(aoi):
logger.exception(' The AOI file does not exist.')
df = gpd.read_file(aoi)
else:
logger.exception(
' The AOI must be a vector file or a GeoDataFrame.')
# Re-project the data to match the image CRS
if isinstance(df.crs, str):
if df.crs.lower().startswith('+proj'):
if data.crs != df.crs:
df = df.to_crs(data.crs)
elif isinstance(df.crs, int):
if data.crs != CRS.from_epsg(df.crs).to_proj4():
df = df.to_crs(data.crs)
else:
if data.crs != CRS.from_dict(df.crs).to_proj4():
df = df.to_crs(data.crs)
if verbose > 0:
logger.info(' Checking geometry validity ...')
# Ensure all geometry is valid
df = df[df['geometry'].apply(lambda x_: x_ is not None)]
if verbose > 0:
logger.info(' Checking geometry extent ...')
# Remove data outside of the image bounds
if type(df.iloc[0].geometry) == Polygon:
df = gpd.overlay(df,
gpd.GeoDataFrame(data=[0],
geometry=[data.gw.meta.geometry],
crs=df.crs),
how='intersection')
else:
# Clip points to the image bounds
df = df[df.geometry.intersects(data.gw.unary_union)]
if isinstance(mask, Polygon) or isinstance(mask, gpd.GeoDataFrame):
if isinstance(mask, gpd.GeoDataFrame):
if CRS.from_dict(mask.crs).to_proj4() != CRS.from_dict(
df.crs).to_proj4():
mask = mask.to_crs(df.crs)
if verbose > 0:
logger.info(' Clipping geometry ...')
df = df[df.within(mask)]
if df.empty:
logger.exception(
' No geometry intersects the user-provided mask.')
# Subset the DataArray
# minx, miny, maxx, maxy = df.total_bounds
#
# obj_subset = self._obj.gw.subset(left=float(minx)-self._obj.res[0],
# top=float(maxy)+self._obj.res[0],
# right=float(maxx)+self._obj.res[0],
# bottom=float(miny)-self._obj.res[0])
# Convert polygons to points
if type(df.iloc[0].geometry) == Polygon:
if verbose > 0:
logger.info(' Converting polygons to points ...')
df = self.polygons_to_points(data,
df,
frac=frac,
all_touched=all_touched,
id_column=id_column,
n_jobs=n_jobs)
# Ensure a unique index
df.index = list(range(0, df.shape[0]))
return df
# Subplot maps
# Load in watershed shapefile boundaries
shapefile_dan = fiona.open(path_shp_dan + '/' + shp_dan_file, 'r')
crop_shape_dan = [feature["geometry"] for feature in shapefile_dan]
shp_dan_extent = list(shapefile_dan.bounds)
output_crs = 'EPSG:4326'
# Subset and reproject the amsr2 SM data at watershed
# 1 km
masked_ds_dan_1km_all = []
for n in range(amsr2_1km_data_stack.shape[0]):
sub_window_dan_1km = Window(col_dan_1km_ind[0], row_dan_1km_ind[0], len(col_dan_1km_ind), len(row_dan_1km_ind))
kwargs_1km_sub = {'driver': 'GTiff', 'dtype': 'float32', 'nodata': 0.0, 'width': len(lon_world_ease_1km),
'height': len(lat_world_ease_1km), 'count': 1, 'crs': CRS.from_dict(init='epsg:6933'),
'transform': Affine(1000.89502334956, 0.0, -17367530.44516138, 0.0, -1000.89502334956, 7314540.79258289)}
amsr2_sm_dan_1km_output = sub_n_reproj(amsr2_1km_data_stack[n, :, :], kwargs_1km_sub, sub_window_dan_1km, output_crs)
masked_ds_dan_1km, mask_transform_ds_dan_1km = mask(dataset=amsr2_sm_dan_1km_output, shapes=crop_shape_dan, crop=True)
masked_ds_dan_1km[np.where(masked_ds_dan_1km == 0)] = np.nan
masked_ds_dan_1km = masked_ds_dan_1km.squeeze()
masked_ds_dan_1km_all.append(masked_ds_dan_1km)
masked_ds_dan_1km_all = np.asarray(masked_ds_dan_1km_all)
# 9 km
masked_ds_dan_9km_all = []
for n in range(amsr2_9km_data_stack.shape[0]):
def test_equality_from_dict(epsg_code):
assert CRS.from_dict(init='epsg:{}'.format(epsg_code)) == CRS.from_dict(init='epsg:{}'.format(epsg_code))
def clip(self, data, df, query=None, mask_data=False, expand_by=0):
"""
Clips a DataArray by vector polygon geometry
Args:
data (DataArray): The ``xarray.DataArray`` to subset.
df (GeoDataFrame or str): The ``geopandas.GeoDataFrame`` or filename to clip to.
query (Optional[str]): A query to apply to ``df``.
mask_data (Optional[bool]): Whether to mask values outside of the ``df`` geometry envelope.
expand_by (Optional[int]): Expand the clip array bounds by ``expand_by`` pixels on each side.
Returns:
``xarray.DataArray``
Examples:
>>> import geowombat as gw
>>>
>>> with gw.open('image.tif') as ds:
>>> ds = gw.clip(ds, df, query="Id == 1")
>>>
>>> # or
>>>
>>> with gw.open('image.tif') as ds:
>>> ds = ds.gw.clip(df, query="Id == 1")
"""
if isinstance(df, str) and os.path.isfile(df):
df = gpd.read_file(df)
if query:
df = df.query(query)
try:
if data.crs.strip() != CRS.from_dict(df.crs).to_proj4().strip():
# Re-project the DataFrame to match the image CRS
df = df.to_crs(data.crs)
except:
if data.crs.strip() != CRS.from_proj4(df.crs).to_proj4().strip():
df = df.to_crs(data.crs)
row_chunks = data.gw.row_chunks
col_chunks = data.gw.col_chunks
left, bottom, right, top = df.total_bounds
# Align the geometry array grid
align_transform, align_width, align_height = align_bounds(
left, bottom, right, top, data.res)
# Get the new bounds
new_left, new_bottom, new_right, new_top = array_bounds(
align_height, align_width, align_transform)
if expand_by > 0:
new_left -= data.gw.cellx * expand_by
new_bottom -= data.gw.celly * expand_by
new_right += data.gw.cellx * expand_by
new_top += data.gw.celly * expand_by
# Subset the array
data = self.subset(data,
left=new_left,
bottom=new_bottom,
right=new_right,
top=new_top)
if mask_data:
# Rasterize the geometry and store as a DataArray
mask = xr.DataArray(data=da.from_array(
features.rasterize(list(df.geometry.values),
out_shape=(align_height, align_width),
transform=align_transform,
fill=0,
out=None,
all_touched=True,
default_value=1,
dtype='int32'),
chunks=(row_chunks, col_chunks)),
dims=['y', 'x'],
coords={
'y': data.y.values,
'x': data.x.values
})
# Return the clipped array
return data.where(mask == 1)
else:
return data
def test_equality_from_dict(epsg_code):
assert CRS.from_dict(init='epsg:{}'.format(epsg_code)) == CRS.from_dict(
init='epsg:{}'.format(epsg_code))
def mask(data, df, query=None, keep='in'):
"""
Masks a DataArray by vector polygon geometry
Args:
data (DataArray): The ``xarray.DataArray`` to mask.
df (GeoDataFrame or str): The ``geopandas.GeoDataFrame`` or filename to use for masking.
query (Optional[str]): A query to apply to ``df``.
keep (Optional[str]): If ``keep`` = 'in', mask values outside of the geometry (keep inside).
Otherwise, if ``keep`` = 'out', mask values inside (keep outside).
Returns:
``xarray.DataArray``
Examples:
>>> import geowombat as gw
>>>
>>> with gw.open('image.tif') as ds:
>>> ds = ds.gw.mask(df)
"""
if isinstance(df, str) and os.path.isfile(df):
df = gpd.read_file(df)
if query:
df = df.query(query)
try:
if data.crs.strip() != CRS.from_dict(df.crs).to_proj4().strip():
# Re-project the DataFrame to match the image CRS
df = df.to_crs(data.crs)
except:
if data.crs.strip() != CRS.from_proj4(df.crs).to_proj4().strip():
df = df.to_crs(data.crs)
# Rasterize the geometry and store as a DataArray
mask = xr.DataArray(data=da.from_array(
features.rasterize(list(df.geometry.values),
out_shape=(data.gw.nrows, data.gw.ncols),
transform=data.transform,
fill=0,
out=None,
all_touched=True,
default_value=1,
dtype='int32'),
chunks=(data.gw.row_chunks, data.gw.col_chunks)),
dims=['y', 'x'],
coords={
'y': data.y.values,
'x': data.x.values
})
# Return the masked array
if keep == 'out':
return data.where(mask != 1)
else:
return data.where(mask == 1)
def write_rasters(
self,
output_dir: PathLike,
variables: Collection[str] = ('sst', 'sses'),
filename_prefix: str = 'abi',
fill_value: float = LEAFLET_NODATA_VALUE,
driver: str = 'GTiff',
correct_sses: bool = False,
):
"""
Write ABI rasters to file using data from given variables.
:param output_dir: path to output directory
:param variables: variable names to write
:param filename_prefix: prefix for output filenames
:param fill_value: desired fill value of output
:param driver: strings of valid GDAL driver (currently one of 'GTiff', 'GPKG', or 'AAIGrid')
:param correct_sses: whether to subtract SSES bias from SST
"""
if not isinstance(output_dir, Path):
output_dir = Path(output_dir)
for variable in variables:
input_data = self.data(variable, correct_sses)
if variable == 'sses':
fill_value = 0
if input_data is not None and not numpy.isnan(input_data).all():
if fill_value is not None:
input_data[numpy.isnan(input_data)] = fill_value
gdal_args = {
'height': input_data.shape[0],
'width': input_data.shape[1],
'count': 1,
'dtype': rasterio.float32,
'crs': CRS.from_dict(OUTPUT_CRS),
'transform': ABIDataset.study_area_transform,
'nodata': fill_value,
}
if driver == 'AAIGrid':
file_extension = 'asc'
gdal_args.update({'FORCE_CELLSIZE': 'YES'})
elif driver == 'GPKG':
file_extension = 'gpkg'
else:
file_extension = 'tiff'
gdal_args.update(TIFF_CREATION_OPTIONS)
output_filename = output_dir / f'{filename_prefix}_{variable}.{file_extension}'
# use rasterio to write to raster with GDAL args
LOGGER.info(f'Writing to {output_filename}')
with rasterio.open(output_filename, 'w', driver,
**gdal_args) as output_raster:
output_raster.write(input_data, 1)
if driver == 'GTiff':
output_raster.build_overviews(
PyOFS.overview_levels(input_data.shape),
Resampling['average'])
output_raster.update_tags(ns='rio_overview',
resampling='average')
def warp_to_transform(src_filename,
dst_transform,
dst_width,
dst_height,
dst_crs_init,
src_band=1,
return_nodata=False,
resampling="nearest"):
"""
Warp content of src_filename to match transform
Inputs
src_filename: str
path to source file
dst_transform: rasterio transform
destination transform
dst_width: int
destination width (no. of columns)
dst_height: int
destination height (no. of rows)
dst_crs_init: str
destination CRS (format "EPSG:code")
src_band: int
index of band to warp, starting from 1 (default = 1)
return_nodata: bool
whether to return no data value (default = False)
resampling: str
resampling mode, one of ["nearest", "average", "cubic", "bilinear", "min", "max"]
Outputs
dst_array: nd array
warped array
nd_value: float
no data value warped array (onli if return_nodata = True)
"""
if resampling == "nearest":
resampling = Resampling.nearest
elif resampling == "average":
resampling = Resampling.average
elif resampling == "cubic":
resampling = Resampling.cubic
elif resampling == "bilinear":
resampling = Resampling.bilinear
elif resampling == "min":
resampling = Resampling.min
elif resampling == "max":
resampling = Resampling.max
else:
print(
"Warning: Resampling method not recognized, switching to default 'nearest'"
)
resampling = Resampling.nearest
if type(src_band) is list:
num_bands = len(src_band)
else:
num_bands = 1
with rasterio.open(src_filename) as src:
if src.nodata is None:
nd_value = 0
else:
nd_value = src.nodata
if num_bands == 1:
dst_array = np.ones(
(dst_height, dst_width), dtype=src.meta["dtype"]) * nd_value
else:
dst_array = np.ones((num_bands, dst_height, dst_width),
dtype=src.meta["dtype"]) * nd_value
warp.reproject(rasterio.band(src, src_band),
destination=dst_array,
dst_transform=dst_transform,
dst_crs=CRS.from_dict(init=dst_crs_init),
dst_resolution=dst_transform[0],
resampling=resampling)
if return_nodata:
return dst_array, nd_value
return dst_array
def prepare_points(self,
data,
aoi,
frac=1.0,
min_frac_area=None,
all_touched=False,
id_column='id',
mask=None,
n_jobs=8,
verbose=0,
**kwargs):
if isinstance(aoi, gpd.GeoDataFrame):
df = aoi
else:
if isinstance(aoi, str):
if not os.path.isfile(aoi):
logger.exception(' The AOI file does not exist.')
raise OSError
df = gpd.read_file(aoi)
else:
logger.exception(
' The AOI must be a vector file or a GeoDataFrame.')
raise TypeError
if id_column not in df.columns.tolist():
df.loc[:, id_column] = df.index.values
df_crs = check_crs(df.crs).to_proj4()
data_crs = check_crs(data.crs).to_proj4()
# Re-project the data to match the image CRS
if data_crs != df_crs:
df = df.to_crs(data_crs)
if verbose > 0:
logger.info(' Checking geometry validity ...')
# Ensure all geometry is valid
df = df[df['geometry'].apply(lambda x_: x_ is not None)]
if verbose > 0:
logger.info(' Checking geometry extent ...')
# Remove data outside of the image bounds
if (type(df.iloc[0].geometry) == Polygon) or (type(df.iloc[0].geometry)
== MultiPolygon):
df = gpd.overlay(df,
gpd.GeoDataFrame(data=[0],
geometry=[data.gw.geometry],
crs=df_crs),
how='intersection').drop(columns=[0])
else:
# Clip points to the image bounds
df = df[df.geometry.intersects(data.gw.geometry)]
if isinstance(mask, Polygon) or isinstance(
mask, MultiPolygon) or isinstance(mask, gpd.GeoDataFrame):
if isinstance(mask, gpd.GeoDataFrame):
if CRS.from_dict(mask.crs).to_proj4() != df_crs:
mask = mask.to_crs(df_crs)
if verbose > 0:
logger.info(' Clipping geometry ...')
df = df[df.within(mask)]
if df.empty:
logger.exception(
' No geometry intersects the user-provided mask.')
raise LookupError
if not df.empty:
# Convert polygons to points
if (type(df.iloc[0].geometry) == Polygon) or (type(
df.iloc[0].geometry) == MultiPolygon):
if verbose > 0:
logger.info(' Converting polygons to points ...')
df = self.polygons_to_points(data,
df,
frac=frac,
min_frac_area=min_frac_area,
all_touched=all_touched,
id_column=id_column,
n_jobs=n_jobs,
**kwargs)
if not df.empty:
# Ensure a unique index
df.index = list(range(0, df.shape[0]))
return df
class Terrain(object):
latlon_crs = CRS.from_dict(init='epsg:4326')
def __init__(self, latlon_bounds, fpath='terrain.tif'):
"""Create container for manipulating GeoTIFF data in the
specified region
Usage
=====
latlon_bounds : list or tuple
Latitude/longitude corresponding to west, south, east, and
north bounds, used to define the source transformation.
fpath : str, optional
Where to save downloaded GeoTIFF (*.tif) data.
"""
self.bounds = list(latlon_bounds)
self._get_utm_crs() # from bounds
self.tiffdata = fpath
self.have_terrain = False
if not hasattr(self, 'have_metadata'):
# set attribute if it hasn't been set already
self.have_metadata = False
def _get_utm_crs(self, datum='WGS84', ellps='WGS84'):
"""Get coordinate system from zone number associated with the
longitude of the northwest corner
Parameters
==========
datum : str, optional
Origin of destination coordinate system, used to describe
PROJ.4 string; default is WGS84.
ellps : str, optional
Ellipsoid defining the shape of the earth in the destination
coordinate system, used to describe PROJ.4 string; default
is WGS84.
"""
#west, south, east, north = self.bounds
self.zone_number = int((self.bounds[0] + 180) / 6) + 1
proj = '+proj=utm +zone={:d} '.format(self.zone_number) \
+ '+datum={:s} +units=m +no_defs '.format(datum) \
+ '+ellps={:s} +towgs84=0,0,0'.format(ellps)
self.utm_crs = CRS.from_proj4(proj)
def _get_bounds_from_metadata(self):
"""This is a stub"""
assert self.have_metadata
raise NotImplementedError()
def to_terrain(self, dx, dy=None, resampling=warp.Resampling.bilinear):
"""Load geospatial raster data and reproject onto specified grid
Usage
=====
dx,dy : float
Grid spacings [m]. If dy is not specified, then uniform
spacing is assumed.
resampling : warp.Resampling value, optional
See `list(warp.Resampling)`.
"""
if dy is None:
dy = dx
# load raster
if not os.path.isfile(self.tiffdata):
raise FileNotFoundError('Need to download()')
dem_raster = rasterio.open(self.tiffdata)
# get source coordinate reference system, transform
west, south, east, north = self.bounds
src_height, src_width = dem_raster.shape
src_crs = dem_raster.crs
src_transform = transform.from_bounds(*self.bounds, src_width,
src_height)
src = dem_raster.read(1)
# calculate destination coordinate reference system, transform
dst_crs = self.utm_crs
print('Projecting from', src_crs, 'to', dst_crs)
# - get origin (the _upper_ left corner) from bounds
orix, oriy = self.to_xy(north, west)
origin = (orix, oriy)
self.origin = origin
dst_transform = transform.from_origin(*origin, dx, dy)
# - get extents from lower right corner
SE_x, SE_y = self.to_xy(south, east)
Lx = SE_x - orix
Ly = oriy - SE_y
Nx = int(Lx / dx)
Ny = int(Ly / dy)
# reproject to uniform grid in the UTM CRS
dem_array = np.empty((Ny, Nx))
warp.reproject(src,
dem_array,
src_transform=src_transform,
src_crs=src_crs,
dst_transform=dst_transform,
dst_crs=dst_crs,
resampling=resampling)
utmx = orix + np.arange(0, Nx * dx, dx)
utmy = oriy + np.arange((-Ny + 1) * dy, dy, dy)
self.x, self.y = np.meshgrid(utmx, utmy, indexing='ij')
self.z = np.flipud(dem_array).T
self.zfun = RectBivariateSpline(utmx, utmy, self.z)
self.have_terrain = True
return self.x, self.y, self.z
def to_latlon(self, x, y):
"""Transform uniform grid to lat/lon space"""
if not hasattr(x, '__iter__'):
assert ~hasattr(x, '__iter__')
x = [x]
y = [y]
xlon, xlat = warp.transform(self.utm_crs, self.latlon_crs, x, y)
try:
shape = x.shape
except AttributeError:
xlat = xlat[0]
xlon = xlon[0]
else:
xlat = np.reshape(xlat, shape)
xlon = np.reshape(xlon, shape)
return xlat, xlon
def to_xy(self, lat, lon, xref=None, yref=None):
"""Transform lat/lon to UTM space"""
if not hasattr(lat, '__iter__'):
assert ~hasattr(lat, '__iter__')
lat = [lat]
lon = [lon]
x, y = warp.transform(self.latlon_crs, self.utm_crs, lon, lat)
try:
shape = lon.shape
except AttributeError:
x = x[0]
y = y[0]
else:
x = np.reshape(x, shape)
y = np.reshape(y, shape)
if xref is not None:
x -= xref
if yref is not None:
y -= yref
return x, y
def xtransect(self, xy=None, latlon=None, wdir=270.0, xrange=(None, None)):
"""Get terrain transect along x for a slice aligned with the
specified wind direction and going through a specified reference
point (defined by xy or latlon)
Usage
=====
xy : list or tuple
Reference location in the UTM coordinate reference system [m]
latlon : list-like
Reference location in latitude and longitude [deg]
wdir : float
Wind direction with which the slice is aligned [deg]
xrange : list or tuple, optional
Range of x values over which slice (or None to use min/max)
"""
assert self.have_terrain, 'Need to call to_terrain()'
assert ((xy is not None) ^
(latlon is not None)), 'Specify xy or latlon'
if xy:
refloc = xy
elif latlon:
x, y = self.to_xy(*latlon)
refloc = (x, y)
ang = 270 - wdir
print('Slice through', refloc, 'at', ang, 'deg')
ang *= np.pi / 180.
# direction specific code
imin = 0 if (xrange[0] is None) else np.where(
self.x <= xrange[0])[0][-1]
imax = None if (xrange[1] is None) else np.where(
self.x > xrange[1])[0][0]
x = self.x[imin:imax, 0]
y = np.tan(ang) * (x - refloc[0]) + refloc[1]
z = self.zfun(x, y, grid=False)
return x - refloc[0], z
def ytransect(self, xy=None, latlon=None, wdir=180.0, yrange=(None, None)):
"""Get terrain transect along x for a slice aligned with the
specified wind direction and going through a specified reference
point (defined by xy or latlon)
Usage
=====
xy : list or tuple
Reference location in the UTM coordinate reference system [m]
latlon : list-like
Reference location in latitude and longitude [deg]
wdir : float
Wind direction with which the slice is aligned [deg]
xrange : list or tuple, optional
Range of x values over which slice (or None to use min/max)
"""
assert self.have_terrain, 'Need to call to_terrain()'
assert ((xy is not None) ^
(latlon is not None)), 'Specify xy or latlon'
if xy:
refloc = xy
elif latlon:
x, y = self.to_xy(*latlon)
refloc = (x, y)
ang = 180 - wdir
print('Slice through', refloc, 'at', ang, 'deg')
ang *= np.pi / 180.
# direction specific code
jmin = 0 if (yrange[0] is None) else np.where(
self.y <= yrange[0])[1][-1]
jmax = None if (yrange[1] is None) else np.where(
self.y > yrange[1])[1][0]
y = self.y[0, jmin:jmax]
x = refloc[0] - np.tan(ang) * (y - refloc[1])
z = self.zfun(x, y, grid=False)
return y - refloc[1], z
