def addLengthMeters(self, stream_network):
"""
Adds length field in meters to network (The added field name will be 'LENGTH_M').
.. note:: This may be needed for generating the kfac file depending on the units of your raster. See: :doc:`gis_tools`.
Parameters:
stream_network(str): Path to stream network file.
Here is an example of how to use this:
.. code:: python
import os
from RAPIDpy.gis.taudem import TauDEM
td = TauDEM()
output_directory = '/path/to/output/files'
td.addLengthMeters(os.path.join(output_directory,"stream_reach_file.shp"))
"""
network_shapefile = ogr.Open(stream_network, 1)
network_layer = network_shapefile.GetLayer()
network_layer_defn = network_layer.GetLayerDefn()
#make sure projection EPSG:4326
network_layer_proj = network_layer.GetSpatialRef()
geographic_proj = osr.SpatialReference()
geographic_proj.ImportFromEPSG(4326)
proj_transform = None
if network_layer_proj != geographic_proj:
proj_transform = osr.CoordinateTransformation(
network_layer_proj, geographic_proj)
#check for field
create_field = True
for i in xrange(network_layer_defn.GetFieldCount()):
field_name = network_layer_defn.GetFieldDefn(i).GetName()
if field_name == 'LENGTH_M':
create_field = False
break
if create_field:
network_layer.CreateField(ogr.FieldDefn('LENGTH_M', ogr.OFTReal))
geo_manager = Geod(ellps="WGS84")
for network_feature in network_layer:
feat_geom = network_feature.GetGeometryRef()
#make sure coordinates are geographic
if proj_transform:
feat_geom.Transform(proj_transform)
line = shapely_loads(feat_geom.ExportToWkb())
lon_list, lat_list = line.xy
az1, az2, dist = geo_manager.inv(lon_list[:-1], lat_list[:-1],
lon_list[1:], lat_list[1:])
network_feature.SetField('LENGTH_M', sum(dist))
network_layer.SetFeature(network_feature)
def addLengthMeters(self, stream_network):
"""
Adds length field in meters to network (The added field name will be 'LENGTH_M').
.. note:: This may be needed for generating the kfac file depending on the units of your raster. See: :doc:`gis_tools`.
Parameters:
stream_network(str): Path to stream network file.
Here is an example of how to use this:
.. code:: python
import os
from RAPIDpy.gis.taudem import TauDEM
td = TauDEM()
output_directory = '/path/to/output/files'
td.addLengthMeters(os.path.join(output_directory,"stream_reach_file.shp"))
"""
network_shapefile = ogr.Open(stream_network, 1)
network_layer = network_shapefile.GetLayer()
network_layer_defn = network_layer.GetLayerDefn()
#make sure projection EPSG:4326
network_layer_proj = network_layer.GetSpatialRef()
geographic_proj = osr.SpatialReference()
geographic_proj.ImportFromEPSG(4326)
proj_transform = None
if network_layer_proj != geographic_proj:
proj_transform = osr.CoordinateTransformation(network_layer_proj, geographic_proj)
#check for field
create_field=True
for i in xrange(network_layer_defn.GetFieldCount()):
field_name = network_layer_defn.GetFieldDefn(i).GetName()
if field_name == 'LENGTH_M':
create_field=False
break
if create_field:
network_layer.CreateField(ogr.FieldDefn('LENGTH_M', ogr.OFTReal))
geo_manager = Geod(ellps="WGS84")
for network_feature in network_layer:
feat_geom = network_feature.GetGeometryRef()
#make sure coordinates are geographic
if proj_transform:
feat_geom.Transform(proj_transform)
line = shapely_loads(feat_geom.ExportToWkb())
lon_list, lat_list = line.xy
az1, az2, dist = geo_manager.inv(lon_list[:-1], lat_list[:-1], lon_list[1:], lat_list[1:])
network_feature.SetField('LENGTH_M', sum(dist))
network_layer.SetFeature(network_feature)
def rasterToPolygon(self, raster_file, polygon_file):
"""
Converts raster to polygon and then dissolves it
"""
print("Process: Raster to Polygon ...")
time_start = datetime.utcnow()
temp_polygon_file = "{0}_temp.shp".format(os.path.splitext(os.path.basename(polygon_file))[0])
cmd = ["gdal_polygonize.py", raster_file,
"-f", "ESRI Shapefile", temp_polygon_file,
os.path.splitext(os.path.basename(temp_polygon_file))[0],
"LINKNO"]
process = Popen(cmd, stdout=PIPE, stderr=PIPE, shell=False)
out, err = process.communicate()
if out:
print("OUTPUT:")
for line in out.split(b'\n'):
print(line)
if err:
print("ERROR:")
print(err)
#raise Exception(err)
print("Time to convert to polygon: {0}".format(datetime.utcnow()-time_start))
print("Dissolving ...")
time_start_dissolve = datetime.utcnow()
ogr_polygin_shapefile = ogr.Open(temp_polygon_file)
ogr_polygon_shapefile_lyr = ogr_polygin_shapefile.GetLayer()
number_of_features = ogr_polygon_shapefile_lyr.GetFeatureCount()
polygon_rivid_list = np.zeros(number_of_features, dtype=np.int32)
for feature_idx, catchment_feature in enumerate(ogr_polygon_shapefile_lyr):
polygon_rivid_list[feature_idx] = catchment_feature.GetField('LINKNO')
shp_drv = ogr.GetDriverByName('ESRI Shapefile')
# Remove output shapefile if it already exists
if os.path.exists(polygon_file):
shp_drv.DeleteDataSource(polygon_file)
dissolve_shapefile = shp_drv.CreateDataSource(polygon_file)
dissolve_layer = dissolve_shapefile.CreateLayer('', ogr_polygon_shapefile_lyr.GetSpatialRef(),
ogr.wkbPolygon)
dissolve_layer.CreateField(ogr.FieldDefn('LINKNO', ogr.OFTInteger))
dissolve_layer_defn = dissolve_layer.GetLayerDefn()
for unique_rivid in np.unique(polygon_rivid_list):
#get indices where it is in the polygon
feature_indices = np.where(polygon_rivid_list==unique_rivid)[0]
new_feat = ogr.Feature(dissolve_layer_defn)
new_feat.SetField('LINKNO', int(unique_rivid))
if len(feature_indices) == 1:
##write feature to file
feature = ogr_polygon_shapefile_lyr.GetFeature(feature_indices[0])
new_feat.SetGeometry(feature.GetGeometryRef())
else:
##dissolve
dissolve_poly_list = []
for feature_index in feature_indices:
feature = ogr_polygon_shapefile_lyr.GetFeature(feature_index)
feat_geom = feature.GetGeometryRef()
dissolve_poly_list.append(shapely_loads(feat_geom.ExportToWkb()))
dissolve_polygon = cascaded_union(dissolve_poly_list)
new_feat.SetGeometry(ogr.CreateGeometryFromWkb(dissolve_polygon.wkb))
dissolve_layer.CreateFeature(new_feat)
#clean up
shp_drv.DeleteDataSource(temp_polygon_file)
print("Time to dissolve: {0}".format(datetime.utcnow()-time_start_dissolve))
print("Total time to convert: {0}".format(datetime.utcnow()-time_start))
def RTreeCreateWeightTable(lsm_grid_lat,
lsm_grid_lon,
in_catchment_shapefile,
river_id,
in_rapid_connect,
out_weight_table,
file_geodatabase=None,
area_id=None):
"""
Create Weight Table for Land Surface Model Grids
"""
time_start_all = datetime.utcnow()
print("Generating LSM Grid Thiessen Array ...")
if file_geodatabase:
gdb_driver = ogr.GetDriverByName("OpenFileGDB")
ogr_file_geodatabase = gdb_driver.Open(file_geodatabase, 0)
ogr_catchment_shapefile_lyr = ogr_file_geodatabase.GetLayer(
in_catchment_shapefile)
else:
ogr_catchment_shapefile = ogr.Open(in_catchment_shapefile)
ogr_catchment_shapefile_lyr = ogr_catchment_shapefile.GetLayer()
ogr_catchment_shapefile_lyr_proj = ogr_catchment_shapefile_lyr.GetSpatialRef(
)
original_catchment_proj = Proj(
ogr_catchment_shapefile_lyr_proj.ExportToProj4())
geographic_proj = Proj(init='EPSG:4326') #geographic
extent = ogr_catchment_shapefile_lyr.GetExtent()
if original_catchment_proj != geographic_proj:
x, y = transform(original_catchment_proj, geographic_proj,
[extent[0], extent[1]], [extent[2], extent[3]])
extent = [min(x), max(x), min(y), max(y)]
lsm_grid_feature_list = pointsToVoronoiGridArray(lsm_grid_lat,
lsm_grid_lon, extent)
##COMMENTED LINES FOR TESTING
##import os
##from .voronoi import pointsToVoronoiGridShapefile
##vor_shp_path = os.path.join(os.path.dirname(in_catchment_shapefile), "test_grid.shp")
##pointsToVoronoiGridShapefile(lsm_grid_lat, lsm_grid_lon, vor_shp_path, extent)
time_end_lsm_grid_thiessen = datetime.utcnow()
print(time_end_lsm_grid_thiessen - time_start_all)
print("Generating LSM Grid Rtree ...")
rtree_idx = rtree.index.Index()
# Populate R-tree index with bounds of ECMWF grid cells
for lsm_grid_pos, lsm_grid_feature in enumerate(lsm_grid_feature_list):
rtree_idx.insert(lsm_grid_pos, lsm_grid_feature['polygon'].bounds)
time_end_lsm_grid_rtree = datetime.utcnow()
print(time_end_lsm_grid_rtree - time_end_lsm_grid_thiessen)
print("Retrieving catchment river id list ...")
number_of_catchment_features = ogr_catchment_shapefile_lyr.GetFeatureCount(
)
catchment_rivid_list = np.zeros(number_of_catchment_features,
dtype=np.int32)
for feature_idx, catchment_feature in enumerate(
ogr_catchment_shapefile_lyr):
catchment_rivid_list[feature_idx] = catchment_feature.GetField(
river_id)
print("Reading in RAPID connect file ...")
rapid_connect_rivid_list = get_rivid_list_from_file(in_rapid_connect)
print("Find LSM grid cells that intersect with each catchment")
print("and write out weight table ...")
dummy_lat_index, dummy_lon_index = _get_lat_lon_indices(
lsm_grid_lat, lsm_grid_lon, lsm_grid_feature_list[0]['lat'],
lsm_grid_feature_list[0]['lon'])
dummy_row_end = [
0, dummy_lon_index, dummy_lat_index, 1,
lsm_grid_feature_list[0]['lon'], lsm_grid_feature_list[0]['lat']
]
with open_csv(out_weight_table, 'w') as csvfile:
connectwriter = csv.writer(csvfile)
connectwriter.writerow([
'rivid', 'area_sqm', 'lon_index', 'lat_index', 'npoints',
'lsm_grid_lon', 'lsm_grid_lat'
])
geographic_proj = Proj(init='EPSG:4326') #geographic
osr_geographic_proj = osr.SpatialReference()
osr_geographic_proj.ImportFromEPSG(4326)
proj_transform = None
if original_catchment_proj != geographic_proj:
proj_transform = osr.CoordinateTransformation(
ogr_catchment_shapefile_lyr_proj, osr_geographic_proj)
for rapid_connect_rivid in rapid_connect_rivid_list:
intersect_grid_info_list = []
try:
catchment_pos = np.where(
catchment_rivid_list == rapid_connect_rivid)[0][0]
except IndexError:
#if it is not in the catchment, add dummy row in its place
connectwriter.writerow([rapid_connect_rivid] + dummy_row_end)
continue
pass
get_catchment_feature = ogr_catchment_shapefile_lyr.GetFeature(
catchment_pos)
feat_geom = get_catchment_feature.GetGeometryRef()
#make sure coordinates are geographic
if proj_transform:
feat_geom.Transform(proj_transform)
catchment_polygon = shapely_loads(feat_geom.ExportToWkb())
for sub_lsm_grid_pos in rtree_idx.intersection(
catchment_polygon.bounds):
if catchment_polygon.intersects(
lsm_grid_feature_list[sub_lsm_grid_pos]['polygon']):
intersect_poly = catchment_polygon.intersection(
lsm_grid_feature_list[sub_lsm_grid_pos]['polygon'])
if not area_id:
#attempt to calculate AREA
poly_area = get_poly_area_geo(intersect_poly)
else:
poly_area = float(
catchment_polygon.GetFeature(area_id)
) * intersect_poly.area / catchment_polygon.area
index_lsm_grid_lat, index_lsm_grid_lon = _get_lat_lon_indices(
lsm_grid_lat, lsm_grid_lon,
lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
lsm_grid_feature_list[sub_lsm_grid_pos]['lon'])
intersect_grid_info_list.append({
'rivid':
rapid_connect_rivid,
'area':
poly_area,
'lsm_grid_lat':
lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
'lsm_grid_lon':
lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
'index_lsm_grid_lon':
index_lsm_grid_lon,
'index_lsm_grid_lat':
index_lsm_grid_lat
})
npoints = len(intersect_grid_info_list)
for intersect_grid_info in intersect_grid_info_list:
connectwriter.writerow([
intersect_grid_info['rivid'], intersect_grid_info['area'],
intersect_grid_info['index_lsm_grid_lon'],
intersect_grid_info['index_lsm_grid_lat'], npoints,
intersect_grid_info['lsm_grid_lon'],
intersect_grid_info['lsm_grid_lat']
])
time_end_all = datetime.utcnow()
print(time_end_all - time_end_lsm_grid_rtree)
print("TOTAL TIME: {0}".format(time_end_all - time_start_all))
def rasterToPolygon(self, raster_file, polygon_file):
"""
Converts raster to polygon and then dissolves it
"""
print("Process: Raster to Polygon ...")
time_start = datetime.utcnow()
temp_polygon_file = "{0}_temp.shp".format(
os.path.splitext(os.path.basename(polygon_file))[0])
cmd = [
"gdal_polygonize.py", raster_file, "-f", "ESRI Shapefile",
temp_polygon_file,
os.path.splitext(os.path.basename(temp_polygon_file))[0], "LINKNO"
]
process = Popen(cmd, stdout=PIPE, stderr=PIPE, shell=False)
out, err = process.communicate()
if out:
print("OUTPUT:")
for line in out.split(b'\n'):
print(line)
if err:
print("ERROR:")
print(err)
#raise Exception(err)
print("Time to convert to polygon: {0}".format(datetime.utcnow() -
time_start))
print("Dissolving ...")
time_start_dissolve = datetime.utcnow()
ogr_polygin_shapefile = ogr.Open(temp_polygon_file)
ogr_polygon_shapefile_lyr = ogr_polygin_shapefile.GetLayer()
number_of_features = ogr_polygon_shapefile_lyr.GetFeatureCount()
polygon_rivid_list = np.zeros(number_of_features, dtype=np.int32)
for feature_idx, catchment_feature in enumerate(
ogr_polygon_shapefile_lyr):
polygon_rivid_list[feature_idx] = catchment_feature.GetField(
'LINKNO')
shp_drv = ogr.GetDriverByName('ESRI Shapefile')
# Remove output shapefile if it already exists
if os.path.exists(polygon_file):
shp_drv.DeleteDataSource(polygon_file)
dissolve_shapefile = shp_drv.CreateDataSource(polygon_file)
dissolve_layer = dissolve_shapefile.CreateLayer(
'', ogr_polygon_shapefile_lyr.GetSpatialRef(), ogr.wkbPolygon)
dissolve_layer.CreateField(ogr.FieldDefn('LINKNO', ogr.OFTInteger))
dissolve_layer_defn = dissolve_layer.GetLayerDefn()
for unique_rivid in np.unique(polygon_rivid_list):
#get indices where it is in the polygon
feature_indices = np.where(polygon_rivid_list == unique_rivid)[0]
new_feat = ogr.Feature(dissolve_layer_defn)
new_feat.SetField('LINKNO', int(unique_rivid))
if len(feature_indices) == 1:
##write feature to file
feature = ogr_polygon_shapefile_lyr.GetFeature(
feature_indices[0])
new_feat.SetGeometry(feature.GetGeometryRef())
else:
##dissolve
dissolve_poly_list = []
for feature_index in feature_indices:
feature = ogr_polygon_shapefile_lyr.GetFeature(
feature_index)
feat_geom = feature.GetGeometryRef()
dissolve_poly_list.append(
shapely_loads(feat_geom.ExportToWkb()))
dissolve_polygon = cascaded_union(dissolve_poly_list)
new_feat.SetGeometry(
ogr.CreateGeometryFromWkb(dissolve_polygon.wkb))
dissolve_layer.CreateFeature(new_feat)
#clean up
shp_drv.DeleteDataSource(temp_polygon_file)
print("Time to dissolve: {0}".format(datetime.utcnow() -
time_start_dissolve))
print("Total time to convert: {0}".format(datetime.utcnow() -
time_start))
def rtree_create_weight_table(lsm_grid_lat,
lsm_grid_lon,
in_catchment_shapefile,
river_id,
in_rapid_connect,
out_weight_table,
file_geodatabase=None,
area_id=None,
lsm_grid_mask=None):
"""
Create Weight Table for Land Surface Model Grids
"""
time_start_all = datetime.utcnow()
if lsm_grid_lat.ndim == 3 and lsm_grid_lon.ndim == 3:
# assume first dimension is time
lsm_grid_lat = lsm_grid_lat[0]
lsm_grid_lon = lsm_grid_lon[0]
log("Generating LSM Grid Thiessen Array ...")
if file_geodatabase:
gdb_driver = ogr.GetDriverByName("OpenFileGDB")
ogr_file_geodatabase = gdb_driver.Open(file_geodatabase, 0)
ogr_catchment_shapefile_lyr = \
ogr_file_geodatabase.GetLayer(in_catchment_shapefile)
else:
ogr_catchment_shapefile = ogr.Open(in_catchment_shapefile)
ogr_catchment_shapefile_lyr = ogr_catchment_shapefile.GetLayer()
ogr_catchment_shapefile_lyr_proj = \
ogr_catchment_shapefile_lyr.GetSpatialRef()
original_catchment_proj = \
Proj(ogr_catchment_shapefile_lyr_proj.ExportToProj4())
geographic_proj = Proj(init='EPSG:4326')
extent = ogr_catchment_shapefile_lyr.GetExtent()
if original_catchment_proj != geographic_proj:
x, y = transform(original_catchment_proj, geographic_proj,
[extent[0], extent[1]], [extent[2], extent[3]])
extent = [min(x), max(x), min(y), max(y)]
lsm_grid_feature_list = \
pointsToVoronoiGridArray(lsm_grid_lat, lsm_grid_lon, extent)
# ##COMMENTED LINES FOR TESTING
# import os
# from .voronoi import pointsToVoronoiGridShapefile
# vor_shp_path = \
# os.path.join(os.path.dirname(in_catchment_shapefile), "test_grid.shp")
# pointsToVoronoiGridShapefile(lsm_grid_lat, lsm_grid_lon,
# vor_shp_path, extent)
time_end_lsm_grid_thiessen = datetime.utcnow()
log(time_end_lsm_grid_thiessen - time_start_all)
log("Generating LSM Grid Rtree ...")
rtree_idx = rtree.index.Index()
# Populate R-tree index with bounds of ECMWF grid cells
for lsm_grid_pos, lsm_grid_feature in enumerate(lsm_grid_feature_list):
rtree_idx.insert(lsm_grid_pos, lsm_grid_feature['polygon'].bounds)
time_end_lsm_grid_rtree = datetime.utcnow()
log(time_end_lsm_grid_rtree - time_end_lsm_grid_thiessen)
log("Retrieving catchment river id list ...")
number_of_catchment_features = \
ogr_catchment_shapefile_lyr.GetFeatureCount()
catchment_rivid_list = \
np.zeros(number_of_catchment_features, dtype=np.int32)
for feature_idx, catchment_feature in \
enumerate(ogr_catchment_shapefile_lyr):
catchment_rivid_list[feature_idx] = \
catchment_feature.GetField(river_id)
log("Reading in RAPID connect file ...")
rapid_connect_rivid_list = np.loadtxt(in_rapid_connect,
delimiter=",",
usecols=(0, ),
ndmin=1,
dtype=int)
log("Find LSM grid cells that intersect with each catchment")
log("and write out weight table ...")
dummy_lat_index, dummy_lon_index = \
_get_lat_lon_indices(lsm_grid_lat,
lsm_grid_lon,
lsm_grid_feature_list[0]['lat'],
lsm_grid_feature_list[0]['lon'])
dummy_row_end = [
0, dummy_lon_index, dummy_lat_index, 1,
lsm_grid_feature_list[0]['lon'], lsm_grid_feature_list[0]['lat']
]
with open_csv(out_weight_table, 'w') as csvfile:
connectwriter = csv.writer(csvfile)
connectwriter.writerow([
'rivid', 'area_sqm', 'lon_index', 'lat_index', 'npoints',
'lsm_grid_lon', 'lsm_grid_lat'
])
geographic_proj = Proj(init='EPSG:4326')
osr_geographic_proj = osr.SpatialReference()
osr_geographic_proj.ImportFromEPSG(4326)
proj_transform = None
if original_catchment_proj != geographic_proj:
proj_transform = \
osr.CoordinateTransformation(ogr_catchment_shapefile_lyr_proj,
osr_geographic_proj)
for rapid_connect_rivid in rapid_connect_rivid_list:
intersect_grid_info_list = []
try:
catchment_pos = \
np.where(catchment_rivid_list == rapid_connect_rivid)[0][0]
except IndexError:
# if it is not in the catchment, add dummy row in its place
connectwriter.writerow([rapid_connect_rivid] + dummy_row_end)
continue
get_catchment_feature = \
ogr_catchment_shapefile_lyr.GetFeature(catchment_pos)
feat_geom = get_catchment_feature.GetGeometryRef()
# make sure coordinates are geographic
if proj_transform:
feat_geom.Transform(proj_transform)
catchment_polygon = shapely_loads(feat_geom.ExportToWkb())
for sub_lsm_grid_pos in \
rtree_idx.intersection(catchment_polygon.bounds):
lsm_grid_polygon = \
lsm_grid_feature_list[sub_lsm_grid_pos]['polygon']
if catchment_polygon.intersects(lsm_grid_polygon):
try:
intersect_poly = \
catchment_polygon.intersection(lsm_grid_polygon)
except TopologicalError:
log('The catchment polygon with id {0} was '
'invalid. Attempting to self clean...'.format(
rapid_connect_rivid))
original_area = catchment_polygon.area
catchment_polygon = catchment_polygon.buffer(0)
area_ratio = original_area / catchment_polygon.area
log('AREA_RATIO: {0}'.format(area_ratio))
msg_level = "INFO"
if round(area_ratio, 5) != 1:
msg_level = "WARNING"
log('The cleaned catchment polygon area '
'differs from the original area by {0}%.'.format(
abs(area_ratio - 1)),
severity=msg_level)
intersect_poly = \
catchment_polygon.intersection(lsm_grid_polygon)
if not area_id:
# attempt to calculate AREA
poly_area = get_poly_area_geo(intersect_poly)
else:
poly_area = \
float(get_catchment_feature.GetField(area_id)) * \
intersect_poly.area/catchment_polygon.area
index_lsm_grid_lat, index_lsm_grid_lon = \
_get_lat_lon_indices(
lsm_grid_lat,
lsm_grid_lon,
lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
lsm_grid_feature_list[sub_lsm_grid_pos]['lon'])
if lsm_grid_mask is not None:
if lsm_grid_mask[int(index_lsm_grid_lat),
int(index_lsm_grid_lon)] > 0:
poly_area /= lsm_grid_mask[int(index_lsm_grid_lat),
int(index_lsm_grid_lon)]
intersect_grid_info_list.append({
'rivid':
rapid_connect_rivid,
'area':
poly_area,
'lsm_grid_lat':
lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
'lsm_grid_lon':
lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
'index_lsm_grid_lon':
index_lsm_grid_lon,
'index_lsm_grid_lat':
index_lsm_grid_lat
})
npoints = len(intersect_grid_info_list)
# If no intersection found, add dummy row
if npoints <= 0:
connectwriter.writerow([rapid_connect_rivid] + dummy_row_end)
for intersect_grid_info in intersect_grid_info_list:
connectwriter.writerow([
intersect_grid_info['rivid'], intersect_grid_info['area'],
intersect_grid_info['index_lsm_grid_lon'],
intersect_grid_info['index_lsm_grid_lat'], npoints,
intersect_grid_info['lsm_grid_lon'],
intersect_grid_info['lsm_grid_lat']
])
time_end_all = datetime.utcnow()
log(time_end_all - time_end_lsm_grid_rtree)
log("TOTAL TIME: {0}".format(time_end_all - time_start_all))
def rasterToPolygon(raster_file, polygon_file):
"""
Converts watershed raster to polygon and then dissolves it.
It dissolves features based on the LINKNO attribute.
"""
log("Process: Raster to Polygon ...")
time_start = datetime.utcnow()
temp_polygon_file = \
"{0}_temp.shp".format(
os.path.splitext(os.path.basename(polygon_file))[0])
GDALGrid(raster_file).to_polygon(out_shapefile=temp_polygon_file,
fieldname="LINKNO",
self_mask=True)
log("Time to convert to polygon: {0}".format(datetime.utcnow() -
time_start))
log("Dissolving ...")
time_start_dissolve = datetime.utcnow()
ogr_polygin_shapefile = ogr.Open(temp_polygon_file)
ogr_polygon_shapefile_lyr = ogr_polygin_shapefile.GetLayer()
number_of_features = ogr_polygon_shapefile_lyr.GetFeatureCount()
polygon_rivid_list = np.zeros(number_of_features, dtype=np.int32)
for feature_idx, catchment_feature in \
enumerate(ogr_polygon_shapefile_lyr):
polygon_rivid_list[feature_idx] = \
catchment_feature.GetField('LINKNO')
shp_drv = ogr.GetDriverByName('ESRI Shapefile')
# Remove output shapefile if it already exists
if os.path.exists(polygon_file):
shp_drv.DeleteDataSource(polygon_file)
dissolve_shapefile = shp_drv.CreateDataSource(polygon_file)
dissolve_layer = \
dissolve_shapefile.CreateLayer(
'',
ogr_polygon_shapefile_lyr.GetSpatialRef(),
ogr.wkbPolygon)
dissolve_layer.CreateField(ogr.FieldDefn('LINKNO', ogr.OFTInteger))
dissolve_layer_defn = dissolve_layer.GetLayerDefn()
for unique_rivid in np.unique(polygon_rivid_list):
# get indices where it is in the polygon
feature_indices = np.where(polygon_rivid_list == unique_rivid)[0]
new_feat = ogr.Feature(dissolve_layer_defn)
new_feat.SetField('LINKNO', int(unique_rivid))
if len(feature_indices) == 1:
# write feature to file
feature = \
ogr_polygon_shapefile_lyr.GetFeature(feature_indices[0])
new_feat.SetGeometry(feature.GetGeometryRef())
else:
# dissolve
dissolve_poly_list = []
for feature_index in feature_indices:
feature = \
ogr_polygon_shapefile_lyr.GetFeature(feature_index)
feat_geom = feature.GetGeometryRef()
dissolve_poly_list.append(
shapely_loads(feat_geom.ExportToWkb()))
dissolve_polygon = cascaded_union(dissolve_poly_list)
new_feat.SetGeometry(
ogr.CreateGeometryFromWkb(dissolve_polygon.wkb))
dissolve_layer.CreateFeature(new_feat)
# clean up
shp_drv.DeleteDataSource(temp_polygon_file)
log("Time to dissolve: {0}".format(datetime.utcnow() -
time_start_dissolve))
log("Total time to convert: {0}".format(datetime.utcnow() -
time_start))
def RTreeCreateWeightTable(lsm_grid_lat, lsm_grid_lon,
in_catchment_shapefile, river_id,
in_rapid_connect, out_weight_table,
file_geodatabase=None, area_id=None):
"""
Create Weight Table for Land Surface Model Grids
"""
time_start_all = datetime.utcnow()
if lsm_grid_lat.ndim == 3 and lsm_grid_lon.ndim == 3:
#assume first dimension is time
lsm_grid_lat = lsm_grid_lat[0]
lsm_grid_lon = lsm_grid_lon[0]
print("Generating LSM Grid Thiessen Array ...")
if file_geodatabase:
gdb_driver = ogr.GetDriverByName("OpenFileGDB")
ogr_file_geodatabase = gdb_driver.Open(file_geodatabase, 0)
ogr_catchment_shapefile_lyr = ogr_file_geodatabase.GetLayer(in_catchment_shapefile)
else:
ogr_catchment_shapefile = ogr.Open(in_catchment_shapefile)
ogr_catchment_shapefile_lyr = ogr_catchment_shapefile.GetLayer()
ogr_catchment_shapefile_lyr_proj = ogr_catchment_shapefile_lyr.GetSpatialRef()
original_catchment_proj = Proj(ogr_catchment_shapefile_lyr_proj.ExportToProj4())
geographic_proj = Proj(init='EPSG:4326') #geographic
extent = ogr_catchment_shapefile_lyr.GetExtent()
if original_catchment_proj != geographic_proj:
x, y = transform(original_catchment_proj,
geographic_proj,
[extent[0], extent[1]],
[extent[2], extent[3]])
extent = [min(x), max(x), min(y), max(y)]
lsm_grid_feature_list = pointsToVoronoiGridArray(lsm_grid_lat, lsm_grid_lon, extent)
##COMMENTED LINES FOR TESTING
# import os
# from .voronoi import pointsToVoronoiGridShapefile
# vor_shp_path = os.path.join(os.path.dirname(in_catchment_shapefile), "test_grid.shp")
# pointsToVoronoiGridShapefile(lsm_grid_lat, lsm_grid_lon, vor_shp_path, extent)
time_end_lsm_grid_thiessen = datetime.utcnow()
print(time_end_lsm_grid_thiessen - time_start_all)
print("Generating LSM Grid Rtree ...")
rtree_idx = rtree.index.Index()
# Populate R-tree index with bounds of ECMWF grid cells
for lsm_grid_pos, lsm_grid_feature in enumerate(lsm_grid_feature_list):
rtree_idx.insert(lsm_grid_pos, lsm_grid_feature['polygon'].bounds)
time_end_lsm_grid_rtree = datetime.utcnow()
print(time_end_lsm_grid_rtree - time_end_lsm_grid_thiessen)
print("Retrieving catchment river id list ...")
number_of_catchment_features = ogr_catchment_shapefile_lyr.GetFeatureCount()
catchment_rivid_list = np.zeros(number_of_catchment_features, dtype=np.int32)
for feature_idx, catchment_feature in enumerate(ogr_catchment_shapefile_lyr):
catchment_rivid_list[feature_idx] = catchment_feature.GetField(river_id)
print("Reading in RAPID connect file ...")
rapid_connect_rivid_list = np.loadtxt(in_rapid_connect,
delimiter=",",
usecols=(0,),
dtype=int)
print("Find LSM grid cells that intersect with each catchment")
print("and write out weight table ...")
dummy_lat_index, dummy_lon_index = _get_lat_lon_indices(lsm_grid_lat, lsm_grid_lon,
lsm_grid_feature_list[0]['lat'],
lsm_grid_feature_list[0]['lon'])
dummy_row_end = [0,
dummy_lon_index,
dummy_lat_index,
1,
lsm_grid_feature_list[0]['lon'],
lsm_grid_feature_list[0]['lat']
]
with open_csv(out_weight_table, 'w') as csvfile:
connectwriter = csv.writer(csvfile)
connectwriter.writerow(['rivid', 'area_sqm', 'lon_index', 'lat_index',
'npoints', 'lsm_grid_lon', 'lsm_grid_lat'])
geographic_proj = Proj(init='EPSG:4326') #geographic
osr_geographic_proj = osr.SpatialReference()
osr_geographic_proj.ImportFromEPSG(4326)
proj_transform = None
if original_catchment_proj != geographic_proj:
proj_transform = osr.CoordinateTransformation(ogr_catchment_shapefile_lyr_proj, osr_geographic_proj)
for rapid_connect_rivid in rapid_connect_rivid_list:
intersect_grid_info_list = []
try:
catchment_pos = np.where(catchment_rivid_list==rapid_connect_rivid)[0][0]
except IndexError:
#if it is not in the catchment, add dummy row in its place
connectwriter.writerow([rapid_connect_rivid] + dummy_row_end)
continue
pass
get_catchment_feature = ogr_catchment_shapefile_lyr.GetFeature(catchment_pos)
feat_geom = get_catchment_feature.GetGeometryRef()
#make sure coordinates are geographic
if proj_transform:
feat_geom.Transform(proj_transform)
catchment_polygon = shapely_loads(feat_geom.ExportToWkb())
for sub_lsm_grid_pos in rtree_idx.intersection(catchment_polygon.bounds):
if catchment_polygon.intersects(lsm_grid_feature_list[sub_lsm_grid_pos]['polygon']):
intersect_poly = catchment_polygon.intersection(lsm_grid_feature_list[sub_lsm_grid_pos]['polygon'])
if not area_id:
#attempt to calculate AREA
poly_area = get_poly_area_geo(intersect_poly)
else:
poly_area = float(catchment_polygon.GetFeature(area_id))*intersect_poly.area/catchment_polygon.area
index_lsm_grid_lat, index_lsm_grid_lon = _get_lat_lon_indices(lsm_grid_lat, lsm_grid_lon,
lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
lsm_grid_feature_list[sub_lsm_grid_pos]['lon'])
intersect_grid_info_list.append({'rivid' : rapid_connect_rivid,
'area' : poly_area,
'lsm_grid_lat': lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
'lsm_grid_lon': lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
'index_lsm_grid_lon': index_lsm_grid_lon,
'index_lsm_grid_lat': index_lsm_grid_lat})
npoints = len(intersect_grid_info_list)
#If no intersection found, add dummy row
if(npoints <=0):
connectwriter.writerow([rapid_connect_rivid] + dummy_row_end)
for intersect_grid_info in intersect_grid_info_list:
connectwriter.writerow([intersect_grid_info['rivid'],
intersect_grid_info['area'],
intersect_grid_info['index_lsm_grid_lon'],
intersect_grid_info['index_lsm_grid_lat'],
npoints,
intersect_grid_info['lsm_grid_lon'],
intersect_grid_info['lsm_grid_lat']])
time_end_all = datetime.utcnow()
print(time_end_all - time_end_lsm_grid_rtree)
print("TOTAL TIME: {0}".format(time_end_all - time_start_all))