def buffer_by_field(in_layer_path: str, out_layer_path, field: str, epsg: int = None, min_buffer=None, centered=False) -> None:
"""generate buffered polygons by value in field
Args:
flowlines (str): feature class of line features to buffer
field (str): field with buffer value
epsg (int): output srs
min_buffer: use this buffer value for field values that are less than this
Returns:
geometry: unioned polygon geometry of buffered lines
"""
log = Logger('buffer_by_field')
with get_shp_or_gpkg(out_layer_path, write=True) as out_layer, get_shp_or_gpkg(in_layer_path) as in_layer:
conversion = in_layer.rough_convert_metres_to_vector_units(1)
# Add input Layer Fields to the output Layer if it is the one we want
out_layer.create_layer(ogr.wkbPolygon, epsg=epsg, fields=in_layer.get_fields())
transform = VectorBase.get_transform(in_layer.spatial_ref, out_layer.spatial_ref)
factor = 0.5 if centered else 1.0
for feature, _counter, progbar in in_layer.iterate_features('Buffering features', write_layers=[out_layer]):
geom = feature.GetGeometryRef()
if geom is None:
progbar.erase() # get around the progressbar
log.warning('Feature with FID={} has no geometry. Skipping'.format(feature.GetFID()))
continue
buffer_dist = feature.GetField(field) * conversion * factor
geom.Transform(transform)
geom_buffer = geom.Buffer(buffer_dist if buffer_dist > min_buffer else min_buffer)
# Create output Feature
out_feature = ogr.Feature(out_layer.ogr_layer_def)
out_feature.SetGeometry(geom_buffer)
# Add field values from input Layer
for i in range(0, out_layer.ogr_layer_def.GetFieldCount()):
out_feature.SetField(out_layer.ogr_layer_def.GetFieldDefn(i).GetNameRef(), feature.GetField(i))
out_layer.ogr_layer.CreateFeature(out_feature)
out_feature = None
def copy_feature_class(in_layer_path: str, out_layer_path: str,
epsg: int = None,
attribute_filter: str = None,
clip_shape: BaseGeometry = None,
clip_rect: List[float] = None,
buffer: float = 0,
) -> None:
"""Copy a Shapefile from one location to another
This method is capable of reprojecting the geometries as they are copied.
It is also possible to filter features by both attributes and also clip the
features to another geometryNone
Args:
in_layer (str): Input layer path
epsg ([type]): EPSG Code to use for the transformation
out_layer (str): Output layer path
attribute_filter (str, optional): [description]. Defaults to None.
clip_shape (BaseGeometry, optional): [description]. Defaults to None.
clip_rect (List[double minx, double miny, double maxx, double maxy)]): Iterate over a subset by clipping to a Shapely-ish geometry. Defaults to None.
buffer (float): Buffer the output features (in meters).
"""
log = Logger('copy_feature_class')
# NOTE: open the outlayer first so that write gets the dataset open priority
with get_shp_or_gpkg(out_layer_path, write=True) as out_layer, \
get_shp_or_gpkg(in_layer_path) as in_layer:
# Add input Layer Fields to the output Layer if it is the one we want
out_layer.create_layer_from_ref(in_layer, epsg=epsg)
transform = VectorBase.get_transform(in_layer.spatial_ref, out_layer.spatial_ref)
buffer_convert = 0
if buffer != 0:
buffer_convert = in_layer.rough_convert_metres_to_vector_units(buffer)
# This is the callback method that will be run on each feature
for feature, _counter, progbar in in_layer.iterate_features("Copying features", write_layers=[out_layer], clip_shape=clip_shape, clip_rect=clip_rect, attribute_filter=attribute_filter):
geom = feature.GetGeometryRef()
if geom is None:
progbar.erase() # get around the progressbar
log.warning('Feature with FID={} has no geometry. Skipping'.format(feature.GetFID()))
continue
if geom.GetGeometryType() in VectorBase.LINE_TYPES:
if geom.Length() == 0.0:
progbar.erase() # get around the progressbar
log.warning('Feature with FID={} has no Length. Skipping'.format(feature.GetFID()))
continue
# Buffer the shape if we need to
if buffer_convert != 0:
geom = geom.Buffer(buffer_convert)
geom.Transform(transform)
# Create output Feature
out_feature = ogr.Feature(out_layer.ogr_layer_def)
out_feature.SetGeometry(geom)
# Add field values from input Layer
for i in range(0, out_layer.ogr_layer_def.GetFieldCount()):
out_feature.SetField(out_layer.ogr_layer_def.GetFieldDefn(i).GetNameRef(), feature.GetField(i))
out_layer.ogr_layer.CreateFeature(out_feature)
out_feature = None
def rvd(huc: int, flowlines_orig: Path, existing_veg_orig: Path, historic_veg_orig: Path,
valley_bottom_orig: Path, output_folder: Path, reach_codes: List[str], flow_areas_orig: Path, waterbodies_orig: Path, meta=None):
"""[Generate segmented reaches on flowline network and calculate RVD from historic and existing vegetation rasters
Args:
huc (integer): Watershed ID
flowlines_orig (Path): Segmented flowlines feature layer
existing_veg_orig (Path): LANDFIRE version 2.00 evt raster, with adjacent xml metadata file
historic_veg_orig (Path): LANDFIRE version 2.00 bps raster, with adjacent xml metadata file
valley_bottom_orig (Path): Vbet polygon feature layer
output_folder (Path): destination folder for project output
reach_codes (List[int]): NHD reach codes for features to include in outputs
flow_areas_orig (Path): NHD flow area polygon feature layer
waterbodies (Path): NHD waterbodies polygon feature layer
meta (Dict[str,str]): dictionary of riverscapes metadata key: value pairs
"""
log = Logger("RVD")
log.info('RVD v.{}'.format(cfg.version))
try:
int(huc)
except ValueError:
raise Exception('Invalid HUC identifier "{}". Must be an integer'.format(huc))
if not (len(huc) == 4 or len(huc) == 8):
raise Exception('Invalid HUC identifier. Must be four digit integer')
safe_makedirs(output_folder)
project, _realization, proj_nodes = create_project(huc, output_folder)
# Incorporate project metadata to the riverscapes project
if meta is not None:
project.add_metadata(meta)
log.info('Adding inputs to project')
_prj_existing_path_node, prj_existing_path = project.add_project_raster(proj_nodes['Inputs'], LayerTypes['EXVEG'], existing_veg_orig)
_prj_historic_path_node, prj_historic_path = project.add_project_raster(proj_nodes['Inputs'], LayerTypes['HISTVEG'], historic_veg_orig)
# TODO: Don't forget the att_filter
# _prj_flowlines_node, prj_flowlines = project.add_project_geopackage(proj_nodes['Inputs'], LayerTypes['INPUTS'], flowlines, att_filter="\"ReachCode\" Like '{}%'".format(huc))
# Copy in the vectors we need
inputs_gpkg_path = os.path.join(output_folder, LayerTypes['INPUTS'].rel_path)
intermediates_gpkg_path = os.path.join(output_folder, LayerTypes['INTERMEDIATES'].rel_path)
outputs_gpkg_path = os.path.join(output_folder, LayerTypes['OUTPUTS'].rel_path)
# Make sure we're starting with empty/fresh geopackages
GeopackageLayer.delete(inputs_gpkg_path)
GeopackageLayer.delete(intermediates_gpkg_path)
GeopackageLayer.delete(outputs_gpkg_path)
# Copy our input layers and also find the difference in the geometry for the valley bottom
flowlines_path = os.path.join(inputs_gpkg_path, LayerTypes['INPUTS'].sub_layers['FLOWLINES'].rel_path)
vbottom_path = os.path.join(inputs_gpkg_path, LayerTypes['INPUTS'].sub_layers['VALLEY_BOTTOM'].rel_path)
copy_feature_class(flowlines_orig, flowlines_path, epsg=cfg.OUTPUT_EPSG)
copy_feature_class(valley_bottom_orig, vbottom_path, epsg=cfg.OUTPUT_EPSG)
with GeopackageLayer(flowlines_path) as flow_lyr:
# Set the output spatial ref as this for the whole project
out_srs = flow_lyr.spatial_ref
meter_conversion = flow_lyr.rough_convert_metres_to_vector_units(1)
distance_buffer = flow_lyr.rough_convert_metres_to_vector_units(1)
# Transform issues reading 102003 as espg id. Using sr wkt seems to work, however arcgis has problems loading feature classes with this method...
raster_srs = ogr.osr.SpatialReference()
ds = gdal.Open(prj_existing_path, 0)
raster_srs.ImportFromWkt(ds.GetProjectionRef())
raster_srs.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER)
transform_shp_to_raster = VectorBase.get_transform(out_srs, raster_srs)
gt = ds.GetGeoTransform()
cell_area = ((gt[1] / meter_conversion) * (-gt[5] / meter_conversion))
# Create the output feature class fields
with GeopackageLayer(outputs_gpkg_path, layer_name='ReachGeometry', delete_dataset=True) as out_lyr:
out_lyr.create_layer(ogr.wkbMultiLineString, spatial_ref=out_srs, options=['FID=ReachID'], fields={
'GNIS_NAME': ogr.OFTString,
'ReachCode': ogr.OFTString,
'TotDASqKm': ogr.OFTReal,
'NHDPlusID': ogr.OFTReal,
'WatershedID': ogr.OFTInteger
})
metadata = {
'RVD_DateTime': datetime.datetime.now().isoformat(),
'Reach_Codes': reach_codes
}
# Execute the SQL to create the lookup tables in the RVD geopackage SQLite database
watershed_name = create_database(huc, outputs_gpkg_path, metadata, cfg.OUTPUT_EPSG, os.path.join(os.path.abspath(os.path.dirname(__file__)), '..', 'database', 'rvd_schema.sql'))
project.add_metadata({'Watershed': watershed_name})
geom_vbottom = get_geometry_unary_union(vbottom_path, spatial_ref=raster_srs)
flowareas_path = None
if flow_areas_orig:
flowareas_path = os.path.join(inputs_gpkg_path, LayerTypes['INPUTS'].sub_layers['FLOW_AREA'].rel_path)
copy_feature_class(flow_areas_orig, flowareas_path, epsg=cfg.OUTPUT_EPSG)
geom_flow_areas = get_geometry_unary_union(flowareas_path)
# Difference with existing vbottom
geom_vbottom = geom_vbottom.difference(geom_flow_areas)
else:
del LayerTypes['INPUTS'].sub_layers['FLOW_AREA']
waterbodies_path = None
if waterbodies_orig:
waterbodies_path = os.path.join(inputs_gpkg_path, LayerTypes['INPUTS'].sub_layers['WATERBODIES'].rel_path)
copy_feature_class(waterbodies_orig, waterbodies_path, epsg=cfg.OUTPUT_EPSG)
geom_waterbodies = get_geometry_unary_union(waterbodies_path)
# Difference with existing vbottom
geom_vbottom = geom_vbottom.difference(geom_waterbodies)
else:
del LayerTypes['INPUTS'].sub_layers['WATERBODIES']
# Add the inputs to the XML
_nd, _in_gpkg_path, _sublayers = project.add_project_geopackage(proj_nodes['Inputs'], LayerTypes['INPUTS'])
# Filter the flow lines to just the required features and then segment to desired length
# TODO: These are brat methods that need to be refactored to use VectorBase layers
cleaned_path = os.path.join(outputs_gpkg_path, 'ReachGeometry')
build_network(flowlines_path, flowareas_path, cleaned_path, waterbodies_path=waterbodies_path, epsg=cfg.OUTPUT_EPSG, reach_codes=reach_codes, create_layer=False)
# Generate Voroni polygons
log.info("Calculating Voronoi Polygons...")
# Add all the points (including islands) to the list
flowline_thiessen_points_groups = centerline_points(cleaned_path, distance_buffer, transform_shp_to_raster)
flowline_thiessen_points = [pt for group in flowline_thiessen_points_groups.values() for pt in group]
simple_save([pt.point for pt in flowline_thiessen_points], ogr.wkbPoint, raster_srs, "Thiessen_Points", intermediates_gpkg_path)
# Exterior is the shell and there is only ever 1
myVorL = NARVoronoi(flowline_thiessen_points)
# Generate Thiessen Polys
myVorL.createshapes()
# Dissolve by flowlines
log.info("Dissolving Thiessen Polygons")
dissolved_polys = myVorL.dissolve_by_property('fid')
# Clip Thiessen Polys
log.info("Clipping Thiessen Polygons to Valley Bottom")
clipped_thiessen = clip_polygons(geom_vbottom, dissolved_polys)
# Save Intermediates
simple_save(clipped_thiessen.values(), ogr.wkbPolygon, raster_srs, "Thiessen", intermediates_gpkg_path)
simple_save(dissolved_polys.values(), ogr.wkbPolygon, raster_srs, "ThiessenPolygonsDissolved", intermediates_gpkg_path)
simple_save(myVorL.polys, ogr.wkbPolygon, raster_srs, "ThiessenPolygonsRaw", intermediates_gpkg_path)
_nd, _inter_gpkg_path, _sublayers = project.add_project_geopackage(proj_nodes['Intermediates'], LayerTypes['INTERMEDIATES'])
# OLD METHOD FOR AUDIT
# dissolved_polys2 = dissolve_by_points(flowline_thiessen_points_groups, myVorL.polys)
# simple_save(dissolved_polys2.values(), ogr.wkbPolygon, out_srs, "ThiessenPolygonsDissolved_OLD", intermediates_gpkg_path)
# Load Vegetation Rasters
log.info(f"Loading Existing and Historic Vegetation Rasters")
vegetation = {}
vegetation["EXISTING"] = load_vegetation_raster(prj_existing_path, outputs_gpkg_path, True, output_folder=os.path.join(output_folder, 'Intermediates'))
vegetation["HISTORIC"] = load_vegetation_raster(prj_historic_path, outputs_gpkg_path, False, output_folder=os.path.join(output_folder, 'Intermediates'))
for epoch in vegetation.keys():
for name in vegetation[epoch].keys():
if not f"{epoch}_{name}" == "HISTORIC_LUI":
project.add_project_raster(proj_nodes['Intermediates'], LayerTypes[f"{epoch}_{name}"])
if vegetation["EXISTING"]["RAW"].shape != vegetation["HISTORIC"]["RAW"].shape:
raise Exception('Vegetation raster shapes are not equal Existing={} Historic={}. Cannot continue'.format(vegetation["EXISTING"]["RAW"].shape, vegetation["HISTORIC"]["RAW"].shape))
# Vegetation zone calculations
riparian_zone_arrays = {}
riparian_zone_arrays["RIPARIAN_ZONES"] = ((vegetation["EXISTING"]["RIPARIAN"] + vegetation["HISTORIC"]["RIPARIAN"]) > 0) * 1
riparian_zone_arrays["NATIVE_RIPARIAN_ZONES"] = ((vegetation["EXISTING"]["NATIVE_RIPARIAN"] + vegetation["HISTORIC"]["NATIVE_RIPARIAN"]) > 0) * 1
riparian_zone_arrays["VEGETATION_ZONES"] = ((vegetation["EXISTING"]["VEGETATED"] + vegetation["HISTORIC"]["VEGETATED"]) > 0) * 1
# Save Intermediate Rasters
for name, raster in riparian_zone_arrays.items():
save_intarr_to_geotiff(raster, os.path.join(output_folder, "Intermediates", f"{name}.tif"), prj_existing_path)
project.add_project_raster(proj_nodes['Intermediates'], LayerTypes[name])
# Calculate Riparian Departure per Reach
riparian_arrays = {f"{epoch.capitalize()}{(name.capitalize()).replace('Native_riparian', 'NativeRiparian')}Mean": array for epoch, arrays in vegetation.items() for name, array in arrays.items() if name in ["RIPARIAN", "NATIVE_RIPARIAN"]}
# Vegetation Cell Counts
raw_arrays = {f"{epoch}": array for epoch, arrays in vegetation.items() for name, array in arrays.items() if name == "RAW"}
# Generate Vegetation Conversions
vegetation_change = (vegetation["HISTORIC"]["CONVERSION"] - vegetation["EXISTING"]["CONVERSION"])
save_intarr_to_geotiff(vegetation_change, os.path.join(output_folder, "Intermediates", "Conversion_Raster.tif"), prj_existing_path)
project.add_project_raster(proj_nodes['Intermediates'], LayerTypes['VEGETATION_CONVERSION'])
# load conversion types dictionary from database
conn = sqlite3.connect(outputs_gpkg_path)
conn.row_factory = dict_factory
curs = conn.cursor()
curs.execute('SELECT * FROM ConversionTypes')
conversion_classifications = curs.fetchall()
curs.execute('SELECT * FROM vwConversions')
conversion_ids = curs.fetchall()
# Split vegetation change classes into binary arrays
vegetation_change_arrays = {
c['FieldName']: (vegetation_change == int(c["TypeValue"])) * 1 if int(c["TypeValue"]) in np.unique(vegetation_change) else None
for c in conversion_classifications
}
# Calcuate average and unique cell counts per reach
progbar = ProgressBar(len(clipped_thiessen.keys()), 50, "Extracting array values by reach...")
counter = 0
discarded = 0
with rasterio.open(prj_existing_path) as dataset:
unique_vegetation_counts = {}
reach_average_riparian = {}
reach_average_change = {}
for reachid, poly in clipped_thiessen.items():
counter += 1
progbar.update(counter)
# we can discount a lot of shapes here.
if not poly.is_valid or poly.is_empty or poly.area == 0 or poly.geom_type not in ["Polygon", "MultiPolygon"]:
discarded += 1
continue
raw_values_unique = {}
change_values_mean = {}
riparian_values_mean = {}
reach_raster = np.ma.masked_invalid(
features.rasterize(
[poly],
out_shape=dataset.shape,
transform=dataset.transform,
all_touched=True,
fill=np.nan))
for raster_name, raster in raw_arrays.items():
if raster is not None:
current_raster = np.ma.masked_array(raster, mask=reach_raster.mask)
raw_values_unique[raster_name] = np.unique(np.ma.filled(current_raster, fill_value=0), return_counts=True)
else:
raw_values_unique[raster_name] = []
for raster_name, raster in riparian_arrays.items():
if raster is not None:
current_raster = np.ma.masked_array(raster, mask=reach_raster.mask)
riparian_values_mean[raster_name] = np.ma.mean(current_raster)
else:
riparian_values_mean[raster_name] = 0.0
for raster_name, raster in vegetation_change_arrays.items():
if raster is not None:
current_raster = np.ma.masked_array(raster, mask=reach_raster.mask)
change_values_mean[raster_name] = np.ma.mean(current_raster)
else:
change_values_mean[raster_name] = 0.0
unique_vegetation_counts[reachid] = raw_values_unique
reach_average_riparian[reachid] = riparian_values_mean
reach_average_change[reachid] = change_values_mean
progbar.finish()
with SQLiteCon(outputs_gpkg_path) as gpkg:
# Ensure all reaches are present in the ReachAttributes table before storing RVD output values
gpkg.curs.execute('INSERT INTO ReachAttributes (ReachID) SELECT ReachID FROM ReachGeometry;')
errs = 0
for reachid, epochs in unique_vegetation_counts.items():
for epoch in epochs.values():
insert_values = [[reachid, int(vegetationid), float(count * cell_area), int(count)] for vegetationid, count in zip(epoch[0], epoch[1]) if vegetationid != 0]
try:
gpkg.curs.executemany('''INSERT INTO ReachVegetation (
ReachID,
VegetationID,
Area,
CellCount)
VALUES (?,?,?,?)''', insert_values)
# Sqlite can't report on SQL errors so we have to print good log messages to help intuit what the problem is
except sqlite3.IntegrityError as err:
# THis is likely a constraint error.
errstr = "Integrity Error when inserting records: ReachID: {} VegetationIDs: {}".format(reachid, str(list(epoch[0])))
log.error(errstr)
errs += 1
except sqlite3.Error as err:
# This is any other kind of error
errstr = "SQL Error when inserting records: ReachID: {} VegetationIDs: {} ERROR: {}".format(reachid, str(list(epoch[0])), str(err))
log.error(errstr)
errs += 1
if errs > 0:
raise Exception('Errors were found inserting records into the database. Cannot continue.')
gpkg.conn.commit()
# load RVD departure levels from DepartureLevels database table
with SQLiteCon(outputs_gpkg_path) as gpkg:
gpkg.curs.execute('SELECT LevelID, MaxRVD FROM DepartureLevels ORDER BY MaxRVD ASC')
departure_levels = gpkg.curs.fetchall()
# Calcuate Average Departure for Riparian and Native Riparian
riparian_departure_values = riparian_departure(reach_average_riparian, departure_levels)
write_db_attributes(outputs_gpkg_path, riparian_departure_values, departure_type_columns)
# Add Conversion Code, Type to Vegetation Conversion
with SQLiteCon(outputs_gpkg_path) as gpkg:
gpkg.curs.execute('SELECT LevelID, MaxValue, NAME FROM ConversionLevels ORDER BY MaxValue ASC')
conversion_levels = gpkg.curs.fetchall()
reach_values_with_conversion_codes = classify_conversions(reach_average_change, conversion_ids, conversion_levels)
write_db_attributes(outputs_gpkg_path, reach_values_with_conversion_codes, rvd_columns)
# # Write Output to GPKG table
# log.info('Insert values to GPKG tables')
# # TODO move this to write_attirubtes method
# with get_shp_or_gpkg(outputs_gpkg_path, layer_name='ReachAttributes', write=True, ) as in_layer:
# # Create each field and store the name and index in a list of tuples
# field_indices = [(field, in_layer.create_field(field, field_type)) for field, field_type in {
# "FromConifer": ogr.OFTReal,
# "FromDevegetated": ogr.OFTReal,
# "FromGrassShrubland": ogr.OFTReal,
# "FromDeciduous": ogr.OFTReal,
# "NoChange": ogr.OFTReal,
# "Deciduous": ogr.OFTReal,
# "GrassShrubland": ogr.OFTReal,
# "Devegetation": ogr.OFTReal,
# "Conifer": ogr.OFTReal,
# "Invasive": ogr.OFTReal,
# "Development": ogr.OFTReal,
# "Agriculture": ogr.OFTReal,
# "ConversionCode": ogr.OFTInteger,
# "ConversionType": ogr.OFTString}.items()]
# for feature, _counter, _progbar in in_layer.iterate_features("Writing Attributes", write_layers=[in_layer]):
# reach = feature.GetFID()
# if reach not in reach_values_with_conversion_codes:
# continue
# # Set all the field values and then store the feature
# for field, _idx in field_indices:
# if field in reach_values_with_conversion_codes[reach]:
# if not reach_values_with_conversion_codes[reach][field]:
# feature.SetField(field, None)
# else:
# feature.SetField(field, reach_values_with_conversion_codes[reach][field])
# in_layer.ogr_layer.SetFeature(feature)
# # Create each field and store the name and index in a list of tuples
# field_indices = [(field, in_layer.create_field(field, field_type)) for field, field_type in {
# "EXISTING_RIPARIAN_MEAN": ogr.OFTReal,
# "HISTORIC_RIPARIAN_MEAN": ogr.OFTReal,
# "RIPARIAN_DEPARTURE": ogr.OFTReal,
# "EXISTING_NATIVE_RIPARIAN_MEAN": ogr.OFTReal,
# "HISTORIC_NATIVE_RIPARIAN_MEAN": ogr.OFTReal,
# "NATIVE_RIPARIAN_DEPARTURE": ogr.OFTReal, }.items()]
# for feature, _counter, _progbar in in_layer.iterate_features("Writing Attributes", write_layers=[in_layer]):
# reach = feature.GetFID()
# if reach not in riparian_departure_values:
# continue
# # Set all the field values and then store the feature
# for field, _idx in field_indices:
# if field in riparian_departure_values[reach]:
# if not riparian_departure_values[reach][field]:
# feature.SetField(field, None)
# else:
# feature.SetField(field, riparian_departure_values[reach][field])
# in_layer.ogr_layer.SetFeature(feature)
# with sqlite3.connect(outputs_gpkg_path) as conn:
# cursor = conn.cursor()
# errs = 0
# for reachid, epochs in unique_vegetation_counts.items():
# for epoch in epochs.values():
# insert_values = [[reachid, int(vegetationid), float(count * cell_area), int(count)] for vegetationid, count in zip(epoch[0], epoch[1]) if vegetationid != 0]
# try:
# cursor.executemany('''INSERT INTO ReachVegetation (
# ReachID,
# VegetationID,
# Area,
# CellCount)
# VALUES (?,?,?,?)''', insert_values)
# # Sqlite can't report on SQL errors so we have to print good log messages to help intuit what the problem is
# except sqlite3.IntegrityError as err:
# # THis is likely a constraint error.
# errstr = "Integrity Error when inserting records: ReachID: {} VegetationIDs: {}".format(reachid, str(list(epoch[0])))
# log.error(errstr)
# errs += 1
# except sqlite3.Error as err:
# # This is any other kind of error
# errstr = "SQL Error when inserting records: ReachID: {} VegetationIDs: {} ERROR: {}".format(reachid, str(list(epoch[0])), str(err))
# log.error(errstr)
# errs += 1
# if errs > 0:
# raise Exception('Errors were found inserting records into the database. Cannot continue.')
# conn.commit()
# Add intermediates and the report to the XML
# project.add_project_geopackage(proj_nodes['Intermediates'], LayerTypes['INTERMEDIATES']) already
# added above
project.add_project_geopackage(proj_nodes['Outputs'], LayerTypes['OUTPUTS'])
# Add the report to the XML
report_path = os.path.join(project.project_dir, LayerTypes['REPORT'].rel_path)
project.add_report(proj_nodes['Outputs'], LayerTypes['REPORT'], replace=True)
report = RVDReport(report_path, project)
report.write()
log.info('RVD complete')