def main():
parser = argparse.ArgumentParser(description='GNAT',
# epilog="This is an epilog"
)
parser.add_argument('huc', help='HUC identifier', type=str)
parser.add_argument('output_folder', help='Output folder', type=str)
parser.add_argument('--verbose',
help='(optional) a little extra logging ',
action='store_true',
default=False)
args = dotenv.parse_args_env(parser)
# Initiate the log file
log = Logger("GNAT")
log.setup(logPath=os.path.join(args.output, "gnat.log"),
verbose=args.verbose)
log.title('GNAT For HUC: {}'.format(args.huc))
try:
gnat(args.hu, args.output_folder)
except Exception as e:
log.error(e)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('folder',
help='Top level folder where BRAT data are stored',
type=str)
parser.add_argument('database', help='Path to SQLite database', type=str)
parser.add_argument(
'--reach_id_field',
help='(Optional) field that uniquely identifies each reach',
default='ReachID',
type=str)
parser.add_argument(
'--reach_geom_buffer',
help='(Optional) reach geometry buffer distance (meters)',
default=100,
type=float)
parser.add_argument(
'--conflict_buffer',
help='(Optional) Conflict attribute buffer distance (meters).',
default=30,
type=float)
parser.add_argument(
'--distance_cell_size',
help='(Optional) Conflict attribute rasterization cell size (meters).',
default=5,
type=float)
args = dotenv.parse_args_env(
parser,
os.path.join(os.path.dirname(__file__), '..', '..', '.env.validation'))
validate_all(args.folder, args.database, args.reach_id_field,
args.reach_geom_buffer, args.conflict_buffer,
args.distance_cell_size)
def main():
""" Combined FIS
"""
parser = argparse.ArgumentParser()
parser.add_argument('database',
help='BRAT SQLite database',
type=argparse.FileType('r'))
parser.add_argument('maxdrainage',
help='Maximum drainage area',
type=float)
parser.add_argument('--verbose',
help='(optional) verbose logging mode',
action='store_true',
default=False)
args = dotenv.parse_args_env(parser)
# Initiate the log file
logg = Logger("Combined FIS")
logfile = os.path.join(os.path.dirname(args.network.name),
"combined_fis.log")
logg.setup(logPath=logfile, verbose=args.verbose)
try:
combined_fis(args.database.name, 'existing', 'EX', args.maxdrainage)
# combined_fis(args.network.name, 'historic', 'HPE', args.maxdrainage)
except Exception as ex:
logg.error(ex)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('lst_xml_folder',
help='Top level data folder containing LST data',
type=str)
parser.add_argument('--verbose',
help='(optional) a little extra logging ',
action='store_true',
default=False)
args = dotenv.parse_args_env(
parser, os.path.join(os.path.dirname(__file__), '.env'))
# Initiate the log file
log = Logger('Land Surface Temperature XML Generator')
log.setup(logPath=os.path.join(os.path.dirname(args.lst_xml_folder),
'lst_xml.log'),
verbose=args.verbose)
try:
process_lst(args.lst_xml_folder)
log.info('Process completed successfully')
except Exception as e:
log.error(e)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('network',
help='Output network ShapeFile path',
type=argparse.FileType('r'))
parser.add_argument('flowaccum',
help='Flow accumulation raster',
type=argparse.FileType('r'))
parser.add_argument('buffer',
help='Distance to buffer reach midpoint',
type=float)
parser.add_argument('--verbose',
help='(optional) verbose logging mode',
action='store_true',
default=False)
args = dotenv.parse_args_env(parser)
# Initiate the log file
logg = Logger("Reach Flow Accum")
logfile = os.path.join(os.path.dirname(args.network.name),
"reach_flowaccum.log")
logg.setup(logPath=logfile, verbose=args.verbose)
try:
reach_drainage_area(args.network.name, args.flowaccum.name,
args.buffer)
except Exception as e:
logg.error(e)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('shapefile', help='Path to full Idaho ShapeFile', type=str)
parser.add_argument('database', help='Output SQLite database (must exist already)', type=str)
args = dotenv.parse_args_env(parser)
load_idaho(args.shapefile, args.database)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('folder',
help='Top level folder where BRAT data are stored',
type=str)
parser.add_argument('database', help='Path to SQLite database', type=str)
parser.add_argument('--buffer',
help='Buffer distance for sampling DEM raster',
default=30,
type=float)
parser.add_argument('--cell_size',
help='Cell size for rasterization',
default=5,
type=float)
parser.add_argument('--reach_id_field',
help='(Optional) Reach ID field',
default='ReachID',
type=str)
args = dotenv.parse_args_env(
parser,
os.path.join(os.path.dirname(__file__), '..', '..', '.env.validation'))
conflict_attributes_validation(args.folder, args.database,
args.reach_id_field, args.buffer,
args.cell_size)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('dem', help='DEM raster', type=str)
parser.add_argument('flowaccum', help='Flow accumulation raster', type=str)
parser.add_argument('drainagearea', help='Drainage Area output raster', type=str)
parser.add_argument('--cleanup', help='Deletes temporary files', action='store_true', default=False)
parser.add_argument('--verbose', help='(optional) verbose logging mode', action='store_true', default=False)
parser.add_argument('--dinfinity', help='(optional) Use the Dinifinity algorthim. D8 used if omitted', action='store_true', default=False)
parser.add_argument('--pitfill', help='(optional) Fill DEM pits before flow direction', action='store_true', default=False)
args = dotenv.parse_args_env(parser)
# Initiate the log file
log = Logger("Flow Accum")
log.setup(logPath=os.path.join(os.path.dirname(args.flowaccum), "flow_accum.log"))
if os.path.isfile(args.flowaccum):
log.info('Deleting existing output raster {}'.format(args.flowaccum))
driver = gdal.GetDriverByName('GTiff')
gdal.Driver.Delete(driver, args.flowaccum)
try:
flow_accumulation(args.dem, args.flowaccum, args.cleanup, args.dinfinity, args.pitfill)
flow_accum_to_drainage_area(args.flowaccum, args.drainagearea)
except Exception as e:
print(e)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser(
description='RVD XML Augmenter',
# epilog="This is an epilog"
)
parser.add_argument('out_project_xml', help='Input XML file', type=str)
parser.add_argument('in_xmls', help='Comma-separated list of XMLs in decreasing priority', type=str)
parser.add_argument('--verbose', help='(optional) a little extra logging ', action='store_true', default=False)
args = dotenv.parse_args_env(parser)
# Initiate the log file
log = Logger('XML Augmenter')
log.setup(verbose=args.verbose)
log.title('XML Augmenter: {}'.format(args.out_project_xml))
try:
out_prj = RSProject(None, args.out_project_xml)
out_prj.rs_meta_augment(
args.in_xmls.split(','),
lyrs_in_out
)
out_prj.XMLBuilder.write()
report_path = out_prj.XMLBuilder.find('.//HTMLFile[@id="RVD_REPORT"]/Path').text
report = RVDReport(os.path.join(out_prj.project_dir, report_path), out_prj)
report.write()
except Exception as e:
log.error(e)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
""" Main hydrology routine
"""
parser = argparse.ArgumentParser()
parser.add_argument('database', help='BRAT SQLite database', type=str)
parser.add_argument('prefix', help='Q2 or Low prefix', type=str)
parser.add_argument('huc', help='HUC identification code', type=str)
parser.add_argument('--verbose',
help='(optional) verbose logging mode',
action='store_true',
default=False)
args = dotenv.parse_args_env(parser)
# Initiate the log file
logg = Logger("Hydrology")
logfile = os.path.join(os.path.dirname(args.database), "hydrology.log")
logg.setup(logPath=logfile, verbose=args.verbose)
try:
hydrology(args.database, args.prefix, args.huc)
except Exception as ex:
logg.error(ex)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('vpuids',
help='Comma separated list of VPUs to process',
type=str)
parser.add_argument(
'data_folder',
help='Top level data folder containing riverscapes context projects',
type=str)
#parser.add_argument('user_name', help='Postgres user name', type=str)
#parser.add_argument('password', help='Postgres password', type=str)
args = dotenv.parse_args_env(
parser, os.path.join(os.path.dirname(__file__), '.env'))
# Initiate the log file
log = Logger('Load NHD')
log.setup(logPath=os.path.join(args.data_folder, 'load_nhd.log'),
verbose=True)
try:
load_nhd(args.vpuids,
args.data_folder) # , args.user_name, args.password)
log.info('Process completed successfully')
except Exception as ex:
log.error(ex)
def main():
""" Vegetation Suitability
"""
parser = argparse.ArgumentParser()
parser.add_argument('database',
help='BRAT database path',
type=argparse.FileType('r'))
parser.add_argument('buffer', help='buffer distance (metres)', type=float)
parser.add_argument('epoch', help='Existing or Historic', type=str)
parser.add_argument('--verbose',
help='(optional) verbose logging mode',
action='store_true',
default=False)
args = dotenv.parse_args_env(parser)
# Initiate the log file
logg = Logger('Veg Summary')
logfile = os.path.join(os.path.dirname(args.database.name),
'vegetation_summary.log')
logg.setup(logPath=logfile, verbose=args.verbose)
try:
vegetation_suitability(args.database.name, args.raster.name,
args.buffer, args.table)
except Exception as e:
logg.error(e)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
""" Main BRAT Run
"""
parser = argparse.ArgumentParser(
description='Run brat against a pre-existing sqlite db:',
# epilog="This is an epilog"
)
parser.add_argument('project',
help='Riverscapes project folder or project xml file',
type=str,
default=None)
parser.add_argument(
'--csv_dir',
help='(optional) directory where we can find updated lookup tables',
action='store_true',
default=False)
parser.add_argument('--verbose',
help='(optional) a little extra logging ',
action='store_true',
default=False)
parser.add_argument(
'--debug',
help=
'(optional) more output about things like memory usage. There is a performance cost',
action='store_true',
default=False)
args = dotenv.parse_args_env(parser)
if os.path.isfile(args.project):
logpath = os.path.dirname(args.project)
elif os.path.isdir(args.project):
logpath = args.project
else:
raise Exception(
'You must supply a valid path to a riverscapes project')
log = Logger('BRAT Run')
log.setup(logPath=os.path.join(logpath, "brat_run.log"),
verbose=args.verbose)
log.title('BRAT Run Tool')
try:
if args.debug is True:
from rscommons.debug import ThreadRun
memfile = os.path.join(logpath, 'brat_run_memusage.log')
retcode, max_obj = ThreadRun(brat_run, memfile, args.project,
args.csv_dir)
log.debug('Return code: {}, [Max process usage] {}'.format(
retcode, max_obj))
else:
brat_run(args.project, args.csv_dir)
except Exception as e:
log.error(e)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('access', help='Input Access database path', type=argparse.FileType('r'))
parser.add_argument('sqlite', help='Output SQLite database path', type=str)
args = dotenv.parse_args_env(parser)
convert(args.access.name, args.sqlite)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('csv', help='CSV of 4 digit HUC IDs', type=argparse.FileType('r'))
args = dotenv.parse_args_env(parser)
download_nhd(args.csv.name)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('watersheds', help='National watershed boundary file geodatabase', type=str)
parser.add_argument('database', help='Path to SQLite database', type=argparse.FileType('r'))
args = dotenv.parse_args_env(parser)
huc_precipitation(args.watersheds, args.database.name)
def main():
parser = argparse.ArgumentParser(
description='RVD',
# epilog="This is an epilog"
)
parser.add_argument('huc', help='HUC identifier', type=str)
parser.add_argument('flowlines', help='Segmented flowlines input.', type=str)
parser.add_argument('existing', help='National existing vegetation raster', type=str)
parser.add_argument('historic', help='National historic vegetation raster', type=str)
parser.add_argument('valley_bottom', help='Valley bottom (.shp, .gpkg/layer_name)', type=str)
parser.add_argument('output_folder', help='Output folder input', type=str)
parser.add_argument('--reach_codes', help='Comma delimited reach codes (FCode) to retain when filtering features. Omitting this option retains all features.', type=str)
parser.add_argument('--flow_areas', help='(optional) path to the flow area polygon feature class containing artificial paths', type=str)
parser.add_argument('--waterbodies', help='(optional) waterbodies input', type=str)
parser.add_argument('--meta', help='riverscapes project metadata as comma separated key=value pairs', type=str)
parser.add_argument('--verbose', help='(optional) a little extra logging ', action='store_true', default=False)
parser.add_argument('--debug', help="(optional) save intermediate outputs for debugging", action='store_true', default=False)
args = dotenv.parse_args_env(parser)
reach_codes = args.reach_codes.split(',') if args.reach_codes else None
meta = parse_metadata(args.meta)
# Initiate the log file
log = Logger("RVD")
log.setup(logPath=os.path.join(args.output_folder, "rvd.log"), verbose=args.verbose)
log.title('RVD For HUC: {}'.format(args.huc))
try:
if args.debug is True:
from rscommons.debug import ThreadRun
memfile = os.path.join(args.output_dir, 'rvd_mem.log')
retcode, max_obj = ThreadRun(rvd, memfile, args.huc,
args.flowlines,
args.existing, args.historic, args.valley_bottom,
args.output_folder,
reach_codes,
args.flow_areas, args.waterbodies,
meta=meta)
log.debug('Return code: {}, [Max process usage] {}'.format(retcode, max_obj))
else:
rvd(args.huc,
args.flowlines,
args.existing, args.historic, args.valley_bottom,
args.output_folder,
reach_codes,
args.flow_areas, args.waterbodies,
meta=meta)
except Exception as e:
log.error(e)
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('csv',
help='CSV file identifying four digit HUCs',
type=argparse.FileType('r'))
args = dotenv.parse_args_env(parser)
sum_lengths(args.csv.name)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('folder', help='Top level folder where BRAT data are stored', type=str)
parser.add_argument('database', help='Path to SQLite database', type=str)
parser.add_argument('buffer', help='Buffer distance for sampling DEM raster', type=float)
args = dotenv.parse_args_env(parser, os.path.join(os.path.dirname(__file__), '..', '..', '.env.validation'))
reach_geometry_validation(args.folder, args.database, args.buffer)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('usu_csv',
help='USU hydrology parameter CSV',
type=str)
parser.add_argument('database', help='BRAT database', type=str)
args = dotenv.parse_args_env(
parser,
os.path.join(os.path.dirname(__file__), '..', '..', '.env.validation'))
hydrology_param_validation(args.usu_csv, args.database)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('reach_network',
help='Reach Network FeatureClass',
type=str)
parser.add_argument('watershed_id',
help='8 digit watershed HUC code',
type=str)
args = dotenv.parse_args_env(parser)
watershed_parameters(args.reach_network, args.watershed_id)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('shapefile',
help='Shapefile with inter-mountain west HUC 12s',
type=argparse.FileType('r'))
args = dotenv.parse_args_env(parser)
identify_huc(args.shapefile.name)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('folder',
help='Top level folder where BRAT data are stored',
type=str)
parser.add_argument('database', help='Path to SQLite database', type=str)
args = dotenv.parse_args_env(
parser,
os.path.join(os.path.dirname(__file__), '..', '..', '.env.validation'))
vegetation_fis_validation(args.folder, args.database)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('database', help='Path to SQLite database', type=str)
parser.add_argument('output', help='Path to output JSON file', type=str)
args = dotenv.parse_args_env(parser)
result = huc_summary_stats(args.database)
with open(args.output, 'w') as jf:
json.dump(result, jf)
print('Process complete. Output written to', args.output)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('boundary', help='HUC boundary polygon shapefile', type=argparse.FileType('r'))
parser.add_argument('ownership', help='National ownership polygon shapefile', type=argparse.FileType('r'))
parser.add_argument('output', help='Output ownership ShapeFile path', type=str)
parser.add_argument('--epsg', help='Output spatial reference EPSG', default=4326, type=int)
parser.add_argument('--buffer', help='Buffer distance in meters', default=10000, type=int)
args = dotenv.parse_args_env(parser)
if os.path.isfile(args.output):
print('Deleting existing output', args.output)
delete_shapefile(args.output)
clip_ownership(args.boundary.name, args.ownership.name, args.output, args.epsg, args.buffer)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('wbdhu12', help='WBD HUC 12 ShapeFile path', type=argparse.FileType('r'))
parser.add_argument('database', help='Output SQLite database path', type=str)
args = dotenv.parse_args_env(parser)
try:
build_watershed_topology(args.wbdhu12.name, args.database)
except Exception as e:
traceback.print_exc(file=sys.stdout)
sys.exit(1)
sys.exit(0)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('host', help='BRAT parameter DB host', type=str)
parser.add_argument('port', help='BRAT parameter DB port', type=str)
parser.add_argument('database', help='BRAT parameter database', type=str)
parser.add_argument('user_name', help='BRAT parameter DB user name', type=str)
parser.add_argument('password', help='BRAT parameter DB password', type=str)
parser.add_argument('--csv_dir', help='directory where the csv lives', type=str)
args = dotenv.parse_args_env(parser)
try:
update_brat_parameters(args.host, args.port, args.database, args.user_name, args.password, args.csv_dir)
print('Processing completed successfully. Review changes using git.')
except Exception as ex:
print('Errors occurred:', str(ex))
def main():
parser = argparse.ArgumentParser()
parser.add_argument('folder',
help='Top level folder where BRAT data are stored',
type=str)
parser.add_argument('database', help='Path to SQLite database', type=str)
parser.add_argument('--id_field',
help='(Optional) Reach ID field',
default='ReachID',
type=str)
args = dotenv.parse_args_env(
parser,
os.path.join(os.path.dirname(__file__), '..', '..', '.env.validation'))
stream_power_validation(args.folder, args.database, args.id_field)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('hucs',
help='National geodatabase of eight digit HUCs',
type=str)
parser.add_argument('database',
help='BRAT database',
type=argparse.FileType('r'))
parser.add_argument(
'ecoregions',
help='Ecoregion Shapefile (not intersected with US states)',
type=argparse.FileType('r'))
args = dotenv.parse_args_env(parser)
assign_hucs_to_ecoregions(args.hucs, args.database.name,
args.ecoregions.name)
def main():
parser = argparse.ArgumentParser(description='Import point observation ShapeFile into PostGIS' )
parser.add_argument('shapefile', help='Point observation ShapeFile path', type=str, default=None)
parser.add_argument('host', help='Postgres password', type=str)
parser.add_argument('port', help='Postgres password', type=str)
parser.add_argument('db', help='Postgres password', type=str)
parser.add_argument('user_name', help='Postgres user name', type=str)
parser.add_argument('password', help='Postgres password', type=str)
parser.add_argument('--verbose', help='(optional) a little extra logging ', action='store_true', default=False)
args = dotenv.parse_args_env(parser)
log = Logger('Import')
log.setup(logPath=os.path.join(os.path.join(os.path.dirname(args.shapefile)), "shapefile_import.log"), verbose=args.verbose)
log.title('Point Observation ImportTool')
import_shapefile(args.shapefile, args.host, args.port, args.user_name, args.password, args.db)
