def raster2shp(rasterfile, vectorshp, layername=None, fieldname=None):
"""Convert raster to ESRI shapefile"""
FileClass.remove_files(vectorshp)
FileClass.check_file_exists(rasterfile)
# raster to polygon vector
exepath = FileClass.get_executable_fullpath("gdal_polygonize.py")
str_cmd = 'python %s -f "ESRI Shapefile" %s %s' % (exepath, rasterfile, vectorshp)
if layername is not None and fieldname is not None:
str_cmd += ' %s %s' % (layername, fieldname)
print (str_cmd)
print (UtilClass.run_command(str_cmd))
def raster2shp(rasterfile,
vectorshp,
layername=None,
fieldname=None,
band_num=1,
mask='default'):
"""Convert raster to ESRI shapefile"""
FileClass.remove_files(vectorshp)
FileClass.check_file_exists(rasterfile)
# this allows GDAL to throw Python Exceptions
gdal.UseExceptions()
src_ds = gdal.Open(rasterfile)
if src_ds is None:
print('Unable to open %s' % rasterfile)
sys.exit(1)
try:
srcband = src_ds.GetRasterBand(band_num)
except RuntimeError as e:
# for example, try GetRasterBand(10)
print('Band ( %i ) not found, %s' % (band_num, e))
sys.exit(1)
if mask == 'default':
maskband = srcband.GetMaskBand()
elif mask is None or mask.upper() == 'NONE':
maskband = None
else:
mask_ds = gdal.Open(mask)
maskband = mask_ds.GetRasterBand(1)
# create output datasource
if layername is None:
layername = FileClass.get_core_name_without_suffix(rasterfile)
drv = ogr_GetDriverByName(str('ESRI Shapefile'))
dst_ds = drv.CreateDataSource(vectorshp)
srs = None
if src_ds.GetProjection() != '':
srs = osr_SpatialReference()
srs.ImportFromWkt(src_ds.GetProjection())
dst_layer = dst_ds.CreateLayer(str(layername), srs=srs)
if fieldname is None:
fieldname = layername.upper()
fd = ogr_FieldDefn(str(fieldname), OFTInteger)
dst_layer.CreateField(fd)
dst_field = 0
result = gdal.Polygonize(srcband,
maskband,
dst_layer,
dst_field, ['8CONNECTED=8'],
callback=None)
return result
def raster2shp(rasterfile, vectorshp, layername=None, fieldname=None,
band_num=1, mask='default'):
"""Convert raster to ESRI shapefile"""
FileClass.remove_files(vectorshp)
FileClass.check_file_exists(rasterfile)
# this allows GDAL to throw Python Exceptions
gdal.UseExceptions()
src_ds = gdal.Open(rasterfile)
if src_ds is None:
print('Unable to open %s' % rasterfile)
sys.exit(1)
try:
srcband = src_ds.GetRasterBand(band_num)
except RuntimeError as e:
# for example, try GetRasterBand(10)
print('Band ( %i ) not found, %s' % (band_num, e))
sys.exit(1)
if mask == 'default':
maskband = srcband.GetMaskBand()
elif mask is None or mask.upper() == 'NONE':
maskband = None
else:
mask_ds = gdal.Open(mask)
maskband = mask_ds.GetRasterBand(1)
# create output datasource
if layername is None:
layername = FileClass.get_core_name_without_suffix(rasterfile)
drv = ogr_GetDriverByName(str('ESRI Shapefile'))
dst_ds = drv.CreateDataSource(vectorshp)
srs = None
if src_ds.GetProjection() != '':
srs = osr_SpatialReference()
srs.ImportFromWkt(src_ds.GetProjection())
dst_layer = dst_ds.CreateLayer(str(layername), srs=srs)
if fieldname is None:
fieldname = layername.upper()
fd = ogr_FieldDefn(str(fieldname), OFTInteger)
dst_layer.CreateField(fd)
dst_field = 0
result = gdal.Polygonize(srcband, maskband, dst_layer, dst_field,
['8CONNECTED=8'], callback=None)
return result
def run(function_name,
in_files,
wp=None,
in_params=None,
out_files=None,
mpi_params=None,
log_params=None):
"""
Run TauDEM function.
1. The command will not execute if any input file does not exist.
2. An error will be detected after running the TauDEM command if
any output file does not exist;
Args:
function_name (str): Full path of TauDEM function.
in_files (dict, required): Dict of pairs of parameter id (string) and file path
(string or list) for input files, e.g.::
{'-z': '/full/path/to/dem.tif'}
wp (str, optional): Workspace for outputs. If not specified, the directory of the
first input file in ``in_files`` will be used.
in_params (dict, optional): Dict of pairs of parameter id (string) and value
(or None for a flag parameter without a value) for input parameters, e.g.::
{'-nc': None}
{'-thresh': threshold}
{'-m': 'ave' 's', '-nc': None}
out_files (dict, optional): Dict of pairs of parameter id (string) and file
path (string or list) for output files, e.g.::
{'-fel': 'filleddem.tif'}
{'-maxS': ['harden.tif', 'maxsimi.tif']}
mpi_params (dict, optional): Dict of pairs of parameter id (string) and value or
path for MPI setting, e.g.::
{'mpipath':'/soft/bin','hostfile':'/soft/bin/cluster.node','n':4}
{'mpipath':'/soft/bin', 'n':4}
{'n':4}
log_params (dict, optional): Dict of pairs of parameter id (string) and value or
path for runtime and log output parameters. e.g.::
{'logfile': '/home/user/log.txt',
'runtimefile': '/home/user/runtime.txt'}
Returns:
True if TauDEM run successfully, otherwise False.
"""
# Check input files
if in_files is None:
TauDEM.error('Input files parameter is required!')
if not isinstance(in_files, dict):
TauDEM.error('The input files parameter must be a dict!')
for (pid, infile) in list(in_files.items()):
if infile is None:
continue
if isinstance(infile, list) or isinstance(infile, tuple):
for idx, inf in enumerate(infile):
if inf is None:
continue
inf, wp = TauDEM.check_infile_and_wp(inf, wp)
in_files[pid][idx] = inf
continue
if os.path.exists(infile):
infile, wp = TauDEM.check_infile_and_wp(infile, wp)
in_files[pid] = os.path.abspath(infile)
else:
# For more flexible input files extension.
# e.g., -inputtags 1 <path/to/tag1.tif> 2 <path/to/tag2.tif> ...
# in such unpredictable circumstance, we cannot check the existance of
# input files, so the developer will check it in other place.
if len(StringClass.split_string(infile, ' ')) > 1:
continue
else: # the infile still should be a existing file, so check in workspace
if wp is None:
TauDEM.error('Workspace should not be None!')
infile = wp + os.sep + infile
if not os.path.exists(infile):
TauDEM.error(
'Input files parameter %s: %s is not existed!' %
(pid, infile))
in_files[pid] = os.path.abspath(infile)
# Make workspace dir if not existed
UtilClass.mkdir(wp)
# Check the log parameter
log_file = None
runtime_file = None
if log_params is not None:
if not isinstance(log_params, dict):
TauDEM.error('The log parameter must be a dict!')
if 'logfile' in log_params and log_params['logfile'] is not None:
log_file = log_params['logfile']
# If log_file is just a file name, then save it in the default workspace.
if os.sep not in log_file:
log_file = wp + os.sep + log_file
log_file = os.path.abspath(log_file)
if 'runtimefile' in log_params and log_params[
'runtimefile'] is not None:
runtime_file = log_params['runtimefile']
# If log_file is just a file name, then save it in the default workspace.
if os.sep not in runtime_file:
runtime_file = wp + os.sep + runtime_file
runtime_file = os.path.abspath(runtime_file)
# remove out_files to avoid any file IO related error
new_out_files = list()
if out_files is not None:
if not isinstance(out_files, dict):
TauDEM.error('The output files parameter must be a dict!')
for (pid, out_file) in list(out_files.items()):
if out_file is None:
continue
if isinstance(out_file, list) or isinstance(out_file, tuple):
for idx, outf in enumerate(out_file):
if outf is None:
continue
outf = FileClass.get_file_fullpath(outf, wp)
FileClass.remove_files(outf)
out_files[pid][idx] = outf
new_out_files.append(outf)
else:
out_file = FileClass.get_file_fullpath(out_file, wp)
FileClass.remove_files(out_file)
out_files[pid] = out_file
new_out_files.append(out_file)
# concatenate command line
commands = list()
# MPI header
if mpi_params is not None:
if not isinstance(mpi_params, dict):
TauDEM.error('The MPI settings parameter must be a dict!')
if 'mpipath' in mpi_params and mpi_params['mpipath'] is not None:
commands.append(mpi_params['mpipath'] + os.sep + 'mpiexec')
else:
commands.append('mpiexec')
if 'hostfile' in mpi_params and mpi_params['hostfile'] is not None \
and not StringClass.string_match(mpi_params['hostfile'], 'none') \
and os.path.isfile(mpi_params['hostfile']):
commands.append('-f')
commands.append(mpi_params['hostfile'])
if 'n' in mpi_params and mpi_params['n'] > 1:
commands.append('-n')
commands.append(str(mpi_params['n']))
else: # If number of processor is less equal than 1, then do not call mpiexec.
commands = []
# append TauDEM function name, which can be full path or just one name
commands.append(function_name)
# append input files
for (pid, infile) in list(in_files.items()):
if infile is None:
continue
if pid[0] != '-':
pid = '-' + pid
commands.append(pid)
if isinstance(infile, list) or isinstance(infile, tuple):
commands.append(' '.join(tmpf for tmpf in infile))
else:
commands.append(infile)
# append input parameters
if in_params is not None:
if not isinstance(in_params, dict):
TauDEM.error('The input parameters must be a dict!')
for (pid, v) in list(in_params.items()):
if pid[0] != '-':
pid = '-' + pid
commands.append(pid)
# allow for parameter which is an flag without value
if v != '' and v is not None:
if MathClass.isnumerical(v):
commands.append(str(v))
else:
commands.append(v)
# append output parameters
if out_files is not None:
for (pid, outfile) in list(out_files.items()):
if outfile is None:
continue
if pid[0] != '-':
pid = '-' + pid
commands.append(pid)
if isinstance(outfile, list) or isinstance(outfile, tuple):
commands.append(' '.join(tmpf for tmpf in outfile))
else:
commands.append(outfile)
# run command
runmsg = UtilClass.run_command(commands)
TauDEM.log(runmsg, log_file)
TauDEM.output_runtime_to_log(function_name, runmsg, runtime_file)
# Check out_files, raise RuntimeError if not exist.
for of in new_out_files:
if not os.path.exists(of):
TauDEM.error('%s failed, and the %s was not generated!' %
(function_name, of))
return False
return True
def run(function_name, in_files, wp=None, in_params=None, out_files=None, mpi_params=None,
log_params=None):
"""
Run TauDEM function.
- 1. The command will not execute if any input file does not exist.
- 2. An error will be detected after running the TauDEM command if
any output file does not exist;
Args:
function_name (str): Full path of TauDEM function.
in_files (dict, required): Dict of pairs of parameter id (string) and file path
(string or list) for input files, e.g.::
{'-z': '/full/path/to/dem.tif'}
wp (str, optional): Workspace for outputs. If not specified, the directory of the
first input file in ``in_files`` will be used.
in_params (dict, optional): Dict of pairs of parameter id (string) and value
(or None for a flag parameter without a value) for input parameters, e.g.::
{'-nc': None}
{'-thresh': threshold}
{'-m': 'ave' 's', '-nc': None}
out_files (dict, optional): Dict of pairs of parameter id (string) and file
path (string or list) for output files, e.g.::
{'-fel': 'filleddem.tif'}
{'-maxS': ['harden.tif', 'maxsimi.tif']}
mpi_params (dict, optional): Dict of pairs of parameter id (string) and value or
path for MPI setting, e.g.::
{'mpipath':'/soft/bin','hostfile':'/soft/bin/cluster.node','n':4}
{'mpipath':'/soft/bin', 'n':4}
{'n':4}
log_params (dict, optional): Dict of pairs of parameter id (string) and value or
path for runtime and log output parameters. e.g.::
{'logfile': '/home/user/log.txt',
'runtimefile': '/home/user/runtime.txt'}
Returns:
True if TauDEM run successfully, otherwise False.
"""
# Check input files
if in_files is None:
TauDEM.error('Input files parameter is required!')
if not isinstance(in_files, dict):
TauDEM.error('The input files parameter must be a dict!')
for (pid, infile) in iteritems(in_files):
if infile is None:
continue
if isinstance(infile, list) or isinstance(infile, tuple):
for idx, inf in enumerate(infile):
if inf is None:
continue
inf, wp = TauDEM.check_infile_and_wp(inf, wp)
in_files[pid][idx] = inf
continue
if os.path.exists(infile):
infile, wp = TauDEM.check_infile_and_wp(infile, wp)
in_files[pid] = os.path.abspath(infile)
else:
# For more flexible input files extension.
# e.g., -inputtags 1 <path/to/tag1.tif> 2 <path/to/tag2.tif> ...
# in such unpredictable circumstance, we cannot check the existance of
# input files, so the developer will check it in other place.
if len(StringClass.split_string(infile, ' ')) > 1:
continue
else: # the infile still should be a existing file, so check in workspace
if wp is None:
TauDEM.error('Workspace should not be None!')
infile = wp + os.sep + infile
if not os.path.exists(infile):
TauDEM.error('Input files parameter %s: %s is not existed!' %
(pid, infile))
in_files[pid] = os.path.abspath(infile)
# Make workspace dir if not existed
UtilClass.mkdir(wp)
# Check the log parameter
log_file = None
runtime_file = None
if log_params is not None:
if not isinstance(log_params, dict):
TauDEM.error('The log parameter must be a dict!')
if 'logfile' in log_params and log_params['logfile'] is not None:
log_file = log_params['logfile']
# If log_file is just a file name, then save it in the default workspace.
if os.sep not in log_file:
log_file = wp + os.sep + log_file
log_file = os.path.abspath(log_file)
if 'runtimefile' in log_params and log_params['runtimefile'] is not None:
runtime_file = log_params['runtimefile']
# If log_file is just a file name, then save it in the default workspace.
if os.sep not in runtime_file:
runtime_file = wp + os.sep + runtime_file
runtime_file = os.path.abspath(runtime_file)
# remove out_files to avoid any file IO related error
new_out_files = list()
if out_files is not None:
if not isinstance(out_files, dict):
TauDEM.error('The output files parameter must be a dict!')
for (pid, out_file) in iteritems(out_files):
if out_file is None:
continue
if isinstance(out_file, list) or isinstance(out_file, tuple):
for idx, outf in enumerate(out_file):
if outf is None:
continue
outf = FileClass.get_file_fullpath(outf, wp)
FileClass.remove_files(outf)
out_files[pid][idx] = outf
new_out_files.append(outf)
else:
out_file = FileClass.get_file_fullpath(out_file, wp)
FileClass.remove_files(out_file)
out_files[pid] = out_file
new_out_files.append(out_file)
# concatenate command line
commands = list()
# MPI header
if mpi_params is not None:
if not isinstance(mpi_params, dict):
TauDEM.error('The MPI settings parameter must be a dict!')
if 'mpipath' in mpi_params and mpi_params['mpipath'] is not None:
commands.append(mpi_params['mpipath'] + os.sep + 'mpiexec')
else:
commands.append('mpiexec')
if 'hostfile' in mpi_params and mpi_params['hostfile'] is not None \
and not StringClass.string_match(mpi_params['hostfile'], 'none') \
and os.path.isfile(mpi_params['hostfile']):
commands.append('-f')
commands.append(mpi_params['hostfile'])
if 'n' in mpi_params and mpi_params['n'] > 1:
commands.append('-n')
commands.append(str(mpi_params['n']))
else: # If number of processor is less equal than 1, then do not call mpiexec.
commands = []
# append TauDEM function name, which can be full path or just one name
commands.append(function_name)
# append input files
for (pid, infile) in iteritems(in_files):
if infile is None:
continue
if pid[0] != '-':
pid = '-' + pid
commands.append(pid)
if isinstance(infile, list) or isinstance(infile, tuple):
commands.append(' '.join(tmpf for tmpf in infile))
else:
commands.append(infile)
# append input parameters
if in_params is not None:
if not isinstance(in_params, dict):
TauDEM.error('The input parameters must be a dict!')
for (pid, v) in iteritems(in_params):
if pid[0] != '-':
pid = '-' + pid
commands.append(pid)
# allow for parameter which is an flag without value
if v != '' and v is not None:
if MathClass.isnumerical(v):
commands.append(str(v))
else:
commands.append(v)
# append output parameters
if out_files is not None:
for (pid, outfile) in iteritems(out_files):
if outfile is None:
continue
if pid[0] != '-':
pid = '-' + pid
commands.append(pid)
if isinstance(outfile, list) or isinstance(outfile, tuple):
commands.append(' '.join(tmpf for tmpf in outfile))
else:
commands.append(outfile)
# run command
runmsg = UtilClass.run_command(commands)
TauDEM.log(runmsg, log_file)
TauDEM.output_runtime_to_log(function_name, runmsg, runtime_file)
# Check out_files, raise RuntimeError if not exist.
for of in new_out_files:
if not os.path.exists(of):
TauDEM.error('%s failed, and the %s was not generated!' % (function_name, of))
return False
return True
