def prep_all(self, parallel=False, removeBinaries=False):
"""
Assumes that all the necessary input files are in ``self.basis_dir``.
This function generates a ``landuse_##`` folder in ``self.basis_dir``
for every land classification number containing a ``fort.13`` file
specific to that land classification number.
.. todo:: Update so that landuse folders can be prepped n at a time and
so that this could be run on a HPC system
"""
first_script = self.setup_landuse_folder(0)
# run grid_all_data in this folder
subprocess.call(['./'+first_script], cwd=self.basis_dir)
# set up remaining land-use classifications
script_list = self.setup_landuse_folders(False)
# run remaining bash scripts
if not parallel:
for s in script_list:
subprocess.call(['./'+s], cwd=self.basis_dir)
else:
print "This needs to be implemented so that we can simultaneously \
run griddata on all of the remaining landuse folders. I \
would sugguest using gnu parallel."
# remove unnecessary files
if removeBinaries:
binaries = glob.glob(self.basis_dir+'/*.asc.binary')
for f in binaries:
os.remove(f)
self.cleanup_landuse_folders()
fm.rename13(basis_dir=self.basis_dir)
def prep_test(self, removeBinaries=False):
"""
Assumes :meth:`~polyadcirc.pyGriddata.prep_mesh.prep_all` has been run
first. Prepares a fort.13 file for testing purposes.
:param binary removeBinaries: flag wheter or not to remove
``*.asc.binary`` files
"""
subprocess.call(['./'+self.setup_folder('test')], cwd=
self.basis_dir)
self.convert(os.path.join(self.basis_dir, 'test'))
# remove unnecessary files
if removeBinaries:
binaries = glob.glob(os.path.join(self.basis_dir, '*.asc.binary'))
for f in binaries:
os.remove(f)
self.cleanup_landuse_folder(os.path.join(self.basis_dir, 'test'))
fm.rename13(['test'], self.basis_dir)
def prep_test(self, removeBinaries=False):
"""
Assumes :meth:`~polyadcirc.pyGriddata.prep_mesh.prep_all` has been run
first. Prepares a fort.13 file for testing purposes.
:param grid: :class:`~polyim.pyGriddata.gridInfo`
:param string path: THIS MUST BE CWD (``'.'``) or ``None``
"""
subprocess.call(['./'+self.setup_folder('test')], cwd=
self.basis_dir)
self.convert(self.basis_dir+'/'+'test')
# remove unnecessary files
if removeBinaries:
binaries = glob.glob(self.basis_dir+'/*.asc.binary')
for f in binaries:
os.remove(f)
self.cleanup_landuse_folder(self.basis_dir+'/test')
fm.rename13(['test'], self.basis_dir)
def prep_all(self, removeBinaries=False, class_nums=None, condense=True,
TOL=None):
"""
Assumes that all the necessary input files are in ``self.basis_dir``.
This function generates a ``landuse_##`` folder in ``self.basis_dir``
for every land classification number containing a ``fort.13`` file
specific to that land classification number.
.. todo:: Update so that landuse folders can be prepped n at a time and
so that this could be run on a HPC system
Currently, the parallel option preps the first folder and then all the
remaining folders at once.
:param binary parallel: Flag whether or not to simultaneously prep
landuse folders.
:param binary removeBinarues: Flag whether or not to remove
``*.asc.binary`` files when completed.
:param list class_nums: List of integers indicating which classes to
prep. This assumes all the ``*.asc.binary`` files are already in
existence.
:param bool condense: Flag whether or not to condense ``fort.13`` to
only non-zero values within a tolerance.
:param double TOL: Tolerance below which to consider a Manning's n
value to be zero if ``condense == True``
"""
if class_nums is None:
class_nums = range(len(self.__landclasses))
if rank > class_nums:
print "There are more MPI TASKS than land classes."
print "This code only scales to MPI_TASKS = len(land_classes)."
print "Extra MPI TASKS will not be used."
return
# Are there any binary files?
binaries = glob.glob(os.path.join(self.basis_dir, '*.asc.binary'))
# If not create them
if not(binaries) and rank == 0:
# set up first landuse folder
first_script = self.setup_landuse_folder(class_nums[0])
# set up remaining land-use classifications
script_list = self.setup_landuse_folders(False)
# run grid_all_data in this folder
subprocess.call(['./'+first_script], cwd=self.basis_dir)
class_nums.remove(0)
landuse_folder = 'landuse_00'
self.cleanup_landuse_folder(os.path.join(self.basis_dir,
landuse_folder))
fm.rename13([landuse_folder], self.basis_dir)
if condense:
print "Removing values below TOL"
landuse_folder_path = os.path.join(self.basis_dir,
landuse_folder)
# read fort.13 file
mann_dict = f13.read_nodal_attr_dict(landuse_folder_path)
# condense fort.13 file
condensed_bv = tmm.condense_bv_dict(mann_dict, TOL)
# write new file
f13.update_mann(condensed_bv, landuse_folder_path)
elif rank == 0:
script_list = self.setup_landuse_folders()
else:
script_list = None
class_nums = None
class_nums = comm.bcast(class_nums, root=0)
script_list = comm.bcast(script_list, root=0)
if len(class_nums) != len(script_list):
temp = [script_list[i] for i in class_nums]
script_list = temp
# run remaining bash scripts
for i in range(0+rank, len(script_list), size):
# run griddata
subprocess.call(['./'+script_list[i]], cwd=self.basis_dir)
# clean up folder
match_string = r"grid_all_(.*)_"+self.file_name[:-3]+r"\.sh"
landuse_folder = re.match(match_string, script_list[i]).groups()[0]
self.cleanup_landuse_folder(os.path.join(self.basis_dir,
landuse_folder))
# rename fort.13 file
fm.rename13([landuse_folder], self.basis_dir)
if condense:
print "Removing values below TOL"
landuse_folder_path = os.path.join(self.basis_dir,
landuse_folder)
# read fort.13 file
mann_dict = f13.read_nodal_attr_dict(landuse_folder_path)
# condense fort.13 file
condensed_bv = tmm.condense_bv_dict(mann_dict, TOL)
# write new file
f13.update_mann(condensed_bv, landuse_folder_path)
print "Done"
# remove unnecessary files
if removeBinaries and rank == 0:
binaries = glob.glob(os.path.join(self.basis_dir, '*.asc.binary'))
for f in binaries:
os.remove(f)
