def calc_jacobian(self, ffs):
jacobian = np.empty((len(ffs[0].data), len(ffs) / 2), dtype=float)
for ff in ffs:
import_weights(ff.data)
for i, index_ff in enumerate(xrange(0, len(ffs), 2)):
# i = 0, 1, 2, ...
# index_ff = 0, 2, 4, ...
for index_datum in xrange(0, len(ffs[0].data)):
dydp = (ffs[index_ff].data[index_datum].value -
ffs[index_ff + 1].data[index_datum].value) / 2
jacobian[index_datum,
i] = ffs[index_ff].data[index_datum].weight * dydp
logger.log(8, 'created {} jacobian'.format(jacobian.shape))
return jacobian
def return_ref_data(args_ref):
logger.log(20, '~~ GATHERING REFERENCE DATA ~~'.rjust(79, '~'))
ref_data = calculate.main(args_ref)
compare.import_weights(ref_data)
return ref_data
def return_ref_data(args_ref):
logger.log(20, '~~ GATHERING REFERENCE DATA ~~'.rjust(79, '~'))
ref_data = calculate.main(args_ref)
compare.import_weights(ref_data)
return ref_data
def main(args):
"""
Arguments
---------
args : string
Evaluated using parser returned by return_calculate_parser().
"""
logger.log(1, ">>> main <<<")
if isinstance(args, basestring):
args.split()
parser = return_calculate_parser()
opts = parser.parse_args(args)
# commands looks like:
# {'me': [['a1.01.mae', 'a2.01.mae', 'a3.01.mae'],
# ['b1.01.mae', 'b2.01.mae']],
# 'mb': [['a1.01.mae'], ['b1.01.mae']],
# 'jeig': [['a1.01.in,a1.out', 'b1.01.in,b1.out']]
# }
commands = {key: value for key, value in opts.__dict__.iteritems() if key in COM_ALL and value}
pretty_all_commands(commands)
# commands_for_filenames looks like:
# {'a1.01.mae': ['me', 'mb'],
# 'a1.01.in': ['jeig'],
# 'a1.out': ['jeig'],
# 'a2.01.mae': ['me'],
# 'a3.01.mae': ['me'],
# 'b1.01.mae': ['me', 'mb'],
# 'b1.01.in': ['jeig'],
# 'b1.out': ['jeig'],
# 'b2.01.mae': ['me']
# }
commands_for_filenames = sort_commands_by_filename(commands)
pretty_commands_for_files(commands_for_filenames)
# inps looks like:
# {'a1.01.mae': <__main__.Mae object at 0x1110e10>,
# 'a1.01.in': None,
# 'a1.out': None,
# 'a2.01.mae': <__main__.Mae object at 0x1733b23>,
# 'a3.01.mae': <__main__.Mae object at 0x1853e12>,
# 'b1.01.mae': <__main__.Mae object at 0x2540e10>,
# 'b1.01.in': None,
# 'b1.out': None,
# 'b2.01.mae': <__main__.Mae object at 0x1353e11>,
# }
inps = {}
for filename, commands_for_filename in commands_for_filenames.iteritems():
if any(x in COM_MACROMODEL for x in commands_for_filename):
if os.path.splitext(filename)[1] == ".mae":
inps[filename] = filetypes.Mae(os.path.join(opts.directory, filename))
inps[filename].commands = commands_for_filename
inps[filename].write_com(sometext=opts.append)
else:
inps[filename] = None
# Check whether or not to skip MacroModel calculations.
if opts.norun:
logger.log(15, " -- Skipping MacroModel calculations.")
else:
for filename, some_class in inps.iteritems():
# Works if some class is None too.
if hasattr(some_class, "run"):
some_class.run(check_tokens=opts.check)
# data is a list comprised of datatypes.Datum objects.
data = collect_data(commands, inps, direc=opts.directory)
if opts.weight:
compare.import_weights(data)
if opts.doprint:
pretty_data(data, log_level=None)
logger.log(1, ">>> data: {}".format(data))
return data