def bridge(input, output, input2 = None, **kwargs):
"""
"""
def load_input(in_path, in_address, table = False, **kwargs):
"""
"""
from MD_toolkit.HDF5_File import HDF5_File as h5
with h5(in_path) as in_h5:
if table: dataset = in_h5.load(in_address, type = "table")
else: dataset = in_h5.load(in_address, type = "array")
attrs = in_h5.attrs("0000/{0}".format(in_address[2:]))
print("Dataset loaded from {0}[{1}]".format(in_path, in_address))
return dataset, attrs
# Load data
dataset, attrs = load_input(in_path=input[0], in_address=input[1],
**kwargs)
if input2 is not None:
dataset2, _ = load_input(in_path=input2[0], in_address=input2[1],
**kwargs)
stacked = np.column_stack((dataset, dataset2))
minimum = np.min(stacked , axis = 1)
dataset = minimum[:, np.newaxis]
block = Bridge_Block(dataset=dataset, attrs=attrs, output=tuple(output))
block_acceptor = Block_Acceptor(outputs=[tuple(output)])
block_acceptor.next()
block_acceptor.send(block)
block_acceptor.close()
def command_line(n_cores = 1, **kwargs):
"""
Provides command line functionality for this analysis
**Arguments:**
:*n_cores*: Number of cores to use
.. todo:
- Figure out syntax to get this into MDclt.primary
"""
from multiprocessing import Pool
block_generator = Association_Block_Generator(**kwargs)
block_accumulator = Association_Block_Accumulator(
preexisting_slice = block_generator.preexisting_slice,
incoming_slice = block_generator.incoming_slice,
**kwargs)
block_accumulator.next()
if n_cores == 1: # Serial
for block in block_generator:
block()
block_accumulator.send(block)
else: # Parallel (processes)
pool = Pool(n_cores)
for block in pool.imap_unordered(pool_director, block_generator):
block_accumulator.send(block)
pool.close()
pool.join()
block_accumulator.close()
block_acceptor = Block_Acceptor(out_path = kwargs["output"], **kwargs)
block_acceptor.next()
block_acceptor.send(block_accumulator)
block_acceptor.close()