def main(argv) :
parser = argparse.ArgumentParser(description='Tool to classify data based on 1-NN of segment data')
parser.add_argument('-i', '--infile', help='Input JSON Segment File')
parser.add_argument('-o', '--outfile', help='Output JSON Learning File')
parser.add_argument('-p', '--pool', default=multiprocessing.cpu_count(), help='Threads of computation to use')
args = parser.parse_args(argv[1:])
segments_json = load_data(args.infile, 'segments', None, None, "Euclidean Segment Distances: ")
if segments_json == None :
print "Could not load --infile : %s" % (args.infile,)
exit()
segments = Segments.fromJSONDict(segments_json)
if int(args.pool) != 1 :
pool = multiprocessing.Pool(int(args.pool))
else :
pool = None
esd = EuclideanDistances(segments.config, segments, pool=pool)
esd.compute_distances()
if (args.outfile == None) :
args.outfile = EuclideanDistances.get_distances_filename(esd.config)
print "Writing %s" % (args.outfile,)
esd.config.status = "EuclideanDistances"
save_data(args.outfile, esd.toJSONDict())
def main(argv) :
parser = argparse.ArgumentParser(description='Tool to classify data based on chaotic invariants of segment data')
parser.add_argument('-i', '--infile', help='Input JSON Segment File')
parser.add_argument('-o', '--outfile', help='Output JSON Learning File')
parser.add_argument('-e', '--epsilon', type=float, default=1.0, help='epsilon value used for generation of chaotic invariants')
parser.add_argument('-p', '--pool', default=max(1,multiprocessing.cpu_count()-2), help='Threads of computation to use')
args = parser.parse_args(argv[1:])
segments_json = load_data(args.infile, 'segments', None, None, "Chaotic Invariant Features: ")
if segments_json == None :
print "Could not load --infile : %s" % (args.infile,)
exit()
segments = Segments.fromJSONDict(segments_json)
if segments.config.segment_size != segments.config.window_size :
print "%s ERROR ill formed input, segment_size != window_size in %s" % (argv[0], args.infile)
sys.exit(1)
if args.epsilon != None :
segments.config.invariant_epsilon = args.epsilon
if int(args.pool) != 1 :
pool = multiprocessing.Pool(int(args.pool))
else :
pool = None
cid = ChaoticInvariantFeatures(segments.config, segments, epsilon=segments.config.invariant_epsilon, pool=pool)
cid.compute_features()
if (args.outfile == None) :
args.outfile = ChaoticInvariantFeatures.get_features_filename(cid.config)
print "Writing %s" % (args.outfile,)
cid.config.status = "ChaoticInvariantFeatures"
save_data(args.outfile, cid.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(description='Post Processing tool for Segment Data')
parser.add_argument('-i', '--infile')
parser.add_argument('-o', '--outfile')
parser.add_argument('-p', '--pool', type=int, default=min(1,multiprocessing.cpu_count()-2))
args = vars(parser.parse_args(argv[1:]))
segments_json = load_data(args['infile'], 'segments', None, None, "ChaosPost: ")
if segments_json == None :
print "Could not load --infile : %s" % (args['infile'],)
exit()
print "input read"
segments = Segments.fromJSONDict(segments_json)
segments.config.post_process="ChaosPost"
dimensions = len(segments.segments[0].windows[0]) / segments.config.window_size
if args['pool'] == 1 :
pool = None
else :
pool = multiprocessing.Pool(args['pool'])
print "%d processes started" % args['pool']
for index in range(dimensions) :
config = copy(segments.config)
config.data_index = segments.segments[0].data_index[index]
post_processed = ChaosPost(config, segments.segments, dimensions=dimensions, index=index, pool=pool)
if args['outfile'] == None:
outfile = ChaosPost.get_segment_filename(config)
else :
outfile = args['outfile']
print "Writing %s" % outfile
post_processed.config.status = "ChaosPost"
save_data(outfile, post_processed.toJSONDict())
def main(argv) :
parser = argparse.ArgumentParser(description='Tool to generate a radial basis kernel from segmented data')
parser.add_argument('-i', '--infile', help='Input JSON Segment file')
parser.add_argument('-o', '--outfile', help='Output JSON RBF Kernel Matrix file')
parser.add_argument('-g', '--kernel-gamma')
parser.add_argument('-p', '--pool', default=multiprocessing.cpu_count(), help='Threads of computation to use')
args = vars(parser.parse_args(argv[1:]))
sf_json = load_data(args['infile'], 'segments', None, None, "RBFKernel: ")
if sf_json == None :
print "Could not load --infile : %s" % (args['infile'],)
exit()
segments = Segments.fromJSONDict(sf_json)
config = segments.config
if (int(args['pool']) > 1) :
pool = multiprocessing.Pool(int(args['pool']))
else :
pool = None
if (args['kernel_gamma'] != None) :
if args['kernel_gamma'] == 'cv' :
config.kernel_gamma = 'cv'
else :
config.kernel_gamma = float(args['kernel_gamma'])
rk = RBFKernel(config, segments, pool=pool)
start = time.clock()
rk.compute_kernel()
stop = time.clock()
print "%f seconds" % (stop - start,)
if args['outfile'] == None :
outfile = RBFKernel.get_kernel_filename(config)
else :
outfile = args['outfile']
print "RBFKernel: Writing %s" % (outfile,)
rk.config.status = "RBFKernel"
save_data(outfile, rk.toJSONDict())
def main(argv) :
parser = argparse.ArgumentParser(description='Tool to generate the scale space similarity between all pairs of persistence diagrams')
parser.add_argument('-i', '--infile', help='Input JSON Persistence Diagram File')
parser.add_argument('-o', '--outfile', help='Output JSON Learning File')
parser.add_argument('-k', '--kernel-scale', type=float, help='Kernel Scale to use for Scale Space Similarity')
parser.add_argument('-d', '--persistence-degree', type=float, help='Persistence degree to consider when computing Scale Space Similarity')
parser.add_argument('--kernel-file', help='translate from PersistenceKernel instead of redoing calculation')
parser.add_argument('-p', '--pool', default=multiprocessing.cpu_count(), help='Threads of computation to use')
args = parser.parse_args(argv[1:])
if args.kernel_file != None :
from Datatypes.Kernel import Kernel
kernel_json = load_data(args.kernel_file, 'kernel', None, None, "Scale Space Similarity: ")
if kernel_json == None :
print "Could not load --kernel-file : %s" % (args.kernel_file, )
exit()
kernel = Kernel.fromJSONDict(kernel_json)
sss = Distances(kernel.config,
[[Distance(mean=k) for k in row] for row in kernel.kernel_matrix],
kernel.segment_info)
if (args.outfile == None) :
args.outfile = ScaleSpaceSimilarity.get_distances_filename(sss.config)
print "Writing %s" % (args.outfile, )
sss.config.status = "ScaleSpaceSimilarity"
save_data(args.outfile, sss.toJSONDict())
else :
persistences_json = load_data(args.infile, 'persistence_diagrams', None, None, "Scale Space Similarity: ")
if persistences_json == None :
print "Could not load --infile : %s" % (args.infile, )
exit()
persistences = PD.fromJSONDict(persistences_json)
if args.kernel_scale == None :
args.kernel_scale = float(persistences.config.kernel_scale)
else :
persistences.config.kernel_scale = args.kernel_scale
if args.pool != 1 :
pool = multiprocessing.Pool(int(args.pool))
else :
pool = None
sss = ScaleSpaceSimilarity(persistences.config, persistences,
persistences.config.kernel_scale, persistences.config.persistence_degree,
pool=pool)
sss.compute_distances()
if (args.outfile == None) :
args.outfile = ScaleSpaceSimilarity.get_distances_filename(sss.config)
print "Writing %s" % (args.outfile, )
sss.config.status = "ScaleSpaceSimilarity"
save_data(args.outfile, sss.toJSONDict())
def main(argv) :
parser = argparse.ArgumentParser(description="Tool to generate Persistence Diagrams from segmented data")
parser.add_argument('-i', '--infile', help='Input JSON Segment Data file')
parser.add_argument('-o', '--outfile', help='Output JSON Persistence Diagram file')
parser.add_argument('-m', '--max-simplices')
parser.add_argument('-e', '--epsilon')
parser.add_argument('-p', '--pool', default=multiprocessing.cpu_count(), help='Threads of computation to use')
args = vars(parser.parse_args(argv[1:]))
if (not os.path.exists(args['infile'])) :
print "Could not find %s for reading" % (args['infile'],)
return
if (int(args['pool']) > 1) :
pool = multiprocessing.Pool(int(args['pool']))
else :
pool = None
segments_json = load_data(args['infile'], 'segments', None, None, "PersistenceGenerator: ")
if segments_json == None :
print "Could not load --infile : %s" % (args['infile'],)
exit()
segments = Segments.fromJSONDict(segments_json)
config = segments.config
if (args['max_simplices'] != None) :
config.max_simplices = int(args['max_simplices'])
config.persistence_epsilon = None
if (args['epsilon'] != None) :
config.persistence_epsilon = float(args['epsilon'])
config.max_simplices = None
def identity(x) :
return x
if pool != None :
persistences = pool.imap(process, itertools.product(segments.segments, [(config.max_simplices, config.persistence_epsilon)]))
else :
persistences = itertools.imap(process, itertools.product(segments.segments, [(config.max_simplices, config.persistence_epsilon)]))
persistences = PDS(config, list(persistences))
if args['outfile'] == None :
outfile = PDS.get_persistence_diagrams_filename(config)
else :
outfile = args['outfile']
print "PersistenceGenerator: Writing %s" % (outfile,)
persistences.config.status = "PersistenceGenerator"
save_data(outfile, persistences.toJSONDict())
def main(argv) :
parser = argparse.ArgumentParser(description='Tool to evaluate the Landscape Distances between two Arrays of Persistence Diagrams')
parser.add_argument('-a', '--infile-a', help="JSON Persistence Diagram file of the first set of Persistence Diagrams")
parser.add_argument('-b', '--infile-b', help="JSON Persistence Diagram file of the second set of Persistence Diagrams")
parser.add_argument('-o', '--outfile', help="JSON Output File")
parser.add_argument('-d', '--degree', type=int, default=1, help="Persistence Degree to consider")
parser.add_argument('-p', '--pool', default=multiprocessing.cpu_count(), help='Threads of computation to use')
args = vars(parser.parse_args(argv[1:]))
if (not os.path.exists(args['infile_a']) or \
((not (args['infile_a'] == args['infile_b'] or args['infile_b'] == None) and not os.path.exists(args['infile_b'])))) :
parser.print_help()
exit()
pfa_json = load_data(args['infile_a'], 'persistence_diagrams', None, None, "LandscapeDistances: ")
if pfa_json == None :
print "Could not load --infile-a : %s" % (args['infile_a'],)
exit()
persistences_a = PD.fromJSONDict(pfa_json)
if args['infile_a'] == args['infile_b'] or args['infile_b'] == None :
persistences_b = persistences_a
else :
pfb_json = load_data(args['infile_b'], 'persistences', None, None, "LandscapeDistances: ")
if pfb_json == None :
print "Could not load --infile-b : %s" % (args['infile_b'],)
exit()
persistences_b = PD.fromJSONDict(pfb_json)
config = persistences_a.config
if args['degree'] != None :
config.persistence_degree = args['degree']
if (int(args['pool']) > 1) :
pool = multiprocessing.Pool(int(args['pool']))
else :
pool = None
start = time.time()
distances = LandscapeDistances(config, persistences_a, persistences_b, pool=pool)
dist = distances.compute_distances()
end = time.time()
print "Time elapsed %f" % (end - start)
if not('outfile' in args) or args['outfile'] == None :
outfile = LandscapeDistances.get_distances_filename(config)
else :
outfile = args['outfile']
print "Writing %s" % (outfile,)
distances.config.status = "LandscapeDistance"
save_data(outfile, distances.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(description='Post Processing tool for Segment Data')
parser.add_argument('-i', '--infile')
parser.add_argument('-o', '--outfile')
args = vars(parser.parse_args(argv[1:]))
segments_json = load_data(args['infile'], 'segments', None, None, "NormalizePost: ")
if segments_json == None :
print "Could not load --infile : %s" % (args['infile'],)
exit()
segments = Segments.fromJSONDict(segments_json)
segments.config.post_process="NormalizePost"
post_processed = NormalizePost(segments.config, segments.segments)
if args['outfile'] == None:
outfile = NormalizePost.get_segment_filename(segments.config)
else :
outfile = args['outfile']
print "Writing %s" % outfile
post_processed.config.status = "NormalizePost"
save_data(outfile, post_processed.toJSONDict())
def main(argv) :
parser = argparse.ArgumentParser(description='Tool to generate a similarity kernel from persistence data')
parser.add_argument('-i', '--infile', help='Input JSON Persistence Diagram file')
parser.add_argument('-o', '--outfile', help='Output JSON Kernel Similarity Matrix file')
parser.add_argument('-p', '--pool', default=multiprocessing.cpu_count(), help='Threads of computation to use')
parser.add_argument('-k', '--kernel-scale')
parser.add_argument('-d', '--persistence-degree', help='Filter persistence to entries of this degree')
args = vars(parser.parse_args(argv[1:]))
persistences_json = load_data(args['infile'], 'persistence_diagrams', None, None, "PersistenceKernel: ")
if persistences_json == None :
print "Could not load --infile : %s" % (args['infile'],)
exit()
persistences = PD.fromJSONDict(persistences_json)
config = persistences.config
if (int(args['pool']) > 1) :
pool = multiprocessing.Pool(int(args['pool']))
else :
pool = None
if (args['kernel_scale'] != None) :
config.kernel_scale = float(args['kernel_scale'])
if (args['persistence_degree'] != None) :
config.persistence_degree = args['persistence_degree']
pk = PersistenceKernel(config, persistences,
kernel_fun=ScaleSpaceWrapper(float(config.kernel_scale)),
pool=pool)
start = time.clock()
pk.compute_kernel()
stop = time.clock()
print "%f seconds" % (stop - start,)
print "Is Positive Semidefinite? %s" % (isPSD(numpy.matrix(pk.kernel_matrix),))
if args['outfile'] == None :
outfile = PersistenceKernel.get_kernel_filename(config)
else :
outfile = args['outfile']
print "PersistenceKernel: Writing %s" % (outfile,)
pk.config.status = "PersistenceKernel"
save_data(outfile, pk.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(
description='Tool to generate a radial basis kernel from segmented data'
)
parser.add_argument('-i', '--infile', help='Input JSON Segment file')
parser.add_argument('-o',
'--outfile',
help='Output JSON RBF Kernel Matrix file')
parser.add_argument('-g', '--kernel-gamma')
parser.add_argument('-p',
'--pool',
default=multiprocessing.cpu_count(),
help='Threads of computation to use')
args = vars(parser.parse_args(argv[1:]))
sf_json = load_data(args['infile'], 'segments', None, None, "RBFKernel: ")
if sf_json == None:
print "Could not load --infile : %s" % (args['infile'], )
exit()
segments = Segments.fromJSONDict(sf_json)
config = segments.config
if (int(args['pool']) > 1):
pool = multiprocessing.Pool(int(args['pool']))
else:
pool = None
if (args['kernel_gamma'] != None):
if args['kernel_gamma'] == 'cv':
config.kernel_gamma = 'cv'
else:
config.kernel_gamma = float(args['kernel_gamma'])
rk = RBFKernel(config, segments, pool=pool)
start = time.clock()
rk.compute_kernel()
stop = time.clock()
print "%f seconds" % (stop - start, )
if args['outfile'] == None:
outfile = RBFKernel.get_kernel_filename(config)
else:
outfile = args['outfile']
print "RBFKernel: Writing %s" % (outfile, )
rk.config.status = "RBFKernel"
save_data(outfile, rk.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(
description='Post Processing tool for Segment Data')
parser.add_argument('-i', '--infile')
parser.add_argument('-o', '--outfile')
args = vars(parser.parse_args(argv[1:]))
segments_json = load_data(args['infile'], 'segments', None, None,
"NormalizePost: ")
if segments_json == None:
print "Could not load --infile : %s" % (args['infile'], )
exit()
segments = Segments.fromJSONDict(segments_json)
segments.config.post_process = "NormalizePost"
post_processed = NormalizePost(segments.config, segments.segments)
if args['outfile'] == None:
outfile = NormalizePost.get_segment_filename(segments.config)
else:
outfile = args['outfile']
print "Writing %s" % outfile
post_processed.config.status = "NormalizePost"
save_data(outfile, post_processed.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(
description='Tool to perform learning on pregenerated features')
parser.add_argument('-i',
'--infile',
help='Input JSON Similarity Feature file')
parser.add_argument('-o', '--outfile', help='Output JSON Learning file')
parser.add_argument('-p',
'--pool',
default=multiprocessing.cpu_count(),
help='Threads of computation to use')
parser.add_argument(
'-c',
'--learning-C',
help=
'C value for SVM. Specify a range for 1-dimensional cross-validation')
parser.add_argument('--timeout', type=int, default=3600)
parser.add_argument('-t',
'--train-test-partitions',
help='Precomputed train / test partitions')
args = vars(parser.parse_args(argv[1:]))
ff_json = load_data(args['infile'], 'features', None, None,
"FeatureLearning: ")
if ff_json == None:
print "Could not load Features from %s" % (args['infile'], )
sys.exit(1)
features = Features.fromJSONDict(ff_json)
config = features.config
segment_info = features.segment_info
if (int(args['pool']) > 1):
pool = multiprocessing.Pool(int(args['pool']))
else:
pool = None
if (args['learning_C'] != None):
learning_C = parse_range(args['learning_C'], t=float)
else:
learning_C = config.learning_C
if not isinstance(learning_C, list):
learning_C = [learning_C]
else:
learning_C = learning_C
if (args['train_test_partitions'] != None):
partitions_json = load_data(args['train_test_partitions'],
'partitions', None, None,
"FeatureLearning: ")
if partitions_json == None:
print "Could not load Train / Test Partitions from %s" % (
args['train_test_partitions'], )
sys.exit(1)
partitions = TrainTestPartitions.fromJSONDict(partitions_json)
else:
partitions = generate_partitions(config,
segment_info,
cv_iterations=5 if
(len(learning_C) > 1) else 0)
if len(learning_C) > 1 and len(partitions.cross_validation) > 0:
num_cv = len(partitions.cross_validation)
learning_wrap = LearningWrapper(features)
if pool != None:
results = pool.imap(
learning_wrap,
itertools.product(partitions.cross_validation, learning_C))
final_results = []
try:
while True:
result = results.next(
args['timeout']) # timeout in case shogun died on us
final_results.append(result)
except StopIteration:
pass
except multiprocessing.TimeoutError as e:
self.pool.terminate()
print traceback.print_exc()
sys.exit(1)
results = final_results
else:
results = map(
learning_wrap,
itertools.product(partitions.cross_validation, learning_C))
max_correct = 0.0
best_C = learning_C[0]
print len(results)
for C in learning_C:
correct = Learning(
config, [_result for (_C, _result) in results if C == _C
]).get_average_correct()
if correct > max_correct:
best_C = C
max_correct = correct
config.learning_C = best_C
print "FeatureLearning: using C = %s, correct = %s" % (
config.learning_C, max_correct)
else:
if isinstance(learning_C, list):
config.learning_C = learning_C[0]
else:
config.learning_C = learning_C
learning_wrap = LearningWrapper(features)
if pool != None:
results = pool.map(
learning_wrap,
itertools.product(partitions.evaluation, [config.learning_C]))
else:
results = map(
learning_wrap,
itertools.product(partitions.evaluation, [config.learning_C]))
learning = Learning(config, [result for (C, result) in results])
if args['outfile'] == None:
learning_filename = FeatureLearning.get_learning_filename(config)
else:
learning_filename = args['outfile']
correct = learning.get_average_correct()
print "%s correct %2.2f%% error %2.2f%% classes %s" % (
"FeatureLearning:", correct * 100.0, (1.0 - correct) * 100.0,
len(set([s.max_label() for s in features.segment_info])))
print "Writing %s" % (learning_filename, )
learning.config.status = "FeatureLearning"
save_data(learning_filename, learning.toJSONDict())
if __name__ == "__main__" :
parser = argparse.ArgumentParser("Tool to generate train / test splits for testing and cross validation")
parser.add_argument("--segments", "-i")
parser.add_argument("--outfile", "-o")
parser.add_argument("--learning-split", "-s", type=float)
parser.add_argument("--learning-iterations", "-I", type=int)
parser.add_argument("--cv-iterations", "-v", default=5, type=int)
parser.add_argument("--seed", "-S")
args = parser.parse_args(sys.argv[1:])
segments_json = load_data(args.segments, 'segments', None, None, sys.argv[0] + " : ")
if segments_json == None :
print "Could not load Segments from %s" % (args.segments,)
sys.exit(1)
segment_info = [SegmentInfo.fromJSONDict(s) for s in segments_json['segments']]
config = Configuration.fromJSONDict(segments_json['config'])
if args.learning_split != None :
config.learning_split = args.learning_split
if args.learning_iterations != None :
config.learning_iterations = args.learning_iterations
output = generate_partitions(config, segment_info, cv_iterations=args.cv_iterations, seed=args.seed)
if args.outfile == None :
args.outfile = TrainTestPartitions.get_partition_filename(config)
print "Writing %s" % (args.outfile,)
save_data(args.outfile, output.toJSONDict())
kernel_matrix = [[numpy.average([k.kernel_matrix[i][j] for k in kernels]) for i in range(kernel_dimension)] for j in range(kernel_dimension)]
return Kernel(config, kernel_matrix, segment_info)
if __name__ == "__main__" :
parser = argparse.ArgumentParser(description="Tool to take multiple Kernels and average them")
parser.add_argument("--infile", "-i", nargs="+")
parser.add_argument("--outfile", "-o")
parser.add_argument("--ratio", "-r", type=float, default=0.5)
parser.add_argument("--pool", "-p")
args = parser.parse_args(sys.argv[1:])
kernels_json = [load_data(infile, 'kernel', None, None, sys.argv[0]+": ") for infile in args.infile]
kernels = [Kernel.fromJSONDict(kernel_json) for kernel_json in kernels_json]
if len(kernels) == 2 :
weights = [args.ratio, 1.0 - args.ratio]
else :
weights = None
average_kernel = AverageKernel(kernels, weights)
if args.outfile == None :
args.outfile = get_filename(average_kernel.config,
['max_simplices', 'persistence_epsilon',
'segment_filename', 'segment_stride', 'segment_size',
'window_size', 'window_stride',
'kernel_scale', 'kernel_gamma', 'invariant_epsilon',
'data_file', 'data_index', 'label_index', 'persistence_degree',
'data_type', 'post_process', 'post_process_arg'], "AverageKernel")
print "Writing %s" % (args.outfile,)
save_data(args.outfile, average_kernel.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(
description=
'Tool to evaluate the Bottleneck Distances between two Arrays of Persistence Diagrams'
)
parser.add_argument(
'-a',
'--infile-a',
help=
"JSON Persistence Diagram file of the first set of Persistence Diagrams"
)
parser.add_argument(
'-b',
'--infile-b',
help=
"JSON Persistence Diagram file of the second set of Persistence Diagrams"
)
parser.add_argument('-o', '--outfile', help="JSON Output File")
parser.add_argument('-d',
'--degree',
type=int,
default=1,
help="Persistence Degree to consider")
parser.add_argument('-p',
'--pool',
default=multiprocessing.cpu_count(),
help='Threads of computation to use')
args = vars(parser.parse_args(argv[1:]))
if (not os.path.exists(args['infile_a']) or \
((not (args['infile_a'] == args['infile_b'] or args['infile_b'] == None) and not os.path.exists(args['infile_b'])))) :
parser.print_help()
exit()
pfa_json = load_data(args['infile_a'], 'persistence_diagrams', None, None,
"BottleneckDistances: ")
if pfa_json == None:
print "Could not load --infile-a : %s" % (args['infile_a'], )
exit()
persistences_a = PersistenceDiagrams.fromJSONDict(pfa_json)
if args['infile_a'] == args['infile_b'] or args['infile_b'] == None:
persistences_b = persistences_a
else:
pfb_json = load_data(args['infile_b'], 'persistence_diagrams', None,
None, "BottleneckDistances: ")
if pfb_json == None:
print "Could not load --infile-b : %s" % (args['infile_b'], )
exit()
persistences_b = PersistenceDiagrams.fromJSONDict(pfb_json)
if (int(args['pool']) > 1):
pool = multiprocessing.Pool(int(args['pool']))
else:
pool = None
start = time.time()
distances = BottleneckDistances(persistences_a.config,
persistences_a,
persistences_b,
pool=pool,
degree=args['degree'])
dist = distances.compute_distances()
end = time.time()
print "Time elapsed %f" % (end - start)
if not ('outfile' in args) or args['outfile'] == None:
outfile = BottleneckDistances.get_distances_filename(distances.config)
else:
outfile = args['outfile']
print "Writing %s" % (outfile, )
distances.config.status = "BottleneckDistance"
save_data(outfile, distances.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(
description=
'Tool to generate the scale space similarity between all pairs of persistence diagrams'
)
parser.add_argument('-i',
'--infile',
help='Input JSON Persistence Diagram File')
parser.add_argument('-o', '--outfile', help='Output JSON Learning File')
parser.add_argument('-k',
'--kernel-scale',
type=float,
help='Kernel Scale to use for Scale Space Similarity')
parser.add_argument(
'-d',
'--persistence-degree',
type=float,
help=
'Persistence degree to consider when computing Scale Space Similarity')
parser.add_argument(
'--kernel-file',
help='translate from PersistenceKernel instead of redoing calculation')
parser.add_argument('-p',
'--pool',
default=multiprocessing.cpu_count(),
help='Threads of computation to use')
args = parser.parse_args(argv[1:])
if args.kernel_file != None:
from Datatypes.Kernel import Kernel
kernel_json = load_data(args.kernel_file, 'kernel', None, None,
"Scale Space Similarity: ")
if kernel_json == None:
print "Could not load --kernel-file : %s" % (args.kernel_file, )
exit()
kernel = Kernel.fromJSONDict(kernel_json)
sss = Distances(kernel.config, [[Distance(mean=k) for k in row]
for row in kernel.kernel_matrix],
kernel.segment_info)
if (args.outfile == None):
args.outfile = ScaleSpaceSimilarity.get_distances_filename(
sss.config)
print "Writing %s" % (args.outfile, )
sss.config.status = "ScaleSpaceSimilarity"
save_data(args.outfile, sss.toJSONDict())
else:
persistences_json = load_data(args.infile, 'persistence_diagrams',
None, None, "Scale Space Similarity: ")
if persistences_json == None:
print "Could not load --infile : %s" % (args.infile, )
exit()
persistences = PD.fromJSONDict(persistences_json)
if args.kernel_scale == None:
args.kernel_scale = float(persistences.config.kernel_scale)
else:
persistences.config.kernel_scale = args.kernel_scale
if args.pool != 1:
pool = multiprocessing.Pool(int(args.pool))
else:
pool = None
sss = ScaleSpaceSimilarity(persistences.config,
persistences,
persistences.config.kernel_scale,
persistences.config.persistence_degree,
pool=pool)
sss.compute_distances()
if (args.outfile == None):
args.outfile = ScaleSpaceSimilarity.get_distances_filename(
sss.config)
print "Writing %s" % (args.outfile, )
sss.config.status = "ScaleSpaceSimilarity"
save_data(args.outfile, sss.toJSONDict())
parser.add_argument("--learning-split", "-s", type=float)
parser.add_argument("--learning-iterations", "-I", type=int)
parser.add_argument("--cv-iterations", "-v", default=5, type=int)
parser.add_argument("--seed", "-S")
args = parser.parse_args(sys.argv[1:])
segments_json = load_data(args.segments, 'segments', None, None,
sys.argv[0] + " : ")
if segments_json == None:
print "Could not load Segments from %s" % (args.segments, )
sys.exit(1)
segment_info = [
SegmentInfo.fromJSONDict(s) for s in segments_json['segments']
]
config = Configuration.fromJSONDict(segments_json['config'])
if args.learning_split != None:
config.learning_split = args.learning_split
if args.learning_iterations != None:
config.learning_iterations = args.learning_iterations
output = generate_partitions(config,
segment_info,
cv_iterations=args.cv_iterations,
seed=args.seed)
if args.outfile == None:
args.outfile = TrainTestPartitions.get_partition_filename(config)
print "Writing %s" % (args.outfile, )
save_data(args.outfile, output.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(description='Tool to perform learning on pregenerated features')
parser.add_argument('-i', '--infile', help='Input JSON Similarity Feature file')
parser.add_argument('-o', '--outfile', help='Output JSON Learning file')
parser.add_argument('-p', '--pool', default=multiprocessing.cpu_count(), help='Threads of computation to use')
parser.add_argument('-c', '--learning-C', help='C value for SVM. Specify a range for 1-dimensional cross-validation')
parser.add_argument('--timeout', type=int, default=3600)
parser.add_argument('-t', '--train-test-partitions', help='Precomputed train / test partitions')
args = vars(parser.parse_args(argv[1:]))
ff_json = load_data(args['infile'], 'features', None, None, "FeatureLearning: ")
if ff_json == None :
print "Could not load Features from %s" % (args['infile'],)
sys.exit(1)
features = Features.fromJSONDict(ff_json)
config = features.config
segment_info = features.segment_info
if (int(args['pool']) > 1) :
pool = multiprocessing.Pool(int(args['pool']))
else :
pool = None
if (args['learning_C'] != None) :
learning_C = parse_range(args['learning_C'], t=float)
else :
learning_C = config.learning_C
if not isinstance(learning_C,list) :
learning_C = [learning_C]
else :
learning_C = learning_C
if (args['train_test_partitions'] != None) :
partitions_json = load_data(args['train_test_partitions'], 'partitions', None, None, "FeatureLearning: ")
if partitions_json == None :
print "Could not load Train / Test Partitions from %s" % (args['train_test_partitions'],)
sys.exit(1)
partitions = TrainTestPartitions.fromJSONDict(partitions_json)
else :
partitions = generate_partitions(config, segment_info,
cv_iterations=5 if (len(learning_C) > 1) else 0)
if len(learning_C) > 1 and len(partitions.cross_validation) > 0 :
num_cv = len(partitions.cross_validation)
learning_wrap = LearningWrapper( features )
if pool != None :
results = pool.imap(learning_wrap, itertools.product(partitions.cross_validation, learning_C))
final_results = []
try:
while True:
result = results.next(args['timeout']) # timeout in case shogun died on us
final_results.append(result)
except StopIteration:
pass
except multiprocessing.TimeoutError as e:
self.pool.terminate()
print traceback.print_exc()
sys.exit(1)
results = final_results
else :
results = map(learning_wrap, itertools.product(partitions.cross_validation, learning_C))
max_correct = 0.0
best_C = learning_C[0]
print len(results)
for C in learning_C :
correct = Learning(config, [_result for (_C, _result) in results if C == _C]).get_average_correct()
if correct > max_correct :
best_C = C
max_correct = correct
config.learning_C = best_C
print "FeatureLearning: using C = %s, correct = %s" % (config.learning_C, max_correct)
else :
if isinstance(learning_C, list) :
config.learning_C = learning_C[0]
else :
config.learning_C = learning_C
learning_wrap = LearningWrapper( features )
if pool != None :
results = pool.map(learning_wrap, itertools.product(partitions.evaluation, [config.learning_C]))
else :
results = map(learning_wrap, itertools.product(partitions.evaluation, [config.learning_C]))
learning = Learning(config, [result for (C,result) in results])
if args['outfile'] == None :
learning_filename = FeatureLearning.get_learning_filename(config)
else :
learning_filename = args['outfile']
correct = learning.get_average_correct()
print "%s correct %2.2f%% error %2.2f%% classes %s" % ("FeatureLearning:", correct * 100.0, (1.0 - correct)*100.0,
len(set([s.max_label() for s in features.segment_info])))
print "Writing %s" % (learning_filename, )
learning.config.status = "FeatureLearning"
save_data(learning_filename, learning.toJSONDict())
def main(argv):
parser = argparse.ArgumentParser(
description=
'Tool to classify data based on 1-NN matching based on the supplied distance matrix'
)
parser.add_argument('-i', '--infile', help='Input JSON Distance File')
parser.add_argument('-o', '--outfile', help='Output JSON Learning File')
parser.add_argument(
'-m',
'--max-mode',
action='store_true',
help=
'Use maximum "Distance" instead of minimum (for Similarity measures"')
parser.add_argument('-t',
'--train-test-partitions',
help='Precomputed train / test partitions')
parser.add_argument('-p', '--pool', default=1, type=int)
args = parser.parse_args(argv[1:])
distances_json = load_data(args.infile, 'distances', None, None,
"DistanceLearning: ")
if distances_json == None:
print "Could not load --infile : %s" % (args.infile, )
sys.exit(1)
distances = Distances.fromJSONDict(distances_json)
if (args.train_test_partitions != None):
partitions_json = load_data(args.train_test_partitions, 'partitions',
None, None, "KernelLearning: ")
if partitions_json == None:
print "Could not load Train / Test Partitions from %s" % (
args.train_test_partitions, )
sys.exit(1)
partitions = TrainTestPartitions.fromJSONDict(partitions_json)
else:
partitions = generate_partitions(distances.config,
distances.segment_info,
cv_iterations=0)
if (args.pool > 1):
pool = multiprocessing.Pool(args.pool)
else:
pool = None
learning_wrap = LearningWrapper(distances, args.max_mode)
if pool != None:
results = pool.map(learning_wrap, partitions.evaluation)
else:
results = map(learning_wrap, partitions.evaluation)
learning = Learning(distances.config, list(results))
if (args.outfile == None):
args.outfile = DistanceLearning.get_learning_filename(learning.config)
print "Writing %s, %2.2f%% correct" % (
args.outfile, learning.get_average_correct() * 100.0)
learning.config.status = "DistanceLearning"
save_data(args.outfile, learning.toJSONDict())