def test_removal_of_error_parameter(self):
filename = make_temp_dir('remove_errored.hdf5')
traj = Trajectory(name='traj', add_time=True, filename=filename)
traj.f_add_result('iii', 42)
traj.f_add_result(FakeResult, 'j.j.josie', 43)
file = traj.v_storage_service.filename
traj.f_store(only_init=True)
with self.assertRaises(RuntimeError):
traj.f_store()
with pt.open_file(file, mode='r') as fh:
jj = fh.get_node(where='/%s/results/j/j' % traj.v_name)
self.assertTrue('josie' not in jj)
traj.j.j.f_remove_child('josie')
traj.j.j.f_add_result(FakeResult2, 'josie2', 444)
traj.f_store()
with self.assertRaises(pex.NoSuchServiceError):
traj.f_store_child('results', recursive=True)
with pt.open_file(file, mode='r') as fh:
jj = fh.get_node(where='/%s/results/j/j' % traj.v_name)
self.assertTrue('josie2' in jj)
josie2 =jj._f_get_child('josie2')
self.assertTrue('hey' in josie2)
self.assertTrue('fail' not in josie2)
def __init__(self, filename, model_state, proposal_state):
"""
Initialize the object.
"""
self.filename = filename
self.ChainRecordDType = state_to_table_dtype(model_state)
self.ChainRecordDType['step'] = pt.UInt32Col()
self.ChainRecordDType['accepted'] = pt.UInt32Col()
self.ChainRecordDType['proposal'] = pt.UInt16Col()
self.ProposalRecordDType = state_to_table_dtype(proposal_state)
self.ChainCounterDType = {'id': pt.UInt16Col(),
'name': pt.StringCol(itemsize=32),
'date': pt.StringCol(itemsize=26)
}
if os.path.exists(filename) and pt.is_pytables_file(filename):
self.fd = pt.open_file(filename, mode='a')
else:
self.fd = pt.open_file(filename, mode='w')
self.fd.create_group('/', 'mcmc',
'Metropolis-Hastings Algorithm Data')
self.fd.create_table('/mcmc', 'proposals',
self.ProposalRecordDType,
'MCMC Proposals')
self.fd.create_table('/mcmc', 'chain_counter',
self.ChainCounterDType, 'Chain Counter')
self.fd.create_group('/mcmc', 'data', 'Collection of Chains')
def validate_results_node(test, expected_path, actual_path, expected_node,
actual_node):
"""Validate results by comparing two specific nodes
:param test: instance of the TestCase.
:param expected_path: path to the reference data.
:param actual_path: path to the output from the test.
:param expected_node: path to the reference node.
:param actual_node: path to the output node from the test.
"""
with tables.open_file(expected_path, 'r') as expected_file, \
tables.open_file(actual_path, 'r') as actual_file:
expected = expected_file.get_node(expected_node)
try:
actual = actual_file.get_node(actual_node)
except tables.NoSuchNodeError:
test.fail("Node '%s' does not exist in datafile" % actual_node)
if type(expected) is tables.table.Table:
validate_tables(test, expected, actual)
elif type(expected) is tables.vlarray.VLArray:
validate_vlarrays(test, expected, actual)
elif type(expected) is tables.array.Array:
validate_arrays(test, expected, actual)
else:
raise NotImplementedError
def test_maximum_overview_size(self):
filename = make_temp_dir('maxisze.hdf5')
env = Environment(trajectory='Testmigrate', filename=filename,
log_config=get_log_config(), add_time=True)
traj = env.v_trajectory
for irun in range(pypetconstants.HDF5_MAX_OVERVIEW_TABLE_LENGTH):
traj.f_add_parameter('f%d.x' % irun, 5)
traj.f_store()
store = pt.open_file(filename, mode='r+')
table = store.root._f_get_child(traj.v_name).overview.parameters_overview
self.assertEquals(table.nrows, pypetconstants.HDF5_MAX_OVERVIEW_TABLE_LENGTH)
store.close()
for irun in range(pypetconstants.HDF5_MAX_OVERVIEW_TABLE_LENGTH,
2*pypetconstants.HDF5_MAX_OVERVIEW_TABLE_LENGTH):
traj.f_add_parameter('f%d.x' % irun, 5)
traj.f_store()
store = pt.open_file(filename, mode='r+')
table = store.root._f_get_child(traj.v_name).overview.parameters_overview
self.assertEquals(table.nrows, pypetconstants.HDF5_MAX_OVERVIEW_TABLE_LENGTH)
store.close()
env.f_disable_logging()
def validate_results(test, expected_path, actual_path):
"""Validate results by comparing in and output HDF5 files
:param test: instance of the TestCase.
:param expected_path: path to the reference data.
:param actual_path: path to the output from the test.
"""
with tables.open_file(expected_path, 'r') as expected_file, \
tables.open_file(actual_path, 'r') as actual_file:
for expected_node in expected_file.walk_nodes('/', 'Leaf'):
try:
actual_node = actual_file.get_node(expected_node._v_pathname)
except tables.NoSuchNodeError:
test.fail("Node '%s' does not exist in datafile" %
expected_node._v_pathname)
if type(expected_node) is tables.table.Table:
validate_tables(test, expected_node, actual_node)
elif type(expected_node) is tables.vlarray.VLArray:
validate_vlarrays(test, expected_node, actual_node)
elif type(expected_node) is tables.array.Array:
validate_arrays(test, expected_node, actual_node)
else:
raise NotImplementedError
validate_attributes(test, expected_node, actual_node)
validate_attributes(test, expected_file.root, actual_file.root)
def test03b_Compare64EArray(self):
"Comparing several written and read 64-bit time values in an EArray."
# Create test EArray with data.
h5file = tables.open_file(self.h5fname, "w", title="Test for comparing Time64 E arrays")
ea = h5file.create_earray("/", "test", tables.Time64Atom(), shape=(0, 2))
# Size of the test.
nrows = ea.nrowsinbuf + 34 # Add some more rows than buffer.
# Only for home checks; the value above should check better
# the I/O with multiple buffers.
# nrows = 10
for i in range(nrows):
j = i * 2
ea.append(((j + 0.012, j + 1 + 0.012),))
h5file.close()
# Check the written data.
h5file = tables.open_file(self.h5fname)
arr = h5file.root.test.read()
h5file.close()
orig_val = numpy.arange(0, nrows * 2, dtype=numpy.int32) + 0.012
orig_val.shape = (nrows, 2)
if common.verbose:
print("Original values:", orig_val)
print("Retrieved values:", arr)
self.assertTrue(allequal(arr, orig_val), "Stored and retrieved values do not match.")
def test02_copy(self):
"""Checking (X)Array.copy() method ('numetic' flavor)"""
srcfile = self._testFilename("oldflavor_numeric.h5")
tmpfile = tempfile.mktemp(".h5")
shutil.copy(srcfile, tmpfile)
try:
# Open the HDF5 with old numeric flavor
with tables.open_file(tmpfile, "r+") as h5file:
# Copy to another location
self.assertWarns(FlavorWarning,
h5file.root.array1.copy, '/', 'array1copy')
h5file.root.array2.copy('/', 'array2copy')
h5file.root.carray1.copy('/', 'carray1copy')
h5file.root.carray2.copy('/', 'carray2copy')
h5file.root.vlarray1.copy('/', 'vlarray1copy')
h5file.root.vlarray2.copy('/', 'vlarray2copy')
if self.close:
h5file.close()
h5file = tables.open_file(tmpfile)
else:
h5file.flush()
# Assert other properties in array
self.assertEqual(h5file.root.array1copy.flavor, 'numeric')
self.assertEqual(h5file.root.array2copy.flavor, 'python')
self.assertEqual(h5file.root.carray1copy.flavor, 'numeric')
self.assertEqual(h5file.root.carray2copy.flavor, 'python')
self.assertEqual(h5file.root.vlarray1copy.flavor, 'numeric')
self.assertEqual(h5file.root.vlarray2copy.flavor, 'python')
finally:
os.remove(tmpfile)
def WriteRead(filename, testTuple):
if common.verbose:
print('\n', '-=' * 30)
print("Running test for object %s" % type(testTuple))
# Create an instance of HDF5 Table
fileh = tables.open_file(filename, mode="w")
root = fileh.root
try:
# Create the array under root and name 'somearray'
a = testTuple
fileh.create_array(root, 'somearray', a, "Some array")
finally:
# Close the file
fileh.close()
# Re-open the file in read-only mode
fileh = tables.open_file(filename, mode="r")
root = fileh.root
# Read the saved array
try:
b = root.somearray.read()
# Compare them. They should be equal.
if not a == b and common.verbose:
print("Write and read lists/tuples differ!")
print("Object written:", a)
print("Object read:", b)
# Check strictly the array equality
assert a == b
finally:
# Close the file
fileh.close()
def test_2D_multiphase(self):
# RELOAD MODULES
self.reload_modules()
pnList = [(twp_navier_stokes_p, twp_navier_stokes_n),
(clsvof_p, clsvof_n)]
self.so = multiphase_so
pList=[]
nList=[]
sList=[]
for (pModule,nModule) in pnList:
pList.append(pModule)
if pList[-1].name == None:
pList[-1].name = pModule.__name__
nList.append(nModule)
for i in range(len(pnList)):
sList.append(default_s)
self.so.name += "_2D_falling_bubble"
# NUMERICAL SOLUTION #
ns = proteus.NumericalSolution.NS_base(self.so,
pList,
nList,
sList,
opts)
ns.calculateSolution('2D_falling_bubble')
# COMPARE VS SAVED FILES #
expected_path = 'comparison_files/multiphase_2D_falling_bubble.h5'
expected = tables.open_file(os.path.join(self._scriptdir,expected_path))
actual = tables.open_file('multiphase_2D_falling_bubble.h5','r')
assert np.allclose(expected.root.phi_t2,actual.root.phi_t2,atol=1e-10)
expected.close()
actual.close()
def compute_rab(self):
'''
Uses the current set of ICA realizations (pytabled) to compute K*(K-1)/2 cross-correlation matrices;
they are indexed via tuples. R(a,b) is much smaller than the ICA realizations (all R(a,b) matrices
are generally smaller than ONE realization), so R(a,b) is also retained in memory. Recomputation of
the R(a,b) matrices is forced.
'''
if not os.path.exists(self.rabDirectory):
try:
os.mkdir(self.rabDirectory)
except OSError:
pass
icaFiles = sorted(os.listdir(self.icaDirectory))
if len(icaFiles) == 0:
raise RAICARICAException
for fi in icaFiles:
fiPtr = tb.open_file(os.path.join(self.icaDirectory,fi),'r')
si = fiPtr.get_node('/decomps/sources').read()
fiPtr.close()
i = np.int(deconstruct_file_name(fi)[1])
print 'Working on R(%d,b)'%i
for fj in icaFiles:
j = np.int(deconstruct_file_name(fj)[1])
if j > i:
# sources assumed to have unit std. dev. but nonzero mean - will behave badly if not!
fjPtr = tb.open_file(os.path.join(self.icaDirectory,fj),'r')
sj = fjPtr.get_node('/decomps/sources').read()
fjPtr.close()
self.RabDict[(i,j)] = np.abs(corrmatrix(si,sj))
# pickle the result
rabPtr = open(os.path.join(self.rabDirectory,'rabmatrix.db'),'wb')
cPickle.dump(self.RabDict,rabPtr,protocol=-1)
rabPtr.close()
def test02_CompareTable(self):
"Comparing written time data with read data in a Table."
wtime = 1234567890.123456
# Create test Table with data.
h5file = tables.open_file(
self.h5fname, 'w', title="Test for comparing Time tables")
tbl = h5file.create_table('/', 'test', self.MyTimeRow)
row = tbl.row
row['t32col'] = int(wtime)
row['t64col'] = (wtime, wtime)
row.append()
h5file.close()
# Check the written data.
h5file = tables.open_file(self.h5fname)
recarr = h5file.root.test.read(0)
h5file.close()
self.assertEqual(recarr['t32col'][0], int(wtime),
"Stored and retrieved values do not match.")
comp = (recarr['t64col'][0] == numpy.array((wtime, wtime)))
self.assertTrue(numpy.alltrue(comp),
"Stored and retrieved values do not match.")
def test01b_Compare64VLArray(self):
"Comparing several written and read 64-bit time values in a VLArray."
# Create test VLArray with data.
h5file = tables.open_file(
self.h5fname, 'w', title="Test for comparing Time64 VL arrays")
vla = h5file.create_vlarray('/', 'test', self.myTime64Atom)
# Size of the test.
nrows = vla.nrowsinbuf + 34 # Add some more rows than buffer.
# Only for home checks; the value above should check better
# the I/O with multiple buffers.
# nrows = 10
for i in xrange(nrows):
j = i * 2
vla.append((j + 0.012, j + 1 + 0.012))
h5file.close()
# Check the written data.
h5file = tables.open_file(self.h5fname)
arr = h5file.root.test.read()
h5file.close()
arr = numpy.array(arr)
orig_val = numpy.arange(0, nrows * 2, dtype=numpy.int32) + 0.012
orig_val.shape = (nrows, 1, 2)
if common.verbose:
print "Original values:", orig_val
print "Retrieved values:", arr
self.assertTrue(allequal(arr, orig_val),
"Stored and retrieved values do not match.")
def test_case_2(self):
# Set parameters for this test
parameters.ct.test_case=2
# RELOAD MODULES
self.reload_modules()
pnList = [(clsvof_p, clsvof_n)]
self.so = default_so
self.so.tnList = clsvof_n.tnList
pList=[]
nList=[]
sList=[]
for (pModule,nModule) in pnList:
pList.append(pModule)
if pList[-1].name == None:
pList[-1].name = pModule.__name__
nList.append(nModule)
for i in range(len(pnList)):
sList.append(default_s)
self.so.name = "clsvof_test_case_2"
# NUMERICAL SOLUTION #
ns = proteus.NumericalSolution.NS_base(self.so,
pList,
nList,
sList,
opts)
ns.calculateSolution('test_case_2')
# COMPARE VS SAVED FILES #
expected_path = 'comparison_files/clsvof_test_case_2.h5'
expected = tables.open_file(os.path.join(self._scriptdir,expected_path))
actual = tables.open_file('clsvof_test_case_2.h5','r')
assert np.allclose(expected.root.u_t2,actual.root.u_t2,atol=1e-10)
expected.close()
actual.close()
def test_EV2(self):
thelper_vof.ct.STABILIZATION_TYPE = 1 # EV
thelper_vof.ct.ENTROPY_TYPE = 2 #logarithmic
thelper_vof.ct.cE = 0.1
thelper_vof.ct.FCT = True
reload(thelper_vof_p)
reload(thelper_vof_n)
self.so.name = self.pList[0].name+"_EV2"
# NUMERICAL SOLUTION #
ns = proteus.NumericalSolution.NS_base(self.so,
self.pList,
self.nList,
self.sList,
opts)
self.sim_names.append(ns.modelList[0].name)
ns.calculateSolution('vof')
# COMPARE VS SAVED FILES #
expected_path = 'comparison_files/vof_level_3_EV2.h5'
expected = tables.open_file(os.path.join(self._scriptdir,expected_path))
actual = tables.open_file('vof_level_3_EV2.h5','r')
assert np.allclose(expected.root.u_t2,
actual.root.u_t2,
atol=1e-10)
expected.close()
actual.close()
def main(argv):
args = parse_args(argv[1:])
fileout = os.path.abspath(args.output)
start = time()
for fin in args.inputs:
filein = os.path.abspath(fin)
print 'Concatenating %s' % filein
if not os.path.exists(fileout):
copyfile(filein, fileout)
else:
# Can't use HdfStorage.readCoordinates because it needs an
# Ice.Communicator object, so there's no point using the
# OMERO.tables interface
tout = tables.open_file(fileout, 'r+')
tin = tables.open_file(filein, 'r')
nrows = tin.root.OME.Measurements.nrows
for a in range(0, nrows, ROW_CHUNK):
b = min(nrows, a + ROW_CHUNK)
print '\tRows %d:%d' % (a, b)
rows = tin.root.OME.Measurements.read_coordinates(range(a, b))
tout.root.OME.Measurements.append(rows)
tin.close()
tout.close()
print '\tCumulative time: %d seconds' % (time() - start)
print 'Done'
def _runTest(self):
self.ns = NumericalSolution.NS_base(self.so,
self.pList,
self.nList,
self.so.sList,
opts)
self.ns.calculateSolution('stokes')
relpath = 'comparison_files/drivenCavityNSE_LSC_expected.h5'
expected = tables.open_file(os.path.join(self._scriptdir,relpath))
actual = tables.open_file('drivenCavityNSETrial.h5','r')
assert numpy.allclose(expected.root.velocity_t7,
actual.root.velocity_t7,
atol=1e-2)
expected.close()
actual.close()
relpath = 'comparison_files/drivenCavityNSE_LSC_expected.log'
actual_log = TestTools.NumericResults.build_from_proteus_log('proteus.log')
expected_log = TestTools.NumericResults.build_from_proteus_log(os.path.join(self._scriptdir,
relpath))
plot_lst = [(3.7,0,3),(3.2,0,2),(2.7,0,2),(2.2,0,1),(1.7,0,1)]
L1 = expected_log.get_ksp_resid_it_info(plot_lst)
L2 = actual_log.get_ksp_resid_it_info(plot_lst)
assert L1 == L2
def test_estimator_pytables():
m1 = MyEstimator(a=1, b='a', c=None, d=False, e=np.zeros(3)).fit(None)
f = tables.open_file(fn, 'w')
m1.to_pytables(f.root)
f.close()
g = tables.open_file(fn)
m2 = MyEstimator.from_pytables(g.root.MyEstimator)
print m1.__dict__
print m2.__dict__
for key, value in m1.get_params().iteritems():
if any(isinstance(value, t) for t in [int, float, str]):
assert value == getattr(m2, key, object())
else:
eq(value, getattr(m2, key, object()), err_msg='error on param key=%s' % key)
for key in m1._get_estimate_names():
value = getattr(m1, key)
if any(isinstance(value, t) for t in [int, float, str]):
assert value == getattr(m2, key, object())
else:
eq(value, getattr(m2, key, object()), err_msg='error on estimate key=%s' % key)
g.close()
def test_3D_hex(self):
# Set parameters for test
parameters_for_poisson.ct.nd = 3
parameters_for_poisson.useHex = True
# Reload _p and _n modules
reload(poisson_p)
reload(poisson_n)
poisson_n.nnx=poisson_p.nn
poisson_n.nny=poisson_p.nn
poisson_n.nnz=poisson_p.nn
# Update name
self.so.name = "3D_"+self.pList[0].name+"_hex_degree2"
# NUMERICAL SOLUTION #
ns = proteus.NumericalSolution.NS_base(self.so,
self.pList,
self.nList,
self.sList,
opts)
self.sim_names.append(ns.modelList[0].name)
ns.calculateSolution('poisson')
# COMPARE VS SAVED FILES #
expected_path = 'comparison_files/'+self.so.name+'.h5'
expected = tables.open_file(os.path.join(self._scriptdir,expected_path))
actual = tables.open_file(self.so.name+'.h5','r')
assert np.allclose(expected.root.u0_t1,
actual.root.u0_t1,
atol=1e-10)
def store_and_sort_corsika_data(source, destination, overwrite=False,
progress=False):
"""First convert the data to HDF5 and create a sorted version"""
if os.path.exists(destination):
if not overwrite:
if progress:
raise Exception("Destination already exists, doing nothing")
return
else:
os.remove(destination)
corsika_data = CorsikaFile(source)
temp_dir = os.path.dirname(destination)
temp_path = create_tempfile_path(temp_dir)
with tables.open_file(temp_path, 'a') as hdf_temp:
store_corsika_data(corsika_data, hdf_temp, progress=progress)
with tables.open_file(temp_path, 'a') as hdf_temp:
create_index(hdf_temp, progress=progress)
with tables.open_file(temp_path, 'r') as hdf_temp, \
tables.open_file(destination, 'w') as hdf_data:
copy_and_sort_node(hdf_temp, hdf_data, progress=progress)
os.remove(temp_path)
def __init__(self, h5_filename_queue):
"""
param h5_filename_queue: a queue of temporary hdf5 files
"""
self.h5_filename_queue = h5_filename_queue
tables.open_file(table_path, 'w').close() #creates a new file
super(WriteHDF5Thread, self).__init__()
def dropfields(input_path, output_path, todrop):
input_file = tables.open_file(input_path, mode="r")
input_root = input_file.root
output_file = tables.open_file(output_path, mode="w")
output_globals = output_file.create_group("/", "globals", "Globals")
print(" * copying globals ...", end=' ')
copy_table(input_root.globals.periodic, output_globals)
print("done.")
output_entities = output_file.create_group("/", "entities", "Entities")
for table in input_file.iterNodes(input_root.entities):
table_fields = get_fields(table)
table_fields = [(fname, ftype) for fname, ftype in table_fields
if fname not in todrop]
size = (len(table) * table.dtype.itemsize) / 1024.0 / 1024.0
#noinspection PyProtectedMember
print(" * copying table %s (%.2f Mb) ..." % (table._v_name, size),
end=' ')
copy_table(table, output_entities, table_fields)
print("done.")
input_file.close()
output_file.close()
def __init__(self, parent, filename):
if not isinstance(filename, string_types):
raise ValueError(
'Pytables requires filename parameter as string. Got {} instead.'
.format(filename.__class__))
self.parent = parent
self.version = HDFPartition.VERSION
self.n_rows = 0
self.n_cols = 0
self.cache = []
if os.path.exists(filename):
self._h5_file = open_file(filename, mode='a')
self.meta = HDFReader._read_meta(self._h5_file)
self.version, self.n_rows, self.n_cols = _get_file_header(
self._h5_file.root.partition.file_header)
else:
# No, doesn't exist
self._h5_file = open_file(filename, mode='w')
self.meta = deepcopy(MPRowsFile.META_TEMPLATE)
self.header_mangler = lambda name: re.sub('_+', '_', re.sub('[^\w_]', '_', name).lower()).rstrip('_')
if self.n_rows == 0:
self.meta['about']['create_time'] = time.time()
def __init__( self,
fnContigLengths,
fnWssd,
overwrite,
openMode,
groupsToCheck=[],
compression=False ):
self.compress = compression
assert os.path.exists(fnContigLengths)
if openMode=='r':
assert not overwrite
assert os.path.exists(fnWssd), fnWssd
debug_output('WssdBase: reading contig lengths from file %s'%fnContigLengths)
self.mContigNameLen = {}
for l in open(fnContigLengths,'r'):
l=l.replace('\n','').split('\t')
self.mContigNameLen[l[0]]=int(l[1])
debug_output('WSSD space: %d contigs totaling %d bp'%( len(self.mContigNameLen), sum(self.mContigNameLen.values()) ))
if overwrite or not os.path.exists(fnWssd):
self.tbl = tables.open_file( fnWssd, 'w' )
else:
if openMode=='r':
self.tbl = tables.open_file( fnWssd, 'r' )
else:
self.tbl = tables.open_file( fnWssd, 'a' )
def create_synth(kind, prec):
prefix_orig = "cellzome/cellzome-"
iname = dirname + prefix_orig + "none-" + prec + ".h5"
f = tb.open_file(iname, "r")
if prec == "single":
type_ = tb.Float32Atom()
else:
type_ = tb.Float64Atom()
prefix = "synth/synth-"
for clevel in range(10):
oname = "%s/%s-%s%d-%s.h5" % (dirname, prefix, kind, clevel, prec)
# print "creating...", iname
f2 = tb.open_file(oname, "w")
if kind in ["none", "numpy"]:
filters = None
else:
filters = tb.Filters(complib=kind, complevel=clevel, shuffle=shuffle)
for name in ["maxarea", "mascotscore"]:
col = f.get_node("/", name)
r = f2.create_carray("/", name, type_, col.shape, filters=filters)
if name == "maxarea":
r[:] = np.arange(col.nrows, dtype=type_.dtype)
else:
r[:] = np.arange(col.nrows, 0, dtype=type_.dtype)
f2.close()
if clevel == 0:
size = 1.5 * float(os.stat(oname)[6])
f.close()
return size
def open(self, mode, ncols=1, nrows=1, xll=0, yll=0, cellsize=1, nodatavalue=-9999.0,
dataset_name="dummy", group_prefix="row", table_prefix="col", index_format="04i", variables=[], units=[]):
# Initialise
fpath = os.path.join(self.folder, self.name);
if (mode[0] == 'w'):
# Open the file
self.__datafile = tables.open_file(fpath, 'w');
# Assign the data attributes
self.ncols = ncols;
self.nrows = nrows;
self.xll = xll;
self.yll = yll;
self.cellsize = cellsize;
self.nodatavalue = nodatavalue;
self.dataset_name = dataset_name;
self.group_prefix = group_prefix;
self.table_prefix = table_prefix;
self.index_format = index_format;
self.variables = variables;
self.units = units;
self.writeheader();
else:
# If file does not exist, then ...
if os.path.exists(fpath):
# Retrieve the data attributes from the header file
self.readheader();
GridEnvelope2D.__init__(self, self.ncols, self.nrows, self.xll, self.yll, self.cellsize, self.cellsize);
self.__datafile = tables.open_file(fpath, 'r');
return True;
else: return False;
def __init__(self, cfg):
self.cfg = cfg
self.path = os.path.join(self.cfg.subsets_path, 'data.db')
self.results = None
if os.path.exists(self.path):
try:
self.h5 = tables.open_file(self.path, 'a')
self.results = self.h5.root.results
except:
# If anything fails, we just create a new database...
log.warning("""Failed to open existing database at %s, or
database is corrupted. Creating a new one""", self.path)
self.results = None
# Something went wrong!
if not self.results:
try:
# Try closing this, just in case
self.h5.close()
except:
pass
# Compression is good -- and faster, according to the pytables docs...
f = tables.Filters(complib='blosc', complevel=5)
self.h5 = tables.open_file(self.path, 'w', filters=f)
self.results = self.h5.create_table(
'/', 'results', cfg.data_layout.data_type)
self.results.cols.subset_id.create_csindex()
assert isinstance(self.results, tables.Table)
assert self.results.indexed
def h5_apply_func(input_path, output_path, node_func):
"""
Apply node_func to all nodes of input_path and store the result in
output_path
Parameters
----------
input_path : str
path to .h5 input file
output_path : str
path to .h5 output file
node_func : function
function that will be applied to all nodes
func(node, new_parent) -> new_node
new_node must be node if node must be copied
None if node must not be copied
another Node if node must not be copied (was already
handled/copied/modified by func)
"""
with tables.open_file(input_path) as input_file, \
tables.open_file(output_path, mode="w") as output_file:
for node in input_file.walk_nodes(classname='Leaf'):
if node is not input_file.root:
print(node._v_pathname, "...", end=' ')
parent_path = node._v_parent._v_pathname
if parent_path in output_file:
new_parent = output_file.get_node(parent_path)
else:
new_parent = output_file._create_path(parent_path)
new_node = node_func(node, new_parent)
if new_node is node:
print("copying (without modifications) ...", end=' ')
node._f_copy(new_parent)
print("done.")
def process(self, rows_slice):
with Worker.hdf5_lock:
with tables.open_file(self.hdf5_file, 'r+') as fileh:
T = fileh.get_node(self.path + '/temporaries')
tmp = T[rows_slice, ...]
ind = np.arange(0, rows_slice.stop - rows_slice.start)
# tmp = - A_new
tmp -= self.rows_sum
diag_A = tmp[ind, rows_slice.start + ind].copy()
np.clip(tmp, 0, np.inf, tmp)
tmp[ind, rows_slice.start + ind] = diag_A
Worker.hdf5_lock.acquire()
with tables.open_file(self.hdf5_file, 'r+') as fileh:
A = fileh.get_node(self.path + '/availabilities')
a = A[rows_slice, ...]
Worker.hdf5_lock.release()
# yet more damping
a = a * self.damping - tmp * (1 - self.damping)
with Worker.hdf5_lock:
with tables.open_file(self.hdf5_file, 'r+') as fileh:
A = fileh.get_node(self.path + '/availabilities')
T = fileh.get_node(self.path + '/temporaries')
A[rows_slice, ...] = a
T[rows_slice, ...] = tmp
del a, tmp
def ptconcat(output_file, input_files, overwrite=False):
"""Concatenate HDF5 Files"""
filt = tb.Filters(
complevel=5, shuffle=True, fletcher32=True, complib='zlib'
)
out_tabs = {}
dt_file = input_files[0]
log.info("Reading data struct '%s'..." % dt_file)
h5struc = tb.open_file(dt_file, 'r')
log.info("Opening output file '%s'..." % output_file)
if overwrite:
outmode = 'w'
else:
outmode = 'a'
h5out = tb.open_file(output_file, outmode)
for node in h5struc.walk_nodes('/', classname='Table'):
path = node._v_pathname
log.debug(path)
dtype = node.dtype
p, n = os.path.split(path)
out_tabs[path] = h5out.create_table(
p, n, description=dtype, filters=filt, createparents=True
)
h5struc.close()
for fname in input_files:
log.info('Reading %s...' % fname)
h5 = tb.open_file(fname)
for path, out in out_tabs.items():
tab = h5.get_node(path)
out.append(tab[:])
h5.close()
h5out.close()
def __init__(self, output_dir, chrom_list):
# combined allele-specific read counts
as_count_filename = "%s/combined_as_count.h5" % output_dir
self.as_count_h5 = tables.open_file(as_count_filename, "w")
# combined mapped read counts
read_count_filename = "%s/combined_read_count.h5" % output_dir
self.read_count_h5 = tables.open_file(read_count_filename, "w")
# counts of genotypes
ref_count_filename = "%s/combined_ref_count.h5" % output_dir
self.ref_count_h5 = tables.open_file(ref_count_filename, "w")
alt_count_filename = "%s/combined_alt_count.h5" % output_dir
self.alt_count_h5 = tables.open_file(alt_count_filename, "w")
het_count_filename = "%s/combined_het_count.h5" % output_dir
self.het_count_h5 = tables.open_file(het_count_filename, "w")
self.filenames = [as_count_filename, read_count_filename,
ref_count_filename, alt_count_filename,
het_count_filename]
self.h5_files = [self.as_count_h5, self.read_count_h5,
self.ref_count_h5, self.alt_count_h5,
self.het_count_h5]
# initialize all of these files
atom = tables.UInt16Atom(dflt=0)
for h5f in self.h5_files:
for chrom in chrom_list:
self.create_carray(h5f, chrom, atom)
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. # # Author: Vicent Mas - [email protected] # # This script is based on a set of scripts by Francesc Alted. """Several simple EArrays.""" import tables import numpy fileh = tables.open_file('earray_samples.h5', mode='w') root = fileh.root a = tables.StringAtom(itemsize=8) # Use ``a`` as the object type for the enlargeable array. array_c = fileh.create_earray(root, 'array_c', a, (0, ), "Chars") array_c.append(numpy.array(['a' * 2, 'b' * 4], dtype='S8')) array_c.append(numpy.array(['a' * 6, 'b' * 8, 'c' * 10], dtype='S8')) # Create an string atom a = tables.StringAtom(itemsize=1) # Use it as a type for the enlargeable array hdfarray = fileh.create_earray(root, 'array_char', a, (0, ), "Character array") hdfarray.append(numpy.array(['a', 'b', 'c'])) # The next is legal: hdfarray.append(numpy.array(['c', 'b', 'c', 'd']))
from snn.optimizer.snnsgd import SNNSGD
import tables
from neurodata.load_data import create_dataloader
from snn.utils.utils_snn import get_acc_and_loss
from snn.utils.utils_snn import get_acc_layered
sample_length = 2000000 # length of samples during training in ms
dt = 25000 # us
polarity = False
T = int(sample_length / dt) # number of timesteps in a sample
input_size = (1 + polarity) * 26 * 26
dataset_path = r"C:\Users\K1804053\OneDrive - King's College London\PycharmProjects\datasets\mnist-dvs\mnist_dvs_events_new.hdf5"
ds = 1
dataset = tables.open_file(dataset_path)
x_max = dataset.root.stats.train_data[1] // ds
dataset.close()
n_outputs = 2
n_hidden = 16
n_neurons_per_layer = [64]
network = LayeredSNN(input_size, n_neurons_per_layer, n_outputs, synaptic_filter=filters.raised_cosine_pillow_08, n_basis_feedforward=[8],
n_basis_feedback=[1], tau_ff=[10], tau_fb=[10], mu=[0.5], device='cpu')
topology = torch.zeros([n_hidden + n_outputs, n_hidden + input_size + n_outputs])
topology[:n_hidden, :input_size] = 1
topology[n_hidden:, input_size:-n_outputs] = 1
network2 = BinarySNN(**make_network_parameters(network_type='snn',
def setUp(self):
self.data_path = self.create_tempfile_from_testdata()
self.data = tables.open_file(self.data_path, 'a')
def __init__(self,parent,subgui=True):
# get the current path
curpath = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
constpath = os.path.join(os.path.split(curpath)[0],'SimISR','const')
# set the root
self.parent = parent
self.subgui = subgui
# set up frames for list
self.frame1 = Tkinter.Frame(self.parent)
self.frame1.grid(row=0,column=0)
self.frame2 = Tkinter.Frame(self.parent)
self.frame2.grid(row=0,column=1)
self.output = []
self.beamhandle = None
if subgui:
self.sizecanv = [500,500]
self.beamcodeent= Tkinter.Entry(self.frame1)
self.beamcodeent.grid(row=1,column=1)
self.beamcodeentlabel = Tkinter.Label(self.frame1,text="Enter Beamcodes")
self.beamcodeentlabel.grid(row=1,column=0,sticky='e')
self.beambuttex = Tkinter.Button(self.frame1, text="Read", command=self.readbcobar)
self.beambuttex.grid(row=1,column=2,sticky='w')
self.beambutt = Tkinter.Button(self.frame1, text="Import", command=self.beambuttonClick)
self.beambutt.grid(row=2,column=2,sticky='w')
canvrow = 3
else:
self.sizecanv = [1000,1000]
self.leb = Tkinter.Label(self.frame1, text="Beam Selector",font=("Helvetica", 16))
self.leb.grid(row=0, sticky=Tkinter.W+Tkinter.E+Tkinter.N+Tkinter.S,columnspan=2)
self.butt = Tkinter.Button(self.frame1, text="Finished", command=self.buttonClick)
self.butt.grid(row=1,column=1,sticky='w')
self.beamcodeent= Tkinter.Entry(self.frame1)
self.beamcodeent.grid(row=2,column=1,sticky='w')
self.beamcodeentlabel = Tkinter.Label(self.frame1,text="Enter Beamcodes")
self.beamcodeentlabel.grid(row=2,column = 0,sticky='e')
self.beambuttex = Tkinter.Button(self.frame1, text="Read", command=self.readbcobar)
self.beambuttex.grid(row=2,column=2,sticky='w')
self.beambutt = Tkinter.Button(self.frame1, text="Import", command=self.beambuttonClick)
self.beambutt.grid(row=3,column=2,sticky='w')
canvrow = 4
self.off_x = self.sizecanv[0]/2
self.off_y = self.sizecanv[1]/2
self.div = 75.0*self.sizecanv[0]/1000.0
self.lat = [80,70,60,50,40,30]
self.angles = np.arange(0,180,30)
self.var = Tkinter.StringVar()
self.var.set("PFISR")
self.choices = {"PFISR":get_files('PFISR_PARAMS.h5'),
"RISR-N":get_files('RISR_PARAMS.h5'),
"Sondrestrom":get_files('Sondrestrom_PARAMS.h5'),
"Millstone":get_files('Millstone_PARAMS.h5')}#, "RISR-S":'file3'}
self.option = Tkinter.OptionMenu(self.frame1, self.var, *self.choices)
self.option.grid(row=1,column=0,sticky='w')
hfile=tables.open_file(self.choices[self.var.get()])
self.lines = hfile.root.Params.Kmat.read()
hfile.close()
self.readfile = Tkinter.StringVar()
# set up the canvas
self.canv = Tkinter.Canvas(self.frame1 , width=self.sizecanv[0], height=self.sizecanv[1],background='white')
self.canv.grid(row=canvrow,column=0,columnspan=2)
self.Drawlines()
self.Drawbeams()
self.canv.bind('<ButtonPress-1>', self.onCanvasClick)
self.canv.bind('<ButtonPress-2>', self.onCanvasRightClick)
self.var.trace('w', self.Changefile)
self.canv.update()
# beam list
self.bidlabel = Tkinter.Label(self.frame2,text="Beam ID")
self.bidlabel.grid(row=0,column=0)
self.azlabel = Tkinter.Label(self.frame2,text="Azimuth")
self.azlabel.grid(row=0,column=1)
self.ellabel = Tkinter.Label(self.frame2,text="Elevation")
self.ellabel.grid(row=0,column=2)
self.scroll = Tkinter.Scrollbar(self.frame2)
self.scroll.grid(row=1,column=3)
self.beamtext = Tkinter.Text(self.frame2,yscrollcommand=self.scroll.set)
self.beamtext.config(width=50,state=Tkinter.DISABLED)
self.beamtext.grid(row = 1,column = 0,columnspan=3)
self.beamlines = []
self.scroll.config(command=self.beamtext.yview)
# bounding box
self.boxbutton= Tkinter.Button(self.frame2, text="Angle Box", command=self.boxbuttonClick)
self.boxbutton.grid(row=2,column=0,sticky='w')
self.azminmaxlabel = Tkinter.Label(self.frame2,text="Az min and max")
self.azminmaxlabel.grid(row=3,column=0,sticky='e')
self.azmin= Tkinter.Entry(self.frame2)
self.azmin.grid(row=3,column=1,sticky='w')
self.azmax= Tkinter.Entry(self.frame2)
self.azmax.grid(row=3,column=2,sticky='w')
self.elminmaxlabel = Tkinter.Label(self.frame2,text="El min and max")
self.elminmaxlabel.grid(row=4,column=0,sticky='e')
self.elmin= Tkinter.Entry(self.frame2)
self.elmin.grid(row=4,column=1,sticky='w')
self.elmax= Tkinter.Entry(self.frame2)
self.elmax.grid(row=4,column=2,sticky='w')
# Az choice
self.azbutton=Tkinter.Button(self.frame2, text="Az Choice", command=self.azbuttonClick)
self.azbutton.grid(row=5,column=0,sticky='w')
self.azchoice= Tkinter.Entry(self.frame2)
self.azchoice.grid(row=5,column=1,sticky='w')
# Az choice
self.elbutton=Tkinter.Button(self.frame2, text="El Choice", command=self.elbuttonClick)
self.elbutton.grid(row=6,column=0,sticky='w')
self.elchoice= Tkinter.Entry(self.frame2)
self.elchoice.grid(row=6,column=1,sticky='w')
self.azsortbutton=Tkinter.Button(self.frame2, text="Az sort", command=self.azsortbuttonClick)
self.azsortbutton.grid(row=7,column=0,sticky='w')
self.elsortbutton=Tkinter.Button(self.frame2, text="El Sort", command=self.elsortbuttonClick)
self.elsortbutton.grid(row=7,column=1,sticky='w')
def h5_read(file):
h5file = tables.open_file(file, driver="H5FD_CORE")
array = h5file.root.somename.read()
#h5file.close()
return array, h5file
def test_source_to_sink():
"""Tests simulations with one facility that has a conversion factor.
The trivial cycle simulation involves only one KFacility which provides
what it requests itself. The conversion factors for requests and bids
are kept the same so that the facility provides exactly what it requests.
The amount of the transactions follow a power law.
Amount = InitialAmount * ConversionFactor ^ Time
This equation is used to test each transaction amount.
"""
if not cyclus_has_coin():
raise SkipTest("Cyclus does not have COIN")
# A reference simulation input for the trivial cycle simulation.
ref_input = os.path.join(INPUT, "trivial_cycle.xml")
# Conversion factors for the three simulations
k_factors = [0.95, 1, 2]
for k_factor in k_factors:
clean_outs()
sim_input = create_sim_input(ref_input, k_factor, k_factor)
holdsrtn = [1] # needed because nose does not send() to test generator
outfile = which_outfile()
cmd = ["cyclus", "-o", outfile, "--input-file", sim_input]
yield check_cmd, cmd, '.', holdsrtn
rtn = holdsrtn[0]
if rtn != 0:
return # don't execute further commands
# tables of interest
paths = ["/AgentEntry", "/Resources", "/Transactions", "/Info"]
# Check if these tables exist
yield assert_true, tables_exist(outfile, paths)
if not tables_exist(outfile, paths):
outfile.close()
clean_outs()
return # don't execute further commands
# Get specific tables and columns
if outfile == h5out:
output = tables.open_file(h5out, mode="r")
agent_entry = output.get_node("/AgentEntry")[:]
info = output.get_node("/Info")[:]
resources = output.get_node("/Resources")[:]
transactions = output.get_node("/Transactions")[:]
output.close()
else:
conn = sqlite3.connect(sqliteout)
conn.row_factory = sqlite3.Row
cur = conn.cursor()
exc = cur.execute
agent_entry = exc('SELECT * FROM AgentEntry').fetchall()
info = exc('SELECT * FROM Info').fetchall()
resources = exc('SELECT * FROM Resources').fetchall()
transactions = exc('SELECT * FROM Transactions').fetchall()
conn.close()
# Find agent ids
agent_ids = to_ary(agent_entry, "AgentId")
spec = to_ary(agent_entry, "Spec")
facility_id = find_ids(":agents:KFacility", spec, agent_ids)
# Test for only one KFacility
yield assert_equal, len(facility_id), 1
sender_ids = to_ary(transactions, "SenderId")
receiver_ids = to_ary(transactions, "ReceiverId")
expected_sender_array = np.empty(sender_ids.size)
expected_sender_array.fill(facility_id[0])
expected_receiver_array = np.empty(receiver_ids.size)
expected_receiver_array.fill(facility_id[0])
yield assert_array_equal, sender_ids, expected_sender_array
yield assert_array_equal, receiver_ids, expected_receiver_array
# Transaction ids must be equal range from 1 to the number of rows
expected_trans_ids = np.arange(0, sender_ids.size, 1)
yield assert_array_equal, \
to_ary(transactions, "TransactionId"), \
expected_trans_ids
# Track transacted resources
resource_ids = to_ary(resources, "ResourceId")
quantities = to_ary(resources, "Quantity")
# Almost equal cases due to floating point k_factors
i = 0
initial_capacity = quantities[0]
for q in quantities:
yield assert_almost_equal, q, initial_capacity * k_factor**i
i += 1
clean_outs()
os.remove(sim_input)
def create_trx(path, n_clusters=6, weights='', window=1):
try:
trx_ = sio.loadmat(path + "/trx.mat")
trx = trx_['trx']
data_types = (
'full_path', 'id', 'numero_larva', 'numero_larva_num', 'protocol',
'pipeline', 'stimuli', 'neuron', 't', 'x_spine', 'y_spine',
'x_contour', 'y_contour', 'x_center', 'y_center', 'straight_proba',
'bend_proba', 'curl_proba', 'ball_proba',
'straight_and_light_bend_proba', 'global_state', 'x_neck_down',
'y_neck_down', 'x_neck_top', 'y_neck_top', 'x_neck', 'y_neck',
'x_head', 'y_head', 'x_tail', 'y_tail', 'S', 'prod_scal_1',
'prod_scal_2', 'S_smooth_5', 'S_deriv_smooth_5',
'angle_upper_lower_smooth_5', 'angle_upper_lower_deriv_smooth_5',
'angle_downer_upper_smooth_5', 'angle_downer_upper_deriv_smooth_5',
'eig_smooth_5', 'eig_deriv_smooth_5',
'head_velocity_norm_smooth_5', 'tail_velocity_norm_smooth_5',
'motion_velocity_norm_smooth_5', 'motion_to_u_tail_head_smooth_5',
'motion_to_v_tail_head_smooth_5', 'd_eff_tail_norm_smooth_5',
'd_eff_tail_norm_deriv_smooth_5', 'd_eff_head_norm_smooth_5',
'd_eff_head_norm_deriv_smooth_5', 'larva_length_smooth_5',
'larva_length_deriv_smooth_5', 'proba_global_state', 'run', 'cast',
'stop', 'hunch', 'back', 'roll', 'small_motion', 'start_stop',
't_start_stop', 'n_duration', 'nb_action', 'As_smooth_5',
'global_state_large_state', 'global_state_small_large_state',
'start_stop_large', 't_start_stop_large', 'duration_large',
'n_duration_large', 'nb_action_large', 'start_stop_large_small',
't_start_stop_large_small', 'duration_large_small',
'n_duration_large_small', 'nb_action_large_small', 'run_large',
'cast_large', 'stop_large', 'hunch_large', 'back_large',
'roll_large', 'run_weak', 'cast_weak', 'stop_weak', 'hunch_weak',
'back_weak', 'roll_weak', 'run_strong', 'cast_strong',
'stop_strong', 'hunch_strong', 'back_strong', 'roll_strong',
'global_state_clustering', 'start_stop_clustering',
't_start_stop_clustering', 'duration_clustering',
'n_duration_clustering', 'nb_action_clustering') + tuple(
'clustering_' + str(i) for i in range(n_clusters))
x = load_transform(path, window=window)
trx_new = []
ae, decoder = autoencoder(
dims=[x[0].shape[-1] - 2, 500, 500, 2000, 10])
n_stacks = len([x[0].shape[-1] - 2, 500, 500, 2000, 10]) - 1
hidden = ae.get_layer(name='encoder_%d' % (n_stacks - 1)).output
clustering_layer = ClusteringLayer(n_clusters,
name='clustering')(hidden)
modele = Model(inputs=ae.input, outputs=[clustering_layer, ae.output])
modele.load_weights(weights)
for j, larva in enumerate(x):
t = larva[:, -1]
X = larva[:, :-2]
res = modele.predict(X)
predictions = res[0].argmax(axis=1)
if predictions[0] != predictions[1]:
predictions[0] = predictions[1]
if predictions[-1] != predictions[-2]:
predictions[-1] = predictions[-2]
for i in range(1, len(predictions) - 1):
if (predictions[i] != predictions[i + 1]) & (
predictions[i] != predictions[i - 1]):
predictions[i] = predictions[i - 1]
predictions = pd.DataFrame(predictions)
global_state_clustering = np.array(
[i + 1 for i in predictions.values])
start_stop_clustering = [[] for i in range(n_clusters)]
t_start_stop_clustering = [[] for i in range(n_clusters)]
duration_clustering = [[] for i in range(n_clusters)]
n_duration_clustering = [[] for i in range(n_clusters)]
nb_action_clustering = [[] for i in range(n_clusters)]
states = []
for i in range(n_clusters):
indices = list(predictions[predictions[0] == i].index)
if len(indices) > 0:
indices_change = [
indices[i] + 1 for i in range(len(indices) - 1)
if (indices[i] + 1 != indices[i + 1]) or
(indices[i - 1] + 1 != indices[i])
] + [indices[-1] + 1]
times_change = [t[i - 1] for i in indices_change]
indices_change = [[
indices_change[i], indices_change[i + 1]
] for i in range(len(indices_change)) if (i % 2 == 0)]
times_change = [[times_change[i], times_change[i + 1]]
for i in range(len(times_change))
if (i % 2 == 0)]
len_behavior = [[sublist[1] - sublist[0]]
for sublist in times_change]
n_duration = [[sublist[1] - sublist[0]]
for sublist in indices_change]
nb_action = len(indices_change)
start_stop_clustering[i] = indices_change
t_start_stop_clustering[i] = times_change
duration_clustering[i] = len_behavior
n_duration_clustering[i] = n_duration
nb_action_clustering[i] = nb_action
states.append([[1] if predictions.values[j] == i else [-1]
for j in range(len(predictions))])
start_stop_clustering = np.array(
[[i for i in start_stop_clustering]])
t_start_stop_clustering = np.array(
[[i for i in t_start_stop_clustering]])
duration_clustering = np.array(
[[i if (len(i) > 0) else [[0]] for i in duration_clustering]])
n_duration_clustering = np.array(
[i if (len(i) > 0) else [[0]] for i in n_duration_clustering])
nb_action_clustering = np.array([[
np.array([i]).astype('O') if (i) else np.array([0]).astype('O')
for i in nb_action_clustering
]])
tmp = [
global_state_clustering, start_stop_clustering,
t_start_stop_clustering, duration_clustering,
n_duration_clustering, nb_action_clustering
]
tmp += states
tmp = tuple(tmp)
trx_new.append(
np.reshape(
np.array(tuple(trx[j][0]) + tmp,
dtype=[(n, d)
for (n, d) in zip(data_types, ["O"] *
len(data_types))]), [
1,
]))
trx_new = np.array(trx_new)
trx_['trx'] = trx_new
sio.savemat(path + '/trx_new_%d_clusters' % n_clusters,
trx_,
long_field_names=True)
except NotImplementedError:
trx_ = tables.open_file(path + "trx.mat")
data_titles_old = (
'full_path', 'id', 'numero_larva', 'numero_larva_num', 'protocol',
'pipeline', 'stimuli', 'neuron', 't', 'x_spine', 'y_spine',
'x_contour', 'y_contour', 'x_center', 'y_center', 'straight_proba',
'bend_proba', 'curl_proba', 'ball_proba',
'straight_and_light_bend_proba', 'global_state', 'x_neck_down',
'y_neck_down', 'x_neck_top', 'y_neck_top', 'x_neck', 'y_neck',
'x_head', 'y_head', 'x_tail', 'y_tail', 'S', 'prod_scal_1',
'prod_scal_2', 'S_smooth_5', 'S_deriv_smooth_5',
'angle_upper_lower_smooth_5', 'angle_upper_lower_deriv_smooth_5',
'angle_downer_upper_smooth_5', 'angle_downer_upper_deriv_smooth_5',
'eig_smooth_5', 'eig_deriv_smooth_5',
'head_velocity_norm_smooth_5', 'tail_velocity_norm_smooth_5',
'motion_velocity_norm_smooth_5', 'motion_to_u_tail_head_smooth_5',
'motion_to_v_tail_head_smooth_5', 'd_eff_tail_norm_smooth_5',
'd_eff_tail_norm_deriv_smooth_5', 'd_eff_head_norm_smooth_5',
'd_eff_head_norm_deriv_smooth_5', 'larva_length_smooth_5',
'larva_length_deriv_smooth_5', 'proba_global_state', 'run', 'cast',
'stop', 'hunch', 'back', 'roll', 'small_motion', 'start_stop',
't_start_stop', 'n_duration', 'nb_action', 'As_smooth_5',
'global_state_large_state', 'global_state_small_large_state',
'start_stop_large', 't_start_stop_large', 'duration_large',
'n_duration_large', 'nb_action_large', 'start_stop_large_small',
't_start_stop_large_small', 'duration_large_small',
'n_duration_large_small', 'nb_action_large_small', 'run_large',
'cast_large', 'stop_large', 'hunch_large', 'back_large',
'roll_large', 'run_weak', 'cast_weak', 'stop_weak', 'hunch_weak',
'back_weak', 'roll_weak', 'run_strong', 'cast_strong',
'stop_strong', 'hunch_strong', 'back_strong', 'roll_strong')
data_titles = (
'full_path', 'id', 'numero_larva', 'numero_larva_num', 'protocol',
'pipeline', 'stimuli', 'neuron', 't', 'x_spine', 'y_spine',
'x_contour', 'y_contour', 'x_center', 'y_center', 'straight_proba',
'bend_proba', 'curl_proba', 'ball_proba',
'straight_and_light_bend_proba', 'global_state', 'x_neck_down',
'y_neck_down', 'x_neck_top', 'y_neck_top', 'x_neck', 'y_neck',
'x_head', 'y_head', 'x_tail', 'y_tail', 'S', 'prod_scal_1',
'prod_scal_2', 'S_smooth_5', 'S_deriv_smooth_5',
'angle_upper_lower_smooth_5', 'angle_upper_lower_deriv_smooth_5',
'angle_downer_upper_smooth_5', 'angle_downer_upper_deriv_smooth_5',
'eig_smooth_5', 'eig_deriv_smooth_5',
'head_velocity_norm_smooth_5', 'tail_velocity_norm_smooth_5',
'motion_velocity_norm_smooth_5', 'motion_to_u_tail_head_smooth_5',
'motion_to_v_tail_head_smooth_5', 'd_eff_tail_norm_smooth_5',
'd_eff_tail_norm_deriv_smooth_5', 'd_eff_head_norm_smooth_5',
'd_eff_head_norm_deriv_smooth_5', 'larva_length_smooth_5',
'larva_length_deriv_smooth_5', 'proba_global_state', 'run', 'cast',
'stop', 'hunch', 'back', 'roll', 'small_motion', 'start_stop',
't_start_stop', 'n_duration', 'nb_action', 'As_smooth_5',
'global_state_large_state', 'global_state_small_large_state',
'start_stop_large', 't_start_stop_large', 'duration_large',
'n_duration_large', 'nb_action_large', 'start_stop_large_small',
't_start_stop_large_small', 'duration_large_small',
'n_duration_large_small', 'nb_action_large_small', 'run_large',
'cast_large', 'stop_large', 'hunch_large', 'back_large',
'roll_large', 'run_weak', 'cast_weak', 'stop_weak', 'hunch_weak',
'back_weak', 'roll_weak', 'run_strong', 'cast_strong',
'stop_strong', 'hunch_strong', 'back_strong', 'roll_strong',
'global_state_clustering', 'start_stop_clustering',
't_start_stop_clustering', 'duration_clustering',
'n_duration_clustering', 'nb_action_clustering') + tuple(
'clustering_' + str(i) for i in range(n_clusters))
x = load_transform(path, window=window)
trx_new = []
ae, decoder = autoencoder(
dims=[x[0].shape[-1] - 2, 500, 500, 2000, 10])
n_stacks = len([x[0].shape[-1] - 2, 500, 500, 2000, 10]) - 1
hidden = ae.get_layer(name='encoder_%d' % (n_stacks - 1)).output
clustering_layer = ClusteringLayer(n_clusters,
name='clustering')(hidden)
modele = Model(inputs=ae.input, outputs=[clustering_layer, ae.output])
modele.load_weights(weights)
for j, larva in enumerate(x):
t = larva[:, -1]
X = larva[:, :-2]
res = modele.predict(X)
predictions = res[0].argmax(axis=1)
if predictions[0] != predictions[1]:
predictions[0] = predictions[1]
if predictions[-1] != predictions[-2]:
predictions[-1] = predictions[-2]
for i in range(1, len(predictions) - 1):
if (predictions[i] != predictions[i + 1]) & (
predictions[i] != predictions[i - 1]):
predictions[i] = predictions[i - 1]
predictions = pd.DataFrame(predictions)
global_state_clustering = np.array(
[i + 1 for i in predictions.values])
start_stop_clustering = [[] for i in range(n_clusters)]
t_start_stop_clustering = [[] for i in range(n_clusters)]
duration_clustering = [[] for i in range(n_clusters)]
n_duration_clustering = [[] for i in range(n_clusters)]
nb_action_clustering = [[] for i in range(n_clusters)]
states = []
for i in range(n_clusters):
indices = list(predictions[predictions[0] == i].index)
if len(indices) > 0:
indices_change = [
indices[i] + 1 for i in range(len(indices) - 1)
if (indices[i] + 1 != indices[i + 1]) or
(indices[i - 1] + 1 != indices[i])
] + [indices[-1] + 1]
times_change = [t[i - 1] for i in indices_change]
indices_change = [[
indices_change[i], indices_change[i + 1]
] for i in range(len(indices_change)) if (i % 2 == 0)]
times_change = [[times_change[i], times_change[i + 1]]
for i in range(len(times_change))
if (i % 2 == 0)]
len_behavior = [[sublist[1] - sublist[0]]
for sublist in times_change]
n_duration = [[sublist[1] - sublist[0]]
for sublist in indices_change]
nb_action = len(indices_change)
start_stop_clustering[i] = indices_change
t_start_stop_clustering[i] = times_change
duration_clustering[i] = len_behavior
n_duration_clustering[i] = n_duration
nb_action_clustering[i] = nb_action
states.append([[1] if predictions.values[j] == i else [-1]
for j in range(len(predictions))])
start_stop_clustering = np.array(
[[i for i in start_stop_clustering]])
t_start_stop_clustering = np.array(
[[i for i in t_start_stop_clustering]])
duration_clustering = np.array(
[[i if (len(i) > 0) else [[0]] for i in duration_clustering]])
n_duration_clustering = np.array(
[i if (len(i) > 0) else [[0]] for i in n_duration_clustering])
nb_action_clustering = np.array([[
np.array([i]).astype('O') if (i) else np.array([0]).astype('O')
for i in nb_action_clustering
]])
tmp = [
global_state_clustering, start_stop_clustering,
t_start_stop_clustering, duration_clustering,
n_duration_clustering, nb_action_clustering
]
tmp += states
tmp = tuple(tmp)
trx_new.append(
np.reshape(
np.array(tuple(trx_.root.trx[k][0][j][0].T
for k in data_titles_old) + tmp,
dtype=[(n, d)
for (n, d) in zip(data_titles, ["O"] *
len(data_titles))]), [
1,
]))
trx_new = np.array(trx_new, ndmin=2)
trx_new = {'__header__': '', '__version__': '', 'trx': trx_new}
sio.savemat(path + '/trx_new_%d_clusters' % n_clusters,
trx_new,
long_field_names=True)
trx_.close()
def test_pmap_writer(config_tmpdir, s1_dataframe_converted,
s2_dataframe_converted, s2si_dataframe_converted):
# setup temporary file
filename = 'test_pmaps_auto.h5'
PMP_file_name = os.path.join(config_tmpdir, filename)
# Get test data
s1_dict, _ = s1_dataframe_converted
s2_dict, _ = s2_dataframe_converted
s2si_dict, _ = s2si_dataframe_converted
#P = PMaps(s1_dict, s2_dict, s2si_dict)
event_numbers = sorted(set(s1_dict).union(set(s2si_dict)))
timestamps = {e: int(time.time() % 1 * 10**9) for e in event_numbers}
run_number = 632
# Write pmaps to disk.
with tb.open_file(PMP_file_name, 'w') as h5out:
write_pmap = pmap_writer(h5out)
write_run_and_event = run_and_event_writer(h5out)
for event_no in event_numbers:
timestamp = timestamps[event_no]
s1 = s1_dict[event_no]
s2 = s2_dict[event_no]
s2si = s2si_dict[event_no]
write_pmap(event_no, s1, s2, s2si)
write_run_and_event(run_number, event_no, timestamp)
# Read back the data we have just written
S1D, S2D, S2SiD = load_pmaps(PMP_file_name)
rundf, evtdf = read_run_and_event_from_pmaps_file(PMP_file_name)
# Convert them into our transient format
# S1D = df_to_s1_dict (s1df)
# S2D = df_to_s2_dict (s2df)
# S2SiD = df_to_s2si_dict(s2df, s2sidf)
######################################################################
# Compare original data to those read back
for event_no, s1 in s1_dict.items():
s1 = s1_dict[event_no]
S1 = S1D[event_no]
for peak_no in s1.peak_collection():
PEAK = S1.peak_waveform(peak_no)
peak = s1.peak_waveform(peak_no)
np.testing.assert_allclose(peak.t, PEAK.t)
np.testing.assert_allclose(peak.E, PEAK.E)
for event_no, s2 in s2_dict.items():
s2 = s2_dict[event_no]
S2 = S2D[event_no]
for peak_no in s2.peak_collection():
PEAK = S2.peak_waveform(peak_no)
peak = s2.peak_waveform(peak_no)
np.testing.assert_allclose(peak.t, PEAK.t)
np.testing.assert_allclose(peak.E, PEAK.E)
for event_no, si in s2si_dict.items():
si = s2si_dict[event_no]
Si = S2SiD[event_no]
for peak_no in si.peak_collection():
PEAK = Si.peak_waveform(peak_no)
peak = si.peak_waveform(peak_no)
np.testing.assert_allclose(peak.t, PEAK.t)
np.testing.assert_allclose(peak.E, PEAK.E)
for sipm_no in si.sipms_in_peak(peak_no):
sipm_wfm = si.sipm_waveform(peak_no, sipm_no)
SIPM_wfm = Si.sipm_waveform(peak_no, sipm_no)
np.testing.assert_allclose(sipm_wfm.t, SIPM_wfm.t)
# Event numbers
np.testing.assert_equal(evtdf.evt_number.values,
np.array(event_numbers, dtype=np.int32))
# Run numbers
np.testing.assert_equal(
rundf.run_number.values,
np.full(len(event_numbers), run_number, dtype=np.int32))
@author: seb18121
"""
import numpy as np
# import matplotlib.pyplot as plt
import tables, sys, gc
# python /mnt/d/My_python_script/feedback_aperp_1D.py XXX_aperp_NO feedbackfactor detuning
basename = sys.argv[1] # retreive the base name
# filename1 = 'CEP_aperp_41'
filename = basename + ".h5"
outfilename = "entrance.h5"
print("Reading the field file ...\n")
h5 = tables.open_file(filename, 'r')
wavelength = h5.root.runInfo._v_attrs.lambda_r
nx = h5.root.runInfo._v_attrs.nX
ny = h5.root.runInfo._v_attrs.nY
nz = h5.root.runInfo._v_attrs.nZ2
Lc = h5.root.runInfo._v_attrs.Lc
Lg = h5.root.runInfo._v_attrs.Lg
meshsizeX = h5.root.runInfo._v_attrs.sLengthOfElmX
meshsizeY = h5.root.runInfo._v_attrs.sLengthOfElmY
meshsizeZ2 = h5.root.runInfo._v_attrs.sLengthOfElmZ2
meshsizeXSI = meshsizeX * np.sqrt(Lc * Lg)
meshsizeYSI = meshsizeY * np.sqrt(Lc * Lg)
meshsizeZSI = meshsizeZ2 * Lc
fieldin = h5.root.aperp.read()
#print("Adding cut: %d" % (storeIdx))
self.add(constraint=cplex.SparsePair(thevars,thecoefs), sense = "G", rhs = (b_Lext[0,minIdx]))
full = int(sys.argv[1])
feuer = int(sys.argv[2])
xnL = int(sys.argv[3])
xnU = int(sys.argv[4])
tnL = int(sys.argv[5])
tnU = int(sys.argv[6])
stepX = int(sys.argv[7])
stepT = int(sys.argv[8])
for timeVar in range(tnL,tnU+1,stepT):
for countVar in range(xnL,xnU+1,stepX):
if feuer:
matlabData = tables.open_file('data/feuerData%d_%d_%d.mat' % (countVar,timeVar,2))
else:
matlabData = tables.open_file('data/contaData%d_%d_%d.mat' % (countVar,timeVar,5))
A2=matlabData.root.A2.data[...]
Amipred=scipy.sparse.csc_matrix((matlabData.root.A2.data[...],matlabData.root.A2.ir[...], matlabData.root.A2.jc[...]))
Amipred=scipy.sparse.lil_matrix(Amipred)
b_Lred=matlabData.root.b_L2[0]
b_Ured=matlabData.root.b_U2[0]
c=matlabData.root.c[0]
xn=int(matlabData.root.xn[0,0])
tn=int(matlabData.root.tn[0,0])
Amipext=scipy.sparse.csc_matrix((matlabData.root.Aext.data[...],matlabData.root.Aext.ir[...], matlabData.root.Aext.jc[...]))
Amipext=scipy.sparse.lil_matrix(Amipext)
b_Uext=matlabData.root.b_Uext
b_Lext=matlabData.root.b_Lext
intVarN=int(matlabData.root.intVarN[0])
def load(self):
"""
Loads a matrix stored in h5 format
:param matrix_filename:
:return: matrix, cut_intervals, nan_bins, distance_counts, correction_factors
"""
log.debug('Load in h5 format')
with tables.open_file(self.matrixFileName, 'r') as f:
parts = {}
try:
for matrix_part in ('data', 'indices', 'indptr', 'shape'):
parts[matrix_part] = getattr(f.root.matrix,
matrix_part).read()
except Exception as e:
log.info(
'No h5 file. Please check parameters concerning the file type!'
)
e
matrix = csr_matrix(tuple(
[parts['data'], parts['indices'], parts['indptr']]),
shape=parts['shape'])
# matrix = hiCMatrix.fillLowerTriangle(matrix)
# get intervals
intvals = {}
for interval_part in ('chr_list', 'start_list', 'end_list',
'extra_list'):
if toString(interval_part) == toString('chr_list'):
chrom_list = getattr(f.root.intervals,
interval_part).read()
intvals[interval_part] = toString(chrom_list)
else:
intvals[interval_part] = getattr(f.root.intervals,
interval_part).read()
cut_intervals = list(
zip(intvals['chr_list'], intvals['start_list'],
intvals['end_list'], intvals['extra_list']))
assert len(cut_intervals) == matrix.shape[0], \
"Error loading matrix. Length of bin intervals ({}) is different than the " \
"size of the matrix ({})".format(len(cut_intervals), matrix.shape[0])
# get nan_bins
try:
if hasattr(f.root, 'nan_bins'):
nan_bins = f.root.nan_bins.read()
else:
nan_bins = np.array([])
except Exception:
nan_bins = np.array([])
# get correction factors
try:
if hasattr(f.root, 'correction_factors'):
correction_factors = f.root.correction_factors.read()
assert len(correction_factors) == matrix.shape[0], \
"Error loading matrix. Length of correction factors does not" \
"match size of matrix"
correction_factors = np.array(correction_factors)
mask = np.isnan(correction_factors)
correction_factors[mask] = 0
mask = np.isinf(correction_factors)
correction_factors[mask] = 0
else:
correction_factors = None
except Exception:
correction_factors = None
try:
# get correction factors
if hasattr(f.root, 'distance_counts'):
distance_counts = f.root.correction_factors.read()
else:
distance_counts = None
except Exception:
distance_counts = None
return matrix, cut_intervals, nan_bins, distance_counts, correction_factors
def main():
dummy_parser = argparse.ArgumentParser(description='train_mm.py')
opts.model_opts(dummy_parser)
dummy_opt = dummy_parser.parse_known_args([])[0]
os.makedirs(os.path.dirname(opt.output), exist_ok=True)
device = torch.device("cpu")
# opt.cuda = opt.gpu > -1
opt.cuda = False
if opt.gpuid:
device = torch.device("cuda:{}".format(opt.gpuid[0]))
cuda.set_device(device)
opt.cuda = True
# torch.cuda.set_device(opt.gpu)
# loading checkpoint just to find multimodal model type
checkpoint = torch.load(opt.model,
map_location=lambda storage, loc: storage)
opt.multimodal_model_type = checkpoint['opt'].multimodal_model_type
del checkpoint
if opt.batch_size > 1:
print(
"Batch size > 1 not implemented! Falling back to batch_size = 1 ..."
)
opt.batch_size = 1
# load test image features
test_file = tables.open_file(opt.path_to_test_img_feats, mode='r')
if opt.multimodal_model_type in ['imgd', 'imge', 'imgw']:
test_img_feats = test_file.root.global_feats[:]
elif opt.multimodal_model_type in ['src+img']:
test_img_feats = test_file.root.local_feats[:]
else:
raise Exception("Model type not implemented: %s" %
opt.multimodal_model_type)
test_file.close()
# Load the model.
fields, model, model_opt = \
onmt.ModelConstructor.load_test_model(opt, dummy_opt.__dict__)
#opt.multimodal_model_type = checkpoint['opt'].multimodal_model_type
# File to write sentences to.
out_file = codecs.open(opt.output, 'w', 'utf-8')
# Test data
data = onmt.io.build_dataset(fields,
opt.data_type,
opt.src,
opt.tgt,
src_dir=opt.src_dir,
sample_rate=opt.sample_rate,
window_size=opt.window_size,
window_stride=opt.window_stride,
window=opt.window,
use_filter_pred=False)
# Sort batch by decreasing lengths of sentence required by pytorch.
# sort=False means "Use dataset's sortkey instead of iterator's".
data_iter = onmt.io.OrderedIterator(dataset=data,
device=device,
batch_size=opt.batch_size,
train=False,
sort=False,
sort_within_batch=True,
shuffle=False)
# Translator
scorer = onmt.translate.GNMTGlobalScorer(opt.alpha, opt.beta)
translator = onmt.translate.TranslatorMultimodal(
model,
fields,
beam_size=opt.beam_size,
n_best=opt.n_best,
global_scorer=scorer,
max_length=opt.max_length,
copy_attn=model_opt.copy_attn,
cuda=opt.cuda,
beam_trace=opt.dump_beam != "",
min_length=opt.min_length,
test_img_feats=test_img_feats,
multimodal_model_type=opt.multimodal_model_type)
builder = onmt.translate.TranslationBuilder(data, translator.fields,
opt.n_best, opt.replace_unk,
opt.tgt)
# Statistics
counter = count(1)
pred_score_total, pred_words_total = 0, 0
gold_score_total, gold_words_total = 0, 0
for sent_idx, batch in enumerate(data_iter):
batch_data = translator.translate_batch(batch, data, sent_idx)
translations = builder.from_batch(batch_data)
for trans in translations:
pred_score_total += trans.pred_scores[0]
pred_words_total += len(trans.pred_sents[0])
if opt.tgt:
gold_score_total += trans.gold_score
gold_words_total += len(trans.gold_sent)
n_best_preds = [
" ".join(pred) for pred in trans.pred_sents[:opt.n_best]
]
out_file.write('\n'.join(n_best_preds))
out_file.write('\n')
out_file.flush()
if opt.verbose:
sent_number = next(counter)
output = trans.log(sent_number)
os.write(1, output.encode('utf-8'))
_report_score('PRED', pred_score_total, pred_words_total)
if opt.tgt:
_report_score('GOLD', gold_score_total, gold_words_total)
if opt.report_bleu:
_report_bleu()
if opt.report_rouge:
_report_rouge()
if opt.dump_beam:
import json
json.dump(translator.beam_accum,
codecs.open(opt.dump_beam, 'w', 'utf-8'))
def get_metadata():
"""
Reads metadata content (i. e. model parametrizations and objectives) of specified .h5 file.
GET parameters:
- datasetName with "dataset".
- drKernelName with "drk".
:return:
"""
app.config["DATASET_NAME"] = InputDataset.check_dataset_name(
request.args.get('datasetName'))
app.config[
"DR_KERNEL_NAME"] = DimensionalityReductionKernel.check_kernel_name(
request.args.get('drKernelName'))
app.config["CACHE_ROOT"] = "/tmp/" + app.config[
"DATASET_NAME"] + "_" + app.config["DR_KERNEL_NAME"]
# Update root storage path with new dataset name.
app.config["STORAGE_PATH"] = app.config["ROOT_STORAGE_PATH"] + app.config[
"DATASET_NAME"] + "/"
app.config["SURROGATE_MODELS_PATH"] = app.config["STORAGE_PATH"] + app.config["DR_KERNEL_NAME"] + \
"_surrogatemodels.pkl"
app.config["EXPLAINER_VALUES_PATH"] = app.config["STORAGE_PATH"] + app.config["DR_KERNEL_NAME"] + \
"_explainervalues.pkl"
dataset_name_class_links = {
"movie": MovieDataset,
"happiness": HappinessDataset
}
app.config["DATASET_CLASS"] = dataset_name_class_links[
app.config["DATASET_NAME"]]
# Compile metadata template.
update_and_get_metadata_template()
# Build file name.
file_name: str = (app.config["STORAGE_PATH"] + "embedding_" +
app.config["DR_KERNEL_NAME"] + ".h5")
app.config["FULL_FILE_NAME"] = file_name
# Open .h5 file, if dataset name and DR kernel name are valid and file exists.
if app.config["DATASET_NAME"] is not None and \
app.config["DR_KERNEL_NAME"] is not None and \
os.path.isfile(file_name):
###################################################
# Load dataset.
###################################################
h5file = tables.open_file(filename=file_name, mode="r")
# Cast to dataframe, then return as JSON.
df = pandas.DataFrame(h5file.root.metadata[:]).set_index("id")
# Close file.
h5file.close()
###################################################
# Preprocess and cache dataset.
###################################################
# Prepare dataframe for ratings.
app.config["RATINGS"] = df.copy(deep=True)
app.config["RATINGS"]["rating"] = 0
# Assemble embedding-level metadata.
app.config["EMBEDDING_METADATA"]["original"] = df
app.config["EMBEDDING_METADATA"]["features_preprocessed"], \
app.config["EMBEDDING_METADATA"]["labels"], \
app.config["EMBEDDING_METADATA"]["features_categorical_encoding_translation"] = \
Utils.preprocess_embedding_metadata_for_predictor(
metadata_template=app.config["METADATA_TEMPLATE"], embeddings_metadata=df
)
###################################################
# Load global surrogate models and local
# explainer values.
###################################################
# Compute regressor for each objective.
with open(app.config["SURROGATE_MODELS_PATH"], "rb") as file:
app.config["GLOBAL_SURROGATE_MODELS"] = pickle.load(file)
# Load explainer values.
# Replace specific metric references with an arbitrary "metric" for parsing in frontend.
app.config["EXPLAINER_VALUES"] = pd.read_pickle(
app.config["EXPLAINER_VALUES_PATH"])
# Return JSON-formatted embedding data.
df["rating"] = app.config["RATINGS"]["rating"]
# todo (remove, generate data cleanly) Hack: Rename target_domain_performance and n_components here, dismiss
# b_nx.
return jsonify(
df.rename(
columns={
"target_domain_performance": "rdp",
"separability_metric": "separability"
}).drop(["b_nx"], axis=1).to_json(orient='index'))
else:
return "File/kernel does not exist.", 400
def save(self, filename, pSymmetric=True, pApplyCorrection=None):
"""
Saves a matrix using hdf5 format
:param filename:
:return: None
"""
log.debug('Save in h5 format')
# self.restoreMaskedBins()
if not filename.endswith(".h5"):
filename += ".h5"
# if the file name already exists
# try to find a new suitable name
if os.path.isfile(filename):
log.warning("*WARNING* File already exists {}\n "
"Overwriting ...\n".format(filename))
unlink(filename)
if self.nan_bins is None:
self.nan_bins = np.array([])
elif not isinstance(self.nan_bins, np.ndarray):
self.nan_bins = np.array(self.nan_bins)
# save only the upper triangle of the
if pSymmetric:
# symmetric matrix
matrix = triu(self.matrix, k=0, format='csr')
else:
matrix = self.matrix
matrix.eliminate_zeros()
filters = tables.Filters(complevel=5, complib='blosc')
with tables.open_file(filename, mode="w",
title="HiCExplorer matrix") as h5file:
matrix_group = h5file.create_group(
"/",
"matrix",
)
# save the parts of the csr matrix
for matrix_part in ('data', 'indices', 'indptr', 'shape'):
arr = np.array(getattr(matrix, matrix_part))
atom = tables.Atom.from_dtype(arr.dtype)
ds = h5file.create_carray(matrix_group,
matrix_part,
atom,
shape=arr.shape,
filters=filters)
ds[:] = arr
# save the matrix intervals
intervals_group = h5file.create_group(
"/",
"intervals",
)
chr_list, start_list, end_list, extra_list = zip(
*self.cut_intervals)
for interval_part in ('chr_list', 'start_list', 'end_list',
'extra_list'):
arr = np.array(eval(interval_part))
atom = tables.Atom.from_dtype(arr.dtype)
ds = h5file.create_carray(intervals_group,
interval_part,
atom,
shape=arr.shape,
filters=filters)
ds[:] = arr
# save nan bins
if len(self.nan_bins):
atom = tables.Atom.from_dtype(self.nan_bins.dtype)
ds = h5file.create_carray(h5file.root,
'nan_bins',
atom,
shape=self.nan_bins.shape,
filters=filters)
ds[:] = self.nan_bins
# save corrections factors
if self.correction_factors is not None and len(
self.correction_factors):
self.correction_factors = np.array(self.correction_factors)
mask = np.isnan(self.correction_factors)
self.correction_factors[mask] = 0
atom = tables.Atom.from_dtype(self.correction_factors.dtype)
ds = h5file.create_carray(h5file.root,
'correction_factors',
atom,
shape=self.correction_factors.shape,
filters=filters)
ds[:] = np.array(self.correction_factors)
# save distance counts
if self.distance_counts is not None and len(self.distance_counts):
atom = tables.Atom.from_dtype(self.distance_counts.dtype)
ds = h5file.create_carray(h5file.root,
'distance_counts',
atom,
shape=self.distance_counts.shape,
filters=filters)
ds[:] = np.array(self.distance_counts)
def read_data(fname,args,p):
data = dict()
c51_data = h5.open_file(fname)
# check how many Nbs are in file
if args.Nbs == None:
Nbs = c51_data.get_node('/gA/'+p['ensembles'][0]+'/bs').read().shape[0]
else:
Nbs = args.Nbs
p['Nbs'] = Nbs
print('using Nbs = %d samples' %Nbs)
ga_bs = np.zeros([Nbs,p['l_d']])
ga_b0 = np.zeros([p['l_d']])
epi_bs = np.zeros_like(ga_bs)
epi_b0 = np.zeros_like(ga_b0)
mL_b0 = np.zeros([p['l_d']])
mL_bs = np.zeros([Nbs,p['l_d']])
aw0_b0 = np.zeros([p['l_d']])
aw0_bs = np.zeros([Nbs,p['l_d']])
aSaw0_b0 = np.zeros([p['l_d']])
aSaw0_bs = np.zeros([Nbs,p['l_d']])
eju_bs = np.zeros_like(ga_bs)
eju_b0 = np.zeros_like(ga_b0)
epqsq_bs = np.zeros_like(ga_bs)
epqsq_b0 = np.zeros_like(ga_b0)
for i,ens in enumerate(p['ensembles']):
ga_bs[:,i] = c51_data.get_node('/gA/'+ens+'/bs').read()[0:Nbs]
ga_b0[i] = float(c51_data.get_node('/gA/'+ens+'/b0').read())
epi_bs[:,i] = c51_data.get_node('/epi/'+ens+'/bs').read()[0:Nbs]
epi_b0[i] = float(c51_data.get_node('/epi/'+ens+'/b0').read())
mL_bs[:,i] = c51_data.get_node('/mpiL/'+ens+'/bs').read()[0:Nbs]
mL_b0[i] = float(c51_data.get_node('/mpiL/'+ens+'/b0').read())
aw0_bs[:,i] = c51_data.get_node('/aw0/'+ens+'/bs').read()[0:Nbs]
aw0_b0[i] = float(c51_data.get_node('/aw0/'+ens+'/b0').read())
# we have to multiply a by sqrt(alpha_S) as a is squared in the extrapolation functions
# to swap sqrt(alpha_S) a in for a
aSaw0_bs[:,i] = aw0_bs[:,i] * np.sqrt(p['afs'][ens])
aSaw0_b0[i] = aw0_b0[i] * np.sqrt(p['afs'][ens])
eju_bs[:,i] = c51_data.get_node('/eju/'+ens+'/bs').read()[0:Nbs]
eju_b0[i] = float(c51_data.get_node('/eju/'+ens+'/b0').read())
epqsq_bs[:,i] = c51_data.get_node('/epqsq/'+ens+'/bs').read()[0:Nbs]
epqsq_b0[i] = float(c51_data.get_node('/epqsq/'+ens+'/b0').read())
print('%s gA = %.4f +- %.4f, epi = %.5f +- %.5f, mpiL = %.4f +- %.4f' \
%(ens,ga_b0[i],ga_bs.std(axis=0)[i],epi_b0[i],epi_bs.std(axis=0)[i],
mL_b0[i],mL_bs.std(axis=0)[i]))
data['ga_bs'] = ga_bs
data['ga_b0'] = ga_b0
data['epi_bs'] = epi_bs
data['epi_b0'] = epi_b0
data['mL_bs'] = mL_bs
data['mL_b0'] = mL_b0
data['aw0_bs'] = aw0_bs
data['aw0_b0'] = aw0_b0
data['eju_b0'] = eju_b0
data['eju_bs'] = eju_bs
data['epqsq_b0'] = epqsq_b0
data['epqsq_bs'] = epqsq_bs
data['aSaw0_bs'] = aSaw0_bs
data['aSaw0_b0'] = aSaw0_b0
c51_data.close()
return data
__author__ = 'zelalem'
import fastcluster
import numpy
import scipy.spatial.distance as dist
import csv
import tables
hdf5_path = "/home/zelalem/Downloads/popular_year.hdf5"
a = tables.StringAtom(itemsize=24)
hdf5_file = tables.open_file(hdf5_path, mode='w')
data_storage = hdf5_file.create_earray(hdf5_file.root, 'e_array',a, (0,))
f = open('/home/zelalem/Desktop/PS_year_month.csv','rb')
reader = list(csv.reader(f))
dataMatrix = []
for row in reader[1:]:
dataMatrix.append(row[1:])
dataMatrix = numpy.array(dataMatrix)
# distanceMatrix = dist.pdist(dataMatrix,'euclidean') # Metric: 'euclidean', 'seuclidean', 'cosine', 'hamming', 'correlation'
data_storage.append(dist.pdist(dataMatrix,'euclidean')) # Metric: 'euclidean', 'seuclidean', 'cosine', 'hamming', 'correlation'
linkage = fastcluster.linkage(data_storage, method='median') # Method 'single','complete','average','weighted','ward','centroid','median'
num_of_cluster = 8
clust_dict = {i: [i] for i in xrange(len(linkage)+1)}
for i in xrange(len(linkage)-num_of_cluster+1):
clust1= int(linkage[i][0])
#print(y)
#print('After processing, sample:', X[0])
# print('After processing, labels:', y_batch[0])
#print('y SHAPE AFTER', np.array(y_batch, dtype=object).shape)
# ======================================================================================================================
# Write pre-processed TRAIN data to csv file
# ======================================================================================================================
# Set the compression level
filters = tables.Filters(complib='blosc', complevel=5)
# Save X batches into file
f = tables.open_file(x_filename + '.hdf', 'a')
ds = f.create_carray(
'/',
'x_data' + str(i),
obj=X_batch,
filters=filters,
)
ds[:] = X_batch
#print(ds)
f.close()
if not x_filename == 'data\\preprocessed_data\\x_TEST_SENTENC_data_preprocessed': # do NOT write for TEST DATA
# Save y batches into file
f = tables.open_file(y_filename + '.hdf', 'a')
ds = f.create_carray('/',
'y_data' + str(i),
print('BAD FILE: ' + str(filelist[nums]))
print("Done!")
print(featuresarray.shape)
return group, truth
#pr = cProfile.Profile()
#pr.enable()
group, truth = test_my_little_function()
#pr.disable()
#s = StringIO.StringIO()
#sortby = 'cumulative'
#ps = pstats.Stats(pr,stream=s).sort_stats(sortby)
#ps.print_stats()
#print(s.getvalue())
print(group.shape)
print(truth.shape)
h5file = 1
if h5file == 1:
import tables
f = tables.open_file(outputname,
'w',
filters=tables.Filters(complib='zlib', complevel=6))
f.create_carray('/', 'features', obj=group)
f.create_carray('/', 'truth', obj=truth)
f.close()
def sub_wrapper(day_datetimes, j):
print day_datetimes[j]
date = day_datetimes[j]
try:
date_1 = date + datetime.timedelta(minutes=13)
global_data, time_slot = pinkdust.load_channels(date,
date_1)
data_087 = global_data[8.7].data
data_108 = global_data[10.8].data
data_120 = global_data[12.0].data
data = np.zeros(
(data_087.shape[0], data_087.shape[1], 3))
data[:, :, 0] = data_087
data[:, :, 1] = data_108
data[:, :, 2] = data_120
except:
print 'Adding date to list of missing dates'
with open('/soge-home/projects/seviri_dust'
'/raw_seviri_data/bt_native/missing_msgnative_dates'
'.txt', 'a') as my_file:
my_file.write('\n')
my_file.write(date.strftime('%Y%m%d%H%M%S'))
data = np.zeros(
(msg_area.shape[0], msg_area.shape[1], 3))
data[:] = np.nan
if (data.shape[0] != msg_area.shape[0]) or (
data.shape[1] !=
msg_area.shape[1]):
print 'Native file data has wrong dimensions - using the second half of the array'
data_copy = deepcopy(data)
data = np.zeros(
(msg_area.shape[0], msg_area.shape[1], 3))
data[:] = data_copy[msg_area.shape[0]:, :]
msg_con_nn = image.ImageContainerNearest(data, msg_area,
radius_of_influence=50000)
area_con_nn = msg_con_nn.resample(target_area)
result_data_nn = area_con_nn.image_data
bt_data = np.zeros((3, lons.shape[0], lons.shape[1]))
bt_data[0] = result_data_nn[:, :, 0]
bt_data[1] = result_data_nn[:, :, 1]
bt_data[2] = result_data_nn[:, :, 2]
cloudmask = None
# Now, instead of writing to day array, you write to hdf
f = tables.open_file('/soge-home/projects/seviri_dust/raw_seviri_data'
'/intermediary_files/BT_087_' + date.strftime(
'%Y%m%d%H%M%S.hdf'),
'w')
atom = tables.Atom.from_dtype(bt_data[0].dtype)
filters = tables.Filters(complib='blosc', complevel=5)
ds = f.create_carray(f.root, 'data', atom,
bt_data[0].shape,
filters=filters)
ds[:] = bt_data[0]
f.close()
f = tables.open_file('/soge-home/projects/seviri_dust/raw_seviri_data'
'/intermediary_files/BT_108_' + date.strftime(
'%Y%m%d%H%M%S.hdf'), 'w')
atom = tables.Atom.from_dtype(bt_data[1].dtype)
filters = tables.Filters(complib='blosc', complevel=5)
ds = f.create_carray(f.root, 'data', atom,
bt_data[0].shape,
filters=filters)
ds[:] = bt_data[1]
f.close()
f = tables.open_file('/soge-home/projects/seviri_dust/raw_seviri_data'
'/intermediary_files/BT_120_' + date.strftime(
'%Y%m%d%H%M%S.hdf'), 'w')
atom = tables.Atom.from_dtype(bt_data[2].dtype)
filters = tables.Filters(complib='blosc', complevel=5)
ds = f.create_carray(f.root, 'data', atom,
bt_data[0].shape,
filters=filters)
ds[:] = bt_data[2]
f.close()
print 'Wrote', day_datetimes[j]
def __enter__(self):
self.file = open_file(self.out_fp, 'w')
self.group = self.file.create_group("/", 'experiments', '')
self.table = self.file.create_table(self.group, self.table_name,
self.row_class, "")
return self
def __enter__(self):
""" Enter context """
if self.hdf is None:
self.hdf = tables.open_file(self.source)
return self
def auto_merge_h5files(file_list,
output_filename='merged.h5',
nodes_keys=None,
merge_arrays=False,
filters=HDF5_ZSTD_FILTERS):
"""
Automatic merge of HDF5 files.
A list of nodes keys can be provided to merge only these nodes. If None, all nodes are merged.
Parameters
----------
file_list: list of path
output_filename: path
nodes_keys: list of path
"""
if nodes_keys is None:
keys = set(get_dataset_keys(file_list[0]))
else:
keys = set(nodes_keys)
bar = tqdm(total=len(file_list))
with open_file(output_filename, 'w', filters=filters) as merge_file:
with open_file(file_list[0]) as f1:
for k in keys:
if type(f1.root[k]) == tables.table.Table:
merge_file.create_table(os.path.join(
'/',
k.rsplit('/', maxsplit=1)[0]),
os.path.basename(k),
createparents=True,
obj=f1.root[k].read())
if type(f1.root[k]) == tables.array.Array:
if merge_arrays:
merge_file.create_earray(os.path.join(
'/',
k.rsplit('/', maxsplit=1)[0]),
os.path.basename(k),
createparents=True,
obj=f1.root[k].read())
else:
merge_file.create_array(os.path.join(
'/',
k.rsplit('/', maxsplit=1)[0]),
os.path.basename(k),
createparents=True,
obj=f1.root[k].read())
bar.update(1)
for filename in file_list[1:]:
common_keys = keys.intersection(get_dataset_keys(filename))
with open_file(filename) as file:
for k in common_keys:
try:
if merge_arrays:
merge_file.root[k].append(file.root[k].read())
else:
if type(file.root[k]) == tables.table.Table:
merge_file.root[k].append(file.root[k].read())
except:
print("Can't append node {} from file {}".format(
k, filename))
bar.update(1)
def run_case(self, stop_at_ignition=False, restart=False):
"""Run simulation case set up ``setup_case``.
:param bool stop_at_ignition: If ``True``, stop integration at ignition point.
:param bool restart: If ``True``, skip if results file exists.
"""
if restart and os.path.isfile(self.meta['save-file']):
print('Skipped existing case ', self.meta['id'])
return
# Save simulation results in hdf5 table format.
table_def = {
'time':
tables.Float64Col(pos=0),
'temperature':
tables.Float64Col(pos=1),
'pressure':
tables.Float64Col(pos=2),
'mass_fractions':
tables.Float64Col(shape=(self.reac.thermo.n_species), pos=3),
}
with tables.open_file(self.save_file, mode='w',
title=str(self.idx)) as h5file:
table = h5file.create_table(where=h5file.root,
name='simulation',
description=table_def)
# Row instance to save timestep information to
timestep = table.row
# Save initial conditions
timestep['time'] = self.reac_net.time
timestep['temperature'] = self.reac.T
timestep['pressure'] = self.reac.thermo.P
timestep['mass_fractions'] = self.reac.Y
# Add ``timestep`` to table
timestep.append()
ignition_flag = False
# Main time integration loop; continue integration while time of
# the ``ReactorNet`` is less than specified end time.
while self.reac_net.time < self.time_end:
self.reac_net.step()
# Save new timestep information
timestep['time'] = self.reac_net.time
timestep['temperature'] = self.reac.T
timestep['pressure'] = self.reac.thermo.P
timestep['mass_fractions'] = self.reac.Y
if self.reac.T > self.properties[
'temperature'] + 400.0 and not ignition_flag:
self.ignition_delay = self.reac_net.time
ignition_flag = True
if stop_at_ignition:
continue
# Add ``timestep`` to table
timestep.append()
# Write ``table`` to disk
table.flush()
return self.ignition_delay
def wrapper(y):
Year_lower = years_list[y]
Year_upper = years_list[y]
Month_lower = 9
Month_upper = 9
Day_lower = 1
Day_upper = 8
Hour_lower = 0
Hour_upper = 23
Minute_lower = 0
Minute_upper = 45
# Generate datetime objects corresponding to these time bounds
time_params = np.array(
[Year_lower, Year_upper, Month_lower, Month_upper,
Day_lower, Day_upper, Hour_lower, Hour_upper,
Minute_lower, Minute_upper])
datetimes = utilities.get_datetime_objects(time_params)
years = np.unique(np.asarray(([j.year for j in datetimes])))
months = np.unique(np.asarray(([j.month for j in datetimes])))
days = np.unique(np.asarray(([j.day for j in datetimes])))
for m in np.arange(0, len(years)):
for k in np.arange(0, len(months)):
for i in np.arange(0, len(days)):
day_datetimes_bool = np.asarray(
[j.day == days[i] and j.month ==
months[k] and j.year ==
years[m] for j in datetimes])
day_datetimes = datetimes[day_datetimes_bool]
if len(day_datetimes) == 0:
continue
ncfile = pinkdust.create_time_nc_file(
'/soge-home/projects/seviri_dust/raw_seviri_data/bt_nc/'
+ day_datetimes[0].strftime(
"%B%Y") + '/BT_' + day_datetimes[
0].strftime(
'%Y%m%d') + '.nc', day_datetimes, lats, lons)
day_array[:] = 0
pool = multiprocessing.Pool()
for j in np.arange(0, len(day_datetimes)):
pool.apply_async(sub_wrapper, args=(day_datetimes, j,))
pool.close()
pool.join()
# Now read back in all the intermediaries and write to nc
for j in np.arange(0, len(day_datetimes)):
f = tables.open_file(
'/soge-home/projects/seviri_dust/raw_seviri_data'
'/intermediary_files/BT_087_' + day_datetimes[
j].strftime(
'%Y%m%d%H%M%S.hdf'))
arrobj = f.get_node('/data')
bt_087 = arrobj.read()
f.close()
f = tables.open_file(
'/soge-home/projects/seviri_dust/raw_seviri_data'
'/intermediary_files/BT_108_' + day_datetimes[
j].strftime(
'%Y%m%d%H%M%S.hdf'))
arrobj = f.get_node('/data')
bt_108 = arrobj.read()
f.close()
f = tables.open_file(
'/soge-home/projects/seviri_dust/raw_seviri_data'
'/intermediary_files/BT_120_' + day_datetimes[
j].strftime(
'%Y%m%d%H%M%S.hdf'))
arrobj = f.get_node('/data')
bt_120 = arrobj.read()
f.close()
ncfile = pinkdust.save_to_existing_nc(ncfile,
bt_087,
bt_108,
bt_120,
None, day_datetimes[j])
print 'Day ' + str(days[i]) + ' done'
ncfile.close()
print 'Month ' + str(months[k]) + ' done'
# FILE INFO ETC.
s = sys.stdin.read()
if (s.split(" ") == ""):
raise ValueError("Please provide at least one directory.")
else:
DIR_TOREAD = s.split(" ")
if CF.VERBOSE:
print("Directories to be read:")
print(DIR_TOREAD)
##### Initialize the file. #####
# Open file connection, writing new file to disk.
myh5 = tables.open_file(CF.FILE_NAME, mode="w", title=CF.FILE_TITLE)
# Create the EArray for actual values.
a = tables.UInt8Atom()
myh5.create_earray(myh5.root,
name="riskLevels",
atom=a,
shape=(0, CF.NUMLAT, CF.NUMLON),
title=CF.DATA_TITLE)
# Create the EArray for grid information, and populate it.
a = tables.Float64Atom()
myh5.create_earray(myh5.root,
name="gridInfo",
atom=a,
shape=(0, len(CF.INFO_LIST)),
elif args.flux == "GaisserHillas" : flux = GaisserHillas() elif args.flux == "Hoerandel" : flux = Hoerandel() elif args.flux == "Hoerandel5" : flux = Hoerandel5() elif args.flux == "Hoerandel_IT" : flux = Hoerandel_IT() eventcount = 0 #generator = weighting.from_simprod(21269,False,'vm-simprod2.icecube.wisc.edu') #generator = weighting.icetop_mc_weights(21269,'/home/tmcelroy/icecube/domeff/datasetConfig.json') nfiles = len(file_list) rand = ROOT.TRandom3() for filename in file_list : h5file = 0 try : h5file = open_file(filename, mode="r") except : continue domtable = h5file.root.doms eventtable = h5file.root.events runtable = h5file.root.runinfo domindex = 0 eventindex = -1 for event in eventtable.iterrows() : eventcount += 1 weight = 1.0 if args.flux != "data" :
import tables
import pandas as pd
import numpy as np
h5_file = tables.open_file("../../../../../restricted_images_national.h5")
table_train = h5_file.get_node("/{}".format("train")) #len=58263
table_validate = h5_file.get_node("/{}".format("validate")) #len=7744
table_test = h5_file.get_node("/{}".format("test")) #len= 13509
#table_train.colnames #Table[0][0:11] ['img0','img1','img_id','inc0','inc1','lat','lng','pop0','pop1','pop_centile','sol0','sol1']
#print(len(table_train[0]), len(table_train[0][0]), len(table_train[0][0][0]), len(table_train[0][0][0][0]))
#(12, 94, 94, 7)
#table.colnames #Table[0][0:11]
lats = [] #latitudes of points
lngs = [] #longitudes of points
pop0 = [] #Population of 2000 of points
pop1 = [] #Population of 2010 of points
popdiff = [] #Pop1 - Pop0
inc0 = [] #Income of 2000
inc1 = [] #Income of 2010 of points
incdiff = [] #inc1 - inc0 of points
for table in [table_train, table_validate, table_test]:
for row in table:
#row[3]=inc0, row[4]=inc1, row[5]=lat, row[6]=lng, row[7]=pop0, row[8]=pop1
inc0.append(row[3])
inc1.append(row[4])
incdiff.append(row[4] - row[3])
lats.append(row[5])
lngs.append(row[6])
pop0.append(row[7])
pop1.append(row[8])
def main():
#reads from hdf5 file (must already exist)
h5file = tables.open_file("t", mode="a", title="Mag Data for AUTUMNX")
stationlist = [
'SALU', 'AKUL', 'PUVR', 'INUK', 'KJPK', 'RADI', 'VLDR', 'STFL', 'SEPT',
'SCHF'
]
table = {}
#get yesterday's date
date = datetime.datetime.utcnow() - datetime.timedelta(days=1)
strd = date.strftime('%Y_%m_%d')
year, month, day = re.split('_', strd)
#main loop
for station in stationlist:
#should probably clean this up, this is pretty bad right now
if station == 'SALU':
table[station] = h5file.root.magnetometer.SALU
elif station == 'AKUL':
table[station] = h5file.root.magnetometer.AKUL
elif station == 'PUVR':
table[station] = h5file.root.magnetometer.PUVR
elif station == 'INUK':
table[station] = h5file.root.magnetometer.INUK
elif station == 'KJPK':
table[station] = h5file.root.magnetometer.KJPK
elif station == 'RADI':
table[station] = h5file.root.magnetometer.RADI
elif station == 'VLDR':
table[station] = h5file.root.magnetometer.VLDR
elif station == 'STFL':
table[station] = h5file.root.magnetometer.STFL
elif station == 'SEPT':
table[station] = h5file.root.magnetometer.SEPT
elif station == 'SCHF':
table[station] = h5file.root.magnetometer.SCHF
print station
#read data from http
url = 'http://autumn.athabascau.ca/magdata/L1/{0}/fluxgate/{1}/{2}/{3}/AUTUMNX_{0}_TGBO_{4}_PT0,5S.txt'.format(
station, year, month, day, strd)
try:
response = urllib2.urlopen(url)
except:
continue
cd = re.split('\n', response.read())
del cd[0:13]
data = []
#parse datetime object into seconds from epoch
for line in cd:
ld = re.split('\s+', line)
try:
datet = ld[0] + ' ' + ld[1] + '000'
datet = (
datetime.datetime.strptime(datet, '%Y-%m-%d %H:%M:%S.%f') -
datetime.datetime.utcfromtimestamp(0)).total_seconds()
ld = [datet, float(ld[3]), float(ld[4]), float(ld[5])]
data.append(ld)
except:
continue
#append data to table in hdf5 file
mag = table[station].row
then = datetime.datetime.now()
print "Starting Data append..."
for line in data:
mag['time'] = line[0]
mag['Bx'] = line[1]
mag['By'] = line[2]
mag['Bz'] = line[3]
mag.append()
#flush table buffer
table[station].flush()
print "{0} s to complete".format(datetime.datetime.now() - then)
#close file
h5file.close()
"length", "x", "y", "z", "r", "energy", "xmin", "ymin", "zmin", "rmin",
"xmax", "ymax", "zmax", "rmax", "xb1", "yb1", "zb1", "eb1", "xb2",
"yb2", "zb2", "eb2", "ovlp_e"
]
data = namedtuple("data", columns) # auxiliar namedtuple
paolina_algorithm = track_blob_info_creator_extractor(**paolina_params)
out_df = pd.DataFrame(columns=columns)
try:
DECO = pd.read_hdf(in_filename, "DECO/Events")
except KeyError:
# save empty file
with tb.open_file(out_filename, "w") as h5out:
df_writer(h5out, out_df, group_name="tracks", table_name="events")
index_tables(out_filename)
sys.exit()
for (event, peak), deco in DECO.groupby(["event", "npeak"]):
# pre-proccess
deco.loc[:, "time"] = 0
deco.loc[:, "Ec"] = deco["E"]
deco.loc[:, "Ep"] = deco["E"]
deco.loc[:, ("Q", "Xrms", "Yrms", "nsipm")] = np.nan
# Paolina
hitc = hits_from_df(deco)[event]
df, voxels, track_hitc, out_of_map = paolina_algorithm(hitc)
print(args)
local_data_path = r'/path/to/datasets'
if args.dataset[:3] == 'shd':
dataset = local_data_path + r'/shd/' + args.dataset
elif args.dataset[:5] == 'mnist':
dataset = local_data_path + r'/mnist-dvs/' + args.dataset
elif args.dataset[:11] == 'dvs_gesture':
dataset = local_data_path + r'/DvsGesture/' + args.dataset
elif args.dataset[:7] == 'swedish':
dataset = local_data_path + r'/SwedishLeaf_processed/' + args.dataset
else:
print('Error: dataset not found')
args.dataset = tables.open_file(dataset)
args.disable_cuda = str2bool(args.disable_cuda)
args.device = None
if not args.disable_cuda and torch.cuda.is_available():
args.device = torch.device('cuda')
else:
args.device = torch.device('cpu')
### Network parameters
args.n_input_neurons = dataset.root.stats.train_data[1]
args.n_output_neurons = dataset.root.stats.train_label[1]
args.n_hidden_neurons = args.n_h
### Learning parameters
if not args.num_samples_train:
