def setup(self):
filePtr = open('tests/icatestsignals.db', 'r')
signalDict = cPickle.load(filePtr)
filePtr.close()
# setup the test data
self.signals = np.vstack([signalDict[k] for k in signalDict])
# standardize signals
self.signals = standardize(self.signals, stdtype='row')
# mixing
self.A = np.random.randn(len(self.signals), len(self.signals))
self.X = np.dot(self.A, self.signals)
# ica options
icaOptions = dict()
icaOptions['nonlinearity'] = 'logcosh'
icaOptions['maxIterations'] = 500
icaOptions['tolerance'] = 1.0e-05
# this is just to get the setup to run; test_has_ica will fail if rpy2ica isn't there
# other tests may pass if you have pyica installed, however
try:
from rpy2ica import fastica
icaMethod = fastica
except:
icaMethod = None
# RAICAR object
self.K = 10
# data logger
self.logger = Logger('tests/runlog.txt')
# raicar object
self.mycar = RAICAR(projDirectory='tests/raicartest',
K=self.K,
nSignals=3,
icaOptions=icaOptions,
icaMethod=icaMethod)
def run(index, ncomponents):
for directory in dirgroups[index:index + 1]:
os.chdir(directory)
raicar = RAICAR(projDirectory='raicar',
nSignals=ncomponents,
icaMethod=ica_method)
melodic_data = MelodicData(directory)
# raicar.clean_project()
raicar.runall(melodic_data.signal)
return raicar
def setup(self):
filePtr = open('tests/icatestsignals.db','r')
signalDict = cPickle.load(filePtr)
filePtr.close()
# setup the test data
self.signals = np.vstack([signalDict[k] for k in signalDict])
# standardize signals
self.signals = standardize(self.signals,stdtype='row')
# mixing
self.A = np.random.randn(len(self.signals),len(self.signals))
self.X = np.dot(self.A,self.signals)
# ica options
icaOptions = dict()
icaOptions['nonlinearity'] = 'logcosh'
icaOptions['maxIterations'] = 500
icaOptions['tolerance'] = 1.0e-05
# this is just to get the setup to run; test_has_ica will fail if rpy2ica isn't there
# other tests may pass if you have pyica installed, however
try:
from rpy2ica import fastica
icaMethod = fastica
except:
icaMethod = None
# RAICAR object
self.K = 10
# data logger
self.logger = Logger('tests/runlog.txt')
# raicar object
self.mycar = RAICAR(projDirectory='tests/raicartest',K=self.K,nSignals=3,icaOptions=icaOptions,icaMethod=icaMethod)
def main():
raicar = RAICAR(projDirectory='raicar', nSignals=10, icaMethod=ica_method)
raicar.clean_project()
x = np.loadtxt('melodic_mix').T
raicar.runall(x)
class TestRAICARrpy2ica:
def setup(self):
filePtr = open('tests/icatestsignals.db', 'r')
signalDict = cPickle.load(filePtr)
filePtr.close()
# setup the test data
self.signals = np.vstack([signalDict[k] for k in signalDict])
# standardize signals
self.signals = standardize(self.signals, stdtype='row')
# mixing
self.A = np.random.randn(len(self.signals), len(self.signals))
self.X = np.dot(self.A, self.signals)
# ica options
icaOptions = dict()
icaOptions['nonlinearity'] = 'logcosh'
icaOptions['maxIterations'] = 500
icaOptions['tolerance'] = 1.0e-05
# this is just to get the setup to run; test_has_ica will fail if rpy2ica isn't there
# other tests may pass if you have pyica installed, however
try:
from rpy2ica import fastica
icaMethod = fastica
except:
icaMethod = None
# RAICAR object
self.K = 10
# data logger
self.logger = Logger('tests/runlog.txt')
# raicar object
self.mycar = RAICAR(projDirectory='tests/raicartest',
K=self.K,
nSignals=3,
icaOptions=icaOptions,
icaMethod=icaMethod)
def test_has_ica(self):
try:
import rpy2ica
rpy2ica_loaded = True
except ImportError:
rpy2ica_loaded = False
assert rpy2ica_loaded, "rpy2ica not installed; you need to use pyica.fastica or supply your own icaMethod and icaOptions!"
def test_clean_project(self):
self.mycar.clean_project()
assert len(
glob.glob('tests/raicartest/ica/*.h5')
) == 0, "project not cleaned succesfully: aligned components exist"
assert len(
glob.glob('tests/raicartest/aln/*.aln')
) == 0, "project not cleaned successfully: ica realizations exist"
assert len(
glob.glob('tests/raicartest/rab/*.db')
) == 0, "project not cleaned successfully: R(a,b) matrices exist"
def test_run_ica(self):
self.mycar.kica(self.X)
assert len(
glob.glob('tests/raicartest/ica/*.h5')
) == self.K, "ica failed: proper number of realizations not produced"
def test_compute_rab(self):
self.mycar.kica(self.X)
self.mycar.compute_rab()
assert (len(self.mycar.RabDict)) == (
self.K * (self.K - 1)
) / 2, "problem with computing Rab: incorrect number of cross-realization matrices"
maxCorr = 0.0
minCorr = 1.0
for k in self.mycar.RabDict:
matrixMax = self.mycar.RabDict[k].max()
matrixMin = self.mycar.RabDict[k].min()
if matrixMax >= maxCorr:
maxCorr = matrixMax
if matrixMin <= minCorr:
minCorr = matrixMin
assert minCorr >= 0.0, "problem with Rab matrices : minimum absolute correlation is < 0.0"
assert maxCorr <= 1.0, "problem with Rab matrices : maximum absolute correlation is > 1.0"
def test_compute_component_alignments(self):
self.mycar.kica(self.X)
self.mycar.compute_rab()
self.mycar.compute_component_alignments()
assert len(
self.mycar.alignDict
) == 3, "problem with computed alignments: wrong number of RAICAR components"
assert len(
self.mycar.alignDict[0]
) == self.K, "problem with computed alignments: wrong number of realization components in RAICAR component"
def test_align_components(self):
self.mycar.kica(self.X)
self.mycar.compute_rab()
self.mycar.compute_component_alignments()
for k in xrange(3):
self.mycar.align_component(k)
assert len(
glob.glob('tests/raicartest/aln/*.h5')
) == 3, "problem with aligned components: not enough components"
assert len(
glob.glob('tests/raicartest/aln/*.db')
) == 1, "problem with aligned components: alignment database was not created"
def test_construct_raicar_components(self):
self.mycar.kica(self.X)
self.mycar.compute_rab()
self.mycar.compute_component_alignments()
for k in xrange(3):
self.mycar.align_component(k)
self.mycar.construct_raicar_components()
assert np.min(self.mycar.reproducibility
) >= 0, "problem with component reproducibility: R < 0"
assert np.max(self.mycar.reproducibility
) <= 1, "problem with component reproducibility: R > 1"
class TestRAICARrpy2ica:
def setup(self):
filePtr = open('tests/icatestsignals.db','r')
signalDict = cPickle.load(filePtr)
filePtr.close()
# setup the test data
self.signals = np.vstack([signalDict[k] for k in signalDict])
# standardize signals
self.signals = standardize(self.signals,stdtype='row')
# mixing
self.A = np.random.randn(len(self.signals),len(self.signals))
self.X = np.dot(self.A,self.signals)
# ica options
icaOptions = dict()
icaOptions['nonlinearity'] = 'logcosh'
icaOptions['maxIterations'] = 500
icaOptions['tolerance'] = 1.0e-05
# this is just to get the setup to run; test_has_ica will fail if rpy2ica isn't there
# other tests may pass if you have pyica installed, however
try:
from rpy2ica import fastica
icaMethod = fastica
except:
icaMethod = None
# RAICAR object
self.K = 10
# data logger
self.logger = Logger('tests/runlog.txt')
# raicar object
self.mycar = RAICAR(projDirectory='tests/raicartest',K=self.K,nSignals=3,icaOptions=icaOptions,icaMethod=icaMethod)
def test_has_ica(self):
try:
import rpy2ica
rpy2ica_loaded = True
except ImportError:
rpy2ica_loaded = False
assert rpy2ica_loaded,"rpy2ica not installed; you need to use pyica.fastica or supply your own icaMethod and icaOptions!"
def test_clean_project(self):
self.mycar.clean_project()
assert len(glob.glob('tests/raicartest/ica/*.h5')) == 0,"project not cleaned succesfully: aligned components exist"
assert len(glob.glob('tests/raicartest/aln/*.aln')) == 0,"project not cleaned successfully: ica realizations exist"
assert len(glob.glob('tests/raicartest/rab/*.db')) == 0,"project not cleaned successfully: R(a,b) matrices exist"
def test_run_ica(self):
self.mycar.kica(self.X)
assert len(glob.glob('tests/raicartest/ica/*.h5')) == self.K,"ica failed: proper number of realizations not produced"
def test_compute_rab(self):
self.mycar.kica(self.X)
self.mycar.compute_rab()
assert(len(self.mycar.RabDict)) == (self.K*(self.K-1))/2,"problem with computing Rab: incorrect number of cross-realization matrices"
maxCorr = 0.0
minCorr = 1.0
for k in self.mycar.RabDict:
matrixMax = self.mycar.RabDict[k].max()
matrixMin = self.mycar.RabDict[k].min()
if matrixMax >= maxCorr:
maxCorr = matrixMax
if matrixMin <= minCorr:
minCorr = matrixMin
assert minCorr >= 0.0,"problem with Rab matrices : minimum absolute correlation is < 0.0"
assert maxCorr <= 1.0,"problem with Rab matrices : maximum absolute correlation is > 1.0"
def test_compute_component_alignments(self):
self.mycar.kica(self.X)
self.mycar.compute_rab()
self.mycar.compute_component_alignments()
assert len(self.mycar.alignDict) == 3,"problem with computed alignments: wrong number of RAICAR components"
assert len(self.mycar.alignDict[0]) == self.K,"problem with computed alignments: wrong number of realization components in RAICAR component"
def test_align_components(self):
self.mycar.kica(self.X)
self.mycar.compute_rab()
self.mycar.compute_component_alignments()
for k in xrange(3):
self.mycar.align_component(k)
assert len(glob.glob('tests/raicartest/aln/*.h5')) == 3,"problem with aligned components: not enough components"
assert len(glob.glob('tests/raicartest/aln/*.db')) == 1,"problem with aligned components: alignment database was not created"
def test_construct_raicar_components(self):
self.mycar.kica(self.X)
self.mycar.compute_rab()
self.mycar.compute_component_alignments()
for k in xrange(3):
self.mycar.align_component(k)
self.mycar.construct_raicar_components()
assert np.min(self.mycar.reproducibility) >= 0,"problem with component reproducibility: R < 0"
assert np.max(self.mycar.reproducibility) <= 1,"problem with component reproducibility: R > 1"