def findMaskPoints(self, image, mask, subscriber=0):
"""
Returns a table of masked points with each row
giving a tuple (coordinate_1, ..., coordindate_n, value).
"""
self.check(image, mask)
subscriber %= 10.0
index = (mask.data == FEATURE_COLOR).nonzero()
zVal = image.data[index]
subscriber %= 60.0
fields = []
for dim, coord in enumerate(index):
newField = FieldContainer(
image.dimensions[dim].data[coord],
image.dimensions[dim].unit,
longname=image.dimensions[dim].longname + " %i" % dim,
shortname=image.dimensions[dim].shortname)
fields.append(newField)
fields.append(
FieldContainer(zVal,
image.unit,
longname=image.longname,
shortname=image.shortname))
res = SampleContainer(
fields, u"Points from %s at %s" % (image.longname, mask.longname),
u"X1")
res.seal()
subscriber %= 100.0
return res
def makeSC(column_data, longnames, shortnames, longname, shortname, attributes={}):
unzipped = zip(*column_data)
assert len(unzipped) == len(longnames) == len(shortnames)
def get_column_fc(col, ln, sn):
try:
from pyphant.quantities import Quantity
unit = Quantity(1.0, col[0].unit)
data = [quant.value for quant in col]
except (KeyError, AttributeError):
unit = 1
data = col
from numpy import array
from pyphant.core.DataContainer import FieldContainer
fc = FieldContainer(data=array(data), unit=unit, longname=ln, shortname=sn)
return fc
columns = [get_column_fc(col, ln, sn) for col, ln, sn in zip(unzipped, longnames, shortnames)]
from pyphant.core.DataContainer import SampleContainer
sc = SampleContainer(longname=longname, shortname=shortname, attributes=attributes, columns=columns)
sc.seal()
return sc
class SampleContainerTestCase(ContainerTestCase):
def setUp(self):
super(SampleContainerTestCase, self).setUp()
self.independent = FieldContainer(
0.3 * numpy.linspace(0, 1, self.testData.shape[0]),
longname='independent variable',
shortname='x',
unit=Quantity('1 mg'),
attributes=copy.copy(self.attributes).update({'independent':
True}))
self.dependent = FieldContainer(9.81 * self.independent.data,
dimensions=[self.independent],
longname='dependent variable',
shortname='f',
unit=Quantity('9.81 nN'),
attributes=copy.copy(
self.attributes).update(
{'independent': False}))
self.sample = SampleContainer([self.dependent, self.field],
longname='Sample',
shortname='X',
attributes=copy.copy(
self.attributes).update(
{'isSample': 'It seems so.'}))
self.sample.seal()
def testSaveRestore(self):
self.eln.create_group(self.eln.root, 'testSaveRestoreSample')
saveSample(self.eln, self.eln.root.testSaveRestoreSample, self.sample)
restoredSample = loadSample(self.eln,
self.eln.root.testSaveRestoreSample)
self.assertEqual(restoredSample, self.sample)
def findMaskPoints(self, image, mask, subscriber=0):
"""
Returns a table of masked points with each row
giving a tuple (coordinate_1, ..., coordindate_n, value).
"""
self.check(image, mask)
subscriber %= 10.0
index = (mask.data == FEATURE_COLOR).nonzero()
zVal = image.data[index]
subscriber %= 60.0
fields = []
for dim, coord in enumerate(index):
newField = FieldContainer(
image.dimensions[dim].data[coord],
image.dimensions[dim].unit,
longname=image.dimensions[dim].longname + " %i" % dim,
shortname=image.dimensions[dim].shortname
)
fields.append(newField)
fields.append(FieldContainer(zVal, image.unit,
longname=image.longname,
shortname=image.shortname)
)
res = SampleContainer(
fields,
u"Points from %s at %s"%(image.longname, mask.longname),
u"X1"
)
res.seal()
subscriber %= 100.0
return res
def checkExpected(self, columns, result):
expected = SampleContainer(columns,
longname='Table',
shortname='T',
attributes=deepcopy(result.attributes))
expected.seal()
self.assertEqual(result, expected)
def makeSC(column_data,
longnames,
shortnames,
longname,
shortname,
attributes=None):
if attributes is None:
attributes = {}
unzipped = zip(*column_data)
assert len(unzipped) == len(longnames) == len(shortnames)
def get_column_fc(col, ln, sn):
try:
from pyphant.quantities import Quantity
unit = Quantity(1.0, col[0].unit)
data = [quant.value for quant in col]
except (KeyError, AttributeError):
unit = 1
data = col
from numpy import array
from pyphant.core.DataContainer import FieldContainer
fc = FieldContainer(data=array(data),
unit=unit,
longname=ln,
shortname=sn)
return fc
columns = [get_column_fc(col, ln, sn) for col, ln, sn \
in zip(unzipped, longnames, shortnames)]
from pyphant.core.DataContainer import SampleContainer
sc = SampleContainer(longname=longname,
shortname=shortname,
attributes=attributes,
columns=columns)
sc.seal()
return sc
def testSCwithSCColumn(self):
fc_child1 = FieldContainer(longname='fc_child1', data=N.ones((10, 10)))
fc_child2 = FieldContainer(longname='fc_child2', data=N.ones((20, 20)))
sc_child = SampleContainer(longname='sc_child', columns=[fc_child1])
sc_parent = SampleContainer(longname='sc_parent',
columns=[sc_child, fc_child2])
sc_parent.seal()
km = KnowledgeManager.getInstance()
km.registerDataContainer(sc_parent, temporary=True)
lnlist = km.search(['longname'], {'col_of': {'longname': 'sc_parent'}})
lnlist = [entry[0] for entry in lnlist]
assert len(lnlist) == 2
assert 'fc_child2' in lnlist
assert 'sc_child' in lnlist
def testSCwithSCColumn(self):
fc_child1 = FieldContainer(longname='fc_child1', data=N.ones((10, 10)))
fc_child2 = FieldContainer(longname='fc_child2', data=N.ones((20, 20)))
sc_child = SampleContainer(longname='sc_child', columns=[fc_child1])
sc_parent = SampleContainer(longname='sc_parent', columns=[sc_child,
fc_child2])
sc_parent.seal()
km = KnowledgeManager.getInstance()
km.registerDataContainer(sc_parent, temporary=True)
lnlist = km.search(['longname'], {'col_of':{'longname':'sc_parent'}})
lnlist = [entry[0] for entry in lnlist]
assert len(lnlist) == 2
assert 'fc_child2' in lnlist
assert 'sc_child' in lnlist
class SampleContainerTestCase(unittest.TestCase):
def setUp(self):
data = NPArray([10.0, -103.5, 1000.43, 0.0, 10.0])
unit = PQ('3s')
error = NPArray([0.1, 0.2, 4.5, 0.1, 0.2])
longname = u'Test: FieldContainer H5FileHandler'
shortname = u'TestH5FC'
attributes = {'custom1': u'testing1...', 'custom2': u'testing2...'}
self.fc = FieldContainer(data, unit, error, None, None, longname,
shortname, attributes)
self.fc.seal()
fc2 = FieldContainer(NPArray([4003.2, 5.3, 600.9]), PQ('0.2m'), None,
None, None, 'FieldContainer 2', 'FC2')
fc2.seal()
columns = [self.fc, fc2]
longname = u'Test: SampleContainer H5FileHandler'
shortname = u'TestH5SC'
self.sc = SampleContainer(columns, longname, shortname, attributes)
self.sc.seal()
class SampleContainerTestCase(unittest.TestCase):
def setUp(self):
data = NPArray([10.0, -103.5, 1000.43, 0.0, 10.0])
unit = PQ('3s')
error = NPArray([0.1, 0.2, 4.5, 0.1, 0.2])
longname = u'Test: FieldContainer H5FileHandler'
shortname = u'TestH5FC'
attributes = {'custom1':u'testing1...', 'custom2':u'testing2...'}
self.fc = FieldContainer(data, unit, error, None, None, longname,
shortname, attributes)
self.fc.seal()
fc2 = FieldContainer(NPArray([4003.2, 5.3, 600.9]), PQ('0.2m'), None,
None, None, 'FieldContainer 2', 'FC2')
fc2.seal()
columns = [self.fc, fc2]
longname = u'Test: SampleContainer H5FileHandler'
shortname = u'TestH5SC'
self.sc = SampleContainer(columns, longname, shortname, attributes)
self.sc.seal()
class SampleContainerInSampleContainerTestCase(SampleContainerTestCase):
def setUp(self):
super(SampleContainerInSampleContainerTestCase,self).setUp()
sample1 = SampleContainer([self.dependent,self.field],longname='First Sample',shortname='X',
attributes = copy.copy(self.attributes).update({'isSample':'It seems so.'}))
self.independent2 = FieldContainer(0.3*numpy.linspace(0,1,self.testData.shape[0]*10),
longname='independent variable',
shortname='x',
unit = Quantity('1 mg'),
attributes = copy.copy(self.attributes).update({'independent':True}))
self.dependent2 = FieldContainer(9.81*self.independent2.data,
dimensions=[self.independent2],
longname='dependent variable',
shortname='f',
unit = Quantity('9.81 nN'),
attributes = copy.copy(self.attributes).update({'independent':False}))
sample2 = SampleContainer([self.dependent2,self.independent2],longname='Second Sample',shortname='Y',
attributes = copy.copy(self.attributes).update({'sample Nr.': 2}))
self.sample = SampleContainer([sample1,sample2],longname='SampleContainer with Samples',shortname='(X,Y)',
attributes = copy.copy(self.attributes).update({'isSample':'It seems so.'}))
self.sample.seal()
class SampleContainerTestCase(ContainerTestCase):
def setUp(self):
super(SampleContainerTestCase,self).setUp()
self.independent = FieldContainer(0.3*numpy.linspace(0,1,self.testData.shape[0]),
longname='independent variable',
shortname='x',
unit = Quantity('1 mg'),
attributes = copy.copy(self.attributes).update({'independent':True}))
self.dependent = FieldContainer(9.81*self.independent.data,
dimensions=[self.independent],
longname='dependent variable',
shortname='f',
unit = Quantity('9.81 nN'),
attributes = copy.copy(self.attributes).update({'independent':False}))
self.sample = SampleContainer([self.dependent,self.field],longname='Sample',shortname='X',
attributes = copy.copy(self.attributes).update({'isSample':'It seems so.'}))
self.sample.seal()
def testSaveRestore(self):
self.eln.createGroup(self.eln.root,'testSaveRestoreSample')
saveSample(self.eln,self.eln.root.testSaveRestoreSample,self.sample)
restoredSample = loadSample(self.eln,self.eln.root.testSaveRestoreSample)
self.assertEqual(restoredSample,self.sample)
def checkExpected(self, columns, result):
expected = SampleContainer(columns, longname="Table", shortname="T", attributes=deepcopy(result.attributes))
expected.seal()
self.assertEqual(result, expected)
def testStringSample(self):
# string = numpy.rec.fromrecords([(s,) for s in [u'Hello',u'World!',u'Bäh!']])
# strings =
uField = FieldContainer(scipy.array([u"Hello", u"World!", u"Bäh!"]), longname=u"Text", shortname="\gamma")
sample = SampleContainer([uField])
sample.seal()