def test_read_layers_cleft(self):
"""
Tests read(mode='layers_cleft')
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# read all
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers_cleft')
# test meta-properties
for category in ['first', 'second']:
np_test.assert_equal(cleft_lay[category].indexed,
self.indexed.union(['normalVolume']))
np_test.assert_equal(cleft_lay[category].properties,
self.properties.union(set(['normalVolume'])))
# test normalized mean
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='normalMean'),
[0, 5, -2, -1, 0, 1, 2, 7, 1])
def test_read_order(self):
"""
Tests read(order)
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# make order and read
order = {'first': ['exp_3', 'exp_2'], 'second': ['exp_4']}
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers',
order=order)
# test catalog properties
np_test.assert_equal(cleft_lay.first.identifiers, ['exp_3', 'exp_2'])
np_test.assert_equal(cleft_lay.second.identifiers, ['exp_4'])
# data
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_2', property='mean'),
self.mean_0 + 1)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_3', property='mean'),
self.mean_0 + 2)
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_4', property='mean'),
self.mean_0 + 3)
# make order and read
order = {'first': ['exp_3', 'exp_5'], 'second': ['exp_4', 'exp_1']}
print("Now a warning should appear:")
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers',
order=order)
# test catalog properties
np_test.assert_equal(cleft_lay.first.identifiers, ['exp_3'])
np_test.assert_equal(cleft_lay.second.identifiers, ['exp_4', 'exp_1'])
def test_read_layers_on_columns(self):
"""
Tests read(mode='layers_on_columns')
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# read all
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers')
cleft_layoncol = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers_on_columns',
reference=cleft_lay)
# test meta-properties
for category in ['first', 'second']:
np_test.assert_equal(cleft_layoncol[category].indexed,
self.indexed)
np_test.assert_equal(cleft_layoncol[category].properties,
self.properties_layers_on_columns)
# ids
np_test.assert_equal(
cleft_layoncol.first.cleftIds,
[list(range(3, 8)), list(range(3, 8))])
# data
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_1', property='mean'),
self.mean_0)
def testGetBoundarySurfaces(self):
"""
Tests getBoundarySurfaces()
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# read all
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers')
# test simple
cleft_lay.getBoundarySurfaces(names=['surfaceBound1', 'surfaceBound2'],
surface='volume')
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_2',
property='surfaceBound1'), 6)
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_2',
property='surfaceBound2'), 6)
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_3',
property='surfaceBound1'), 6)
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='surfaceBound1'), 6)
# test factor = 10
cleft_lay.getBoundarySurfaces(names=['surfaceBound1', 'surfaceBound2'],
factor=10,
surface='volume')
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_3',
property='surfaceBound2'), 60)
def testGetRelative(self):
"""
Tests getRelative()
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# read layers
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers')
# test regions
cleft_lay.getRelative(fraction=0.5,
new='half',
name='mean',
region=['bound', 'cleft'])
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1', property='half'),
(33 / 4. + 5) / 2)
cleft_lay.getRelative(fraction=0.3,
new='point_three',
name='mean',
region=['bound', 'cleft'])
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_2',
property='point_three'),
37 / 4. + (6 - 37 / 4.) * 0.3)
# test regions with volume
cleft_lay.getRelative(fraction=0.5,
new='half',
name='mean',
region=['bound', 'cleft'],
weight='volume')
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1', property='half'),
(33 / 4. + 5) / 2)
cleft_lay.second.setValue(identifier='exp_1',
property='volumeX',
value=numpy.array(
[6, 6, 6, 6, 6, 10, 10, 6, 6]))
cleft_lay.second.setValue(identifier='exp_4',
property='volumeX',
value=numpy.array(
[6, 6, 6, 6, 6, 10, 10, 6, 6]))
cleft_lay.getRelative(fraction=0.5,
new='half',
name='mean',
region=['bound', 'cleft'],
weight='volumeX',
categories=['second'])
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1', property='half'),
(33 / 4. + (130 + 12 * 6) / 38.) / 2)
# test ids
cleft_lay.getRelative(fraction=0.5,
new='half',
ids=[[1, 2, 8, 9], [3, 4, 5, 6, 7]])
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1', property='half'),
(33 / 4. + 5) / 2)
def testNormalizeByMean(self):
"""
Tests normalizeByMean() for layers, layers on columns and columns
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# make cleft layers
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers')
# absolute, specified ids
cleft_lay.normalizeByMean(name='mean',
normalName='normalized',
ids=[3, 4, 5],
mode='absolute')
np_test.assert_equal('normalized' in cleft_lay.first.properties, True)
np_test.assert_equal('normalized' in cleft_lay.second.properties, True)
np_test.assert_equal('normMean' in cleft_lay.first.properties, False)
np_test.assert_equal('normMean' in cleft_lay.second.properties, False)
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='normalized'),
[1, 6, -1, 0, 1, 2, 3, 8, 2])
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_4',
property='normalized'),
[1, 6, -1, 0, 1, 2, 3, 8, 2])
# absolute, specified ids, reference
cleft_lay.normalizeByMean(name='mean',
normalName='normalized',
ids=[3, 4, 5],
mode='absolute',
reference=cleft_lay)
np_test.assert_equal('normalized' in cleft_lay.first.properties, True)
np_test.assert_equal('normalized' in cleft_lay.second.properties, True)
np_test.assert_equal('normMean' in cleft_lay.first.properties, False)
np_test.assert_equal('normMean' in cleft_lay.second.properties, False)
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='normalized'),
[1, 6, -1, 0, 1, 2, 3, 8, 2])
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_4',
property='normalized'),
[1, 6, -1, 0, 1, 2, 3, 8, 2])
# relative, all ids
cleft_lay.normalizeByMean(name='mean',
normalName='normalized',
mode='relative')
np_test.assert_equal('normalized' in cleft_lay.first.properties, True)
np_test.assert_equal('normalized' in cleft_lay.second.properties, True)
np_test.assert_equal('normMean' in cleft_lay.first.properties, False)
np_test.assert_equal('normMean' in cleft_lay.second.properties, False)
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='normalized'),
(self.mean_0 - self.mean_0.mean()) / self.mean_0.mean())
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_2',
property='normalized'),
(self.mean_0 - self.mean_0.mean()) / (self.mean_0.mean() + 1))
# relative, all ids, reference
cleft_lay.normalizeByMean(name='mean',
normalName='normalized',
mode='relative',
reference=cleft_lay)
np_test.assert_equal('normalized' in cleft_lay.first.properties, True)
np_test.assert_equal('normalized' in cleft_lay.second.properties, True)
np_test.assert_equal('normMean' in cleft_lay.first.properties, False)
np_test.assert_equal('normMean' in cleft_lay.second.properties, False)
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='normalized'),
(self.mean_0 - self.mean_0.mean()) / self.mean_0.mean())
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_2',
property='normalized'),
(self.mean_0 - self.mean_0.mean()) / (self.mean_0.mean() + 1))
# 0to1, regions
cleft_lay.normalizeByMean(name='mean',
normalName='normal0to1',
region=['bound', 'cleft'],
mode='0to1')
np_test.assert_equal('normal0to1' in cleft_lay.first.properties, True)
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='normal0to1'),
(common.cleft_layers_density_mean - 33 / 4.) / (5 - 33 / 4.))
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_2',
property='normal0to1'),
(common.cleft_layers_density_mean - 33 / 4.) / (5 - 33 / 4.))
# 0to1, regions, with reference
cleft_lay.normalizeByMean(name='mean',
normalName='normal0to1',
region=['bound', 'cleft'],
mode='0to1',
reference=cleft_lay)
np_test.assert_equal('normal0to1' in cleft_lay.first.properties, True)
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='normal0to1'),
(common.cleft_layers_density_mean - 33 / 4.) / (5 - 33 / 4.))
np_test.assert_almost_equal(
cleft_lay.first.getValue(identifier='exp_2',
property='normal0to1'),
(common.cleft_layers_density_mean - 33 / 4.) / (5 - 33 / 4.))
# 0to1, ids
cleft_lay.normalizeByMean(name='mean',
normalName='normal0to1',
ids=[[1, 2, 8, 9], [3, 4, 5, 6, 7]],
mode='0to1')
np_test.assert_equal('normal0to1' in cleft_lay.first.properties, True)
np_test.assert_almost_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='normal0to1'),
(common.cleft_layers_density_mean - 33 / 4.) / (5 - 33 / 4.))
# 0to1 layers on columns, simple
cleft_layoncol = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers_on_columns',
reference=cleft_lay)
np_test.assert_almost_equal(
cleft_layoncol.second.getValue(identifier='exp_1',
property='normalMean'),
(common.cleft_layers_density_mean - 33 / 4.) / (5 - 33 / 4.))
# make another layers with simple values
cleft_lay_2 = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers')
cleft_lay_2.second.setValue(identifier='exp_1',
property='mean',
value=numpy.array(
[0., 0, 10, 10, 10, 10, 10, 0, 0.]))
cleft_lay_2.first.setValue(identifier='exp_2',
property='mean',
value=numpy.array(
[0., 0, 10, 10, 10, 10, 10, 0, 0.]))
cleft_lay_2.second.setValue(identifier='exp_4',
property='mean',
value=numpy.array(
[0., 0, 10, 10, 10, 10, 10, 0, 0.]))
# 0to1, layers on columns, with reference 0
cleft_layoncol.normalizeByMean(name='mean',
normalName='nor',
ids=[[1, 2, 8, 9], [3, 4, 5, 6, 7]],
mode='0to1',
reference=[cleft_lay_2, None])
np_test.assert_almost_equal(
cleft_layoncol.second.getValue(identifier='exp_1', property='nor'),
(common.cleft_layers_density_mean - 0.) / (5.))
np_test.assert_almost_equal(
cleft_layoncol.first.getValue(identifier='exp_2', property='nor'),
(common.cleft_layers_density_mean + 1 - 0.) / (6.))
# 0to1, layers on columns, with references 0 and 1
cleft_layoncol.normalizeByMean(name='mean',
normalName='nor',
ids=[[1, 2, 8, 9], [3, 4, 5, 6, 7]],
mode='0to1',
reference=[cleft_lay_2, cleft_lay_2])
np_test.assert_almost_equal(
cleft_layoncol.second.getValue(identifier='exp_1', property='nor'),
(common.cleft_layers_density_mean - 0.) / (10.))
# 0to1, layers on columns, with references 0 and 1, shortcut
cleft_layoncol.normalizeByMean(name='mean',
normalName='nor',
ids=[[1, 2, 8, 9], [3, 4, 5, 6, 7]],
mode='0to1',
reference=cleft_lay_2)
np_test.assert_almost_equal(
cleft_layoncol.second.getValue(identifier='exp_1', property='nor'),
(common.cleft_layers_density_mean - 0.) / (10.))
# absolute, columns, with references 0 and 1
cleft_col = CleftRegions.read(files=catal.cleft_columns_obj,
catalog=catal,
mode='columns',
reference=cleft_lay_2)
cleft_col.normalizeByMean(name='mean',
normalName='nor',
ids=[1, 2, 8, 9],
mode='absolute',
reference=cleft_lay_2)
np_test.assert_almost_equal(
cleft_col.second.getValue(identifier='exp_1', property='nor'),
common.cleft_columns_density_mean)
# 0to1, columns, with references 0 and 1
cleft_col = CleftRegions.read(files=catal.cleft_columns_obj,
catalog=catal,
mode='columns',
reference=cleft_lay_2)
cleft_col.normalizeByMean(name='mean',
normalName='nor',
ids=[[1, 2, 8, 9], [3, 4, 5, 6, 7]],
mode='0to1',
reference=[cleft_lay_2, cleft_lay_2])
np_test.assert_almost_equal(
cleft_col.second.getValue(identifier='exp_1', property='nor'),
(common.cleft_columns_density_mean - 0.) / (10.))
np_test.assert_almost_equal(
cleft_col.second.getValue(identifier='exp_4', property='nor'),
(common.cleft_columns_density_mean + 3 - 0.) / (10.))
def test_read_columns(self):
"""
Tests read(mode='columns')
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# read all
cleft_col = CleftRegions.read(files=catal.cleft_columns_obj,
catalog=catal,
mode='columns')
# test meta-properties
for category in ['first', 'second']:
np_test.assert_equal(cleft_col[category].indexed,
self.indexed_columns)
np_test.assert_equal(cleft_col[category].properties,
self.properties_columns)
# read columns with layers as reference
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers')
cleft_col = CleftRegions.read(files=catal.cleft_columns_obj,
catalog=catal,
mode='columns',
reference=cleft_lay)
# test meta-properties
for category in ['first', 'second']:
np_test.assert_equal(
cleft_col[category].indexed,
self.indexed_columns.union(set(['normalMean'])))
np_test.assert_equal(
cleft_col[category].properties,
self.properties_columns.union(set(['normalMean'])))
# test catalog properties
np_test.assert_equal(set(cleft_col.first.identifiers),
set(['exp_2', 'exp_3']))
np_test.assert_equal(set(cleft_col.second.identifiers),
set(['exp_1', 'exp_4']))
# test category
for category in ['first', 'second']:
np_test.assert_equal(cleft_col[category].ids,
[self.ids_columns, self.ids_columns])
# identifiers
np_test.assert_equal(set(cleft_col.first.identifiers),
set(['exp_2', 'exp_3']))
np_test.assert_equal(set(cleft_col.second.identifiers),
set(['exp_1', 'exp_4']))
# data
np_test.assert_equal(
cleft_col.second.getValue(identifier='exp_1', property='mean'),
self.mean_0_columns)
np_test.assert_equal(
cleft_col.first.getValue(identifier='exp_2', property='mean'),
self.mean_0_columns + 1)
np_test.assert_equal(
cleft_col.first.getValue(identifier='exp_3', property='mean'),
self.mean_0_columns + 2)
np_test.assert_equal(
cleft_col.second.getValue(identifier='exp_4', property='mean'),
self.mean_0_columns + 3)
np_test.assert_equal(
cleft_col.first.getValue(identifier='exp_2', property='volume'),
self.volume_columns)
def test_read_layers(self):
"""
Tests read(mode='layers')
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# read all
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers')
# test meta-properties
for category in ['first', 'second']:
np_test.assert_equal(cleft_lay[category].indexed, self.indexed)
np_test.assert_equal(cleft_lay[category].properties,
self.properties.union(set(['normalMean'])))
# test catalog properties
np_test.assert_equal(set(cleft_lay.first.identifiers),
set(['exp_2', 'exp_3']))
np_test.assert_equal(set(cleft_lay.second.identifiers),
set(['exp_1', 'exp_4']))
# test category
for category in ['first', 'second']:
np_test.assert_equal(cleft_lay[category].ids, [self.ids, self.ids])
np_test.assert_equal(cleft_lay[category].width,
[self.width, self.width])
# identifiers
np_test.assert_equal(set(cleft_lay.first.identifiers),
set(['exp_2', 'exp_3']))
np_test.assert_equal(set(cleft_lay.second.identifiers),
set(['exp_1', 'exp_4']))
# data
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_1', property='mean'),
self.mean_0)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_2', property='mean'),
self.mean_0 + 1)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_3', property='mean'),
self.mean_0 + 2)
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_4', property='mean'),
self.mean_0 + 3)
# ids
np_test.assert_equal(
cleft_lay.first.cleftIds,
[list(range(3, 8)), list(range(3, 8))])
np_test.assert_equal(cleft_lay.first.bound1Ids, [[1, 2], [1, 2]])
np_test.assert_equal(cleft_lay.first.bound2Ids, [[8, 9], [8, 9]])
np_test.assert_equal(cleft_lay.first.boundIds,
[[1, 2, 8, 9], [1, 2, 8, 9]])
def test_read(self):
"""
Tests read(mode=None)
"""
# make catalog
curr_dir, base = os.path.split(os.path.abspath(__file__))
cat_dir = os.path.join(curr_dir, common.rel_catalogs_dir)
catal = Catalog()
catal.read(dir=cat_dir,
catalog=r'catalog_[0-9]*\.',
type='distributed')
catal.makeGroups(feature='category')
# read all
cleft_lay = CleftRegions.read(files=catal.results_obj,
catalog=catal,
mode='layers')
# test meta-properties
for category in ['first', 'second']:
np_test.assert_equal(cleft_lay[category].indexed, self.indexed)
np_test.assert_equal(cleft_lay[category].properties,
self.properties)
# test catalog properties
np_test.assert_equal(set(cleft_lay.first.identifiers),
set(['exp_2', 'exp_3']))
np_test.assert_equal(set(cleft_lay.second.identifiers),
set(['exp_1', 'exp_4']))
# test category
for category in ['first', 'second']:
np_test.assert_equal(cleft_lay[category].ids, [self.ids, self.ids])
np_test.assert_equal(cleft_lay[category].width,
[self.width, self.width])
# identifiers
np_test.assert_equal(set(cleft_lay.first.identifiers),
set(['exp_2', 'exp_3']))
np_test.assert_equal(set(cleft_lay.second.identifiers),
set(['exp_1', 'exp_4']))
# data
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_1', property='mean'),
self.mean_0)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_2', property='mean'),
self.mean_0 + 1)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_3', property='mean'),
self.mean_0 + 2)
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_4', property='mean'),
self.mean_0 + 3)
# width and volume in nm
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_1', property='width_nm'),
self.width * 3.1)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_2', property='width_nm'),
self.width * 3.2)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_3', property='width_nm'),
self.width * 3.3)
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_4', property='width_nm'),
self.width * 3.4)
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_1',
property='volume_nm'),
self.volume * 3.1**3)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_2', property='volume_nm'),
self.volume * 3.2**3)
np_test.assert_equal(
cleft_lay.first.getValue(identifier='exp_3', property='volume_nm'),
self.volume * 3.3**3)
np_test.assert_equal(
cleft_lay.second.getValue(identifier='exp_4',
property='volume_nm'),
self.volume * 3.4**3)