def testAddLinked(self):
"""
Tests addLinked() and getNLinked()
"""
# read svs
sv = Vesicles.read(files=self.sv_files, catalog=self.catalog,
membrane=self.mem_files, lumen=self.lum_files)
# read connectors
conn_files = {
'rim_wt' : {'77_4': 'segmentations/conn_77-4_new_rest.pkl',
'78_3': 'segmentations/conn_78-3_new_rest.pkl'},
'rim_altered' : {'75_4' : 'segmentations/conn_75-4_new_rest.pkl'}}
# calculate linked and N linked
sv.addLinked(files=self.catalog.connector_files)
sv.getNLinked()
# test 77_4
np_test.assert_equal(
sv.rim_wt.getValue(identifier='77_4', property='linked', ids=3),
[4, 30])
np_test.assert_equal(
sv.rim_wt.getValue(identifier='77_4', property='n_linked', ids=3),
2)
np_test.assert_equal(
sv.rim_wt.getValue(identifier='77_4', property='linked', ids=5),
[4, 22, 88])
np_test.assert_equal(
sv.rim_wt.getValue(identifier='77_4', property='n_linked', ids=5),
3)
def testReadCatalogs(self):
"""
Tests read() with catalogs
"""
# read
sv = Vesicles.read(files=self.sv_files, catalog=self.catalog,
membrane=self.mem_files, lumen=self.lum_files)
# test general
np_test.assert_equal(sv.rim_wt.identifiers, ['77_4', '78_3'])
np_test.assert_equal(sv.rim_altered.identifiers, ['75_4'])
# test 77_4
np_test.assert_equal(
sv.rim_wt.getValue(identifier='77_4', property='ids'),
list(range(2, 144)))
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='density', ids=7),
-0.02, decimal=2)
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='membrane_density',
ids=7),
-0.04, decimal=2)
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='lumen_density',
ids=7),
0.00, decimal=2)
# test 78_3
np_test.assert_equal(
sv.rim_wt.getValue(identifier='78_3', property='ids'),
list(range(2,81)))
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='78_3', property='meanDistance',
ids=7),
50.4, decimal=1)
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='78_3', property='minDistance',
ids=7),
44.0, decimal=1)
# test 75_4
np_test.assert_equal(
sv.rim_altered.getValue(identifier='75_4', property='ids'),
list(range(2, 133)))
np_test.assert_almost_equal(
sv.rim_altered.getValue(identifier='75_4', property='radius',
ids=7),
6.3, decimal=1)
np_test.assert_almost_equal(
sv.rim_altered.getValue(identifier='75_4', property='radius_nm',
ids=7),
16.5, decimal=1)
def testRead_order(self):
"""
Tests read() with specified order
"""
# make order and read
order = {'rim_wt' : ['78_3', '77_4'], 'rim_altered' : ['75_4']}
sv = Vesicles.read(
files=self.sv_files, catalog=self.catalog, order=order,
membrane=self.mem_files, lumen=self.lum_files)
# test general
np_test.assert_equal(sv.rim_wt.identifiers, ['78_3', '77_4'])
np_test.assert_equal(sv.rim_altered.identifiers, ['75_4'])
def testGetN(self):
"""
Tests getN()
"""
# read svs
sv = Vesicles.read(files=self.sv_files, catalog=self.catalog,
membrane=self.mem_files, lumen=self.mem_files)
pixel_size = self.catalog.pixel_size['rim_wt']['77_4']
# n vesicles
sv.getNVesicles(name='n_ves')
np_test.assert_equal(
sv.rim_wt.getValue(identifier='77_4', property='n_ves'), 142)
np_test.assert_equal(
sv.rim_wt.getValue(identifier='78_3', property='n_ves'), 79)
np_test.assert_equal(
sv.rim_altered.getValue(identifier='75_4', property='n_ves'), 131)
# n vesicles per unit layer area
sv.getNVesicles(name='n_area', layer=self.layer)
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='n_area'),
142 / (7557 * pixel_size**2 * 1e-6),
decimal=1)
# n vesicles per unit layer area, layer_factor=0.001
sv.getNVesicles(name='n_area', layer=self.layer, layer_factor=0.001)
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='n_area'),
142 / (7557 * pixel_size**2 * 0.001),
decimal=4)
# unit layer area in nm^2
sv.getNVesicles(name='area_nm', layer=self.layer, inverse=True,
fixed=1, layer_factor=1.)
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='area_nm'),
7557 * pixel_size**2,
decimal=1)
# unit layer area in nm^3
sv.getNVesicles(name='area_um', layer=self.layer, inverse=True,
fixed=1, layer_factor=1.e-6)
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='area_um'),
7557 * pixel_size**2 * 1.e-6,
decimal=1)
def testGetMeanConnectionLength(self):
"""
Tests getMeanConnectionLength()
"""
# read svs
sv = Vesicles.read(files=self.sv_files, catalog=self.catalog,
membrane=self.mem_files, lumen=self.mem_files)
# calculate mean tether lengths
sv.getMeanConnectionLength(conn=self.tether, name='mean_tether_nm')
# test 77_4
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='mean_tether_nm',
ids=3),
5.54 * self.catalog.pixel_size['rim_wt']['77_4'],
decimal=1)
np_test.assert_almost_equal(
sv.rim_wt.getValue(identifier='77_4', property='mean_tether_nm',
ids=5),
4.88 * self.catalog.pixel_size['rim_wt']['77_4'],
decimal=1)
def testGetNearestNeighbor(self):
"""
Tests getNearestNeighbor()
"""
# setup
sv = Vesicles()
sv['group_a'] = Observations()
clust = Clusters()
clust['group_a'] = Observations()
ids_1 = [1, 4, 5, 7]
sv['group_a'].setValue(
identifier='exp_1', name='ids', indexed=True, value=ids_1)
clust['group_a'].setValue(
identifier='exp_1', name='bound_ids', indexed=False, value=ids_1)
clust['group_a'].setValue(
identifier='exp_1', name='bound_dist', indexed=False,
value=[3., 2, 4, 3, 1, 2.5])
clust['group_a'].setValue(
identifier='exp_1', name='bound_dist_nm', indexed=False,
value=[41., 51, 71, 54, 74, 75])
ids_2 = [1, 8, 5, 7, 4]
sv['group_a'].setValue(
identifier='exp_2', name='ids', indexed=True, value=ids_2)
clust['group_a'].setValue(
identifier='exp_2', name='bound_ids', indexed=False,
value=[4, 8, 3, 5])
clust['group_a'].setValue(
identifier='exp_2', name='bound_dist', indexed=False,
value=[48., 34, 45, 38, 58, 35])
clust['group_a'].setValue(
identifier='exp_2', name='bound_dist_nm', indexed=False,
value=[84., 43, 54, 83, 85, 53])
# in pixels
sv.getNearestNeighbor(cluster=clust, dist_name='bound_dist')
near_dist = sv['group_a'].getValue(
identifier='exp_1', name='nearest_distance')
np_test.assert_equal(near_dist, [2, 1, 2, 1.])
near_ids = sv['group_a'].getValue(
identifier='exp_1', name='nearest_ids')
np_test.assert_equal(near_ids, [5, 7, 1, 4])
# different sv ids and clust bound_ids
sv.getNearestNeighbor(cluster=clust, dist_name='bound_dist')
near_dist = sv['group_a'].getValue(
identifier='exp_2', name='nearest_distance')
np_test.assert_equal(near_dist, [-1, 48, 45, -1, 45])
near_ids = sv['group_a'].getValue(
identifier='exp_2', name='nearest_ids')
np_test.assert_equal(near_ids, [-1, 4, 4, -1, 5])
# in pixels and in nm
clust['group_a'].setValue(
identifier='exp_1', name='bound_dist_nm', indexed=True,
value=2*numpy.array([3., 2, 4, 3, 1, 2.5]))
sv.getNearestNeighbor(
cluster=clust, dist_name='bound_dist', name='foo', default=-2)
near_dist = sv['group_a'].getValue(
identifier='exp_1', name='foo_distance')
np_test.assert_equal(near_dist, [2, 1, 2, 1.])
near_ids = sv['group_a'].getValue(
identifier='exp_1', name='foo_ids')
np_test.assert_equal(near_ids, [5, 7, 1, 4])
near_dist_nm = sv['group_a'].getValue(
identifier='exp_1', name='foo_distance_nm')
np_test.assert_equal(near_dist_nm, 2*numpy.array([2, 1, 2, 1.]))
near_dist = sv['group_a'].getValue(
identifier='exp_2', name='foo_distance')
np_test.assert_equal(near_dist, [-2, 48, 45, -2, 45])
near_dist = sv['group_a'].getValue(
identifier='exp_2', name='foo_distance_nm')
np_test.assert_equal(near_dist, [-2, 84, 54, -2, 54])
near_ids = sv['group_a'].getValue(
identifier='exp_2', name='foo_ids')
np_test.assert_equal(near_ids, [-2, 4, 4, -2, 5])
# consistency check
sv['group_b'] = Observations()
sv['group_b'].setValue(
identifier='exp_1', name='ids', indexed=True, value=ids_1)
clust['group_b'] = Observations()
clust['group_b'].setValue(
identifier='exp_1', name='bound_ids', indexed=False, value=ids_1)
clust['group_b'].setValue(
identifier='exp_1', name='bound_dist', indexed=False,
value=[3., 2, 4, 3])
# this way because assert_raises doesn't work for some reason
caught = False
try:
sv.getNearestNeighbor(cluster=clust, dist_name='bound_dist')
except ValueError:
caught = True
np_test.assert_equal(caught, True)
def setUp(self):
"""
"""
# set sv files and adjust paths
dir_, base = os.path.split(__file__)
sv_files = {
'rim_wt' : {'77_4': 'segmentations/sv_77-4_vesicles.pkl',
'78_3': 'segmentations/sv_78-3_vesicles.pkl'},
'rim_altered' : {'75_4' : 'segmentations/sv_75-4_vesicles.pkl'}}
for categ in sv_files:
for ident, name in list(sv_files[categ].items()):
sv_files[categ][ident] = os.path.join(dir_, name)
self.sv_files = sv_files
# set membrane files and adjust paths
mem_files = {
'rim_wt' : {'77_4': 'segmentations/sv_77-4_mem.pkl',
'78_3': 'segmentations/sv_78-3_mem.pkl'},
'rim_altered' : {'75_4' : 'segmentations/sv_75-4_mem.pkl'}}
for categ in mem_files:
for ident, name in list(mem_files[categ].items()):
mem_files[categ][ident] = os.path.join(dir_, name)
self.mem_files = mem_files
# set lumen files and adjust paths
lum_files = {
'rim_wt' : {'77_4': 'segmentations/sv_77-4_lum.pkl',
'78_3': 'segmentations/sv_78-3_lum.pkl'},
'rim_altered' : {'75_4' : 'segmentations/sv_75-4_lum.pkl'}}
for categ in lum_files:
for ident, name in list(lum_files[categ].items()):
lum_files[categ][ident] = os.path.join(dir_, name)
self.lum_files = lum_files
# set catalog for tethers and connectors
dir_, base = os.path.split(__file__)
catalog = pyto.analysis.Catalog()
catalog._db = {
'category' : {'77_4' : 'rim_wt', '78_3' : 'rim_wt',
'75_4' : 'rim_altered'},
'tether_files' : {'77_4': 'segmentations/conn_77-4_new_AZ.pkl',
'78_3': 'segmentations/conn_78-3_new_AZ.pkl',
'75_4' : 'segmentations/conn_75-4_new_AZ.pkl'},
'connector_files' : {'77_4': 'segmentations/conn_77-4_new_rest.pkl',
'78_3': 'segmentations/conn_78-3_new_rest.pkl',
'75_4' : 'segmentations/conn_75-4_new_rest.pkl'},
'layer_files' : {'77_4': 'segmentations/layers_77-4.dat',
'78_3': 'segmentations/layers_78-3.dat',
'75_4' : 'segmentations/layers_75-4.dat'},
'pixel_size' : {'77_4' : 2.644, '78_3' : 2.644, '75_4' : 2.644},
'operator' : {'77_4' : 'emerson', '78_3' : 'lake',
'75_4' : 'palmer'}
}
for ident, name in list(catalog._db['tether_files'].items()):
catalog._db['tether_files'][ident] = os.path.join(dir_, name)
for ident, name in list(catalog._db['connector_files'].items()):
catalog._db['connector_files'][ident] = os.path.join(dir_, name)
for ident, name in list(catalog._db['layer_files'].items()):
catalog._db['layer_files'][ident] = os.path.join(dir_, name)
catalog.makeGroups()
self.catalog = catalog
# read tethers and connectors
from pyto.analysis.connections import Connections
self.tether = Connections.read(files=catalog.tether_files,
mode='connectors', catalog=catalog)
self.connector = Connections.read(
files=catalog.connector_files, mode='connectors', catalog=catalog,
order=self.tether)
# read layers
from pyto.analysis.layers import Layers
self.layer = Layers.read(
files=catalog.layer_files, catalog=catalog, order=self.tether)
# read vesicles
self.sv = Vesicles.read(files=self.sv_files, catalog=self.catalog,
membrane=self.mem_files, lumen=self.mem_files)
def setUp(self):
"""
"""
# local path
dir_, base = os.path.split(__file__)
# set catalog
catalog = pyto.analysis.Catalog()
catalog._db = {
'category': {
'77_4': 'rim_wt',
'78_3': 'rim_wt',
'75_4': 'rim_altered'
},
'tether_files': {
'77_4': 'segmentations/conn_77-4_new_AZ.pkl',
'78_3': 'segmentations/conn_78-3_new_AZ.pkl',
'75_4': 'segmentations/conn_75-4_new_AZ.pkl'
},
'sv_files': {
'77_4': 'segmentations/sv_77-4_vesicles.pkl',
'78_3': 'segmentations/sv_78-3_vesicles.pkl',
'75_4': 'segmentations/sv_75-4_vesicles.pkl'
},
'pixel_size': {
'77_4': 2.644,
'78_3': 2.644,
'75_4': 2.644
},
'operator': {
'77_4': 'emerson',
'78_3': 'lake',
'75_4': 'palmer'
}
}
for ident, name in list(catalog._db['tether_files'].items()):
catalog._db['tether_files'][ident] = os.path.join(dir_, name)
for ident, name in list(catalog._db['sv_files'].items()):
catalog._db['sv_files'][ident] = os.path.join(dir_, name)
catalog.makeGroups()
self.catalog = catalog
# read tethers and sv
self.tether = Connections.read(files=catalog.tether_files,
mode='connectors',
catalog=catalog)
from pyto.analysis.vesicles import Vesicles
self.sv = Vesicles.read(files=catalog.sv_files, catalog=catalog)
# set segmentation files and adjust paths
tether_files = {
'rim_wt': {
'77_4': 'segmentations/conn_77-4_AZ_all.pkl',
'78_3': 'segmentations/conn_78-3_AZ_all.pkl'
},
'rim_altered': {
'75_4': 'segmentations/conn_75-4_AZ_all.pkl'
}
}
for categ in tether_files:
for ident, name in list(tether_files[categ].items()):
tether_files[categ][ident] = os.path.join(dir_, name)
self.tether_files = tether_files
# set pixel size
self.pixel_size = {
'rim_wt': {
'77_4': 2.644,
'78_3': 2.644
},
'rim_altered': {
'75_4': 2.644
}
}