def test_n_FindPaths(self):
tprob = scipy.io.mmread(os.path.join(ReferenceDir, "Data", "tProb.mtx"))
sources = [0]
sinks = [70]
paths, bottlenecks, fluxes = FindPaths.run(tprob, sources, sinks, 10)
# paths are hard to test due to type issues, adding later --TJL
bottlenecks_ref = io.loadh(os.path.join(ReferenceDir, "transition_path_theory_reference", "dijkstra_bottlenecks.h5"), 'Data')
fluxes_ref = io.loadh(os.path.join(ReferenceDir, "transition_path_theory_reference", "dijkstra_fluxes.h5"), 'Data')
npt.assert_array_almost_equal(bottlenecks, bottlenecks_ref)
npt.assert_array_almost_equal(fluxes, fluxes_ref)
def test_FindPaths():
tprob = get("transition_path_theory_reference/tProb.mtx")
sources = [0]
sinks = [70]
paths, bottlenecks, fluxes = FindPaths.run(tprob, sources, sinks, 10)
# paths are hard to test due to type issues, adding later --TJL
bottlenecks_ref = get(pjoin("transition_path_theory_reference",
"dijkstra_bottlenecks.h5"))['Data']
fluxes_ref = get(pjoin("transition_path_theory_reference",
"dijkstra_fluxes.h5"))['Data']
eq(bottlenecks, bottlenecks_ref)
eq(fluxes, fluxes_ref)
def test_multi_state_path_calculations(self):
path_output = FindPaths.run(self.tprob, self.multi_sources, self.multi_sinks, self.num_paths)
path_result_ref = io.loadh(tpt_get("many_state/Paths.h5"))
paths_ref = path_result_ref['Paths']
bottlenecks_ref = path_result_ref['Bottlenecks']
fluxes_ref = path_result_ref['fluxes']
npt.assert_array_almost_equal(path_output[0], paths_ref)
npt.assert_array_almost_equal(path_output[1], bottlenecks_ref)
npt.assert_array_almost_equal(path_output[2], fluxes_ref)
def test_FindPaths():
tprob = get("transition_path_theory_reference/tProb.mtx")
sources = [0]
sinks = [70]
paths, bottlenecks, fluxes = FindPaths.run(tprob, sources, sinks, 10)
# paths are hard to test due to type issues, adding later --TJL
bottlenecks_ref = get(pjoin("transition_path_theory_reference",
"dijkstra_bottlenecks.h5"))['Data']
fluxes_ref = get(pjoin("transition_path_theory_reference",
"dijkstra_fluxes.h5"))['Data']
eq(bottlenecks, bottlenecks_ref)
eq(fluxes, fluxes_ref)
def test_multi_state_path_calculations(self):
path_output = FindPaths.run(self.tprob, self.multi_sources, self.multi_sinks, self.num_paths)
path_result_ref = io.loadh(tpt_get("many_state/Paths.h5"))
paths_ref = path_result_ref['Paths']
bottlenecks_ref = path_result_ref['Bottlenecks']
fluxes_ref = path_result_ref['fluxes']
npt.assert_array_almost_equal(path_output[0], paths_ref)
npt.assert_array_almost_equal(path_output[1], bottlenecks_ref)
npt.assert_array_almost_equal(path_output[2], fluxes_ref)
def test_n_FindPaths(self):
tprob = scipy.io.mmread(os.path.join(ReferenceDir, "Data",
"tProb.mtx"))
sources = [0]
sinks = [70]
paths, bottlenecks, fluxes = FindPaths.run(tprob, sources, sinks, 10)
# paths are hard to test due to type issues, adding later --TJL
bottlenecks_ref = io.loadh(
os.path.join(ReferenceDir, "transition_path_theory_reference",
"dijkstra_bottlenecks.h5"), 'Data')
fluxes_ref = io.loadh(
os.path.join(ReferenceDir, "transition_path_theory_reference",
"dijkstra_fluxes.h5"), 'Data')
npt.assert_array_almost_equal(bottlenecks, bottlenecks_ref)
npt.assert_array_almost_equal(fluxes, fluxes_ref)