def test_averEff(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "aver.prb"
options.configfilename = "standard.conf"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
def test_stepFunctionBelowReject(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "step.prb"
options.configfilename = "stepreject.conf"
options.expbfile = "expbursts.bst"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
def test_output(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.binaryofile = "binary.pkl"
options.burstcompofile = "burstcomp.txt"
options.burstsizeofile = "burstsizes.txt"
options.decaytimeofile = "decaytimes.txt"
options.endtimeofile = "endtimes.txt"
options.pbfile = "high.prb"
options.configfilename = "standard.conf"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 1., delta = 0.05)
def test_invalidTrajFormat(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.trajformat = "inv"
options.pbfile = "step.prb"
options.configfilename = "stepreject.conf"
options.expbfile = "expbursts.bst"
self.assertRaises(ValueError, runMCFRET, options)
def test_trajFormat(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.trajformat = "dat"
options.pbfile = "step.prb"
options.configfilename = "stepreject.conf"
options.expbfile = "expbursts.bst"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
def test_invalidPhotongenerator(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "step.prb"
options.configfilename = "invalid_photongenerator.conf"
options.expbfile = "expbursts.bst"
self.assertRaises(ValueError, runMCFRET, options)
def test_invalidMinMaxStartTraj(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "aver.prb"
options.configfilename = "wrongminmaxstart2.conf"
options.expbfile = "expbursts.bst"
self.assertRaises(ValueError, runMCFRET, options)
def test_cannotAssignClass(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "invalid.prb"
options.configfilename = "expbstcorr.conf"
options.expbfile = "expbursts.bst"
self.assertRaises(ValueError, runMCFRET, options)
def test_profiling(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "high.prb"
options.configfilename = "standard.conf"
options.prffile = "profile.log"
runMCFRET(options)
self.assertTrue(os.path.exists("profile.log"))
def test_invalidDir(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "high.prb"
options.configfilename = "standard.conf"
os.mkdir(os.path.join(self.workdir, "empty"))
options.trajdirectory = "empty"
self.assertRaises(ValueError, runMCFRET, options)
def test_rejectPhotonTest(self):
for i in ("trajectory", "same-species", "all"):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "aver.prb"
options.configfilename = "rejecttest-%s.conf" % i
options.expbfile = "expbursts.bst"
self.assertRaises(ValueError, runMCFRET, options)
def test_expBurstCorrected(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "aver.prb"
options.configfilename = "expbstcorr.conf"
options.expbfile = "expbursts.bst"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
def test_cextensionPhotongenerator(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "step.prb"
options.configfilename = "cextension.conf"
options.expbfile = "expbursts.bst"
try:
# from FRETUtils.PhotonGenerator import tryGetCPhoton #@UnusedImport
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
except ImportError:
pass
def test_invalidBSCutOff(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "aver.prb"
options.configfilename = "invalidbscutoff.conf"
self.assertRaises(ValueError, runMCFRET, options)
def test_invalidBurstGenMethod(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "aver.prb"
options.configfilename = "invalidburstacc.conf"
self.assertRaises(ValueError, runMCFRET, options)