def testCalculatorQueries(self):
""" Test that the calculator queries return the correct calculators. """
# Setup a minimal experiment simulation.
source_input = TestUtilities.generateTestFilePath('FELsource_out.h5')
diffr_input = TestUtilities.generateTestFilePath('pmi_out.h5')
pmi_input = TestUtilities.generateTestFilePath('prop_out.h5')
photon_source = XFELPhotonSource(parameters=None,
input_path=source_input,
output_path='FELsource_out.h5')
photon_propagator = XFELPhotonPropagator(parameters=None,
input_path='FELsource_out.h5',
output_path='prop_out.h5')
photon_interactor = FakePhotonMatterInteractor(
parameters=None, input_path=pmi_input, output_path='pmi_out.h5')
diffraction_parameters = {
'uniform_rotation': True,
'calculate_Compton': False,
'slice_interval': 100,
'number_of_slices': 2,
'pmi_start_ID': 1,
'pmi_stop_ID': 1,
'number_of_diffraction_patterns': 2,
'beam_parameter_file':
TestUtilities.generateTestFilePath('s2e.beam'),
'beam_geometry_file':
TestUtilities.generateTestFilePath('s2e.geom'),
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=diffr_input,
output_path='diffr_out.h5')
photon_detector = PerfectPhotonDetector(parameters=None,
input_path='diffr_out.h5',
output_path='detector_out.h5')
photon_analyzer = S2EReconstruction(parameters=None,
input_path='detector_out.h5',
output_path='analyzer_out.h5')
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
# Check queries.
self.assertIs(pxs.photon_source, photon_source)
self.assertIs(pxs.photon_propagator, photon_propagator)
self.assertIs(pxs.photon_interactor, photon_interactor)
self.assertIs(pxs.photon_diffractor, photon_diffractor)
self.assertIs(pxs.photon_detector, photon_detector)
self.assertIs(pxs.photon_analyzer, photon_analyzer)
'slice_interval': 100,
'number_of_slices': 2,
'pmi_start_ID': 1,
'pmi_stop_ID': 1,
'number_of_diffraction_patterns': 2,
'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'),
'beam_geometry_file': TestUtilities.generateTestFilePath('s2e.geom'),
}
photon_diffractor = SingFELPhotonDiffractor(parameters=diffraction_parameters,
input_path='pmi',
output_path='diffr')
# Perfect detector.
photon_detector = PerfectPhotonDetector(parameters=None,
input_path='diffr',
output_path='detector')
# Reconstruction: EMC+DM
emc_parameters = {
'initial_number_of_quaternions': 1,
'max_number_of_quaternions': 9,
'max_number_of_iterations': 100,
'min_error': 1.0e-8,
'beamstop': 1.0e-5,
'detailed_output': False
}
dm_parameters = {
'number_of_trials': 5,
'number_of_iterations': 2,
def testSimS2EWorkflowSingleFile(self):
""" Testing that a workflow akin to the simS2E example workflow works. Only one I/O file per calculator. """
# These directories and files are expected to be present after a successfull calculation.
expected_dirs = [
'pmi',
'diffr',
]
expected_symlinks = ['detector']
expected_files = [
'FELsource_out.h5',
'prop_out.h5',
'pmi/pmi_out_0000001.h5',
'diffr/diffr_out_0000001.h5',
'detector/diffr_out_0000001.h5',
'recon.h5',
'orient_out.h5',
]
# Ensure proper cleanup.
self.__files_to_remove = expected_files + expected_symlinks
self.__files_to_remove.append('prepHDF5.py')
self.__dirs_to_remove = expected_dirs
# Location of the FEL source file.
source_input = TestUtilities.generateTestFilePath(
'FELsource_out/FELsource_out_0000001.h5')
# Photon source.
photon_source = XFELPhotonSource(parameters=None,
input_path=source_input,
output_path='FELsource_out.h5')
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None,
input_path='FELsource_out.h5',
output_path='prop_out.h5')
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path='prop_out.h5',
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Diffraction with parameters.
diffraction_parameters = {
'uniform_rotation': True,
'calculate_Compton': False,
'slice_interval': 100,
'number_of_slices': 2,
'pmi_start_ID': 1,
'pmi_stop_ID': 1,
'number_of_diffraction_patterns': 1,
'beam_parameter_file':
TestUtilities.generateTestFilePath('s2e.beam'),
'beam_geometry_file':
TestUtilities.generateTestFilePath('s2e.geom'),
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path='pmi',
output_path='diffr')
# Perfect detector.
photon_detector = PerfectPhotonDetector(parameters=None,
input_path='diffr',
output_path='detector')
# Reconstruction: EMC+DM
emc_parameters = {
'initial_number_of_quaternions': 1,
'max_number_of_quaternions': 9,
'max_number_of_iterations': 3,
'min_error': 1.0e-8,
'beamstop': 1.0e-5,
'detailed_output': False
}
dm_parameters = {
'number_of_trials': 5,
'number_of_iterations': 2,
'averaging_start': 15,
'leash': 0.2,
'number_of_shrink_cycles': 2,
}
reconstructor = S2EReconstruction(parameters={
'EMC_Parameters': emc_parameters,
'DM_Parameters': dm_parameters
},
input_path='detector',
output_path='recon.h5')
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
# Check that all output files and directories are present.
for directory in expected_dirs + expected_symlinks:
self.assertTrue(os.path.isdir(directory))
for f in expected_files:
print f
self.assertTrue(os.path.isfile(f))
def testConstructionExceptions(self):
""" Test that the appropriate exceptions are thrown if the object is constructed incorrectly. """
# Setup a minimal experiment simulation.
source_input = TestUtilities.generateTestFilePath('FELsource_out.h5')
diffr_input = TestUtilities.generateTestFilePath('pmi_out.h5')
pmi_input = TestUtilities.generateTestFilePath('prop_out.h5')
photon_source = XFELPhotonSource(parameters=None,
input_path=source_input,
output_path='FELsource_out.h5')
photon_propagator = XFELPhotonPropagator(parameters=None,
input_path='FELsource_out.h5',
output_path='prop_out.h5')
photon_interactor = FakePhotonMatterInteractor(
parameters=None, input_path=pmi_input, output_path='pmi_out.h5')
diffraction_parameters = {
'uniform_rotation': True,
'calculate_Compton': False,
'slice_interval': 100,
'number_of_slices': 2,
'pmi_start_ID': 1,
'pmi_stop_ID': 1,
'number_of_diffraction_patterns': 2,
'beam_parameter_file':
TestUtilities.generateTestFilePath('s2e.beam'),
'beam_geometry_file':
TestUtilities.generateTestFilePath('s2e.geom'),
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=diffr_input,
output_path='diffr_out.h5')
photon_detector = PerfectPhotonDetector(parameters=None,
input_path='diffr_out.h5',
output_path='detector_out.h5')
photon_analyzer = S2EReconstruction(parameters=None,
input_path='detector_out.h5',
output_path='analyzer_out.h5')
# Check wrong source.
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=None,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_propagator,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
# Check wrong propagator.
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_source,
photon_propagator=None,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_source,
photon_propagator=photon_source,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
# Check wrong interactor.
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=None,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_source,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
# Check wrong diffractor.
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=None,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_source,
photon_detector=photon_detector,
photon_analyzer=photon_analyzer,
)
# Check wrong analyzer.
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=None,
)
self.assertRaises(
TypeError,
PhotonExperimentSimulation,
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=photon_diffractor,
)