def testCheckInterfaceConsistency(self):
""" Test if the check for interface consistency works correctly. """
# Setup a minimal experiment simulation.
source_input = TestUtilities.generateTestFilePath('FELsource_out.h5')
diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.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')
pmi_parameters = {
'sample_path': TestUtilities.generateTestFilePath('sample.h5')
}
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=pmi_input,
output_path='pmi_out.h5',
sample_path=self.__sample_path)
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'),
'number_of_MPI_processes': 2,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=diffr_input,
output_path='diffr_out.h5')
photon_detector = IdealPhotonDetector(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,
)
interfaces_are_consistent = pxs._checkInterfaceConsistency()
self.assertTrue(interfaces_are_consistent)
def testCheckInterfaceConsistency(self):
""" Test if the check for interface consistency works correctly. """
# Setup a minimal experiment simulation.
source_input = TestUtilities.generateTestFilePath("FELsource_out.h5")
diffr_input = TestUtilities.generateTestFilePath("pmi_out_0000001.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"
)
pmi_parameters = {"sample_path": TestUtilities.generateTestFilePath("sample.h5")}
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None, input_path=pmi_input, output_path="pmi_out.h5", sample_path=self.__sample_path
)
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"),
"number_of_MPI_processes": 2,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters, input_path=diffr_input, output_path="diffr_out.h5"
)
photon_detector = IdealPhotonDetector(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,
)
interfaces_are_consistent = pxs._checkInterfaceConsistency()
self.assertTrue(interfaces_are_consistent)
def testCheckInterfaceConsistency(self):
""" Test if the check for interface consistency works correctly. """
# Setup a minimal experiment simulation.
source_input = TestUtilities.generateTestFilePath('FELsource_out.h5')
diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.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')
pmi_parameters = {
'sample_path': TestUtilities.generateTestFilePath('sample.h5')
}
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=pmi_input,
output_path='pmi_out.h5',
sample_path=self.__sample_path)
diffraction_parameters = self.diffractorParam_1
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=diffr_input,
output_path='diffr_out.h5')
photon_detector = IdealPhotonDetector(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,
)
interfaces_are_consistent = pxs._checkInterfaceConsistency()
self.assertTrue(interfaces_are_consistent)
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)
def testConstruction(self):
""" Test the default constructor of this class. """
# Setup a minimal experiment simulation.
source_input = TestUtilities.generateTestFilePath('FELsource_out.h5')
diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.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 = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=pmi_input,
output_path='pmi_out.h5',
sample_path=self.__sample_path)
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'),
'number_of_MPI_processes': 2,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=diffr_input,
output_path='diffr_out.h5')
photon_detector = IdealPhotonDetector(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 instance.
self.assertIsInstance(pxs, PhotonExperimentSimulation)
def testCheckInterfaceConsistency(self):
""" Test if the check for interface consistency works correctly. """
# 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,
)
interfaces_are_consistent = pxs._checkInterfaceConsistency()
self.assertTrue( interfaces_are_consistent )
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_0000001.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 = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=pmi_input,
output_path='pmi_out.h5',
sample_path=self.__sample_path)
diffraction_parameters = self.diffractorParam_2
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=diffr_input,
output_path='diffr_out.h5')
photon_detector = IdealPhotonDetector(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)
def testConstruction(self):
""" Test the default constructor of this class. """
# Setup a minimal experiment simulation.
source_input = TestUtilities.generateTestFilePath('FELsource_out.h5')
diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.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 = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=pmi_input,
output_path='pmi_out.h5',
sample_path=self.__sample_path)
diffraction_parameters = self.diffractorParam_1
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=diffr_input,
output_path='diffr_out.h5')
photon_detector = IdealPhotonDetector(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 instance.
self.assertIsInstance(pxs, PhotonExperimentSimulation)
'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()
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 testSimS2EWorkflowDirectories(self):
""" Testing that a workflow akin to the simS2E example workflow works.
Two sources, two diffraction patterns."""
# Setup directories.
working_directory = 'SPI'
source_dir = os.path.join(working_directory, 'FELsource')
prop_dir = os.path.join(working_directory, 'prop')
pmi_dir = os.path.join(working_directory, 'pmi')
diffr_dir = os.path.join(working_directory, 'diffr')
detector_dir = os.path.join(working_directory, 'detector')
recon_dir = os.path.join(working_directory, 'recon')
# Make directories.
os.mkdir(working_directory)
os.mkdir(source_dir)
os.mkdir(prop_dir)
os.mkdir(pmi_dir)
os.mkdir(diffr_dir)
os.mkdir(detector_dir)
os.mkdir(recon_dir)
# Ensure proper cleanup.
self.__dirs_to_remove.append(working_directory)
# Location of the FEL source file.
source_input = TestUtilities.generateTestFilePath('FELsource_out')
# Photon source.
photon_source = XFELPhotonSource(parameters=None,
input_path=source_input,
output_path=source_dir)
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None,
input_path=source_dir,
output_path=prop_dir)
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=prop_dir,
output_path=pmi_dir,
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': 2,
'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_dir,
output_path=diffr_dir)
# 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=diffr_dir,
output_path=recon_dir)
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=None,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
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 ) )
'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,
'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()
def testHistory(self):
""" Testing that all generated output files contain the history """
# Setup directories.
working_directory = 'SPI'
self.__dirs_to_remove.append(working_directory)
source_dir = os.path.join(working_directory, 'FELsource')
prop_dir = os.path.join(working_directory, 'prop')
pmi_dir = os.path.join(working_directory, 'pmi')
diffr_dir = os.path.join(working_directory, 'diffr')
detector_dir = os.path.join(working_directory, 'detector')
recon_dir = os.path.join(working_directory, 'recon')
# Make directories.
os.mkdir(working_directory)
os.mkdir(source_dir)
os.mkdir(prop_dir)
os.mkdir(pmi_dir)
os.mkdir(diffr_dir)
os.mkdir(detector_dir)
os.mkdir(recon_dir)
# Location of the FEL source file.
source_input = TestUtilities.generateTestFilePath('FELsource_out')
# Photon source.
photon_source = XFELPhotonSource(parameters=None,
input_path=source_input,
output_path=source_dir)
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None,
input_path=source_dir,
output_path=prop_dir)
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=prop_dir,
output_path=pmi_dir,
sample_path=self.__sample_path)
# Diffraction with parameters.
diffraction_parameters = self.diffractorParam_2
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path=diffr_dir)
# 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': True,
'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=diffr_dir,
output_path=recon_dir)
# Perfect detector.
photon_detector = IdealPhotonDetector(parameters=None,
input_path='diffr',
output_path='detector')
# 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 histories.
# prop.
with h5py.File(os.path.join(prop_dir, 'prop_out_0000000.h5'),
'r') as prop_h5:
self.assertIn('history', list(prop_h5.keys()))
self.assertIn('parent', list(prop_h5['history'].keys()))
self.assertIn('detail', list(prop_h5['history/parent'].keys()))
self.assertIn('parent', list(prop_h5['history/parent'].keys()))
prop_h5.close()
# pmi.
with h5py.File(os.path.join(pmi_dir, 'pmi_out_0000001.h5'),
'r') as pmi_h5:
self.assertIn('history', list(pmi_h5.keys()))
self.assertIn('parent', list(pmi_h5['history'].keys()))
self.assertIn('detail', list(pmi_h5['history/parent'].keys()))
self.assertIn('parent', list(pmi_h5['history/parent'].keys()))
self.assertIn('detail',
list(pmi_h5['history/parent/parent'].keys()))
self.assertIn('parent',
list(pmi_h5['history/parent/parent'].keys()))
pmi_h5.close()
# diffr.
with h5py.File(os.path.join(diffr_dir, 'diffr_out_0000001.h5'),
'r') as diffr_h5:
tasks = list(diffr_h5['data'].keys())
for task in tasks:
self.assertIn('history', list(diffr_h5["data"][task].keys()))
self.assertIn('parent',
list(diffr_h5["data"][task]['history'].keys()))
self.assertIn(
'detail',
list(diffr_h5["data"][task]['history/parent'].keys()))
self.assertIn(
'parent',
list(diffr_h5["data"][task]['history/parent'].keys()))
self.assertIn(
'parent',
list(diffr_h5["data"][task]
['history/parent/parent'].keys()))
self.assertIn(
'detail',
list(diffr_h5["data"][task]
['history/parent/parent'].keys()))
self.assertIn(
'parent',
list(diffr_h5["data"][task]
['history/parent/parent/parent'].keys()))
self.assertIn(
'detail',
list(diffr_h5["data"][task]
['history/parent/parent/parent'].keys()))
diffr_h5.close()
# phase.
with h5py.File(os.path.join(recon_dir, 'phase_out.h5'), 'r') as dm_h5:
self.assertIn('history', list(dm_h5.keys()))
self.assertIn('error', list(dm_h5['history'].keys()))
self.assertIn('object', list(dm_h5['history'].keys()))
dm_h5.close()
def testSimS2EWorkflowDefaultPaths(self):
""" Testing that a workflow akin to the simS2E example workflow works. No IO paths specified. """
# These directories and files are expected to be present after a successfull calculation.
expected_dirs = [
'source_in',
'source',
'prop',
'pmi',
'diffr',
'analysis',
]
expected_files = [
'source/FELsource_out_0000000.h5',
'source/FELsource_out_0000001.h5',
'prop/prop_out_0000000.h5',
'prop/prop_out_0000001.h5',
'pmi/pmi_out_0000001.h5',
'pmi/pmi_out_0000002.h5',
'diffr/diffr_out_0000001.h5',
'analysis/orient_out.h5',
'analysis/phase_out.h5',
]
# Ensure proper cleanup.
self.__dirs_to_remove = expected_dirs
self.__files_to_remove.append('diffr.h5')
self.__files_to_remove.append('detector')
# Get proper FEL source files to start from.
shutil.copytree(TestUtilities.generateTestFilePath('FELsource_out'),
'source_in')
# Photon source.
photon_source = XFELPhotonSource(input_path='source_in')
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator()
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
sample_path=self.__sample_path)
# 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': 2,
'number_of_diffraction_patterns': 1,
'beam_parameter_file':
TestUtilities.generateTestFilePath('s2e.beam'),
'beam_geometry_file':
TestUtilities.generateTestFilePath('s2e.geom'),
'number_of_MPI_processes': 2
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'))
photon_diffractor.parameters.cpus_per_task = 1
# Reconstruction: EMC+DM
emc_parameters = {
'initial_number_of_quaternions': 1,
'max_number_of_quaternions': 2,
'max_number_of_iterations': 10,
'min_error': 1.0e-6,
'beamstop': True,
'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
})
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
# Check that all output files and directories are present.
for directory in expected_dirs:
print(directory)
self.assertTrue(os.path.isdir(directory))
for f in expected_files:
print(f)
self.assertTrue(os.path.isfile(f))
def testHistory(self):
""" Testing that all generated output files contain the history """
# Setup directories.
working_directory = "SPI"
self.__dirs_to_remove.append(working_directory)
source_dir = os.path.join(working_directory, "FELsource")
prop_dir = os.path.join(working_directory, "prop")
pmi_dir = os.path.join(working_directory, "pmi")
diffr_dir = os.path.join(working_directory, "diffr")
detector_dir = os.path.join(working_directory, "detector")
recon_dir = os.path.join(working_directory, "recon")
# Make directories.
os.mkdir(working_directory)
os.mkdir(source_dir)
os.mkdir(prop_dir)
os.mkdir(pmi_dir)
os.mkdir(diffr_dir)
os.mkdir(detector_dir)
os.mkdir(recon_dir)
# Location of the FEL source file.
source_input = TestUtilities.generateTestFilePath("FELsource_out")
# Photon source.
photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path=source_dir)
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None, input_path=source_dir, output_path=prop_dir)
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None, input_path=prop_dir, output_path=pmi_dir, sample_path=self.__sample_path
)
# 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": 2,
"number_of_diffraction_patterns": 2,
"beam_parameter_file": TestUtilities.generateTestFilePath("s2e.beam"),
"beam_geometry_file": TestUtilities.generateTestFilePath("s2e.geom"),
"number_of_MPI_processes": 2,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath("pmi_out"),
output_path=diffr_dir,
)
# 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": True,
"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=diffr_dir,
output_path=recon_dir,
)
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=None,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
# Check histories.
# prop.
with h5py.File(os.path.join(prop_dir, "prop_out_0000000.h5"), "r") as prop_h5:
self.assertIn("history", prop_h5.keys())
self.assertIn("parent", prop_h5["history"].keys())
self.assertIn("detail", prop_h5["history/parent"].keys())
self.assertIn("parent", prop_h5["history/parent"].keys())
prop_h5.close()
# pmi.
with h5py.File(os.path.join(pmi_dir, "pmi_out_0000001.h5"), "r") as pmi_h5:
self.assertIn("history", pmi_h5.keys())
self.assertIn("parent", pmi_h5["history"].keys())
self.assertIn("detail", pmi_h5["history/parent"].keys())
self.assertIn("parent", pmi_h5["history/parent"].keys())
self.assertIn("detail", pmi_h5["history/parent/parent"].keys())
self.assertIn("parent", pmi_h5["history/parent/parent"].keys())
pmi_h5.close()
# diffr.
with h5py.File(os.path.join(diffr_dir, "diffr_out_0000001.h5"), "r") as diffr_h5:
self.assertIn("history", diffr_h5.keys())
self.assertIn("parent", diffr_h5["history"].keys())
self.assertIn("detail", diffr_h5["history/parent"].keys())
self.assertIn("parent", diffr_h5["history/parent"].keys())
self.assertIn("parent", diffr_h5["history/parent/parent"].keys())
self.assertIn("detail", diffr_h5["history/parent/parent"].keys())
self.assertIn("parent", diffr_h5["history/parent/parent/parent"].keys())
self.assertIn("detail", diffr_h5["history/parent/parent/parent"].keys())
diffr_h5.close()
# phase.
with h5py.File(os.path.join(recon_dir, "phase_out.h5"), "r") as dm_h5:
self.assertIn("history", dm_h5.keys())
self.assertIn("error", dm_h5["history"].keys())
self.assertIn("object", dm_h5["history"].keys())
dm_h5.close()
def testSimS2EWorkflowDirectories(self):
""" Testing that a workflow akin to the simS2E example workflow works.
Two sources, two diffraction patterns."""
# Setup directories.
working_directory = 'SPI'
source_dir = os.path.join( working_directory, 'FELsource' )
prop_dir = os.path.join( working_directory, 'prop' )
pmi_dir = os.path.join( working_directory, 'pmi' )
diffr_dir = os.path.join( working_directory, 'diffr' )
detector_dir = os.path.join( working_directory, 'detector' )
recon_dir = os.path.join( working_directory, 'recon' )
# Make directories.
os.mkdir(working_directory)
os.mkdir(source_dir)
os.mkdir(prop_dir)
os.mkdir(pmi_dir)
os.mkdir(diffr_dir)
os.mkdir(detector_dir)
os.mkdir(recon_dir)
# Ensure proper cleanup.
self.__dirs_to_remove.append(working_directory)
# Location of the FEL source file.
source_input = TestUtilities.generateTestFilePath('FELsource_out')
# Photon source.
photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path=source_dir)
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None, input_path=source_dir, output_path=prop_dir)
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None,
input_path=prop_dir,
output_path=pmi_dir,
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' : 2,
'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_dir,
output_path=diffr_dir)
# 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=diffr_dir,
output_path = recon_dir
)
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=None,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
def testSimS2EWorkflowDirectories(self):
""" Testing that a workflow akin to the simS2E example workflow works.
Two sources, two diffraction patterns."""
# Setup directories.
working_directory = "SPI"
self.__dirs_to_remove.append(working_directory)
source_dir = os.path.join(working_directory, "FELsource")
prop_dir = os.path.join(working_directory, "prop")
pmi_dir = os.path.join(working_directory, "pmi")
diffr_dir = os.path.join(working_directory, "diffr")
detector_dir = os.path.join(working_directory, "detector")
recon_dir = os.path.join(working_directory, "recon")
# Make directories.
os.mkdir(working_directory)
os.mkdir(source_dir)
os.mkdir(prop_dir)
os.mkdir(pmi_dir)
os.mkdir(diffr_dir)
os.mkdir(detector_dir)
os.mkdir(recon_dir)
# Location of the FEL source file.
source_input = TestUtilities.generateTestFilePath("FELsource_out")
# Photon source.
photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path=source_dir)
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None, input_path=source_dir, output_path=prop_dir)
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None, input_path=prop_dir, output_path=pmi_dir, sample_path=self.__sample_path
)
# 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": 2,
"number_of_diffraction_patterns": 2,
"beam_parameter_file": TestUtilities.generateTestFilePath("s2e.beam"),
"beam_geometry_file": TestUtilities.generateTestFilePath("s2e.geom"),
"number_of_MPI_processes": 2,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath("pmi_out"),
output_path=diffr_dir,
)
# 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": True,
"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=diffr_dir,
output_path=recon_dir,
)
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=None,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
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_files = [
"FELsource_out.h5",
"prop_out.h5",
"pmi/pmi_out_0000001.h5",
"diffr/diffr_out_0000001.h5",
"orient_out.h5",
"recon.h5",
]
# Ensure proper cleanup.
self.__files_to_remove = expected_files
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=self.__sample_path
)
# 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"),
"number_of_MPI_processes": 2,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath("pmi_out"),
output_path="diffr",
)
# Reconstruction: EMC+DM
emc_parameters = {
"initial_number_of_quaternions": 1,
"max_number_of_quaternions": 2,
"max_number_of_iterations": 10,
"min_error": 1.0e-6,
"beamstop": True,
"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=TestUtilities.generateTestFilePath(
"diffr"
), # Cheeting here to provide more realistic data for emc.
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=None,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
# Check that all output files and directories are present.
for directory in expected_dirs:
self.assertTrue(os.path.isdir(directory))
for f in expected_files:
print f
self.assertTrue(os.path.isfile(f))
def testSimS2EWorkflowDefaultPaths(self):
""" Testing that a workflow akin to the simS2E example workflow works. No IO paths specified. """
# These directories and files are expected to be present after a successfull calculation.
expected_dirs = ["source_in", "source", "prop", "pmi", "diffr", "analysis"]
expected_files = [
"source/FELsource_out_0000000.h5",
"source/FELsource_out_0000001.h5",
"prop/prop_out_0000000.h5",
"prop/prop_out_0000001.h5",
"pmi/pmi_out_0000001.h5",
"pmi/pmi_out_0000002.h5",
"diffr/diffr_out_0000001.h5",
"diffr/diffr_out_0000002.h5",
"diffr.h5",
"detector",
"analysis/orient_out.h5",
"analysis/phase_out.h5",
]
# Ensure proper cleanup.
self.__dirs_to_remove = expected_dirs
self.__files_to_remove.append("diffr.h5")
self.__files_to_remove.append("detector")
# Get proper FEL source files to start from.
shutil.copytree(TestUtilities.generateTestFilePath("FELsource_out"), "source_in")
# Photon source.
photon_source = XFELPhotonSource(input_path="source_in")
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator()
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(sample_path=self.__sample_path)
# 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": 2,
"number_of_diffraction_patterns": 1,
"beam_parameter_file": TestUtilities.generateTestFilePath("s2e.beam"),
"beam_geometry_file": TestUtilities.generateTestFilePath("s2e.geom"),
"number_of_MPI_processes": 2,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters, input_path=TestUtilities.generateTestFilePath("pmi_out")
)
# Reconstruction: EMC+DM
emc_parameters = {
"initial_number_of_quaternions": 1,
"max_number_of_quaternions": 2,
"max_number_of_iterations": 10,
"min_error": 1.0e-6,
"beamstop": True,
"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})
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
# Check that all output files and directories are present.
for directory in expected_dirs:
print directory
self.assertTrue(os.path.isdir(directory))
for f in expected_files:
print f
self.assertTrue(os.path.isfile(f))
