def testDataInterfaceQueries(self):
""" Check that the data interface queries work. """
# Get test instance.G
# Setup pmi parameters.
pmi_parameters = {
'number_of_trajectories': 1,
'number_of_steps': 100,
'sample_path': TestUtilities.generateTestFilePath('sample.h5')
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi_out.h5',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Get expected and provided data descriptors.
expected_data = test_interactor.expectedData()
provided_data = test_interactor.providedData()
# Check types are correct.
self.assertIsInstance(expected_data, list)
self.assertIsInstance(provided_data, list)
for d in expected_data:
self.assertIsInstance(d, str)
self.assertEqual(d[0], '/')
for d in provided_data:
self.assertIsInstance(d, str)
self.assertEqual(d[0], '/')
def testRotationRandom(self):
""" Check that by default no rotation is applied and that random rotation has an effect."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 1,
'number_of_steps': 100,
'random_rotation': True,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
# Check rotation angle.
with h5py.File(
os.path.join(test_interactor.output_path,
'pmi_out_0000001.h5'), 'r') as h5:
angle = h5['data/angle'].value[0]
# Check we have a non-zero rotation.
self.assertNotEqual(numpy.linalg.norm(angle), 0.)
def testIssue53(self):
""" Check that xmdyn_demo writes the Nph variable according to bugfix 53."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 10,
'number_of_steps': 100,
}
pmi = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('2nip.pdb'))
# Call backengine
status = pmi.backengine()
h5 = h5py.File('pmi/pmi_out_0000001.h5')
Nph = h5['/data/snp_0000001/Nph']
self.assertEqual(Nph.shape, (1, ))
def testBackengine(self):
""" Check that the backengine method works correctly. """
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {'number_of_trajectories' : 1,
'number_of_steps' : 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path = TestUtilities.generateTestFilePath('sample.h5') )
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
self.assertTrue( 'pmi_out_0000001.h5' in os.listdir( test_interactor.output_path ) )
def testBackengine(self):
""" Check that the backengine method works correctly. """
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 1,
'number_of_steps': 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
self.assertTrue(
'pmi_out_0000001.h5' in os.listdir(test_interactor.output_path))
def testDataInterfaceQueries(self):
""" Check that the data interface queries work. """
# Get test instance.
# Setup pmi parameters.
pmi_parameters = {'number_of_trajectories' : 1,
'number_of_steps' : 100,
'sample_path' : TestUtilities.generateTestFilePath('sample.h5')
}
test_interactor = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi_out.h5',
sample_path = TestUtilities.generateTestFilePath('sample.h5') )
# Get expected and provided data descriptors.
expected_data = test_interactor.expectedData()
provided_data = test_interactor.providedData()
# Check types are correct.
self.assertIsInstance(expected_data, list)
self.assertIsInstance(provided_data, list)
for d in expected_data:
self.assertIsInstance(d, str)
self.assertEqual(d[0], '/')
for d in provided_data:
self.assertIsInstance(d, str)
self.assertEqual(d[0], '/')
def testRotationNone(self):
""" Check that by default no rotation is applied and that random rotation has an effect."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 1,
'number_of_steps': 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
# Check rotation angle.
with h5py.File(
os.path.join(test_interactor.output_path,
'pmi_out_0000001.h5'), 'r') as h5:
angle = h5['data/angle'].value
self.assertEqual(angle[0, 0], 0.)
self.assertEqual(angle[0, 1], 0.)
self.assertEqual(angle[0, 2], 0.)
self.assertEqual(angle[0, 3], 0.)
# Get atom positions.
atom_positions = h5['data/snp_0000001/r'].value
# Now do same calculation again.
test_interactor.backengine()
# Get atom positions from new calculation.
with h5py.File(
os.path.join(test_interactor.output_path,
'pmi_out_0000001.h5'), 'r') as h5:
new_atom_positions = h5['data/snp_0000001/r'].value
# They should coincide since no rotation has been applied.
self.assertAlmostEqual(
1e10 * numpy.linalg.norm(atom_positions - new_atom_positions), 0.0,
7)
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 testDefaultConstruction(self):
""" Testing the default construction of the class. """
# Construct the object.
interactor = XMDYNDemoPhotonMatterInteractor(
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
self.assertIsInstance(interactor, XMDYNDemoPhotonMatterInteractor)
def testConstruction(self):
""" Testing the default construction of the class. """
# Construct the object.
diffractor = XMDYNDemoPhotonMatterInteractor(parameters=None,
input_path=self.input_h5,
output_path='pmi')
self.assertIsInstance(diffractor, XMDYNDemoPhotonMatterInteractor)
def testDataInterfaceQueries(self):
""" Check that the data interface queries work. """
# Get test instance.
test_interactor = XMDYNDemoPhotonMatterInteractor(parameters=None, input_path=self.input_h5, output_path='pmi_out.h5')
# Get expected and provided data descriptors.
expected_data = test_interactor.expectedData()
provided_data = test_interactor.providedData()
# Check types are correct.
self.assertIsInstance(expected_data, list)
self.assertIsInstance(provided_data, list)
for d in expected_data:
self.assertIsInstance(d, str)
self.assertEqual(d[0], '/')
for d in provided_data:
self.assertIsInstance(d, str)
self.assertEqual(d[0], '/')
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 testBackengineDefaultPaths(self):
""" Check that the backengine method works correctly. """
# Prepare input.
shutil.copytree( TestUtilities.generateTestFilePath('prop_out'), os.path.abspath( 'prop' ) )
self.__dirs_to_remove.append( 'prop' )
self.__dirs_to_remove.append( 'pmi' )
test_interactor = XMDYNDemoPhotonMatterInteractor(sample_path=TestUtilities.generateTestFilePath('sample.h5') )
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
self.assertTrue( os.path.isdir( os.path.abspath( 'prop' ) ) )
self.assertIn( 'pmi_out_0000001.h5' , os.listdir( test_interactor.output_path ) )
self.assertIn( 'pmi_out_0000002.h5' , os.listdir( test_interactor.output_path ) )
def testLoadPDBFile(self):
""" Check that the sample can be taken from a pdb directly. """
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {'number_of_trajectories' : 10,
'number_of_steps' : 100,
}
pmi = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('2nip.pdb') )
# Call backengine
status = pmi.backengine()
self.assertEqual(status, 0 )
def testOPMD(self):
""" Check that the input directory scanner filters out the opmd files."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Setup parameters.
pmi_parameters = {'number_of_trajectories' : 10,
'number_of_steps' : 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=TestUtilities.generateTestFilePath('prop_out'),
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5') )
# Call backengine
status = test_interactor.backengine()
self.assertEqual(status, 0 )
def reference2NIP(self):
""" Testing that diffraction intensities with 9fs 5keV pulses through SPB-SFX KB beamline are of the order of Yoon 2016. """
source_file = "/data/netapp/grotec/datadump/5keV_9fs_2015_slice12_fromYoon2016.h5"
#source_file = TestUtilities.generateTestFilePath("FELsource_out.h5")
# Propagate
propagator = XFELPhotonPropagator(parameters=None,
input_path=source_file,
output_path="prop_out.h5")
propagator.backengine()
propagator.saveH5()
pmi = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=propagator.output_path,
output_path="pmi",
sample_path=TestUtilities.generateTestFilePath("sample.h5"))
pmi.backengine()
# Diffraction with parameters.
diffraction_parameters = {
'uniform_rotation': True,
'calculate_Compton': False,
'slice_interval': 100,
'number_of_slices': 100,
'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': 8,
}
diffractor = SingFELPhotonDiffractor(parameters=diffraction_parameters,
input_path=pmi.output_path,
output_path="diffr_out.h5")
diffractor.backengine()
def testDataInterfaceQueries(self):
""" Check that the data interface queries work. """
# Get test instance.
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=self.input_h5,
output_path='pmi_out.h5')
# Get expected and provided data descriptors.
expected_data = test_interactor.expectedData()
provided_data = test_interactor.providedData()
# Check types are correct.
self.assertIsInstance(expected_data, list)
self.assertIsInstance(provided_data, list)
for d in expected_data:
self.assertIsInstance(d, str)
self.assertEqual(d[0], '/')
for d in provided_data:
self.assertIsInstance(d, str)
self.assertEqual(d[0], '/')
def testLoadPDBFile(self):
""" Check that the sample can be taken from a pdb directly. """
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 10,
'number_of_steps': 100,
}
pmi = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('2nip.pdb'))
# Call backengine
status = pmi.backengine()
self.assertEqual(status, 0)
def testOPMD(self):
""" Check that the input directory scanner filters out the opmd files."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Setup parameters.
pmi_parameters = {
'number_of_trajectories': 10,
'number_of_steps': 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=TestUtilities.generateTestFilePath('prop_out'),
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
self.assertEqual(status, 0)
def testIssue53(self):
""" Check that xmdyn_demo writes the Nph variable according to bugfix 53."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {'number_of_trajectories' : 10,
'number_of_steps' : 100,
}
pmi = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('2nip.pdb') )
# Call backengine
status = pmi.backengine()
h5 = h5py.File('pmi/pmi_out_0000001.h5')
Nph = h5['/data/snp_0000001/Nph']
self.assertEqual(Nph.shape, (1,))
def testBackengineDefaultPaths(self):
""" Check that the backengine method works correctly. """
# Prepare input.
shutil.copytree(TestUtilities.generateTestFilePath('prop_out'),
os.path.abspath('prop'))
self.__dirs_to_remove.append('prop')
self.__dirs_to_remove.append('pmi')
test_interactor = XMDYNDemoPhotonMatterInteractor(
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
self.assertTrue(os.path.isdir(os.path.abspath('prop')))
self.assertIn('pmi_out_0000001.h5',
os.listdir(test_interactor.output_path))
self.assertIn('pmi_out_0000002.h5',
os.listdir(test_interactor.output_path))
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_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 testShapedConstruction(self):
""" Testing the construction of the class with parameters. """
# Setup pmi parameters.
pmi_parameters = {
'number_of_trajectories': 1,
'number_of_steps': 100,
}
interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
output_path='pmi_out',
input_path='pmi_in',
sample_path=TestUtilities.generateTestFilePath('sample.h5'),
)
self.assertIsInstance(interactor, XMDYNDemoPhotonMatterInteractor)
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)
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))
from SimEx.PhotonExperimentSimulation.PhotonExperimentSimulation import PhotonExperimentSimulation
# 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_0000001.h5')
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out_0000001.h5', output_path='prop_out_0000001.h5')
# Photon interactor with default parameters.
pmi_parameters= {'sample_path' :TestUtilities.generateTestFilePath('sample.h5')}
photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=pmi_parameters,
input_path='prop_out_0000001.h5',
output_path='pmi')
# Diffraction with parameters.
diffraction_parameters={ 'uniform_rotation': 1,
'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(
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 = 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 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_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')
# 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,
)
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_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')
# 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,
)
'FELsource_out/FELsource_out_0000001.h5')
# Photon source.
photon_source = XFELPhotonSource(parameters=None,
input_path=source_input,
output_path='FELsource_out_0000001.h5')
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None,
input_path='FELsource_out_0000001.h5',
output_path='prop_out_0000001.h5')
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path='prop_out_0000001.h5',
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Diffraction with parameters.
diffraction_parameters = {
'uniform_rotation': 1,
'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'),
}
import sys
from SimEx.Calculators.XMDYNDemoPhotonMatterInteractor import XMDYNDemoPhotonMatterInteractor
# Define the input path (location of propagated pulse data).
prop_path = "prop_out/prop_s2e_example.h5"
# Define the sample as pdb code + ".pdb" extension.
sample="2NIP.pdb"
# Setup propagation parameters.
parameters=None
# Construct the propagator
pmi_calculator = XMDYNDemoPhotonMatterInteractor( parameters=parameters, input_path=prop_path,
sample_path=sample)
# Read the data.
pmi_calculator._readH5()
# Call the backengine.
status = pmi_calculator.backengine()
if status != 0:
print("PMI calculation failed, check output.")
sys.exit()
print("PMI calculation succeeded.")
