def testBackengineAutoMPICommand(self):
""" Test that we can start a test calculation. """
# Cleanup.
self.__dirs_to_remove.append('diffr')
parameters = SingFELPhotonDiffractorParameters(
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_parameters=self.beam,
detector_geometry=self.detector_geometry,
)
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path=self.input_h5,
output_path='diffr')
# Call backengine.
status = diffractor.backengine()
# Check successful completion.
self.assertEqual(status, 0)
def testBackengineInputDir(self):
""" Test that we can start a test calculation if the input path is a directory. """
# Cleanup.
self.__dirs_to_remove.append('diffr')
parameters = SingFELPhotonDiffractorParameters(
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,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun -np 2',
)
# Construct the object.
diffractor = SingFELPhotonDiffractor(
parameters=parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr')
# Call backengine.
status = diffractor.backengine()
# Check successful completion.
self.assertEqual(status, 0)
def testBackengineInputDir(self):
""" Test that we can start a test calculation if the input path is a directory. """
# Cleanup.
self.__dirs_to_remove.append('diffr')
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,
}
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters, input_path=TestUtilities.generateTestFilePath('pmi_out'), output_path='diffr')
# Call backengine.
status = diffractor.backengine()
# Check successful completion.
self.assertEqual(status, 0)
def testBackengineInputDir(self):
""" Test that we can start a test calculation if the input path is a directory. """
# Cleanup.
self.__dirs_to_remove.append('diffr')
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'),
}
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path=os.path.dirname(
self.input_h5),
output_path='diffr')
# Call backengine.
status = diffractor.backengine()
# Check successful completion.
self.assertEqual(status, 0)
def testBackengineDefaultPaths(self):
""" Test that we can start a calculation with default paths given. """
# Prepare input.
shutil.copytree( TestUtilities.generateTestFilePath( 'pmi_out' ), os.path.abspath( 'pmi' ) )
# Ensure proper cleanup.
self.__dirs_to_remove.append( os.path.abspath( 'pmi') )
self.__dirs_to_remove.append( os.path.abspath( 'diffr' ) )
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,
}
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters)
# Call backengine.
status = diffractor.backengine()
# Check successful completion.
self.assertEqual(status, 0)
# Check expected files exist.
self.assertTrue( os.path.isdir( os.path.abspath( 'diffr' ) ) )
self.assertIn( 'diffr_out_0000001.h5', os.listdir( os.path.abspath( 'diffr' ) ) )
self.assertIn( 'diffr_out_0000002.h5', os.listdir( os.path.abspath( 'diffr' ) ) )
def testDefaultConstructionLegacy(self):
""" Testing the default construction of the class with MPI parameter. """
# Prepare input.
shutil.copytree(TestUtilities.generateTestFilePath('pmi_out'),
os.path.abspath('pmi'))
# Ensure proper cleanup.
self.__dirs_to_remove.append(os.path.abspath('pmi'))
self.__dirs_to_remove.append(os.path.abspath('diffr'))
# Set up parameters.
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_parameters': None,
'detector_geometry': self.detector_geometry,
'number_of_MPI_processes': 2,
}
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path='pmi')
# Check type.
self.assertIsInstance(diffractor, SingFELPhotonDiffractor)
# Check default output_path.
self.assertEqual(diffractor.output_path, os.path.abspath('diffr'))
def testDefaultConstructionLegacy(self):
""" Testing the default construction of the class with MPI parameter. """
# Prepare input.
shutil.copytree(TestUtilities.generateTestFilePath('pmi_out'),
os.path.abspath('pmi'))
# Ensure proper cleanup.
self.__dirs_to_remove.append(os.path.abspath('pmi'))
self.__dirs_to_remove.append(os.path.abspath('diffr'))
# Set up parameters.
parameters = SingFELPhotonDiffractorParameters(
sample=None,
uniform_rotation=False,
calculate_Compton=False,
slice_interval=100,
number_of_slices=3,
pmi_start_ID=1,
pmi_stop_ID=1,
number_of_diffraction_patterns=2,
beam_parameters=self.beam,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun -np 2',
)
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path='pmi')
# Check type.
self.assertIsInstance(diffractor, SingFELPhotonDiffractor)
# Check default output_path.
self.assertEqual(diffractor.output_path, os.path.abspath('diffr'))
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 testConstructionWithSample(self):
""" Testing the construction with sample passed via parameters."""
# Ensure proper cleanup.
sample_file = TestUtilities.generateTestFilePath('2nip.pdb')
self.__dirs_to_remove.append(os.path.abspath('diffr'))
# Set up parameters.
parameters = SingFELPhotonDiffractorParameters(
sample=sample_file,
uniform_rotation=False,
calculate_Compton=False,
slice_interval=100,
number_of_slices=5,
pmi_start_ID=1,
pmi_stop_ID=1,
number_of_diffraction_patterns=1,
beam_parameters=self.beam,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun')
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters)
self.assertIsInstance(diffractor, SingFELPhotonDiffractor)
self.assertEqual(diffractor.input_path, os.path.abspath(sample_file))
self.assertEqual(diffractor.output_path, os.path.abspath('diffr'))
def testSingleFile(self):
""" Test that saveH5() generates only one linked hdf. """
diffraction_parameters={ 'uniform_rotation': True,
'calculate_Compton' : True,
'slice_interval' : 100,
'number_of_slices' : 2,
'pmi_start_ID' : 1,
'pmi_stop_ID' : 4,
'number_of_diffraction_patterns' : 2,
'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'),
'beam_geometry_file' : TestUtilities.generateTestFilePath('s2e.geom'),
'number_of_MPI_processes' : 8,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr_newstyle')
# Cleanup.
self.__dirs_to_remove.append(photon_diffractor.output_path)
# Run backengine and convert files.
photon_diffractor.backengine()
photon_diffractor.saveH5()
# Cleanup new style files.
self.__files_to_remove.append(photon_diffractor.output_path)
# Check that only one file was generated.
self.assertTrue( os.path.isfile( photon_diffractor.output_path ))
# Open the file for reading.
h5_filehandle = h5py.File( photon_diffractor.output_path, 'r')
# Count groups under /data.
number_of_patterns = len(h5_filehandle.keys()) - 3
self.assertEqual( number_of_patterns, 8 )
# Assert global metadata is present.
self.assertIn("params", h5_filehandle.keys() )
self.assertIn("version", h5_filehandle.keys() )
self.assertIn("info", h5_filehandle.keys() )
self.assertIn("geom", h5_filehandle["params"].keys() )
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 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 testBug53(self):
""" Tests a script that was found to raise if run in parallel mode. """
self.__dirs_to_remove.append('diffr')
diffraction_parameters = SingFELPhotonDiffractorParameters(
uniform_rotation=True,
calculate_Compton=True,
slice_interval=100,
number_of_slices=2,
pmi_start_ID=1,
pmi_stop_ID=9,
number_of_diffraction_patterns=1,
detector_geometry=self.detector_geometry,
)
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr')
photon_diffractor.backengine()
def testBackengineWithSample(self):
""" Test that we can start a test calculation if the sample was given via the parameters . """
# Cleanup.
sample_file = TestUtilities.generateTestFilePath('2nip.pdb')
self.__dirs_to_remove.append('diffr')
# Make sure sample file does not exist.
if sample_file in os.listdir(os.getcwd()):
os.remove(sample_file)
parameters = SingFELPhotonDiffractorParameters(
sample=sample_file,
uniform_rotation=False,
calculate_Compton=False,
number_of_diffraction_patterns=2,
beam_parameters=self.beam,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun -np 2 -x OMP_NUM_THREADS=2',
)
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path=None,
output_path='diffr')
# Call backengine.
status = diffractor.backengine()
# Check successful completion.
self.assertEqual(status, 0)
# Check expected files exist.
self.assertTrue(os.path.isdir(os.path.abspath('diffr')))
self.assertIn('diffr_out_0000001.h5',
os.listdir(diffractor.output_path))
self.assertIn('diffr_out_0000002.h5',
os.listdir(diffractor.output_path))
def testBug53(self):
""" Tests a script that was found to raise if run in parallel mode. """
self.__dirs_to_remove.append('diffr')
diffraction_parameters={ 'uniform_rotation': True,
'calculate_Compton' : True,
'slice_interval' : 100,
'number_of_slices' : 2,
'pmi_start_ID' : 1,
'pmi_stop_ID' : 9,
'number_of_diffraction_patterns' : 1,
'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'),
'beam_geometry_file' : TestUtilities.generateTestFilePath('s2e.geom'),
'number_of_MPI_processes' : 10,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr')
photon_diffractor.backengine()
def testH5Output(self):
""" Test that data, params and misc are present in hdf5 output file. """
# Ensure proper cleanup.
sample_file = TestUtilities.generateTestFilePath('2nip.pdb')
self.__dirs_to_remove.append(os.path.abspath('diffr'))
self.__files_to_remove.append(os.path.abspath('diffr.h5'))
# Set up parameters.
parameters = SingFELPhotonDiffractorParameters(
sample=sample_file,
uniform_rotation=False,
calculate_Compton=False,
slice_interval=100,
number_of_slices=3,
pmi_start_ID=1,
pmi_stop_ID=1,
number_of_diffraction_patterns=2,
beam_parameters=self.beam,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun -np 2',
)
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters)
# Run and save.
diffractor.backengine()
diffractor.saveH5()
# Examine content of results hdf.
with h5py.File(diffractor.output_path, 'r') as h5:
# Datagroups in /"
self.assertIn("data", h5.keys())
self.assertIn("params", h5.keys())
self.assertIn("misc", h5.keys())
# Data.
data = h5["data"]
self.assertIn("0000001", data.keys())
# Parameters
params = h5["params"]
self.assertIn("beam", params.keys())
self.assertIn("geom", params.keys())
# Beam
beam = h5["params/beam"]
self.assertIn("focusArea", beam.keys())
self.assertIn("photonEnergy", beam.keys())
# Geometry
geom = h5["params/geom"]
self.assertIn("detectorDist", geom.keys())
self.assertIn("mask", geom.keys())
self.assertIn("pixelHeight", geom.keys())
self.assertIn("pixelWidth", geom.keys())
def testBackengineDefaultPaths(self):
""" Test that we can start a calculation with default paths given. """
# Prepare input.
shutil.copytree(TestUtilities.generateTestFilePath('pmi_out'),
os.path.abspath('pmi'))
# Ensure proper cleanup.
self.__dirs_to_remove.append(os.path.abspath('pmi'))
self.__dirs_to_remove.append(os.path.abspath('diffr'))
parameters = SingFELPhotonDiffractorParameters(
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,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun -np 2',
)
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path='pmi')
# Call backengine.
status = diffractor.backengine()
# Check successful completion.
self.assertEqual(status, 0)
# Check expected files exist.
self.assertTrue(os.path.isdir(os.path.abspath('diffr')))
self.assertIn('diffr_out_0000001.h5',
os.listdir(os.path.abspath('diffr')))
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 testConstructionParameters(self):
""" Check we can construct with a parameter object. """
parameters = SingFELPhotonDiffractorParameters(
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_parameters=self.beam,
detector_geometry=self.detector_geometry,
)
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path=self.input_h5,
output_path='diffr_out.h5')
# Check instance.
self.assertIsInstance(diffractor, SingFELPhotonDiffractor)
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 testSingleFile(self):
""" Test that saveH5() generates only one linked hdf. """
parameters = SingFELPhotonDiffractorParameters(
sample=None,
uniform_rotation=False,
calculate_Compton=False,
slice_interval=100,
number_of_slices=3,
pmi_start_ID=1,
pmi_stop_ID=1,
number_of_diffraction_patterns=8,
beam_parameters=self.beam,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun -np 8',
)
photon_diffractor = SingFELPhotonDiffractor(
parameters=parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr_newstyle')
# Cleanup.
self.__dirs_to_remove.append(photon_diffractor.output_path)
# Run backengine and convert files.
photon_diffractor.backengine()
photon_diffractor.saveH5()
linked_h5 = photon_diffractor.output_path + '.h5'
# Cleanup new style files.
self.__files_to_remove.append(linked_h5)
# Check that only one file was generated.
self.assertTrue(os.path.isfile(linked_h5))
# Open the file for reading.
h5_filehandle = h5py.File(linked_h5, 'r')
# Count groups under /data.
number_of_patterns = len(list(h5_filehandle['data'].keys()))
self.assertEqual(number_of_patterns, 8)
# Assert global metadata is present.
self.assertIn("params", list(h5_filehandle.keys()))
self.assertIn("version", list(h5_filehandle.keys()))
self.assertIn("info", list(h5_filehandle.keys()))
def testShapedConstructionDict(self):
""" Testing the construction of the class with parameters given as a dict. """
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_parameters': self.beam,
'detector_geometry': self.detector_geometry,
}
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path=self.input_h5,
output_path='diffr_out.h5')
self.assertIsInstance(diffractor, SingFELPhotonDiffractor)
def testShapedConstructionDict(self):
""" Testing the construction of the class with parameters given as a dict. """
parameters = SingFELPhotonDiffractorParameters(
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_parameters=self.beam,
detector_geometry=self.detector_geometry,
)
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path=self.input_h5,
output_path='diffr_out.h5')
self.assertIsInstance(diffractor, SingFELPhotonDiffractor)
def testSingleFile(self):
""" Test that saveH5() generates only one linked hdf. """
diffraction_parameters = {
'uniform_rotation': True,
'calculate_Compton': True,
'slice_interval': 100,
'number_of_slices': 2,
'pmi_start_ID': 1,
'pmi_stop_ID': 4,
'number_of_diffraction_patterns': 2,
'beam_parameters': None,
'detector_geometry': self.detector_geometry,
'number_of_MPI_processes': 8,
}
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr_newstyle')
# Cleanup.
self.__dirs_to_remove.append(photon_diffractor.output_path)
# Run backengine and convert files.
photon_diffractor.backengine()
photon_diffractor.saveH5()
# Cleanup new style files.
self.__files_to_remove.append(photon_diffractor.output_path)
# Check that only one file was generated.
self.assertTrue(os.path.isfile(photon_diffractor.output_path))
# Open the file for reading.
h5_filehandle = h5py.File(photon_diffractor.output_path, 'r')
# Count groups under /data.
number_of_patterns = len(h5_filehandle['data'].keys())
self.assertEqual(number_of_patterns, 8)
# Assert global metadata is present.
self.assertIn("params", h5_filehandle.keys())
self.assertIn("version", h5_filehandle.keys())
self.assertIn("info", h5_filehandle.keys())
def testConstruction(self):
""" Testing the default construction of the class. """
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'),
}
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path=self.input_h5,
output_path='diffr_out.h5')
self.assertIsInstance(diffractor, SingFELPhotonDiffractor)
def testConstructionExceptions(self):
""" Check that proper exceptions are thrown if object is constructed incorrectly. """
# Parameter not a dict.
self.assertRaises(TypeError, SingFELPhotonDiffractor, 1, self.input_h5,
'diffr.h5')
# Setup parameters that are ok
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'),
}
# Check construction with sane parameters.
singfel = SingFELPhotonDiffractor(parameters, self.input_h5,
'diffr.h5')
self.assertIsInstance(singfel, SingFELPhotonDiffractor)
# uniform_rotation not a bool.
parameters['uniform_rotation'] = 1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# Reset.
parameters['uniform_rotation'] = True
# calculate_Compton not a bool.
parameters['calculate_Compton'] = 1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# Reset.
parameters['calculate_Compton'] = False
# slice_interval not positive integer.
parameters['slice_interval'] = -1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# slice_interval not a number
parameters['slice_interval'] = 'one'
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# Reset.
parameters['slice_interval'] = 1
# number_of_slices not positive integer.
parameters['number_of_slices'] = -1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# number_of_slices not a number
parameters['number_of_slices'] = 'one'
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# Reset.
parameters['number_of_slices'] = 2
# number_of_diffraction_patterns not positive integer.
parameters['number_of_diffraction_patterns'] = -1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# number_of_diffraction_patterns not a number
parameters['number_of_diffraction_patterns'] = 'one'
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# Reset.
parameters['number_of_diffraction_patterns'] = 2
# pmi_start_ID not positive integer.
parameters['pmi_start_ID'] = -1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# pmi_start_ID not a number
parameters['pmi_start_ID'] = 'one'
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# Reset.
parameters['pmi_start_ID'] = 1
# pmi_stop_ID not positive integer.
parameters['pmi_stop_ID'] = -1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# pmi_stop_ID not a number
parameters['pmi_stop_ID'] = 'one'
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# Reset.
parameters['pmi_stop_ID'] = 1
# beam_parameter_file not a string.
parameters['beam_parameter_file'] = 1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# beam_parameter_file not a file.
parameters['beam_parameter_file'] = 's2e.beam'
self.assertRaises(IOError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
parameters['beam_parameter_file'] = TestUtilities.generateTestFilePath(
's2e.beam')
# beam_geometry_file not a string.
parameters['beam_geometry_file'] = 1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# beam_geometry_file not a file.
parameters['beam_geometry_file'] = 's2e.geom'
self.assertRaises(IOError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
parameters['beam_geometry_file'] = TestUtilities.generateTestFilePath(
's2e.geom'),
# Unknown parameter name.
parameters['number_of_nonexisting_parameter'] = 3
self.assertRaises(RuntimeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.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'),
}
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
def testReference(self, debug=False):
""" Check that singfel reproduces a given set of reference data. """
self.__dirs_to_remove.append('diffr')
beam_file = TestUtilities.generateTestFilePath('s2e.beam')
geom_file = TestUtilities.generateTestFilePath('s2e.geom')
# Setup diffraction parameters (no rotation because reference test).
parameters = SingFELPhotonDiffractorParameters(
uniform_rotation=False,
calculate_Compton=True,
slice_interval=100,
number_of_slices=100,
pmi_start_ID=1,
pmi_stop_ID =1,
number_of_diffraction_patterns=1,
beam_parameter_file=beam_file,
beam_geometry_file=geom_file,
number_of_MPI_processes=2,
)
# Setup diffraction calculator.
diffractor = SingFELPhotonDiffractor(
parameters=parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr'
)
# Run (reads input and write output, as well).
diffractor.backengine()
# Open results file.
h5_handle = h5py.File(os.path.join(diffractor.output_path,'diffr_out_0000001.h5'),'r')
# Get data (copy).
diffraction_data = h5_handle['/data/diffr'].value
h5_handle.close()
# Get total intensity.
intensity = diffraction_data.sum()
# Get hash of the data.
this_hash = hash( diffraction_data.tostring() )
if debug:
print "%15.14e" % (intensity)
# Save wavefront data for reference.
#########################################################################################
## ATTENTION: Overwrites reference data, use only if you're sure you want to do this. ###
#########################################################################################
#with open(TestUtilities.generateTestFilePath("singfel_reference.hash.txt"), 'w') as hashfile:
#hashfile.write(str(this_hash))
#hashfile.close()
#########################################################################################
self.assertEqual(math.pi, 22./7.)
# Load reference hash.
with open( TestUtilities.generateTestFilePath("singfel_reference.hash.txt"), 'r') as hashfile:
ref_hash = hashfile.readline()
hashfile.close()
# Weak test.
reference_intensity = '5.18647193908691e+01'
self.assertEqual( "%15.14e" % (intensity), reference_intensity)
# Strong test.
self.assertEqual( ref_hash, str(this_hash) )
def plot_diffr_vs_detector(self):
""" Compare patterns before and after detector sim. """
# Cleanup.
#self.__files_to_remove.append('5mzd.pdb')
#self.__files_to_remove.append('diffr.h5')
#self.__dirs_to_remove.append('diffr')
# Avoid crash due to multiple instances of G4RunManager
del self._detector
# Setup detector geometry.
detector_panel = DetectorPanel(
ranges={
'fast_scan_min': 0,
'fast_scan_max': 511,
'slow_scan_min': 0,
'slow_scan_max': 511
},
pixel_size=2.2e-4 * Units.meter,
photon_response=1.0,
distance_from_interaction_plane=0.13 * Units.meter,
corners={
'x': -256,
'y': -256
},
)
detector_geometry = DetectorGeometry(panels=[detector_panel])
# Setup photon beam.
beam = PhotonBeamParameters(
photon_energy=4.96e3 * Units.electronvolt,
beam_diameter_fwhm=1.0e-6 * Units.meter,
pulse_energy=1.0e-3 * Units.joule,
photon_energy_relative_bandwidth=0.001,
divergence=1e-3 * Units.radian,
photon_energy_spectrum_type="SASE",
)
# Setup and run the diffraction sim.
diffraction_parameters = SingFELPhotonDiffractorParameters(
uniform_rotation=None,
calculate_Compton=False,
number_of_diffraction_patterns=1,
detector_geometry=detector_geometry,
beam_parameters=beam,
sample="5mzd.pdb",
forced_mpi_command='mpirun -np 1',
)
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
output_path='diffr',
)
photon_diffractor.backengine()
photon_diffractor.saveH5()
analysis1 = DiffractionAnalysis(photon_diffractor.output_path,
pattern_indices=[1],
poissonize=True)
analysis1.plotPattern(
operation=None,
logscale=False,
)
parameters = XCSITPhotonDetectorParameters(
detector_type="AGIPDSPB",
patterns=[0],
)
detector = XCSITPhotonDetector(
parameters=parameters,
input_path="diffr.h5",
output_path="detector_out.h5",
)
detector._readH5()
detector.backengine()
detector.saveH5()
# Weak test Check we have photons in the signal.
pattern = h5py.File("detector_out.h5", 'r')['data/0000001/data'].value
analysis2 = DiffractionAnalysis(detector.output_path,
pattern_indices=[1],
poissonize=True)
analysis2.plotPattern(
operation=None,
logscale=False,
)
mpl.pyplot.show()
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 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,
)
