beam_diameter_fwhm=226.0e-9 * meter, #sqrt(250*160/pi)*2
pulse_energy=4.0e-3 * joule,
)
diffraction_parameters = SingFELPhotonDiffractorParameters(
uniform_rotation=True,
calculate_Compton=False,
number_of_diffraction_patterns=36,
detector_geometry=detector_geometry,
beam_parameters=beam,
forced_mpi_command='mpirun -np 36')
out_path = "diffr"
cleanUp(out_path)
diffractor = SingFELPhotonDiffractor(parameters=diffraction_parameters,
input_path='./4V7V.pdb',
output_path=out_path)
from timeit import default_timer as timer
start = timer()
diffractor.backengine()
end = timer()
print(end - start, 's') # Time in seconds
# Link the .h5 output generated from mpirun together
diffractor.saveH5()
geom = "s2e.geom" # e.g. s2e.geom
parameters = SingFELPhotonDiffractorParameters(
uniform_rotation=True, # Uniform sampling of rotation space.
calculate_Compton=False, # Do not calculate Compton scattering
slice_interval=100, # Take interval of 100 pmi snapshots
number_of_slices=2, # Take two snapshots from this interval
pmi_start_ID=1, # Start with this pmi file ID.
pmi_stop_ID=1, # Stop after this pmi file ID.
number_of_diffraction_patterns=
100, # Calculate 100 patterns from each trajectory.
beam_parameter_file=beam, # Beam file.
beam_geometry_file=geom, # Geometry file (detector).
cpus_per_task=
1, # Use one CPU per MPI process. Number of processes is guessed from machine parameters.
)
# Construct the object.
diffractor = SingFELPhotonDiffractor(parameters=parameters,
input_path=pmi_path,
output_path='diffr')
# Call backengine.
status = diffractor.backengine()
if status != 0:
print("Diffraction calculation failed, check output.")
sys.exit()
print("Diffraction calculation succeeded.")
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(
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 testSimS2EWorkflowSingleFile(self):
""" Testing that a workflow akin to the simS2E example workflow works. Only one I/O file per calculator. """
# These directories and files are expected to be present after a successfull calculation.
expected_dirs = [
'pmi',
'diffr',
]
expected_files = [
'FELsource_out.h5', 'prop_out.h5', 'pmi/pmi_out_0000001.h5',
'diffr/diffr_out_0000001.h5', 'orient_out.h5', 'recon.h5'
]
# Ensure proper cleanup.
self.__files_to_remove = expected_files
self.__dirs_to_remove = expected_dirs
# Location of the FEL source file.
source_input = TestUtilities.generateTestFilePath(
'FELsource_out/FELsource_out_0000001.h5')
# Photon source.
photon_source = XFELPhotonSource(parameters=None,
input_path=source_input,
output_path='FELsource_out.h5')
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None,
input_path='FELsource_out.h5',
output_path='prop_out.h5')
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path='prop_out.h5',
output_path='pmi',
sample_path=self.__sample_path)
# Diffraction with parameters.
diffraction_parameters = 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=1,
beam_parameter_file=TestUtilities.generateTestFilePath('s2e.beam'),
detector_geometry=TestUtilities.generateTestFilePath('s2e.geom'),
number_of_MPI_processes=2,
)
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr')
# Reconstruction: EMC+DM
emc_parameters = {
'initial_number_of_quaternions': 1,
'max_number_of_quaternions': 2,
'max_number_of_iterations': 10,
'min_error': 1.0e-6,
'beamstop': True,
'detailed_output': False
}
dm_parameters = {
'number_of_trials': 5,
'number_of_iterations': 2,
'averaging_start': 15,
'leash': 0.2,
'number_of_shrink_cycles': 2,
}
reconstructor = S2EReconstruction(
parameters={
'EMC_Parameters': emc_parameters,
'DM_Parameters': dm_parameters
},
input_path=TestUtilities.generateTestFilePath(
'diffr'
), # Cheeting here to provide more realistic data for emc.
output_path='recon.h5')
photon_detector = IdealPhotonDetector(parameters=None,
input_path='diffr',
output_path='detector')
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=None,
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:
self.assertTrue(os.path.isdir(directory))
for f in expected_files:
print(f)
self.assertTrue(os.path.isfile(f))
def testSimS2EWorkflowDefaultPaths(self):
""" Testing that a workflow akin to the simS2E example workflow works. No IO paths specified. """
# These directories and files are expected to be present after a successfull calculation.
expected_dirs = [
'source_in',
'source',
'prop',
'pmi',
'diffr',
'analysis',
]
expected_files = [
'source/FELsource_out_0000000.h5',
'source/FELsource_out_0000001.h5',
'prop/prop_out_0000000.h5',
'prop/prop_out_0000001.h5',
'pmi/pmi_out_0000001.h5',
'pmi/pmi_out_0000002.h5',
'diffr/diffr_out_0000001.h5',
'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 testSimS2EWorkflowDirectories(self):
""" Testing that a workflow akin to the simS2E example workflow works.
Two sources, two diffraction patterns."""
# Setup directories.
working_directory = 'SPI'
self.__dirs_to_remove.append(working_directory)
source_dir = os.path.join(working_directory, 'FELsource')
prop_dir = os.path.join(working_directory, 'prop')
pmi_dir = os.path.join(working_directory, 'pmi')
diffr_dir = os.path.join(working_directory, 'diffr')
detector_dir = os.path.join(working_directory, 'detector')
recon_dir = os.path.join(working_directory, 'recon')
# Make directories.
os.mkdir(working_directory)
os.mkdir(source_dir)
os.mkdir(prop_dir)
os.mkdir(pmi_dir)
os.mkdir(diffr_dir)
os.mkdir(detector_dir)
os.mkdir(recon_dir)
# Location of the FEL source file.
source_input = TestUtilities.generateTestFilePath('FELsource_out')
# Photon source.
photon_source = XFELPhotonSource(parameters=None,
input_path=source_input,
output_path=source_dir)
# Photon propagator, default parameters.
photon_propagator = XFELPhotonPropagator(parameters=None,
input_path=source_dir,
output_path=prop_dir)
# Photon interactor with default parameters.
photon_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=prop_dir,
output_path=pmi_dir,
sample_path=self.__sample_path)
diffraction_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)
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()
def testSimS2EWorkflowTwoDiffractionPatterns(self):
""" Testing that a workflow akin to the simS2E example workflow works. """
# These directories and files are expected to be present after a successfull calculation.
expected_dirs = [
'pmi',
'diffr',
]
expected_symlinks = ['detector']
expected_files = [
'FELsource_out_0000001.h5',
'prop_out_0000001.h5',
'pmi/pmi_out_0000001.h5',
'diffr/diffr_out_0000001.h5',
'detector/diffr_out_0000001.h5',
'orient_out.h5',
]
# Ensure proper cleanup.
self.__files_to_remove = expected_files + expected_symlinks + [
'recon.h5'
]
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_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=self.__sample_path)
# Diffraction with parameters.
diffraction_parameters = self.diffractorParam_1
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr')
# Perfect detector.
photon_detector = IdealPhotonDetector(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': 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='detector',
output_path='recon.h5')
# Setup the photon experiment.
pxs = PhotonExperimentSimulation(
photon_source=photon_source,
photon_propagator=photon_propagator,
photon_interactor=photon_interactor,
photon_diffractor=photon_diffractor,
photon_detector=photon_detector,
photon_analyzer=reconstructor,
)
# Run the experiment.
pxs.run()
# Check that all output files and directories are present.
for directory in expected_dirs + expected_symlinks:
self.assertTrue(os.path.isdir(directory))
for f in expected_files:
print(f)
self.assertTrue(os.path.isfile(f))
def testConstructionExceptions(self):
""" Test that the appropriate exceptions are thrown if the object is constructed incorrectly. """
# Setup a minimal experiment simulation.
source_input = TestUtilities.generateTestFilePath('FELsource_out.h5')
diffr_input = TestUtilities.generateTestFilePath('pmi_out_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,
)
def plot_diffr_vs_detector(self):
""" Compare patterns before and after detector sim. """
# Cleanup.
#self.__files_to_remove.append('6r43.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="6r43.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 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_parameters': self.beam,
'detector_geometry': self.detector_geometry,
}
# 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(ValueError, 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(ValueError, 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(ValueError, 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(ValueError, 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(ValueError, 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_parameters not a string.
parameters['beam_parameters'] = 1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# beam_parameters not a file.
parameters['beam_parameters'] = 'xyz.beam'
self.assertRaises(IOError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
parameters['beam_parameters'] = self.beam
# detector_geometry not a string.
parameters['detector_geometry'] = 1
self.assertRaises(TypeError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
# detector_geometry not a file.
parameters['detector_geometry'] = 'xyz.geom'
self.assertRaises(IOError, SingFELPhotonDiffractor, parameters,
self.input_h5, 'diffr.h5')
parameters['detector_geometry'] = self.detector_geometry
