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 testBackengineMultipleInputFile(self):
""" Test a backengine run with multiple input files. """
# Construct the object.
xfel_propagator = XFELPhotonPropagator( parameters=None, input_path=TestUtilities.generateTestFilePath( 'FELsource_out' ), output_path='prop_out' )
# Call the backengine.
status = xfel_propagator.backengine()
# Check backengine returned sanely.
self.assertEqual( status, 0 )
# Ensure clean-up.
self.__dirs_to_remove.append(xfel_propagator.output_path)
def testBackengineSingleInputFile(self):
""" Test a backengine run with a single input file. """
# Ensure clean-up.
self.__files_to_remove.append('prop_out_0000001.h5')
# Construct the object.
xfel_propagator = XFELPhotonPropagator( parameters=None, input_path=self.input_h5, output_path='prop_out_0000001.h5' )
# Call the backengine.
status = xfel_propagator.backengine()
# Check backengine returned sanely.
self.assertEqual( status, 0 )
def testBackengineMultipleInputFile(self):
""" Test a backengine run with multiple input files. """
# Construct the object.
xfel_propagator = XFELPhotonPropagator( parameters=None, input_path=TestUtilities.generateTestFilePath( 'FELsource_out' ), output_path='prop_out' )
# Call the backengine.
status = xfel_propagator.backengine()
# Check backengine returned sanely.
self.assertEqual( status, 0 )
# Ensure clean-up.
self.__dirs_to_remove.append(xfel_propagator.output_path)
def testBackengineSingleInputFile(self):
""" Test a backengine run with a single input file. """
# Construct the object.
xfel_propagator = XFELPhotonPropagator( parameters=None, input_path=self.input_h5, output_path='prop_out_0000001.h5' )
# Call the backengine.
status = xfel_propagator.backengine()
# Check backengine returned sanely.
self.assertEqual( status, 0 )
# Ensure clean-up.
self.__files_to_remove.append(xfel_propagator.output_path)
def testBackengineDefaultPaths(self):
""" Test a backengine run with a default io paths."""
# Prepare source.
shutil.copytree(TestUtilities.generateTestFilePath('FELsource_out'), os.path.abspath('source') )
self.__dirs_to_remove.append( 'source' )
self.__dirs_to_remove.append( 'prop' )
# Construct the object.
xfel_propagator = XFELPhotonPropagator()
# Call the backengine.
status = xfel_propagator.backengine()
# Check backengine returned sanely.
self.assertEqual( status, 0 )
# Check expected files exist.
self.assertTrue( os.path.isdir, os.path.abspath('prop') )
self.assertIn( 'prop_out_0000000.h5', os.listdir( 'prop' ) )
self.assertIn( 'prop_out_0000001.h5', os.listdir( 'prop' ) )
import sys
# Setup propagation parameters. Here we must specify the beamline.
parameters = WavePropagatorParameters(beamline=beamline)
# Path to source files (ADJUST ME).
input_files_path = "source/3fs_5keV_nz35_0000001.h5"
# Construct the propagator
propagator = XFELPhotonPropagator(
parameters=parameters,
input_path=input_files_path,
output_path='prop_out/prop_s2e_example.h5',
use_opmd=False # Set to True if openPMD output is required
)
# Read the data.
propagator._readH5()
# Call the backengine.
status = propagator.backengine()
if status != 0:
print "Wave propagation failed, check output."
sys.exit()
propagator.saveH5()
print "Wave propagation succeeded."