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 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 testBackengineNoBeam(self):
""" Test that we can start a test calculation with no explicit beam parameters. """
# 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=None,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun -np 2',
)
# 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 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 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()
# 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(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 testNoRotation(self):
""" Test that we can run singfel with no-rotation option."""
diffraction_parameters = SingFELPhotonDiffractorParameters(
uniform_rotation=None,
calculate_Compton=False,
slice_interval=100,
number_of_slices=3,
pmi_start_ID=1,
pmi_stop_ID=1,
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_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)
pattern = h5py.File(
photon_diffractor.output_path)['data/0000001/diffr'].value
# 2nd run.
photon_diffractor = SingFELPhotonDiffractor(
parameters=diffraction_parameters,
input_path=TestUtilities.generateTestFilePath('pmi_out'),
output_path='diffr_newstyle')
# Run backengine and convert files.
photon_diffractor.backengine()
photon_diffractor.saveH5()
new_pattern = h5py.File(
photon_diffractor.output_path)['data/0000001/diffr'].value
self.assertAlmostEqual(numpy.linalg.norm(pattern - new_pattern), 0.0,
10)
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 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 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 testH5OutputThrice(self):
""" Test whether the backengine behaves normally after multiple calculation"""
# Ensure proper cleanup.
sample_file = TestUtilities.generateTestFilePath('2nip.pdb')
# 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,
output_path='tmp/diffr')
# Run and save.
diffractor.backengine()
diffractor.saveH5()
self.__dirs_to_remove.append(os.path.abspath('tmp'))
self.__files_to_remove.append(
os.path.abspath(diffractor.output_path + '.h5'))
os.remove('tmp/diffr.h5')
shutil.rmtree('tmp/diffr')
diffractor.backengine()
diffractor.saveH5()
try:
os.remove('tmp/diffr.h5')
shutil.rmtree('tmp/diffr')
except IsADirectoryError:
shutil.rmtree('tmp')
print(sys.exc_info()[0])
raise
diffractor.backengine()
diffractor.saveH5()
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 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 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()
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.")
