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 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=2,
detector_geometry=self.detector_geometry,
forced_mpi_command='mpirun -np 2',
)
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.
# Ensure removal of directory.
self.__dirs_to_remove.append(photon_diffractor.output_path)
photon_diffractor.backengine()
photon_diffractor.saveH5()
# Cleanup new style files.
# Ensure removal of linked hdf.
self.__files_to_remove.append(photon_diffractor.output_path)
with h5py.File(photon_diffractor.output_path) as handle:
pattern = handle['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()
with h5py.File(photon_diffractor.output_path) as handle:
new_pattern = handle['data/0000001/diffr'].value
self.assertAlmostEqual(numpy.linalg.norm(pattern - new_pattern), 0.0,
5)
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 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. """
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 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 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()
