def setUpClass(cls):
""" Setting up the test class. """
# Setup parameters.
cls.__beam_parameters = PhotonBeamParameters(
photon_energy=4.96e3 * electronvolt,
photon_energy_relative_bandwidth=0.01,
beam_diameter_fwhm=2e-6 * meter,
divergence=2e-6 * radian,
pulse_energy=1e-3 * joule,
photon_energy_spectrum_type='tophat')
cls.__geometry = DetectorGeometry(panels=DetectorPanel(
ranges={
"fast_scan_min": 0,
"fast_scan_max": 63,
"slow_scan_min": 0,
"slow_scan_max": 63
},
pixel_size=220.0e-6 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.1 * meter,
corners={
"x": -32,
"y": -32
},
saturation_adu=1e4,
))
def testBackengineGPU(self):
""" Check a backengine calculation with openCL enabled. """
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
self.__files_to_remove.append("diffr.h5")
# Clean up to make sure no old files mess things up.
self.tearDown()
beam_parameters = PhotonBeamParameters(
photon_energy=4.96e3 * electronvolt,
photon_energy_relative_bandwidth=0.01,
beam_diameter_fwhm=2e-6 * meter,
divergence=2e-6 * radian,
pulse_energy=1e-3 * joule,
photon_energy_spectrum_type='tophat')
geometry = DetectorGeometry(panels=DetectorPanel(
ranges={
"fast_scan_min": 0,
"fast_scan_max": 63,
"slow_scan_min": 0,
"slow_scan_max": 63
},
pixel_size=220.0e-6 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.1 * meter,
corners={
"x": -32,
"y": -32
},
saturation_adu=1e4,
))
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
beam_parameters=beam_parameters,
detector_geometry=geometry,
number_of_diffraction_patterns=10,
use_gpu=True)
# Get calculator.
diffractor = CrystFELPhotonDiffractor(parameters=parameters,
input_path=None,
output_path='diffr')
# Run backengine
status = diffractor.backengine()
# Check return code.
self.assertEqual(status, 0)
output_path = "%s" % diffractor.output_path
# Check output dir was created.
self.assertTrue(os.path.isdir(output_path))
# Check pattern was written.
diffractor.saveH5()
self.assertIn("diffr_out_0000001.h5", os.listdir(output_path))
def setUpClass(cls):
detector_panel = DetectorPanel(
ranges={
'fast_scan_min': 0,
'fast_scan_max': 1023,
'slow_scan_min': 0,
'slow_scan_max': 1023
},
pixel_size=2.2e-4 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.13 * meter,
corners={
'x': -512,
'y': 512
},
)
cls.detector_geometry = DetectorGeometry(panels=[detector_panel])
cls.beam = PhotonBeamParameters(
photon_energy=8.6e3 * electronvolt,
beam_diameter_fwhm=1.0e-6 * meter,
pulse_energy=1.0e-3 * joule,
photon_energy_relative_bandwidth=0.001,
divergence=None,
photon_energy_spectrum_type="SASE",
)
def setUpClass(cls):
""" Setting up the test class. """
cls.input_h5 = TestUtilities.generateTestFilePath('pmi_out_0000001.h5')
detector_panel = DetectorPanel(
ranges={
'fast_scan_min': 0,
'fast_scan_max': 21,
'slow_scan_min': 0,
'slow_scan_max': 21
},
pixel_size=2.2e-4 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.13 * meter,
corners={
'x': -11,
'y': -11
},
)
cls.detector_geometry = DetectorGeometry(panels=[detector_panel])
cls.beam = PhotonBeamParameters(
photon_energy=8.6e3 * electronvolt,
beam_diameter_fwhm=1.0e-6 * meter,
pulse_energy=1.0e-3 * joule,
photon_energy_relative_bandwidth=0.001,
divergence=1e-3 * radian,
photon_energy_spectrum_type="SASE",
)
def testBackengineWithBeamParametersObject(self):
""" Check beam parameter logic if they are set as parameters. """
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
# Setup beam parameters.
beam_parameters = PhotonBeamParameters(
photon_energy=16.0e3 * electronvolt,
photon_energy_relative_bandwidth=0.001,
pulse_energy=2.0e-3 * joule,
beam_diameter_fwhm=100e-9 * meter,
divergence=None,
photon_energy_spectrum_type="tophat",
)
# Get parameters.
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
detector_geometry=self.__geometry,
beam_parameters=beam_parameters,
number_of_diffraction_patterns=2,
uniform_rotation=True,
)
# Get calculator.
diffractor = CrystFELPhotonDiffractor(parameters=parameters,
input_path=None,
output_path='diffr')
# Run backengine
status = diffractor.backengine()
# Check return code.
self.assertEqual(status, 0)
def testSaveH5(self):
""" Check that saveh5() creates correct filenames. """
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
self.__files_to_remove.append("5udc.pdb")
self.__files_to_remove.append("diffr.h5")
# Setup beam parameters.
beam_parameters = PhotonBeamParameters(photon_energy=5e3*electronvolt,
pulse_energy=2e-3*joule,
photon_energy_relative_bandwidth=1e-3,
photon_energy_spectrum_type="tophat",
beam_diameter_fwhm=3e-6*meter,
)
# Get parameters.
parameters = CrystFELPhotonDiffractorParameters(sample="5udc.pdb",
detector_geometry=TestUtilities.generateTestFilePath("simple.geom"),
beam_parameters=beam_parameters,
number_of_diffraction_patterns=2)
# Get calculator.
diffractor = CrystFELPhotonDiffractor(parameters=parameters, input_path=None, output_path='diffr')
# Run backengine
status = diffractor.backengine()
# Check return code.
self.assertEqual(status, 0)
# Check output dir was created.
self.assertTrue( os.path.isdir( diffractor.output_path ) )
# Save correctly.
diffractor.saveH5()
# Check output file was created.
self.assertTrue( os.path.isfile( diffractor.output_path ) )
# Check pattern was written.
self.assertIn( "diffr_out_0000001.h5" , os.listdir( "diffr" ))
self.assertIn( "diffr_out_0000002.h5" , os.listdir( "diffr" ))
# Open linked h5 file.
with h5py.File(diffractor.output_path, 'r') as h5:
self.assertIn("data" , h5.keys())
self.assertIn("0000001" , h5["data"].keys())
self.assertIn("0000002" , h5["data"].keys())
self.assertIn("data" , h5["data/0000001"].keys())
self.assertIn("data" , h5["data/0000002"].keys())
self.assertIn("params" , h5.keys())
self.assertIn("beam" , h5["params"].keys())
self.assertIn("photonEnergy" , h5["params/beam"].keys())
self.assertIn("focusArea" , h5["params/beam"].keys())
# Check metafile was created.
self.assertIn( os.path.split(diffractor.output_path)[-1], os.listdir( os.path.dirname( diffractor.output_path) ) )
def testBackengine(self):
# Get calculator.
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
# Setup parameters.
beam_parameters = PhotonBeamParameters(
photon_energy=4.96e3 * electronvolt,
photon_energy_relative_bandwidth=0.01,
beam_diameter_fwhm=2e-6 * meter,
divergence=2e-6 * radian,
pulse_energy=1e-3 * joule,
photon_energy_spectrum_type='tophat')
self.assertIsInstance(beam_parameters, PhotonBeamParameters)
geometry = DetectorGeometry(panels=DetectorPanel(
ranges={
"fast_scan_min": 0,
"fast_scan_max": 63,
"slow_scan_min": 0,
"slow_scan_max": 63
},
pixel_size=220.0e-6 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.1 * meter,
corners={
"x": -32,
"y": -32
},
saturation_adu=1e4,
))
sys.stdout.flush()
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
beam_parameters=beam_parameters,
detector_geometry=geometry,
number_of_diffraction_patterns=10)
diffractor = CrystFELPhotonDiffractor(parameters=parameters,
input_path=None,
output_path='diffr')
# Run backengine
status = diffractor.backengine()
# Check return code.
self.assertEqual(status, 0)
# Check output dir was created.
output_path = "%s" % diffractor.output_path
self.assertTrue(os.path.isdir(output_path))
# Check pattern was written.
self.assertIn("diffr_out-1.h5", os.listdir(output_path))
def setUpClass(cls):
cls.beam = PhotonBeamParameters(
photon_energy=8.6e3 * electronvolt,
beam_diameter_fwhm=1.0e-6 * meter,
pulse_energy=1.0e-3 * joule,
photon_energy_relative_bandwidth=0.001,
divergence=None,
photon_energy_spectrum_type="SASE",
)
def testShapedConstructionGeometry(self):
""" Testing the construction with a geometry object. """
beam_parameters = PhotonBeamParameters(
photon_energy=4.96e3 * electronvolt,
photon_energy_relative_bandwidth=0.01,
beam_diameter_fwhm=2e-6 * meter,
divergence=2e-6 * radian,
pulse_energy=1e-3 * joule)
geometry = DetectorGeometry(panels=DetectorPanel(
ranges={
"fast_scan_min": 0,
"fast_scan_max": 63,
"slow_scan_min": 0,
"slow_scan_max": 63
},
pixel_size=220.0e-6 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.1 * meter,
corners={
"x": -32,
"y": -32
},
saturation_adu=1e4,
))
# Attempt to construct an instance of the class.
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
powder=True,
number_of_diffraction_patterns=10,
number_of_background_photons=100,
poissonize=True,
suppress_fringes=True,
crystal_size_min=10.0e-9 * meter,
crystal_size_max=100.0e-9 * meter,
uniform_rotation=False,
beam_parameters=beam_parameters,
detector_geometry=geometry,
)
# Check all parameters are set as intended.
self.assertFalse(parameters.uniform_rotation)
self.assertEqual(parameters.number_of_diffraction_patterns, 10)
self.assertTrue(parameters.powder)
self.assertEqual(parameters.crystal_size_min.m_as(meter), 10.e-9)
self.assertEqual(parameters.crystal_size_max.m_as(meter), 100.e-9)
self.assertTrue(parameters.poissonize)
self.assertEqual(parameters.number_of_background_photons, 100)
self.assertTrue(parameters.suppress_fringes)
self.assertIsInstance(parameters.beam_parameters, PhotonBeamParameters)
self.assertEqual(
parameters.beam_parameters.photon_energy.m_as(electronvolt),
4.96e3)
self.assertEqual(parameters.detector_geometry, geometry)
def testBackengineWithBeamAndGeometry(self):
""" Check geom parameter logic if they are set as parameters. """
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
# Setup beam parameters.
beam_parameters = PhotonBeamParameters(
photon_energy=16.0e3 * electronvolt,
photon_energy_relative_bandwidth=0.001,
pulse_energy=2.0e-3 * joule,
beam_diameter_fwhm=100e-9 * meter,
divergence=None,
photon_energy_spectrum_type="tophat",
)
geometry = DetectorGeometry(panels=DetectorPanel(
ranges={
"fast_scan_min": 0,
"fast_scan_max": 63,
"slow_scan_min": 0,
"slow_scan_max": 63
},
pixel_size=220.0e-6 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.1 * meter,
corners={
"x": -32,
"y": -32
},
saturation_adu=1e4,
))
# Get parameters.
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
detector_geometry=geometry,
beam_parameters=beam_parameters,
number_of_diffraction_patterns=2,
uniform_rotation=True,
)
# Get calculator.
diffractor = CrystFELPhotonDiffractor(parameters=parameters,
input_path=None,
output_path='diffr')
# Run backengine
status = diffractor.backengine()
# Check return code.
self.assertEqual(status, 0)
def testShapedConstruction(self):
""" Testing the construction of the class with parameters. """
# Attempt to construct an instance of the class.
parameters = PhotonBeamParameters(
photon_energy=4.96e3 * electronvolt,
photon_energy_relative_bandwidth=2e-2,
photon_energy_spectrum_type="SASE",
pulse_energy=2e-3 * joule,
beam_diameter_fwhm=2e-6 * meter,
divergence=1e-6 * radian,
)
# Check all parameters are set as intended.
self.assertEqual(parameters.photon_energy, 4.96e3 * electronvolt)
self.assertEqual(parameters.photon_energy_relative_bandwidth, 2e-2)
self.assertEqual(parameters.photon_energy_spectrum_type, "SASE")
self.assertEqual(parameters.pulse_energy, 2e-3 * joule)
self.assertEqual(parameters.beam_diameter_fwhm, 2e-6 * meter)
self.assertEqual(parameters.divergence, 1e-6 * radian)
def testShapedConstruction(self):
""" Testing the construction with parameters of the class. """
beam_parameters = PhotonBeamParameters(
photon_energy=4.96e3 * electronvolt,
photon_energy_relative_bandwidth=0.01,
beam_diameter_fwhm=2e-6 * meter,
divergence=2e-6 * radian,
pulse_energy=1e-3 * joule)
# Attempt to construct an instance of the class.
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
powder=True,
number_of_diffraction_patterns=10,
number_of_background_photons=100,
poissonize=True,
suppress_fringes=True,
crystal_size_min=10.0e-9 * meter,
crystal_size_max=100.0e-9 * meter,
uniform_rotation=False,
beam_parameters=beam_parameters,
detector_geometry=TestUtilities.generateTestFilePath(
'simple.geom'))
# Check all parameters are set as intended.
self.assertFalse(parameters.uniform_rotation)
self.assertEqual(parameters.number_of_diffraction_patterns, 10)
self.assertTrue(parameters.powder)
self.assertEqual(parameters.crystal_size_min.m_as(meter), 10.e-9)
self.assertEqual(parameters.crystal_size_max.m_as(meter), 100.e-9)
self.assertTrue(parameters.poissonize)
self.assertEqual(parameters.number_of_background_photons, 100)
self.assertTrue(parameters.suppress_fringes)
self.assertIsInstance(parameters.beam_parameters, PhotonBeamParameters)
self.assertEqual(
parameters.beam_parameters.photon_energy.m_as(electronvolt),
4.96e3)
self.assertEqual(parameters.detector_geometry,
TestUtilities.generateTestFilePath('simple.geom'))
def testSettersAndQueries(self):
""" Testing the default construction of the class using a dictionary. """
# Attempt to construct an instance of the class.
parameters = PhotonBeamParameters(
photon_energy=4.96e3 * electronvolt,
pulse_energy=2e-3 * joule,
beam_diameter_fwhm=2e-6 * meter,
)
# Set via methods.
parameters.photon_energy = 8.0e3 * electronvolt
parameters.pulse_energy = 2.5e-3 * joule
parameters.beam_diameter_fwhm = 100e-9 * meter
parameters.photon_energy_relative_bandwidth = 1e-3
parameters.divergence = 5e-6 * radian
parameters.photon_energy_spectrum_type = "tophat"
# Check all parameters are set as intended.
self.assertEqual(parameters.photon_energy, 8.0e3 * electronvolt)
self.assertEqual(parameters.photon_energy_relative_bandwidth, 1e-3)
self.assertEqual(parameters.pulse_energy.magnitude, 2.5e-3)
self.assertEqual(parameters.beam_diameter_fwhm.magnitude, 1e-7)
self.assertEqual(parameters.divergence.magnitude, 5e-6)
self.assertEqual(parameters.photon_energy_spectrum_type, "tophat")
def testConstructionWithParametersNoProp(self):
""" Testing the construction of the class with a parameter dictionary without propagation input. """
beam = PhotonBeamParameters(
photon_energy = 8.6e3*Units.electronvolt,
pulse_energy=1.5e-3*Units.joule,
photon_energy_relative_bandwidth=1e-4,
divergence=1.0e-3*Units.radian,
beam_diameter_fwhm=5.0e-3*Units.meter,
)
# Setup pmi parameters.
pmi_parameters = PhotonMatterInteractorParameters(
number_of_trajectories=1,
beam_parameters=beam,
)
interactor = XMDYNPhotonMatterInteractor(
parameters=pmi_parameters,
output_path='pmi_out',
sample_path=TestUtilities.generateTestFilePath('sample.h5'),
)
self.assertIsInstance(interactor, XMDYNPhotonMatterInteractor)
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()
},
pixel_size=560e-6 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.13 * meter,
corners={
'x': -49.5,
'y': -49.5
},
fast_scan_xyz='1.0x',
slow_scan_xyz='1.0y')
detector_geometry = DetectorGeometry(panels=[p0])
beam = PhotonBeamParameters(
photon_energy=6.0e3 * electronvolt,
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)
def testSaveH5(self):
""" Check that saveh5() creates correct filenames. """
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
self.__files_to_remove.append("diffr.h5")
# Setup beam parameters.
beam_parameters = PhotonBeamParameters(
photon_energy=5e3 * electronvolt,
pulse_energy=2e-3 * joule,
photon_energy_relative_bandwidth=1e-3,
photon_energy_spectrum_type="tophat",
beam_diameter_fwhm=3e-6 * meter,
)
geometry = DetectorGeometry(panels=DetectorPanel(
ranges={
"fast_scan_min": 0,
"fast_scan_max": 63,
"slow_scan_min": 0,
"slow_scan_max": 63
},
pixel_size=220.0e-6 * meter,
photon_response=1.0,
distance_from_interaction_plane=0.1 * meter,
corners={
"x": -32,
"y": -32
},
saturation_adu=1e4,
))
# Get parameters.
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
detector_geometry=geometry,
beam_parameters=beam_parameters,
number_of_diffraction_patterns=2,
uniform_rotation=True,
)
# Get calculator.
diffractor = CrystFELPhotonDiffractor(parameters=parameters,
input_path=None,
output_path='diffr')
# Run backengine
status = diffractor.backengine()
# Check return code.
self.assertEqual(status, 0)
# Check output dir was created.
self.assertTrue(os.path.isdir(diffractor.output_path))
# Save correctly.
diffractor.saveH5()
# Check output file was created.
self.assertTrue(os.path.isfile(diffractor.output_path))
# Check pattern was written.
self.assertIn("diffr_out_0000001.h5", os.listdir("diffr"))
self.assertIn("diffr_out_0000002.h5", os.listdir("diffr"))
# Open linked h5 file.
with h5py.File(diffractor.output_path, 'r') as h5:
self.assertIn("data", list(h5.keys()))
self.assertIn("0000001", list(h5["data"].keys()))
self.assertIn("0000002", list(h5["data"].keys()))
self.assertIn("data", list(h5["data/0000001"].keys()))
self.assertIn("data", list(h5["data/0000002"].keys()))
self.assertIn("params", list(h5.keys()))
self.assertIn("beam", list(h5["params"].keys()))
self.assertIn("photonEnergy", list(h5["params/beam"].keys()))
self.assertIn("focusArea", list(h5["params/beam"].keys()))
# Check metafile was created.
self.assertIn(
os.path.split(diffractor.output_path)[-1],
os.listdir(os.path.dirname(diffractor.output_path)))
