def testSettersAndQueries(self):
""" Testing the default construction of the class using a dictionary. """
self.__files_to_remove.append("5udc.pdb")
# Construct with defaults.
parameters = CrystFELPhotonDiffractorParameters(self.__sample)
# Set some members to non-defaults.
parameters.powder = True
parameters.number_of_diffraction_patterns = 10
parameters.number_of_background_photons = 100
parameters.poissonize = True
parameters.suppress_fringes = True
parameters.crystal_size_min = 10.0e-9 * meter
parameters.crystal_size_max = 100.0e-9 * meter
parameters.uniform_rotation = False
# 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, 10.0e-9 * meter)
self.assertEqual(parameters.crystal_size_max, 100.0e-9 * meter)
self.assertTrue(parameters.poissonize)
self.assertEqual(parameters.number_of_background_photons, 100)
self.assertTrue(parameters.suppress_fringes)
def testBackengineMultiplePatterns(self):
""" Check we can run pattern_sim with a minimal set of parameter. """
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
# Get parameters.
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
detector_geometry=self.__geometry,
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))
# Check pattern was written.
self.assertIn("diffr_out-1.h5", os.listdir(diffractor.output_path))
self.assertIn("diffr_out-2.h5", os.listdir(diffractor.output_path))
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 testBackengine(self):
# Get calculator.
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
sys.stdout.flush()
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
beam_parameters=self.__beam_parameters,
detector_geometry=self.__geometry,
number_of_diffraction_patterns=10,
uniform_rotation=True,
)
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 testConstructionWithPropInput(self):
""" Check that beam parameters can be taken from a given propagation output file."""
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
detector_geometry=TestUtilities.generateTestFilePath(
"simple.geom"),
beam_parameters=None,
number_of_diffraction_patterns=1,
)
diffractor = CrystFELPhotonDiffractor(
parameters=parameters,
input_path=TestUtilities.generateTestFilePath(
"prop_out_0000001.h5"),
output_path="diffr",
)
# Set spectrum type to tophat otherwise calculation will never finish.
diffractor.parameters.beam_parameters.photon_energy_spectrum_type = "tophat"
# Check that beam parameters have been updated from prop output.
self.assertAlmostEqual(
diffractor.parameters.beam_parameters.photon_energy.m_as(
electronvolt), 4972.8402471221643, 5)
def testBackengineWithPropInput(self):
""" Check that beam parameters can be taken from a given propagation output file."""
self.__dirs_to_remove.append("diffr")
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
detector_geometry=self.__geometry,
beam_parameters=None,
number_of_diffraction_patterns=1,
uniform_rotation=True,
)
diffractor = CrystFELPhotonDiffractor(
parameters=parameters,
input_path=TestUtilities.generateTestFilePath(
"prop_out/prop_out_0000011.h5"),
output_path="diffr",
)
# Set spectrum type to tophat otherwise calculation will never finish.
diffractor.parameters.beam_parameters.photon_energy_spectrum_type = "tophat"
# Check that beam parameters have been updated from prop output.
diffractor.backengine()
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 testBackengineSinglePattern(self):
""" Check we can run pattern_sim with a minimal set of parameter. """
# Ensure cleanup.
self.__dirs_to_remove.append("diffr")
# Get parameters.
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
detector_geometry=TestUtilities.generateTestFilePath(
"simple.geom"),
number_of_diffraction_patterns=1)
# 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))
# Check pattern was written.
self.assertIn("diffr_out_0000001.h5",
os.listdir(diffractor.output_path))
def testDefaultConstruction(self):
""" Testing the default construction. """
# Attempt to construct an instance of the class.
parameters = CrystFELPhotonDiffractorParameters(sample=self.__sample)
# Check instance and inheritance.
self.assertIsInstance(parameters, CrystFELPhotonDiffractorParameters)
self.assertIsInstance(parameters, AbstractCalculatorParameters)
# Check all parameters are set to default values.
self.assertEqual(parameters.sample, self.__sample)
self.assertTrue(parameters.uniform_rotation)
self.assertEqual(parameters.beam_parameters, None)
self.assertEqual(parameters.detector_geometry, None)
self.assertTrue(parameters.uniform_rotation)
self.assertEqual(parameters.number_of_diffraction_patterns, 1)
self.assertFalse(parameters.powder)
self.assertEqual(parameters.intensities_file, None)
self.assertEqual(parameters.crystal_size_min, None)
self.assertEqual(parameters.crystal_size_max, None)
self.assertFalse(parameters.poissonize, False)
self.assertEqual(parameters.number_of_background_photons, 0)
self.assertFalse(parameters.suppress_fringes)
self.assertEqual(parameters.beam_parameters, None)
self.assertEqual(parameters.detector_geometry, None)
def testCrystalSizes(self):
""" Test the various ways to set the crystal size range. """
# Construct with only minimum size.
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,
uniform_rotation=False,
)
self.assertEqual(parameters.crystal_size_min,
parameters.crystal_size_max)
# Construct with only max size.
parameters = CrystFELPhotonDiffractorParameters(
sample=self.__sample,
powder=True,
number_of_diffraction_patterns=10,
number_of_background_photons=100,
poissonize=True,
suppress_fringes=True,
crystal_size_max=10.0e-9 * meter,
uniform_rotation=False,
)
self.assertEqual(parameters.crystal_size_min,
parameters.crystal_size_max)
# Construct with both sizes set.
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,
)
self.assertNotEqual(parameters.crystal_size_min,
parameters.crystal_size_max)
def testUseGPU(self):
""" Check the use_gpu parameter handling."""
# Check default.
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,
uniform_rotation=False,
)
self.assertTrue(parameters.gpus_per_task == 0)
# Switch to True and check new value.
parameters.gpus_per_task = 1
self.assertTrue(parameters.gpus_per_task == 1)
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 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 testShapedConstruction(self):
""" Testing the construction of the class with parameters. """
# Setup parameters.
parameters=CrystFELPhotonDiffractorParameters(sample="5udc.pdb")
# Construct the object.
diffractor = CrystFELPhotonDiffractor(parameters=parameters, input_path=None)
# Check type.
self.assertIsInstance(diffractor, CrystFELPhotonDiffractor)
self.assertIsInstance(diffractor, AbstractPhotonDiffractor)
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 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 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)))
