def testDeSerialize(self):
""" Test deserialization (i.e. construction from a file/string). """
# Setup geometry.
geometry = DetectorGeometry(panels=[self.__panel0, self.__panel1])
# Serialize
stream = io.StringIO()
geometry.serialize(stream=stream)
serialized_panel = stream.getvalue()
stream.close()
# Deserialize
deserialized_geometry = _detectorGeometryFromString(serialized_panel)
# Compare.
for i, panel in enumerate(geometry.panels):
self.assertAlmostEqual(panel.ranges,
deserialized_geometry.panels[i].ranges)
self.assertAlmostEqual(panel.corners,
deserialized_geometry.panels[i].corners)
self.assertEqual(panel.fast_scan_xyz,
deserialized_geometry.panels[i].fast_scan_xyz)
self.assertEqual(panel.slow_scan_xyz,
deserialized_geometry.panels[i].slow_scan_xyz)
self.assertAlmostEqual(
panel.pixel_size.magnitude,
deserialized_geometry.panels[i].pixel_size.magnitude)
self.assertAlmostEqual(
panel.distance_from_interaction_plane.magnitude,
deserialized_geometry.panels[i].
distance_from_interaction_plane.magnitude)
def testSerializeFilename(self):
""" Test the serialization of the DetectorGeometry. """
# Get panels
panel0 = self.__panel0
panel1 = self.__panel1
# Setup the detector geometry.
detector_geometry = DetectorGeometry(panels=[panel0, panel1])
# Serialize to stream
geom_file = "simex.geom"
#self.__files_to_remove.append(geom_file)
# Serialize into file handle.
detector_geometry.serialize(geom_file)
reference_string = """;panel 0
panel0/min_fs = 0
panel0/max_fs = 511
panel0/min_ss = 512
panel0/max_ss = 1023
panel0/px = 512
panel0/py = 512
panel0/corner_x = -512
panel0/corner_y = -256
panel0/fs = 1.0x
panel0/ss = 1.0y
panel0/clen = 1.3000000e-01
panel0/res = 4.5454545e+03
panel0/pix_width = 2.2000000e-04
panel0/coffset = 0.0000000e+00
panel0/adu_per_photon= 1.0000000e+00
panel0/max_adu = 1.0000000e+04
;panel 1
panel1/min_fs = 0
panel1/max_fs = 511
panel1/min_ss = 1024
panel1/max_ss = 1535
panel1/px = 512
panel1/py = 512
panel1/corner_x = -512
panel1/corner_y = 256
panel1/fs = 1.0x
panel1/ss = 1.0y
panel1/clen = 1.3000000e-01
panel1/res = 4.5454545e+03
panel1/pix_width = 2.2000000e-04
panel1/coffset = 0.0000000e+00
panel1/adu_per_photon= 1.0000000e+00
panel1/max_adu = 1.0000000e+04
"""
# Open for reading.
with open(geom_file, 'r') as stream:
lines = "".join(stream.readlines())
self.assertEqual(lines, reference_string)
def testSerializeHandle(self):
""" Test the serialization of the DetectorGeometry. """
# Get panels
panel0 = self.__panel0
panel1 = self.__panel1
# Setup the detector geometry.
detector_geometry = DetectorGeometry(panels=[panel0, panel1])
# Serialize to stream
geom_file = "simex.geom"
self.__files_to_remove.append(geom_file)
# Open for writing.
with open("simex.geom", 'w') as stream:
# Serialize into file handle.
detector_geometry.serialize(stream)
reference_string = self.__reference_serialization_string
# Open for reading.
with open(geom_file, 'r') as stream:
lines = "".join(stream.readlines())
self.assertEqual(lines, reference_string)
def testSerialize(self):
""" Test the serialization of the DetectorGeometry. """
# Get panels
panel0 = self.__panel0
panel1 = self.__panel1
# Setup the detector geometry.
detector_geometry = DetectorGeometry(panels=[panel0, panel1])
# Serialize to stream
stream = StringIO.StringIO()
detector_geometry.serialize(stream)
reference_string = """;panel 0
panel0/min_fs = 0
panel0/max_fs = 511
panel0/min_ss = 512
panel0/max_ss = 1023
panel0/px = 512
panel0/py = 512
panel0/corner_x = -512
panel0/corner_y = -256
panel0/fs = 1.0x
panel0/ss = 1.0y
panel0/clen = 1.3000000e-01
panel0/res = 4.5454545e+03
panel0/pix_width = 2.2000000e-04
panel0/coffset = 0.0000000e+00
panel0/adu_per_photon= 1.0000000e+00
panel0/max_adu = 1.0000000e+04
;panel 1
panel1/min_fs = 0
panel1/max_fs = 511
panel1/min_ss = 1024
panel1/max_ss = 1535
panel1/px = 512
panel1/py = 512
panel1/corner_x = -512
panel1/corner_y = 256
panel1/fs = 1.0x
panel1/ss = 1.0y
panel1/clen = 1.3000000e-01
panel1/res = 4.5454545e+03
panel1/pix_width = 2.2000000e-04
panel1/coffset = 0.0000000e+00
panel1/adu_per_photon= 1.0000000e+00
panel1/max_adu = 1.0000000e+04
"""
self.assertEqual(stream.getvalue(), reference_string)
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 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 testSerialize(self):
""" Test the serialization of the DetectorGeometry. """
# Get panels
panel0 = self.__panel0
panel1 = self.__panel1
# Setup the detector geometry.
detector_geometry = DetectorGeometry(panels=[panel0, panel1])
# Serialize to stream
stream = io.StringIO()
detector_geometry.serialize(stream)
reference_string = self.__reference_serialization_string
self.assertEqual(stream.getvalue(), reference_string)
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 testShapedConstructionMultiPanels(self):
# Get a panel
panel0 = self.__panel0
panel1 = self.__panel1
# Construct the detector geometry.
detector_geometry = DetectorGeometry(panels=[panel0, panel1])
# Check members.
self.assertEqual(panel0, detector_geometry.panels[0])
self.assertEqual(panel1, detector_geometry.panels[1])
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])
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 testShapedConstructionSinglePanel(self):
# Get a panel
detector_panel = self.__panel0
# Construct the detector geometry.
detector_geometry = DetectorGeometry(panels=detector_panel)
# Check type and inheritance.
self.assertIsInstance(detector_geometry, DetectorGeometry)
self.assertIsInstance(detector_geometry, AbstractCalculatorParameters)
# Check members.
self.assertEqual(detector_panel, detector_geometry.panels[0])
def detector_geometry(self, value):
""" Set the 'detector_geometry' parameter to a given value.
:param value: The value to set 'detector_geometry' to.
"""
if value is None:
print(
"WARNING: Geometry not set, calculation will most probably fail."
)
else:
value = checkAndSetInstance((str, DetectorGeometry), value, None)
if isinstance(value, str):
if not os.path.isfile(value):
raise IOError(
'The parameter "detector_geometry" %s is not a valid file or filename.'
% (value))
value = DetectorGeometry(filename=value)
# Store on object and return.
self.__detector_geometry = value
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()
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)))
'fast_scan_min': 0,
'fast_scan_max': 99,
'slow_scan_min': 0,
'slow_scan_max': 99
},
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')
