def testLoadPDB(self):
""" Check that we can load a pdb and convert it to a dict. """
# Setup path to pdb file.
pdb_path = generateTestFilePath("2nip.pdb")
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
return_dict = IOUtilities.loadPDB(pdb_path)
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (4728,) )
self.assertEqual( return_dict['r'].shape, (4728,3) )
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check exception on corrupt file.
# does not raise due to highly tolerant default acceptance levels in Bio.PDB.
#self.assertRaises( IOError, IOUtilities.loadPDB, generateTestFilePath("2nip_corrupt.pdb" ) )
# Check exception on wrong input type.
self.assertRaises( IOError, IOUtilities.loadPDB, [1,2] )
# Check exception on wrong file type.
self.assertRaises( IOError, IOUtilities.loadPDB, generateTestFilePath("sample.h5") )
def testLoadPDB(self):
""" Check that we can load a pdb and convert it to a dict. """
# Setup path to pdb file.
pdb_path = generateTestFilePath("2nip.pdb")
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
return_dict = IOUtilities.loadPDB(pdb_path)
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (4728,) )
self.assertEqual( return_dict['r'].shape, (4728,3) )
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check exception on wrong input type.
self.assertRaises( IOError, IOUtilities.loadPDB, [1,2] )
# Check exception on wrong file type.
self.assertRaises( IOError, IOUtilities.loadPDB, generateTestFilePath("sample.h5") )
def testLegacyDictionary(self):
""" Check parameter object can be initialized via a old-style dictionary. """
parameters_dict = {
'uniform_rotation': False,
'calculate_Compton': True,
'slice_interval': 12,
'number_of_slices': 2,
'pmi_start_ID': 4,
'pmi_stop_ID': 5,
'number_of_diffraction_patterns': 2,
'beam_parameters': None,
'detector_geometry': self.detector_geometry,
'number_of_MPI_processes': 4, # Legacy, has no effect.
'sample': generateTestFilePath('2nip.pdb')
}
parameters = SingFELPhotonDiffractorParameters(**parameters_dict)
# Check all parameters are set correctly.
self.assertFalse(parameters.uniform_rotation)
self.assertTrue(parameters.calculate_Compton)
self.assertEqual(parameters.slice_interval, 12)
self.assertEqual(parameters.number_of_slices, 2)
self.assertEqual(parameters.pmi_start_ID, 4)
self.assertEqual(parameters.pmi_stop_ID, 5)
self.assertEqual(parameters.beam_parameters, None)
self.assertEqual(parameters.detector_geometry, self.detector_geometry)
self.assertEqual(parameters.sample, generateTestFilePath('2nip.pdb'))
def testGenesisDFLToWPGWavefront(self):
""" Check the conversion from genesis dfl to wpg readable hdf5. """
genesis_out_file = generateTestFilePath("genesis/lcls/lcls.out")
genesis_dfl_file = generateTestFilePath("genesis/lcls/lcls.out.dfl")
wf = IOUtilities.genesis_dfl_to_wavefront(genesis_out_file, genesis_dfl_file)
self.assertIsInstance(wf, Wavefront)
def setUp(self):
""" Setting up a test. """
self.__files_to_remove = []
self.__dirs_to_remove = []
path_to_field_data = generateTestFilePath(
os.path.join("issue-sample", "no_particles", "data%T.h5"))
path_to_particle_data = generateTestFilePath(
os.path.join("issue-sample", "no_fields", "data%T.h5"))
path_to_data = generateTestFilePath(
os.path.join("git-sample", "data%T.h5"))
mode = api.Access_Type.read_only
self.__field_series = api.Series(path_to_field_data, mode)
self.__particle_series = api.Series(path_to_particle_data, mode)
self.__series = api.Series(path_to_data, mode)
def testWpgToOPMDLegacyConverter(self):
""" Test the conversion of wpg output to openPMD conform file, omitting the openpmd-api."""
# Get sample file.
h5_input = generateTestFilePath('prop_out/prop_out_0000011.h5')
# Convert.
convertToOPMDLegacy(h5_input)
# New file name.
opmd_h5_file = h5_input.replace(".h5", ".opmd.h5")
# Make sure we clean up after test.
self.__files_to_remove.append(opmd_h5_file)
# Check new file was generated.
self.assertTrue(os.path.isfile(opmd_h5_file))
# Validate the new file.
g = opmd_validator.open_file(opmd_h5_file)
# Setup result array.
result_array = numpy.array([0, 0])
result_array += opmd_validator.check_root_attr(g, False)
# Go through all the iterations, checking both the particles and the meshes
extensions = {'ED-PIC': False, 'HYDRO1D': False}
result_array += opmd_validator.check_iterations(g, False, extensions)
# Assert that no errors nor warnings were issued.
self.assertEqual(result_array[0], 0)
self.assertEqual(result_array[1], 0)
def testHydroTxtToOPMDConverter(self):
""" Test the conversion of esther output to openPMD conform hdf5 file."""
# Get sample file.
esther_output = generateTestFilePath('hydroTests')
# Convert.
convertTxtToOPMD(esther_output)
# New file name.
opmd_h5_file = esther_output + '/output.opmd.h5'
# Make sure we clean up after test.
self.__files_to_remove.append(opmd_h5_file)
# Check new file was generated.
self.assertTrue(os.path.isfile(opmd_h5_file))
# Validate the new file.
g = opmd_validator.open_file(opmd_h5_file)
# Setup result array.
result_array = numpy.array([0, 0])
result_array += opmd_validator.check_root_attr(g, False)
# Go through all the iterations, checking both the particles.
# and the meshes.
extensions = {'ED-PIC': False, 'HYDRO1D': True}
result_array += opmd_validator.check_iterations(g, False, extensions)
# Assert that no errors nor warnings were issued.
self.assertEqual(result_array[0], 0)
self.assertEqual(result_array[1], 0)
def test_sample2h5(self):
""" Test the conversion utility to convert a sample directory to hdf5. """
# Expected file to be generated.
sample_file = 'sample.h5'
# Clean up.
self.__files_to_remove.append(sample_file)
# Input dir.
sample_dir = generateTestFilePath("sample_dir")
# Run utility.
sample2h5(sample_dir)
# Check file was generated.
self.assertIn(sample_file, os.listdir('.'))
self.assertTrue(os.path.isfile(sample_file))
# Check data is sane.
expected_keys = ['Z', 'r']
with h5py.File(sample_file, 'r') as h5:
present_keys = h5.keys()
for pk in present_keys:
self.assertIn(pk, expected_keys)
Z = h5['Z'].value
r = h5['r'].value
# Check data shapes are consistent.
self.assertEqual(r.shape, (len(Z), 3))
def testHydroTxtToOPMDConverter(self):
""" Test the conversion of esther output to openPMD conform hdf5 file."""
# Get sample file.
esther_output = generateTestFilePath('hydroTests')
# Convert.
convertTxtToOPMD(esther_output)
# New file name.
opmd_h5_file = esther_output + '.opmd.h5'
# Make sure we clean up after test.
self.__files_to_remove.append(opmd_h5_file)
# Check new file was generated.
self.assertTrue( os.path.isfile( opmd_h5_file ) )
# Validate the new file.
g = opmd_validator.open_file(opmd_h5_file)
# Setup result array.
result_array = numpy.array([0, 0])
result_array += opmd_validator.check_root_attr(g, False)
# Go through all the iterations, checking both the particles.
# and the meshes.
extensions = {'ED-PIC': False, 'HYDRO1D': True}
result_array += opmd_validator.check_iterations(g,False,extensions)
# Assert that no errors nor warnings were issued.
self.assertEqual( result_array[0], 0 )
self.assertEqual( result_array[1], 0 )
def testWpgToOPMDConverter(self):
""" Test the conversion of wpg output to openPMD conform file."""
# Get sample file.
h5_input = generateTestFilePath('prop_out/prop_out_0000011.h5')
# Convert.
convertToOPMD(h5_input)
# New file name.
opmd_h5_file = h5_input.replace(".h5", ".opmd.h5")
self.__files_to_remove.append(opmd_h5_file)
# Check new file was generated.
self.assertTrue(os.path.isfile(opmd_h5_file))
# Read the file back in through the API.
series = opmd.Series(opmd_h5_file, opmd.Access_Type.read_only)
self.assertIsInstance(series, opmd.Series)
# Check attributes are present.
try:
series.author
series.date
series.software
series.software_version
series.get_attribute("radius of curvature in x")
series.get_attribute("z coordinate")
series.get_attribute("Rx_Unit_Dimension")
series.get_attribute("Rx_UnitSI")
series.get_attribute("radius of curvature in y")
series.get_attribute("Ry_Unit_Dimension")
series.get_attribute("Ry_UnitSI")
series.get_attribute("Delta radius of curvature in x")
series.get_attribute("DRx_Unit_Dimension")
series.get_attribute("DRx_UnitSI")
series.get_attribute("Delta radius of curvature in y")
series.get_attribute("DRy_Unit_Dimension")
series.get_attribute("DRy_UnitSI")
series.get_attribute("photon energy")
series.get_attribute("photon energy unit dimension")
series.get_attribute("photon energy UnitSI")
except RuntimeError:
self.fail("Error while querying attribute.")
except:
raise
# Check the beamline serialization
self.assertIsInstance(series.get_attribute("beamline"), str)
def testConstructionWithSample(self):
""" Testing the construction of the class with a PhotonBeamParameters instance. """
# Attempt to construct an instance of the class.
parameters = SingFELPhotonDiffractorParameters(
sample=generateTestFilePath('2nip.pdb'),
detector_geometry=self.detector_geometry,
beam_parameters=self.beam)
# Check instance and inheritance.
self.assertIsInstance(parameters, SingFELPhotonDiffractorParameters)
self.assertIsInstance(parameters, AbstractCalculatorParameters)
# Check all parameters are set to default values.
self.assertEqual(parameters.sample, generateTestFilePath('2nip.pdb'))
self.assertEqual(parameters.uniform_rotation, False)
self.assertFalse(parameters.calculate_Compton)
self.assertEqual(parameters.slice_interval, 100)
self.assertEqual(parameters.number_of_slices, 1)
self.assertEqual(parameters.pmi_start_ID, 1)
self.assertEqual(parameters.pmi_stop_ID, 1)
self.assertEqual(parameters.beam_parameters, self.beam)
self.assertEqual(parameters.detector_geometry, self.detector_geometry)
def testLoadOPMDWavefront(self):
""" Test if loading a wavefront from openpmd-hdf into a WPG structure works."""
# Get sample file.
h5_input = generateTestFilePath('prop_out/prop_out_0000011.h5')
# Convert.
convertToOPMD(h5_input)
# New file name.
opmd_h5_file = h5_input.replace(".h5", ".opmd.h5")
self.__files_to_remove.append(opmd_h5_file)
# Reconstruct the series.
series = opmd.Series(opmd_h5_file, opmd.Access_Type.read_only)
wavefront = wpg.Wavefront()
def testLoadXYZ(self):
""" Check that we can load a xyz file and convert it to a dict. """
# Setup path to xyz file.
xyz_path = generateTestFilePath("Fe2O3_poly_test.xyz")
# Attempt to load it.
return_dict = IOUtilities.loadXYZ(xyz_path)
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (100,) )
self.assertEqual( return_dict['r'].shape, (100,3) )
def testPdbToS2ESampleDict(self):
""" Check the utility that converts a pdb file to an s2e sample dict.
"""
# Setup path to pdb file.
pdb_path = generateTestFilePath("2nip.pdb")
# Attempt to load it.
return_dict = IOUtilities._pdbToS2ESampleDict(pdb_path)
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (4728,) )
self.assertEqual( return_dict['r'].shape, (4728,3) )
def testDefaultConstruction(self):
""" Testing the default construction of the class using a dictionary. """
# Attempt to construct an instance of the class.
parameters = SingFELPhotonDiffractorParameters(
sample=generateTestFilePath("2nip.pdb"))
# Check instance and inheritance.
self.assertIsInstance(parameters, SingFELPhotonDiffractorParameters)
self.assertIsInstance(parameters, AbstractCalculatorParameters)
# Check all parameters are set to default values.
self.assertEqual(parameters.uniform_rotation, False)
self.assertFalse(parameters.calculate_Compton)
self.assertEqual(parameters.slice_interval, 100)
self.assertEqual(parameters.number_of_slices, 1)
self.assertEqual(parameters.pmi_start_ID, 1)
self.assertEqual(parameters.pmi_stop_ID, 1)
self.assertEqual(parameters.beam_parameters, None)
self.assertEqual(parameters.detector_geometry, None)
def testWPGDataPropConstruction(self):
""" Testing the construction of the class with the prop hdf5 file. """
file_path = generateTestFilePath("prop_out_0000001.h5")
print("Testing path: ", file_path)
prop_data = WPGdata(file_path)
self.assertIsInstance(prop_data.wavefront, Wavefront)
def testWPGDataSourceConstruction(self):
""" Testing the construction of the class with the source hdf5 file. """
file_path = generateTestFilePath("FELsource_out.h5")
print("Testing path: ", file_path)
FELsource_data = WPGdata(file_path)
self.assertIsInstance(FELsource_data.wavefront, Wavefront)
