def testBackengine(self): """ Test that we can start a test calculation. """ self.__files_to_remove.append('orient_out.h5') self.__files_to_remove.append('recon_out.h5') emc_parameters = { 'initial_number_of_quaternions': 1, 'max_number_of_quaternions': 2, 'max_number_of_iterations': 10, 'min_error': 1.0e-6, 'beamstop': True, 'detailed_output': False } dm_parameters = { 'number_of_trials': 5, 'number_of_iterations': 2, 'averaging_start': 15, 'leash': 0.2, 'number_of_shrink_cycles': 2, } # Construct the object. analyzer = S2EReconstruction(parameters={ 'EMC_Parameters': emc_parameters, 'DM_Parameters': dm_parameters }, input_path=self.input_h5, output_path='recon_out.h5') # Call backengine. status = analyzer.backengine() self.assertEqual(status, 0)
def testCheckInterfaceConsistency(self): """ Test if the check for interface consistency works correctly. """ # Setup a minimal experiment simulation. source_input = TestUtilities.generateTestFilePath('FELsource_out.h5') diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.h5') pmi_input = TestUtilities.generateTestFilePath('prop_out.h5') photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') pmi_parameters = { 'sample_path': TestUtilities.generateTestFilePath('sample.h5') } photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path=pmi_input, output_path='pmi_out.h5', sample_path=self.__sample_path) diffraction_parameters = { 'uniform_rotation': True, 'calculate_Compton': False, 'slice_interval': 100, 'number_of_slices': 2, 'pmi_start_ID': 1, 'pmi_stop_ID': 1, 'number_of_diffraction_patterns': 2, 'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'), 'beam_geometry_file': TestUtilities.generateTestFilePath('s2e.geom'), 'number_of_MPI_processes': 2, } photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=diffr_input, output_path='diffr_out.h5') photon_detector = IdealPhotonDetector(parameters=None, input_path='diffr_out.h5', output_path='detector_out.h5') photon_analyzer = S2EReconstruction(parameters=None, input_path='detector_out.h5', output_path='analyzer_out.h5') pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) interfaces_are_consistent = pxs._checkInterfaceConsistency() self.assertTrue(interfaces_are_consistent)
def testShapedConstruction(self): """ Testing the default construction of the class. """ self.__files_to_remove.append('orient_out.h5') self.__files_to_remove.append('recon_out.h5') # Construct the object. analyzer = S2EReconstruction(parameters=None, input_path=self.input_h5, output_path='recon_out.h5') self.assertIsInstance(analyzer, S2EReconstruction)
def testCalculatorQueries(self): """ Test that the calculator queries return the correct calculators. """ # Setup a minimal experiment simulation. source_input = TestUtilities.generateTestFilePath('FELsource_out.h5') diffr_input = TestUtilities.generateTestFilePath('pmi_out.h5') pmi_input = TestUtilities.generateTestFilePath('prop_out.h5') photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') photon_interactor = FakePhotonMatterInteractor( parameters=None, input_path=pmi_input, output_path='pmi_out.h5') diffraction_parameters = { 'uniform_rotation': True, 'calculate_Compton': False, 'slice_interval': 100, 'number_of_slices': 2, 'pmi_start_ID': 1, 'pmi_stop_ID': 1, 'number_of_diffraction_patterns': 2, 'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'), 'beam_geometry_file': TestUtilities.generateTestFilePath('s2e.geom'), } photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=diffr_input, output_path='diffr_out.h5') photon_detector = PerfectPhotonDetector(parameters=None, input_path='diffr_out.h5', output_path='detector_out.h5') photon_analyzer = S2EReconstruction(parameters=None, input_path='detector_out.h5', output_path='analyzer_out.h5') pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check queries. self.assertIs(pxs.photon_source, photon_source) self.assertIs(pxs.photon_propagator, photon_propagator) self.assertIs(pxs.photon_interactor, photon_interactor) self.assertIs(pxs.photon_diffractor, photon_diffractor) self.assertIs(pxs.photon_detector, photon_detector) self.assertIs(pxs.photon_analyzer, photon_analyzer)
def testConstruction(self): """ Test the default constructor of this class. """ # Setup a minimal experiment simulation. source_input = TestUtilities.generateTestFilePath('FELsource_out.h5') diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.h5') pmi_input = TestUtilities.generateTestFilePath('prop_out.h5') photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path=pmi_input, output_path='pmi_out.h5', sample_path=self.__sample_path) diffraction_parameters = { 'uniform_rotation': True, 'calculate_Compton': False, 'slice_interval': 100, 'number_of_slices': 2, 'pmi_start_ID': 1, 'pmi_stop_ID': 1, 'number_of_diffraction_patterns': 2, 'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'), 'beam_geometry_file': TestUtilities.generateTestFilePath('s2e.geom'), 'number_of_MPI_processes': 2, } photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=diffr_input, output_path='diffr_out.h5') photon_detector = IdealPhotonDetector(parameters=None, input_path='diffr_out.h5', output_path='detector_out.h5') photon_analyzer = S2EReconstruction(parameters=None, input_path='detector_out.h5', output_path='analyzer_out.h5') pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check instance. self.assertIsInstance(pxs, PhotonExperimentSimulation)
def testDefaultConstruction(self): """ Testing the default construction of the class. """ # Ensure proper cleanup. self.__dirs_to_remove.append('analysis') # Construct the object. analyzer = S2EReconstruction() self.assertIsInstance(analyzer, S2EReconstruction) # Check. self.assertEqual(analyzer.input_path, os.path.abspath('detector')) self.assertEqual(analyzer.output_path, os.path.abspath('analysis'))
def testCheckInterfaceConsistency(self): """ Test if the check for interface consistency works correctly. """ # Setup a minimal experiment simulation. source_input = TestUtilities.generateTestFilePath('FELsource_out.h5') diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.h5') pmi_input = TestUtilities.generateTestFilePath('prop_out.h5') photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') pmi_parameters = { 'sample_path': TestUtilities.generateTestFilePath('sample.h5') } photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path=pmi_input, output_path='pmi_out.h5', sample_path=self.__sample_path) diffraction_parameters = self.diffractorParam_1 photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=diffr_input, output_path='diffr_out.h5') photon_detector = IdealPhotonDetector(parameters=None, input_path='diffr_out.h5', output_path='detector_out.h5') photon_analyzer = S2EReconstruction(parameters=None, input_path='detector_out.h5', output_path='analyzer_out.h5') pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) interfaces_are_consistent = pxs._checkInterfaceConsistency() self.assertTrue(interfaces_are_consistent)
def testCalculatorQueries(self): """ Test that the calculator queries return the correct calculators. """ # Setup a minimal experiment simulation. source_input = TestUtilities.generateTestFilePath('FELsource_out.h5') diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.h5') pmi_input = TestUtilities.generateTestFilePath('prop_out.h5') photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path=pmi_input, output_path='pmi_out.h5', sample_path=self.__sample_path) diffraction_parameters = self.diffractorParam_2 photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=diffr_input, output_path='diffr_out.h5') photon_detector = IdealPhotonDetector(parameters=None, input_path='diffr_out.h5', output_path='detector_out.h5') photon_analyzer = S2EReconstruction(parameters=None, input_path='detector_out.h5', output_path='analyzer_out.h5') pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check queries. self.assertIs(pxs.photon_source, photon_source) self.assertIs(pxs.photon_propagator, photon_propagator) self.assertIs(pxs.photon_interactor, photon_interactor) self.assertIs(pxs.photon_diffractor, photon_diffractor) self.assertIs(pxs.photon_detector, photon_detector) self.assertIs(pxs.photon_analyzer, photon_analyzer)
def testBackengineDefaultPath(self): """ Test that we can start a test calculation. """ # Prepare path. shutil.copytree(TestUtilities.generateTestFilePath('diffr'), 'detector') # Ensure proper cleanup. self.__dirs_to_remove.append('detector') self.__dirs_to_remove.append('analysis') emc_parameters = { 'initial_number_of_quaternions': 1, 'max_number_of_quaternions': 2, 'max_number_of_iterations': 10, 'min_error': 1.0e-6, 'beamstop': True, 'detailed_output': False } dm_parameters = { 'number_of_trials': 5, 'number_of_iterations': 2, 'averaging_start': 15, 'leash': 0.2, 'number_of_shrink_cycles': 2, } # Construct the object. analyzer = S2EReconstruction(parameters={ 'EMC_Parameters': emc_parameters, 'DM_Parameters': dm_parameters }) # Call backengine. status = analyzer.backengine() # Check return value. self.assertEqual(status, 0) # Check presence of output files. self.assertTrue(os.path.isdir('analysis')) self.assertIn('orient_out.h5', os.listdir('analysis')) self.assertIn('phase_out.h5', os.listdir('analysis'))
def testConstruction(self): """ Test the default constructor of this class. """ # Setup a minimal experiment simulation. source_input = TestUtilities.generateTestFilePath('FELsource_out.h5') diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.h5') pmi_input = TestUtilities.generateTestFilePath('prop_out.h5') photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path=pmi_input, output_path='pmi_out.h5', sample_path=self.__sample_path) diffraction_parameters = self.diffractorParam_1 photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=diffr_input, output_path='diffr_out.h5') photon_detector = IdealPhotonDetector(parameters=None, input_path='diffr_out.h5', output_path='detector_out.h5') photon_analyzer = S2EReconstruction(parameters=None, input_path='detector_out.h5', output_path='analyzer_out.h5') pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check instance. self.assertIsInstance(pxs, PhotonExperimentSimulation)
def testConstructionExceptions(self): """ Test that the appropriate exceptions are thrown if the object is constructed incorrectly. """ # Setup a minimal experiment simulation. source_input = TestUtilities.generateTestFilePath('FELsource_out.h5') diffr_input = TestUtilities.generateTestFilePath('pmi_out_0000001.h5') pmi_input = TestUtilities.generateTestFilePath('prop_out.h5') photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path=pmi_input, output_path='pmi_out.h5', sample_path=self.__sample_path) diffraction_parameters = self.diffractorParam_1 photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=diffr_input, output_path='diffr_out.h5') photon_detector = IdealPhotonDetector(parameters=None, input_path='diffr_out.h5', output_path='detector_out.h5') photon_analyzer = S2EReconstruction(parameters=None, input_path='detector_out.h5', output_path='analyzer_out.h5') # Check wrong source. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=None, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_propagator, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check wrong propagator. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=None, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_source, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check wrong interactor. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=None, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_source, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check wrong diffractor. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=None, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_source, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check wrong analyzer. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=None, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_diffractor, )
'min_error': 1.0e-8, 'beamstop': 1.0e-5, 'detailed_output': False } dm_parameters = { 'number_of_trials': 5, 'number_of_iterations': 2, 'averaging_start': 15, 'leash': 0.2, 'number_of_shrink_cycles': 2, } reconstructor = S2EReconstruction(parameters={ 'EMC_Parameters': emc_parameters, 'DM_Parameters': dm_parameters }, input_path='detector', output_path='recon.h5') # Setup the photon experiment. pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=reconstructor, ) # Run the experiment. pxs.run()
def testHistory(self): """ Testing that all generated output files contain the history """ # Setup directories. working_directory = 'SPI' self.__dirs_to_remove.append(working_directory) source_dir = os.path.join(working_directory, 'FELsource') prop_dir = os.path.join(working_directory, 'prop') pmi_dir = os.path.join(working_directory, 'pmi') diffr_dir = os.path.join(working_directory, 'diffr') detector_dir = os.path.join(working_directory, 'detector') recon_dir = os.path.join(working_directory, 'recon') # Make directories. os.mkdir(working_directory) os.mkdir(source_dir) os.mkdir(prop_dir) os.mkdir(pmi_dir) os.mkdir(diffr_dir) os.mkdir(detector_dir) os.mkdir(recon_dir) # Location of the FEL source file. source_input = TestUtilities.generateTestFilePath('FELsource_out') # Photon source. photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path=source_dir) # Photon propagator, default parameters. photon_propagator = XFELPhotonPropagator(parameters=None, input_path=source_dir, output_path=prop_dir) # Photon interactor with default parameters. photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path=prop_dir, output_path=pmi_dir, sample_path=self.__sample_path) # Diffraction with parameters. diffraction_parameters = self.diffractorParam_2 photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=TestUtilities.generateTestFilePath('pmi_out'), output_path=diffr_dir) # Reconstruction: EMC+DM emc_parameters = { 'initial_number_of_quaternions': 1, 'max_number_of_quaternions': 9, 'max_number_of_iterations': 3, 'min_error': 1.0e-8, 'beamstop': True, 'detailed_output': False } dm_parameters = { 'number_of_trials': 5, 'number_of_iterations': 2, 'averaging_start': 15, 'leash': 0.2, 'number_of_shrink_cycles': 2, } reconstructor = S2EReconstruction(parameters={ 'EMC_Parameters': emc_parameters, 'DM_Parameters': dm_parameters }, input_path=diffr_dir, output_path=recon_dir) # Perfect detector. photon_detector = IdealPhotonDetector(parameters=None, input_path='diffr', output_path='detector') # Setup the photon experiment. pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=reconstructor, ) # Run the experiment. pxs.run() # Check histories. # prop. with h5py.File(os.path.join(prop_dir, 'prop_out_0000000.h5'), 'r') as prop_h5: self.assertIn('history', list(prop_h5.keys())) self.assertIn('parent', list(prop_h5['history'].keys())) self.assertIn('detail', list(prop_h5['history/parent'].keys())) self.assertIn('parent', list(prop_h5['history/parent'].keys())) prop_h5.close() # pmi. with h5py.File(os.path.join(pmi_dir, 'pmi_out_0000001.h5'), 'r') as pmi_h5: self.assertIn('history', list(pmi_h5.keys())) self.assertIn('parent', list(pmi_h5['history'].keys())) self.assertIn('detail', list(pmi_h5['history/parent'].keys())) self.assertIn('parent', list(pmi_h5['history/parent'].keys())) self.assertIn('detail', list(pmi_h5['history/parent/parent'].keys())) self.assertIn('parent', list(pmi_h5['history/parent/parent'].keys())) pmi_h5.close() # diffr. with h5py.File(os.path.join(diffr_dir, 'diffr_out_0000001.h5'), 'r') as diffr_h5: tasks = list(diffr_h5['data'].keys()) for task in tasks: self.assertIn('history', list(diffr_h5["data"][task].keys())) self.assertIn('parent', list(diffr_h5["data"][task]['history'].keys())) self.assertIn( 'detail', list(diffr_h5["data"][task]['history/parent'].keys())) self.assertIn( 'parent', list(diffr_h5["data"][task]['history/parent'].keys())) self.assertIn( 'parent', list(diffr_h5["data"][task] ['history/parent/parent'].keys())) self.assertIn( 'detail', list(diffr_h5["data"][task] ['history/parent/parent'].keys())) self.assertIn( 'parent', list(diffr_h5["data"][task] ['history/parent/parent/parent'].keys())) self.assertIn( 'detail', list(diffr_h5["data"][task] ['history/parent/parent/parent'].keys())) diffr_h5.close() # phase. with h5py.File(os.path.join(recon_dir, 'phase_out.h5'), 'r') as dm_h5: self.assertIn('history', list(dm_h5.keys())) self.assertIn('error', list(dm_h5['history'].keys())) self.assertIn('object', list(dm_h5['history'].keys())) dm_h5.close()
def testSimS2EWorkflowDefaultPaths(self): """ Testing that a workflow akin to the simS2E example workflow works. No IO paths specified. """ # These directories and files are expected to be present after a successfull calculation. expected_dirs = [ 'source_in', 'source', 'prop', 'pmi', 'diffr', 'analysis', ] expected_files = [ 'source/FELsource_out_0000000.h5', 'source/FELsource_out_0000001.h5', 'prop/prop_out_0000000.h5', 'prop/prop_out_0000001.h5', 'pmi/pmi_out_0000001.h5', 'pmi/pmi_out_0000002.h5', 'diffr/diffr_out_0000001.h5', 'analysis/orient_out.h5', 'analysis/phase_out.h5', ] # Ensure proper cleanup. self.__dirs_to_remove = expected_dirs self.__files_to_remove.append('diffr.h5') self.__files_to_remove.append('detector') # Get proper FEL source files to start from. shutil.copytree(TestUtilities.generateTestFilePath('FELsource_out'), 'source_in') # Photon source. photon_source = XFELPhotonSource(input_path='source_in') # Photon propagator, default parameters. photon_propagator = XFELPhotonPropagator() # Photon interactor with default parameters. photon_interactor = XMDYNDemoPhotonMatterInteractor( sample_path=self.__sample_path) # Diffraction with parameters. diffraction_parameters = { 'uniform_rotation': True, 'calculate_Compton': False, 'slice_interval': 100, 'number_of_slices': 2, 'pmi_start_ID': 1, 'pmi_stop_ID': 2, 'number_of_diffraction_patterns': 1, 'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'), 'beam_geometry_file': TestUtilities.generateTestFilePath('s2e.geom'), 'number_of_MPI_processes': 2 } photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=TestUtilities.generateTestFilePath('pmi_out')) photon_diffractor.parameters.cpus_per_task = 1 # Reconstruction: EMC+DM emc_parameters = { 'initial_number_of_quaternions': 1, 'max_number_of_quaternions': 2, 'max_number_of_iterations': 10, 'min_error': 1.0e-6, 'beamstop': True, 'detailed_output': False } dm_parameters = { 'number_of_trials': 5, 'number_of_iterations': 2, 'averaging_start': 15, 'leash': 0.2, 'number_of_shrink_cycles': 2, } reconstructor = S2EReconstruction(parameters={ 'EMC_Parameters': emc_parameters, 'DM_Parameters': dm_parameters }) # Setup the photon experiment. pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_analyzer=reconstructor, ) # Run the experiment. pxs.run() # Check that all output files and directories are present. for directory in expected_dirs: print(directory) self.assertTrue(os.path.isdir(directory)) for f in expected_files: print(f) self.assertTrue(os.path.isfile(f))
def testSimS2EWorkflowSingleFile(self): """ Testing that a workflow akin to the simS2E example workflow works. Only one I/O file per calculator. """ # These directories and files are expected to be present after a successfull calculation. expected_dirs = [ 'pmi', 'diffr', ] expected_symlinks = ['detector'] expected_files = [ 'FELsource_out.h5', 'prop_out.h5', 'pmi/pmi_out_0000001.h5', 'diffr/diffr_out_0000001.h5', 'detector/diffr_out_0000001.h5', 'recon.h5', 'orient_out.h5', ] # Ensure proper cleanup. self.__files_to_remove = expected_files + expected_symlinks self.__files_to_remove.append('prepHDF5.py') self.__dirs_to_remove = expected_dirs # Location of the FEL source file. source_input = TestUtilities.generateTestFilePath( 'FELsource_out/FELsource_out_0000001.h5') # Photon source. photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') # Photon propagator, default parameters. photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') # Photon interactor with default parameters. photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path='prop_out.h5', output_path='pmi', sample_path=TestUtilities.generateTestFilePath('sample.h5')) # Diffraction with parameters. diffraction_parameters = { 'uniform_rotation': True, 'calculate_Compton': False, 'slice_interval': 100, 'number_of_slices': 2, 'pmi_start_ID': 1, 'pmi_stop_ID': 1, 'number_of_diffraction_patterns': 1, 'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'), 'beam_geometry_file': TestUtilities.generateTestFilePath('s2e.geom'), } photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path='pmi', output_path='diffr') # Perfect detector. photon_detector = PerfectPhotonDetector(parameters=None, input_path='diffr', output_path='detector') # Reconstruction: EMC+DM emc_parameters = { 'initial_number_of_quaternions': 1, 'max_number_of_quaternions': 9, 'max_number_of_iterations': 3, 'min_error': 1.0e-8, 'beamstop': 1.0e-5, 'detailed_output': False } dm_parameters = { 'number_of_trials': 5, 'number_of_iterations': 2, 'averaging_start': 15, 'leash': 0.2, 'number_of_shrink_cycles': 2, } reconstructor = S2EReconstruction(parameters={ 'EMC_Parameters': emc_parameters, 'DM_Parameters': dm_parameters }, input_path='detector', output_path='recon.h5') # Setup the photon experiment. pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=reconstructor, ) # Run the experiment. pxs.run() # Check that all output files and directories are present. for directory in expected_dirs + expected_symlinks: self.assertTrue(os.path.isdir(directory)) for f in expected_files: print f self.assertTrue(os.path.isfile(f))
def testSimS2EWorkflowDirectories(self): """ Testing that a workflow akin to the simS2E example workflow works. Two sources, two diffraction patterns.""" # Setup directories. working_directory = 'SPI' source_dir = os.path.join(working_directory, 'FELsource') prop_dir = os.path.join(working_directory, 'prop') pmi_dir = os.path.join(working_directory, 'pmi') diffr_dir = os.path.join(working_directory, 'diffr') detector_dir = os.path.join(working_directory, 'detector') recon_dir = os.path.join(working_directory, 'recon') # Make directories. os.mkdir(working_directory) os.mkdir(source_dir) os.mkdir(prop_dir) os.mkdir(pmi_dir) os.mkdir(diffr_dir) os.mkdir(detector_dir) os.mkdir(recon_dir) # Ensure proper cleanup. self.__dirs_to_remove.append(working_directory) # Location of the FEL source file. source_input = TestUtilities.generateTestFilePath('FELsource_out') # Photon source. photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path=source_dir) # Photon propagator, default parameters. photon_propagator = XFELPhotonPropagator(parameters=None, input_path=source_dir, output_path=prop_dir) # Photon interactor with default parameters. photon_interactor = XMDYNDemoPhotonMatterInteractor( parameters=None, input_path=prop_dir, output_path=pmi_dir, sample_path=TestUtilities.generateTestFilePath('sample.h5')) # Diffraction with parameters. diffraction_parameters = { 'uniform_rotation': True, 'calculate_Compton': False, 'slice_interval': 100, 'number_of_slices': 2, 'pmi_start_ID': 1, 'pmi_stop_ID': 2, 'number_of_diffraction_patterns': 2, 'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'), 'beam_geometry_file': TestUtilities.generateTestFilePath('s2e.geom'), } photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=pmi_dir, output_path=diffr_dir) # Reconstruction: EMC+DM emc_parameters = { 'initial_number_of_quaternions': 1, 'max_number_of_quaternions': 9, 'max_number_of_iterations': 3, 'min_error': 1.0e-8, 'beamstop': 1.0e-5, 'detailed_output': False } dm_parameters = { 'number_of_trials': 5, 'number_of_iterations': 2, 'averaging_start': 15, 'leash': 0.2, 'number_of_shrink_cycles': 2, } reconstructor = S2EReconstruction(parameters={ 'EMC_Parameters': emc_parameters, 'DM_Parameters': dm_parameters }, input_path=diffr_dir, output_path=recon_dir) # Setup the photon experiment. pxs = PhotonExperimentSimulation( photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=None, photon_analyzer=reconstructor, ) # Run the experiment. pxs.run()
def testConstructionExceptions(self): """ Test that the appropriate exceptions are thrown if the object is constructed incorrectly. """ # Setup a minimal experiment simulation. source_input = TestUtilities.generateTestFilePath('FELsource_out.h5') diffr_input = TestUtilities.generateTestFilePath('pmi_out.h5') pmi_input = TestUtilities.generateTestFilePath('prop_out.h5') photon_source = XFELPhotonSource(parameters=None, input_path=source_input, output_path='FELsource_out.h5') photon_propagator = XFELPhotonPropagator(parameters=None, input_path='FELsource_out.h5', output_path='prop_out.h5') photon_interactor = FakePhotonMatterInteractor( parameters=None, input_path=pmi_input, output_path='pmi_out.h5') diffraction_parameters = { 'uniform_rotation': True, 'calculate_Compton': False, 'slice_interval': 100, 'number_of_slices': 2, 'pmi_start_ID': 1, 'pmi_stop_ID': 1, 'number_of_diffraction_patterns': 2, 'beam_parameter_file': TestUtilities.generateTestFilePath('s2e.beam'), 'beam_geometry_file': TestUtilities.generateTestFilePath('s2e.geom'), } photon_diffractor = SingFELPhotonDiffractor( parameters=diffraction_parameters, input_path=diffr_input, output_path='diffr_out.h5') photon_detector = PerfectPhotonDetector(parameters=None, input_path='diffr_out.h5', output_path='detector_out.h5') photon_analyzer = S2EReconstruction(parameters=None, input_path='detector_out.h5', output_path='analyzer_out.h5') # Check wrong source. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=None, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_propagator, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check wrong propagator. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=None, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_source, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check wrong interactor. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=None, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_source, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check wrong diffractor. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=None, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_source, photon_detector=photon_detector, photon_analyzer=photon_analyzer, ) # Check wrong analyzer. self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=None, ) self.assertRaises( TypeError, PhotonExperimentSimulation, photon_source=photon_source, photon_propagator=photon_propagator, photon_interactor=photon_interactor, photon_diffractor=photon_diffractor, photon_detector=photon_detector, photon_analyzer=photon_diffractor, )