def testSingleDiffrFileMultiplePatterns(self):
""" Test that EMC accepts a single (new style) input file from diffraction containing multiple patterns. """
# Cleanup.
self.__files_to_remove.append('orient_out.h5')
# Construct the object.
emc_parameters = {"initial_number_of_quaternions" : 3,
"max_number_of_quaternions" : 4,
"max_number_of_iterations" : 3,
"min_error" : 1.e-6,
"beamstop" : True,
"detailed_output" : True,
}
emc = EMCOrientation(parameters=emc_parameters,
input_path=TestUtilities.generateTestFilePath("diffr_newstyle.h5"),
output_path='orient_out.h5',
tmp_files_path=None,
run_files_path=None,)
# Call backengine.
status = emc.backengine()
# Check success.
self.assertEqual(status, 0)
def testPaths(self):
""" Test that we can start a test calculation. """
self.__files_to_remove.append('orient_out.h5')
# Construct the object.
analyzer = EMCOrientation(parameters=None, input_path=self.input_h5, output_path='orient_out.h5')
# Keep the test short.
analyzer.parameters.max_number_of_iterations=2
# Call backengine.
status = analyzer.backengine()
# Check paths exist and are populated.
run_files_path = analyzer.run_files_path
tmp_files_path = analyzer.tmp_files_path
self.assertTrue( os.path.isdir( run_files_path ) )
self.assertTrue( os.path.isdir( tmp_files_path ) )
expected_run_files = ["finish_intensity.dat", "quaternion.dat",
"detector.dat",
"most_likely_orientations.dat",
"start_intensity.dat",
"EMC_extended.log",
"mutual_info.dat",
"EMC.log",
"photons.dat",
]
for ef in expected_run_files:
self.assertIn( ef, os.listdir(run_files_path) )
def testBackengine(self):
""" Test that we can start a test calculation. """
self.__files_to_remove.append('orient_out.h5')
# Construct the object.
analyzer = EMCOrientation(parameters=None, input_path=self.input_h5, output_path='orient_out.h5')
# Call backengine.
status = analyzer.backengine()
self.assertEqual(status, 0)
def testPaths(self):
""" Test that we can start a test calculation. """
self.__files_to_remove.append('orient_out.h5')
# Construct the object with very nonsensical iteration control parameters.
emc_parameters = {
"initial_number_of_quaternions": 1,
"max_number_of_quaternions": 2,
"max_number_of_iterations": 2,
"min_error": 5.e-6,
"beamstop": True,
"detailed_output": True,
}
# Case 1: no paths given, make dirs in /tmp
emc = EMCOrientation(
parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path=None,
run_files_path=None,
)
# Construct the object.
# Keep the test short.
emc.parameters.max_number_of_iterations = 2
# Call backengine.
status = emc.backengine()
# Check paths exist and are populated.
run_files_path = emc.run_files_path
tmp_files_path = emc.tmp_files_path
self.assertTrue(os.path.isdir(run_files_path))
self.assertTrue(os.path.isdir(tmp_files_path))
expected_run_files = [
"finish_intensity.dat",
"quaternion.dat",
"detector.dat",
"most_likely_orientations.dat",
"start_intensity.dat",
"EMC_extended.log",
"mutual_info.dat",
"EMC.log",
"photons.dat",
]
for ef in expected_run_files:
self.assertIn(ef, os.listdir(run_files_path))
def testBackengine(self):
""" Test that we can start a test calculation. """
self.__files_to_remove.append('orient_out.h5')
# Construct the object.
analyzer = EMCOrientation(parameters=None,
input_path=self.input_h5,
output_path='orient_out.h5')
# Call backengine.
status = analyzer.backengine()
self.assertEqual(status, 0)
def testConstruction(self):
""" Testing the default construction of the class. """
# Construct the object.
analyzer = EMCOrientation(parameters=None,
input_path=self.input_h5,
output_path='orient_out.h5')
self.assertIsInstance(analyzer, EMCOrientation)
def testConstruction(self):
""" Testing the default construction of the class. """
# Construct the object.
analyzer = EMCOrientation()
# Test a parameter.
self.assertEqual(analyzer.parameters.initial_number_of_quaternions, 1)
self.assertIsInstance(analyzer, EMCOrientation)
def testDiffr0_2(self):
""" Test that we can handle diffr input version 0.2 """
self.__files_to_remove.append('orient_out.h5')
# Construct the object.
emc_parameters = {
"initial_number_of_quaternions": 2,
"max_number_of_quaternions": 4,
"max_number_of_iterations": 10,
"min_error": 1.e-6,
"beamstop": True,
"detailed_output": True,
}
emc = EMCOrientation(
parameters=emc_parameters,
input_path=TestUtilities.generateTestFilePath("diffr_0.2"),
output_path='orient_out.h5',
tmp_files_path=None,
run_files_path=None,
)
# Call backengine.
status = emc.backengine()
self.assertEqual(status, 0)
# Cleanup.
self.__files_to_remove.append('orient_out.h5')
# Construct the object.
emc_parameters = {
"initial_number_of_quaternions": 3,
"max_number_of_quaternions": 4,
"max_number_of_iterations": 3,
"min_error": 1.e-6,
"beamstop": True,
"detailed_output": True,
}
emc = EMCOrientation(
parameters=emc_parameters,
input_path=TestUtilities.generateTestFilePath("diffr_newstyle.h5"),
output_path='orient_out.h5',
tmp_files_path=None,
run_files_path=None,
)
# Call backengine.
status = emc.backengine()
# Check success.
self.assertEqual(status, 0)
def testConstructionParameters(self):
""" Testing the construction of the class with a parameters object. """
# Construct the object.
emc_parameters = EMCOrientationParameters(
initial_number_of_quaternions=2,
max_number_of_quaternions=4,
max_number_of_iterations=5,
min_error=1.e-6,
beamstop=False,
detailed_output=False)
analyzer = EMCOrientation(parameters=emc_parameters)
# Test a parameter.
self.assertEqual(analyzer.parameters.initial_number_of_quaternions, 2)
self.assertIsInstance(analyzer, EMCOrientation)
def testConstructionParametersDict(self):
""" Testing the construction of the class with a parameters dictionary. """
# Construct the object.
emc_parameters = {
'initial_number_of_quaternions': 2,
'max_number_of_quaternions': 4,
'max_number_of_iterations': 5,
'min_error': 1.e-6,
'beamstop': False,
'detailed_output': False
}
analyzer = EMCOrientation(parameters=emc_parameters)
# Test a parameter.
self.assertEqual(analyzer.parameters.initial_number_of_quaternions, 2)
self.assertIsInstance(analyzer, EMCOrientation)
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: The parameters for the reconstruction.
:type parameters: dict
:example parameters: parameters={'EMC_Parameters' : EMCOrientationParameters(), 'DM_Parameters' : DMPhasingParameters()} # Use default parameters for EMC and DM.
:param input_path: Path for input data.
:type input_path: str
:param output_path: Path where to write output to.
:type output_path: str
"""
# Initialize base class.
super(S2EReconstruction, self).__init__(parameters, input_path,
output_path)
self.__provided_data = [
'/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
self.__expected_data = [
'/data/data',
'/data/diffr',
'/data/angle',
'/history/parent/detail',
'/history/parent/parent',
'/info/package_version',
'/info/contact',
'/info/data_description',
'/info/method_description',
'/params/geom/detectorDist',
'/params/geom/pixelWidth',
'/params/geom/pixelHeight',
'/params/geom/mask',
'/params/beam/photonEnergy',
'/params/beam/photons',
'/params/beam/focusArea',
'/params/info',
]
emc_parameters = None
dm_parameters = None
# Construct emc and dm calculators.
if self.parameters != {}:
emc_parameters = self.parameters['EMC_Parameters']
dm_parameters = self.parameters['DM_Parameters']
if os.path.isdir(self.output_path):
intermediate_output_path = os.path.join(self.output_path,
'orient_out.h5')
else:
intermediate_output_path = 'orient_out.h5'
self.__emc = EMCOrientation(emc_parameters, self.input_path,
intermediate_output_path)
self.__dm = DMPhasing(dm_parameters, intermediate_output_path,
self.output_path)
class S2EReconstruction(AbstractPhotonAnalyzer):
"""
:class S2EReconstruction: Class representing photon data analysis for electron density reconstruction from 2D diffraction patterns.
Wraps the EMC orientation module and the DM phasing module.
"""
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: The parameters for the reconstruction.
:type parameters: dict
:example parameters: parameters={'EMC_Parameters' : EMCOrientationParameters(), 'DM_Parameters' : DMPhasingParameters()} # Use default parameters for EMC and DM.
:param input_path: Path for input data.
:type input_path: str
:param output_path: Path where to write output to.
:type output_path: str
"""
# Initialize base class.
super(S2EReconstruction, self).__init__(parameters, input_path,
output_path)
self.__provided_data = [
'/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
self.__expected_data = [
'/data/data',
'/data/diffr',
'/data/angle',
'/history/parent/detail',
'/history/parent/parent',
'/info/package_version',
'/info/contact',
'/info/data_description',
'/info/method_description',
'/params/geom/detectorDist',
'/params/geom/pixelWidth',
'/params/geom/pixelHeight',
'/params/geom/mask',
'/params/beam/photonEnergy',
'/params/beam/photons',
'/params/beam/focusArea',
'/params/info',
]
emc_parameters = None
dm_parameters = None
# Construct emc and dm calculators.
if self.parameters != {}:
emc_parameters = self.parameters['EMC_Parameters']
dm_parameters = self.parameters['DM_Parameters']
if os.path.isdir(self.output_path):
intermediate_output_path = os.path.join(self.output_path,
'orient_out.h5')
else:
intermediate_output_path = 'orient_out.h5'
self.__emc = EMCOrientation(emc_parameters, self.input_path,
intermediate_output_path)
self.__dm = DMPhasing(dm_parameters, intermediate_output_path,
self.output_path)
def expectedData(self):
""" Query for the data expected by the Analyzer. """
return self.__expected_data
def providedData(self):
""" Query for the data provided by the Analyzer. """
return self.__provided_data
@property
def data(self):
""" Query for the field data. """
return self.__data
def _readH5(self):
""" """
""" Private method for reading the hdf5 input and extracting the parameters and data relevant to initialize the object. """
pass # Nothing to be done since IO happens in backengine.
def saveH5(self):
""" """
"""
Private method to save the object to a file.
:param output_path: The file where to save the object's data.
:type output_path: str
"""
pass # No action required since output is written in backengine.
def backengine(self):
""" Run the EMC and DM backengine executables. """
# Run EMC.
emc_status = self.__emc.backengine()
# If EMC was not successful, return with error code.
if emc_status != 0:
return emc_status
# Else run DM.
return self.__dm.backengine()
def testPhotonFileConsecutiveRuns(self):
""" Check that the photons.dat from the previous run is reused. """
self.__files_to_remove.append('orient_out.h5')
self.__files_to_remove.append('orient_out2.h5')
# Construct the object.
emc_parameters = {
"initial_number_of_quaternions": 1,
"max_number_of_quaternions": 2,
"max_number_of_iterations": 2,
"min_error": 1.e-6,
"beamstop": True,
"detailed_output": True,
}
emc = EMCOrientation(
parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path=None,
run_files_path=None,
)
# Call backengine.
status = emc.backengine()
# Check paths exist and are populated.
run_files_path = emc.run_files_path
tmp_files_path = emc.tmp_files_path
self.assertTrue(os.path.isdir(run_files_path))
self.assertTrue(os.path.isdir(tmp_files_path))
expected_run_files = [
"finish_intensity.dat",
"quaternion.dat",
"detector.dat",
"most_likely_orientations.dat",
"start_intensity.dat",
"EMC_extended.log",
"mutual_info.dat",
"EMC.log",
"photons.dat",
]
for ef in expected_run_files:
self.assertIn(ef, os.listdir(run_files_path))
# Second run.
emc2 = EMCOrientation(parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out2.h5',
tmp_files_path=emc.tmp_files_path,
run_files_path=None)
# Call backengine.
status = emc2.backengine()
# Check paths exist and are populated.
run_files_path2 = emc2.run_files_path
tmp_files_path2 = emc2.tmp_files_path
self.assertNotEqual(run_files_path, run_files_path2)
self.assertEqual(tmp_files_path, tmp_files_path2)
expected_run_files2 = [
"finish_intensity.dat",
"quaternion.dat",
"detector.dat",
"most_likely_orientations.dat",
"start_intensity.dat",
"EMC_extended.log",
"mutual_info.dat",
"EMC.log",
"photons.dat",
]
for ef in expected_run_files2:
self.assertIn(ef, os.listdir(run_files_path2))
def testSetupPaths(self):
""" Check that setting up paths works correctly. """
# Clean up no matter how tests go.
self.__dirs_to_remove.append("emc_run")
self.__dirs_to_remove.append("emc_tmp")
# Construct the object with very nonsensical iteration control parameters.
emc_parameters = {
"initial_number_of_quaternions": 1,
"max_number_of_quaternions": 2,
"max_number_of_iterations": 2,
"min_error": 5.e-6,
"beamstop": True,
"detailed_output": True,
}
# Case 1: no paths given, make dirs in /tmp
emc = EMCOrientation(
parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path=None,
run_files_path=None,
)
run, tmp = emc._setupPaths()
# Check.
self.assertTrue(os.path.isdir(emc.run_files_path))
self.assertTrue(os.path.isdir(emc.tmp_files_path))
self.assertEqual(run, emc.run_files_path)
self.assertEqual(tmp, emc.tmp_files_path)
# Case 1: non-existing paths given, make dirs.
emc2 = EMCOrientation(
parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path="emc_tmp",
run_files_path="emc_run",
)
run, tmp = emc2._setupPaths()
# Check.
self.assertEqual(emc2.run_files_path, "emc_run")
self.assertEqual(emc2.tmp_files_path, "emc_tmp")
self.assertEqual(emc2.run_files_path, run)
self.assertEqual(emc2.tmp_files_path, tmp)
# Case 3: existing tmp path given, make dirs.
emc3 = EMCOrientation(
parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path="emc_tmp",
run_files_path=None,
)
run, tmp = emc3._setupPaths()
# Check.
self.assertTrue(os.path.dirname(emc3.run_files_path), "tmp")
self.assertEqual(emc3.tmp_files_path, "emc_tmp")
self.assertEqual(emc3.run_files_path, run)
self.assertEqual(emc3.tmp_files_path, tmp)
# Case 4: existing run path given, raise exception.
self.assertRaises(IOError,
EMCOrientation,
parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path="emc_tmp",
run_files_path=emc3.run_files_path)
def testPhotonFileConsecutiveRuns(self):
""" Check that the photons.dat from the previous run is reused. """
self.__files_to_remove.append('orient_out.h5')
self.__files_to_remove.append('orient_out2.h5')
# Construct the object.
emc_parameters = {"initial_number_of_quaternions" : 1,
"max_number_of_quaternions" : 2,
"max_number_of_iterations" : 2,
"min_error" : 1.e-6,
"beamstop" : True,
"detailed_output" : True,
}
emc = EMCOrientation(parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path=None,
run_files_path=None,)
# Call backengine.
status = emc.backengine()
# Check paths exist and are populated.
run_files_path = emc.run_files_path
tmp_files_path = emc.tmp_files_path
self.assertTrue( os.path.isdir( run_files_path ) )
self.assertTrue( os.path.isdir( tmp_files_path ) )
expected_run_files = ["finish_intensity.dat", "quaternion.dat",
"detector.dat",
"most_likely_orientations.dat",
"start_intensity.dat",
"EMC_extended.log",
"mutual_info.dat",
"EMC.log",
"photons.dat",
]
for ef in expected_run_files:
self.assertIn( ef, os.listdir(run_files_path) )
# Second run.
emc2 = EMCOrientation(parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out2.h5',
tmp_files_path=emc.tmp_files_path,
run_files_path=None)
# Call backengine.
status = emc2.backengine()
# Check paths exist and are populated.
run_files_path2 = emc2.run_files_path
tmp_files_path2 = emc2.tmp_files_path
self.assertNotEqual( run_files_path, run_files_path2 )
self.assertEqual( tmp_files_path, tmp_files_path2 )
expected_run_files2 = ["finish_intensity.dat", "quaternion.dat",
"detector.dat",
"most_likely_orientations.dat",
"start_intensity.dat",
"EMC_extended.log",
"mutual_info.dat",
"EMC.log",
"photons.dat",
]
for ef in expected_run_files2:
self.assertIn( ef, os.listdir(run_files_path2) )
def testSetupPaths( self ):
""" Check that setting up paths works correctly. """
# Clean up no matter how tests go.
self.__dirs_to_remove.append("emc_run")
self.__dirs_to_remove.append("emc_tmp")
# Construct the object with very nonsensical iteration control parameters.
emc_parameters = {"initial_number_of_quaternions" : 1,
"max_number_of_quaternions" : 2,
"max_number_of_iterations" : 2,
"min_error" : 5.e-6,
"beamstop" : True,
"detailed_output" : True,
}
# Case 1: no paths given, make dirs in /tmp
emc = EMCOrientation(parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path=None,
run_files_path=None,)
run, tmp = emc._setupPaths()
# Check.
self.assertTrue( os.path.isdir( emc.run_files_path ) )
self.assertTrue( os.path.isdir( emc.tmp_files_path ) )
self.assertEqual( run, emc.run_files_path )
self.assertEqual( tmp, emc.tmp_files_path )
# Case 1: non-existing paths given, make dirs.
emc2 = EMCOrientation(parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path="emc_tmp",
run_files_path="emc_run",)
run, tmp = emc2._setupPaths()
# Check.
self.assertEqual( emc2.run_files_path, "emc_run" )
self.assertEqual( emc2.tmp_files_path, "emc_tmp" )
self.assertEqual( emc2.run_files_path, run )
self.assertEqual( emc2.tmp_files_path, tmp )
# Case 3: existing tmp path given, make dirs.
emc3 = EMCOrientation(parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path="emc_tmp",
run_files_path=None,)
run, tmp = emc3._setupPaths()
# Check.
self.assertTrue( os.path.dirname( emc3.run_files_path ), "tmp" )
self.assertEqual( emc3.tmp_files_path, "emc_tmp" )
self.assertEqual( emc3.run_files_path, run )
self.assertEqual( emc3.tmp_files_path, tmp )
# Case 4: existing run path given, raise exception.
self.assertRaises( IOError, EMCOrientation,
parameters=emc_parameters,
input_path=self.input_h5,
output_path='orient_out.h5',
tmp_files_path="emc_tmp",
run_files_path=emc3.run_files_path
)