def test_getTables(self):
dictDnaTables = UtilsDnaTables.getDict(
self.dataPath / "indexingTwoImagesDnaTables.xml")
listTables = UtilsDnaTables.getTables(dictDnaTables,
"autoindex_solutions")
# logger.info(pprint.pformat(listTables))
self.assertGreaterEqual(len(list(listTables)), 1)
def test_getListParam(self):
dictDnaTables = UtilsDnaTables.getDict(
self.dataPath / 'indexingTwoImagesDnaTables.xml')
listTables = UtilsDnaTables.getTables(dictDnaTables,
'autoindex_solutions')
listParameter = UtilsDnaTables.getListParam(listTables[0])
# logger.info(pprint.pformat(listParameter))
self.assertGreaterEqual(len(listParameter), 1)
def test_getListValue(self):
# Mosaicity
dictDnaTables = UtilsDnaTables.getDict(
self.dataPath / "indexingTwoImagesDnaTables.xml")
listTables = UtilsDnaTables.getTables(dictDnaTables,
"mosaicity_estimation")
listParameter = UtilsDnaTables.getListParam(listTables[0])
# logger.info(pprint.pformat(listParameter))
self.assertEqual(
UtilsDnaTables.getListValue(listParameter, "mosaicity", "value"),
0.1)
# Refinement
listTablesRefinement = UtilsDnaTables.getTables(
dictDnaTables, "refinement")
tableRefinement = listTablesRefinement[0]
listParamRefinement = UtilsDnaTables.getListParam(tableRefinement)
# logger.info(pprint.pformat(listParamRefinement))
self.assertEqual(
UtilsDnaTables.getListValue(listParamRefinement, "parameters",
"used"), 204)
self.assertEqual(
UtilsDnaTables.getListValue(listParamRefinement, "results",
"detector_distance"),
305.222015,
)
self.assertEqual(
UtilsDnaTables.getListValue(listParamRefinement, "deviations",
"positional"),
1.351692,
)
def test_getListValue(self):
# Mosaicity
dictDnaTables = UtilsDnaTables.getDict(
self.dataPath / 'indexingTwoImagesDnaTables.xml')
listTables = UtilsDnaTables.getTables(dictDnaTables,
'mosaicity_estimation')
listParameter = UtilsDnaTables.getListParam(listTables[0])
# logger.info(pprint.pformat(listParameter))
self.assertEqual(
UtilsDnaTables.getListValue(listParameter, 'mosaicity', 'value'),
0.1)
# Refinement
listTablesRefinement = UtilsDnaTables.getTables(
dictDnaTables, 'refinement')
tableRefinement = listTablesRefinement[0]
listParamRefinement = UtilsDnaTables.getListParam(tableRefinement)
# logger.info(pprint.pformat(listParamRefinement))
self.assertEqual(
UtilsDnaTables.getListValue(listParamRefinement, 'parameters',
'used'), 204)
self.assertEqual(
UtilsDnaTables.getListValue(listParamRefinement, 'results',
'detector_distance'), 305.222015)
self.assertEqual(
UtilsDnaTables.getListValue(listParamRefinement, 'deviations',
'positional'), 1.351692)
def test_getItemValue(self):
dictDnaTables = UtilsDnaTables.getDict(
self.dataPath / "indexingTwoImagesDnaTables.xml")
listTables = UtilsDnaTables.getTables(dictDnaTables,
"autoindex_solutions")
listParameter = UtilsDnaTables.getListParam(listTables[0])
dictParam = listParameter[0]
# logger.info(pprint.pformat(dictParam))
self.assertEqual(UtilsDnaTables.getItemValue(dictParam, "penalty"),
999)
self.assertEqual(UtilsDnaTables.getItemValue(dictParam, "lattice"),
"cI")
self.assertEqual(UtilsDnaTables.getItemValue(dictParam, "a"),
121.869148)
def test_getItemValue(self):
dictDnaTables = UtilsDnaTables.getDict(
self.dataPath / 'indexingTwoImagesDnaTables.xml')
listTables = UtilsDnaTables.getTables(dictDnaTables,
'autoindex_solutions')
listParameter = UtilsDnaTables.getListParam(listTables[0])
dictParam = listParameter[0]
# logger.info(pprint.pformat(dictParam))
self.assertEqual(UtilsDnaTables.getItemValue(dictParam, 'penalty'),
999)
self.assertEqual(UtilsDnaTables.getItemValue(dictParam, 'lattice'),
'cI')
self.assertEqual(UtilsDnaTables.getItemValue(dictParam, 'a'),
121.869148)
def test_getDict(self):
dictDnaTables = UtilsDnaTables.getDict(
self.dataPath / "indexingTwoImagesDnaTables.xml")
# logger.info(pprint.pformat(dictDnaTables))
self.assertTrue(dictDnaTables is not None)
def parseIndexingMosflmOutput(self, newMatFilePath, dnaTablesFilePath):
outData = {}
# Read Newmat file
newmat = self.getNewmat(newMatFilePath)
if newmat is None:
errorMessage = "MOSFLM indexing error : No solution was obtained!"
logger.error(errorMessage)
self.setFailure()
else:
outData['newmat'] = self.getNewmat(newMatFilePath)
# Then read the XML file
dictDnaTables = UtilsDnaTables.getDict(dnaTablesFilePath)
# Mosaicity estimation
listTablesMosaicity = UtilsDnaTables.getTables(
dictDnaTables, 'mosaicity_estimation')
mosaicityValueSum = 0.0
nValues = 0
for table in listTablesMosaicity:
listParam = UtilsDnaTables.getListParam(table)
mosaicityValue = UtilsDnaTables.getListValue(
listParam, 'mosaicity', 'value')
mosaicityValueSum += mosaicityValue
nValues += 1
outData['mosaicityEstimation'] = mosaicityValueSum / nValues
# Refinement
listTablesRefinement = UtilsDnaTables.getTables(
dictDnaTables, 'refinement')
tableRefinement = listTablesRefinement[0]
listParamRefinement = UtilsDnaTables.getListParam(tableRefinement)
outData['deviationAngular'] = UtilsDnaTables.getListValue(
listParamRefinement, 'deviations', 'angular')
outData['refinedDistance'] = UtilsDnaTables.getListValue(
listParamRefinement, 'results', 'detector_distance')
outData['spotsUsed'] = UtilsDnaTables.getListValue(
listParamRefinement, 'parameters', 'used')
outData['spotsTotal'] = UtilsDnaTables.getListValue(
listParamRefinement, 'parameters', 'out_of')
# Solution refinement
listTablesSolutionRefinement = UtilsDnaTables.getTables(
dictDnaTables, 'solution_refinement')
tableSolutionRefinement = listTablesSolutionRefinement[0]
listSolutionRefinement = UtilsDnaTables.getListParam(
tableSolutionRefinement)
outData['selectedSolutionNumber'] = UtilsDnaTables.getListValue(
listSolutionRefinement, 'selection', 'number')
outData[
'selectedSolutionSpaceGroup'] = UtilsDnaTables.getListValue(
listSolutionRefinement, 'selection', 'spacegroup')
outData[
'selectedSolutionSpaceGroupNumber'] = UtilsDnaTables.getListValue(
listSolutionRefinement, 'selection', 'spacegroup_number')
# Autoindex solutions
listTablesAutoIndexSolution = UtilsDnaTables.getTables(
dictDnaTables, 'autoindex_solutions')
listIndexingSolution = []
tablesAutoIndexSolution = listTablesAutoIndexSolution[0]
listAutoindexSolutions = UtilsDnaTables.getListParam(
tablesAutoIndexSolution)
for autoIndexSolution in listAutoindexSolutions:
indexingSolution = {
'index':
UtilsDnaTables.getItemValue(autoIndexSolution, 'index'),
'penalty':
UtilsDnaTables.getItemValue(autoIndexSolution, 'penalty'),
'lattice':
UtilsDnaTables.getItemValue(autoIndexSolution, 'lattice'),
'a':
UtilsDnaTables.getItemValue(autoIndexSolution, 'a'),
'b':
UtilsDnaTables.getItemValue(autoIndexSolution, 'b'),
'c':
UtilsDnaTables.getItemValue(autoIndexSolution, 'c'),
'alpha':
UtilsDnaTables.getItemValue(autoIndexSolution, 'alpha'),
'beta':
UtilsDnaTables.getItemValue(autoIndexSolution, 'beta'),
'gamma':
UtilsDnaTables.getItemValue(autoIndexSolution, 'gamma')
}
listIndexingSolution.append(indexingSolution)
outData['indexingSolution'] = listIndexingSolution
# Beam refinement
listTablesBeamRefinement = UtilsDnaTables.getTables(
dictDnaTables, 'beam_refinement')
tableBeamRefinement = listTablesBeamRefinement[0]
listRefinedBeam = UtilsDnaTables.getListParam(tableBeamRefinement)
initialBeamPositionX = UtilsDnaTables.getListValue(
listRefinedBeam, 'initial_beam', 'x')
initialBeamPositionY = UtilsDnaTables.getListValue(
listRefinedBeam, 'initial_beam', 'y')
refinedBeamPositionX = UtilsDnaTables.getListValue(
listRefinedBeam, 'refined_beam', 'x')
refinedBeamPositionY = UtilsDnaTables.getListValue(
listRefinedBeam, 'refined_beam', 'y')
beamPositionRefined = {
'x': refinedBeamPositionX,
'y': refinedBeamPositionY
}
outData['refinedBeam'] = beamPositionRefined
beamPositionShift = {
'x': initialBeamPositionX - refinedBeamPositionX,
'y': initialBeamPositionY - refinedBeamPositionY,
}
outData['beamShift'] = beamPositionShift
return outData