def tes_execute_MosflmIndexingTask_TRYP_X1_4(self):
UtilsTest.loadTestImage('ref-TRYP-X1_4_0001.cbf')
UtilsTest.loadTestImage('ref-TRYP-X1_4_0002.cbf')
UtilsTest.loadTestImage('ref-TRYP-X1_4_0003.cbf')
UtilsTest.loadTestImage('ref-TRYP-X1_4_0004.cbf')
referenceDataPath = self.dataPath / 'mosflm_indexing_TRYP-X1_4.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
mosflmIndexingTask = MosflmIndexingTask(inData=inData)
mosflmIndexingTask.execute()
self.assertTrue(mosflmIndexingTask.isSuccess())
def test_generateMOSFLMCommands_indexing(self):
tempdir = tempfile.mkdtemp(prefix='generateMOSFLMCommands_indexing_test_')
tmpWorkingDir = pathlib.Path(tempdir)
referenceDataPath = self.dataPath / 'mosflm_abstract_input.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
task = MosflmIndexingTask(inData)
listCommands = task.generateMOSFLMCommands(inData, tmpWorkingDir)
for requiredItem in ['BEAM', 'DETECTOR', 'OMEGA', 'REVERSEPHI',
'DIRECTORY', 'TEMPLATE', 'LIMITS EXCLUDE',
'RASTER', 'POLARIZATION']:
self.assertTrue(requiredItem in ' '.join(listCommands))
shutil.rmtree(tempdir)
def test_parseIndexingMosflmOutput(self):
newMatFilePath = self.dataPath / 'newmat.txt'
dnaTablesPath = self.dataPath / 'indexingTwoImagesDnaTables.xml'
task = MosflmIndexingTask(inData={})
outData = task.parseIndexingMosflmOutput(newMatFilePath, dnaTablesPath)
for parameter in ['newmat', 'mosaicityEstimation', 'deviationAngular',
'refinedDistance', 'spotsUsed', 'spotsTotal',
'selectedSolutionNumber',
'selectedSolutionSpaceGroup',
'selectedSolutionSpaceGroupNumber',
'indexingSolution']:
self.assertTrue(parameter in outData, parameter)
def test_parseIndexingMosflmOutput(self):
newMatFilePath = self.dataPath / "newmat.txt"
dnaTablesPath = self.dataPath / "indexingTwoImagesDnaTables.xml"
task = MosflmIndexingTask(inData={})
outData = task.parseIndexingMosflmOutput(newMatFilePath, dnaTablesPath)
for parameter in [
"newmat",
"mosaicityEstimation",
"deviationAngular",
"refinedDistance",
"spotsUsed",
"spotsTotal",
"selectedSolutionNumber",
"selectedSolutionSpaceGroup",
"selectedSolutionSpaceGroupNumber",
"indexingSolution",
]:
self.assertTrue(parameter in outData, parameter)
def test_generateMOSFLMCommands_indexing(self):
tempdir = tempfile.mkdtemp(
prefix="generateMOSFLMCommands_indexing_test_")
tmpWorkingDir = pathlib.Path(tempdir)
referenceDataPath = self.dataPath / "mosflm_abstract_input.json"
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
task = MosflmIndexingTask(inData)
listCommands = task.generateMOSFLMCommands(inData, tmpWorkingDir)
for requiredItem in [
"BEAM",
"DETECTOR",
"OMEGA",
"REVERSEPHI",
"DIRECTORY",
"TEMPLATE",
"LIMITS EXCLUDE",
"RASTER",
"POLARIZATION",
]:
self.assertTrue(requiredItem in " ".join(listCommands))
shutil.rmtree(tempdir)
def test_execute_MosflmIndexingTask_TRYP_X1_4(self):
referenceDataPath = self.dataPath / 'TRYP-X1_4.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
mosflmIndexingTask = MosflmIndexingTask(inData=inData)
mosflmIndexingTask.execute()
self.assertTrue(mosflmIndexingTask.isSuccess())
def test_execute_MosflmIndexingTask_fae_3(self):
referenceDataPath = self.dataPath / "mosflm_indexing_fae_3.json"
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
mosflmIndexingTask = MosflmIndexingTask(inData=inData)
mosflmIndexingTask.execute()
self.assertTrue(mosflmIndexingTask.isSuccess())