def _createSubSetFromMicrographsTiltPair(self, micrographsTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = MicrographsTiltPair(filename=self._getPath('micrographs_pairs.sqlite'))
print "self._dbName=%s" % self._dbName
modifiedSet = MicrographsTiltPair(filename=self._dbName, prefix=self._dbPrefix)
inputU = micrographsTiltPair.getUntilted()
inputT = micrographsTiltPair.getTilted()
outputU = SetOfMicrographs(filename=self._getPath('mics_untilted.sqlite'))
outputT = SetOfParticles(filename=self._getPath('mics_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
for micPairI in modifiedSet:
untilted = micPairI.getUntilted()
tilted = micPairI.getTilted()
if micPairI.isEnabled():
micPairO = TiltPair()
micPairO.setUntilted(untilted)
micPairO.setTilted(tilted)
output.append(micPairO)
outputU.append(untilted)
outputT.append(tilted)
output.setUntilted(outputU)
output.setTilted(outputT)
# Register outputs
outputDict = {'outputMicrographsTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(micrographsTiltPair, output)
return output
def _createSubSetFromMicrographsTiltPair(self, micrographsTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = MicrographsTiltPair(
filename=self._getPath('micrographs_pairs.sqlite'))
modifiedSet = MicrographsTiltPair(filename=self._dbName,
prefix=self._dbPrefix)
inputU = micrographsTiltPair.getUntilted()
inputT = micrographsTiltPair.getTilted()
outputU = SetOfMicrographs(
filename=self._getPath('mics_untilted.sqlite'))
outputT = SetOfParticles(filename=self._getPath('mics_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
for micPairI in modifiedSet:
untilted = micPairI.getUntilted()
tilted = micPairI.getTilted()
if micPairI.isEnabled():
micPairO = TiltPair()
micPairO.setUntilted(untilted)
micPairO.setTilted(tilted)
output.append(micPairO)
outputU.append(untilted)
outputT.append(tilted)
output.setUntilted(outputU)
output.setTilted(outputT)
# Register outputs
outputDict = {'outputMicrographsTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(micrographsTiltPair, output)
return output
def createTiltedPairsStep(self):
args = {}
self.micsPairsSqlite = self._getPath('micrographs_pairs.sqlite')
cleanPath(self.micsPairsSqlite) # Delete if exists
micsTiltPair = MicrographsTiltPair(filename=self.micsPairsSqlite)
micsU = self.importMicrographs(self.patternUntilted.get(), 'Untilted',
self.voltage.get(), self.sphericalAberration.get(), self.ampContrast.get())
micsT = self.importMicrographs(self.patternTilted.get(), 'Tilted',
self.voltage.get(), self.sphericalAberration.get(), self.ampContrast.get())
micsTiltPair.setUntilted(micsU)
micsTiltPair.setTilted(micsT)
for micU, micT in izip(micsU, micsT):
micsTiltPair.append(TiltPair(micU, micT))
args[self.OUTPUT_NAME] = micsTiltPair
self._defineOutputs(**args)
def _createSubSetFromMicrographsTiltPair(self, micrographsTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = MicrographsTiltPair(filename=self._getPath('micrographs_pairs.sqlite'))
print "self._dbName=%s" % self._dbName
modifiedSet = MicrographsTiltPair(filename=self._dbName, prefix=self._dbPrefix)
for micPairI in modifiedSet:
untilted = micPairI.getUntilted()
tilted = micPairI.getTilted()
if micPairI.isEnabled():
micPairO = TiltPair()
micPairO.setUntilted(untilted)
micPairO.setTilted(tilted)
output.append(micPairO)
# Register outputs
outputDict = {'outputMicrographsTiltPair': output}
self._defineOutputs(**outputDict)
return output
def createTiltedPairsStep(self):
args = {}
self.micsPairsSqlite = self._getPath('micrographs_pairs.sqlite')
cleanPath(self.micsPairsSqlite) # Delete if exists
micsTiltPair = MicrographsTiltPair(filename=self.micsPairsSqlite)
micsU = self.importMicrographs(self.patternUntilted.get(), 'Untilted',
self.voltage.get(),
self.sphericalAberration.get(),
self.ampContrast.get())
micsT = self.importMicrographs(self.patternTilted.get(), 'Tilted',
self.voltage.get(),
self.sphericalAberration.get(),
self.ampContrast.get())
micsTiltPair.setUntilted(micsU)
micsTiltPair.setTilted(micsT)
for micU, micT in izip(micsU, micsT):
micsTiltPair.append(TiltPair(micU, micT))
args[self.OUTPUT_NAME] = micsTiltPair
self._defineOutputs(**args)
def _createSubSetFromMicrographsTiltPair(self, micrographsTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = MicrographsTiltPair(filename=self._getPath('micrographs_pairs.sqlite'))
modifiedSet = MicrographsTiltPair(filename=self._dbName,
prefix=self._dbPrefix)
inputU = micrographsTiltPair.getUntilted()
inputT = micrographsTiltPair.getTilted()
outputU = SetOfMicrographs(filename=self._getPath('mics_untilted.sqlite'))
outputT = SetOfMicrographs(filename=self._getPath('mics_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
for micPair, u, t in izip(modifiedSet, inputU, inputT):
if micPair.isEnabled():
output.append(micPair)
outputU.append(u)
outputT.append(t)
output.setUntilted(outputU)
output.setTilted(outputT)
# Register outputs
outputDict = {'outputMicrographsTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(micrographsTiltPair, output)
return output