def createOutputStep(self):
posDir = self._getExtraPath()
coordSet = self._createSetOfCoordinates(self.inputMics)
readSetOfCoordinates(posDir, self.inputMics, coordSet)
self._defineOutputs(outputCoordinates=coordSet)
self._defineSourceRelation(self.inputMicrographs, coordSet)
boxSize = Integer(coordSet.getBoxSize())
self._defineOutputs(boxsize=boxSize)
self._defineSourceRelation(self.inputMicrographs.get(), boxSize)
def createDiscardedStep(self):
posDir = self._getExtraPath()
suffixRoot = self._ProtParticlePicking__getOutputSuffix()
suffix = '' if suffixRoot=='2' or suffixRoot=='' \
else str(int(suffixRoot)-1)
coordSetDisc = self._createSetOfCoordinates(self.inputMics,
suffix='Discarded'+suffix)
readSetOfCoordinates(posDir, self.inputMics, coordSetDisc,
readDiscarded=True)
if coordSetDisc.getSize()>0:
outputName = 'outputDiscardedCoordinates' + suffix
outputs = {outputName: coordSetDisc}
self._defineOutputs(**outputs)
self._defineSourceRelation(self.inputMicrographs, coordSetDisc)
def _readCoordinates(self, coordsDir, suffix=''):
micTiltPairs = self.inputMicrographsTiltedPair.get()
uSuffix = 'Untilted' + suffix
tSuffix = 'Tilted' + suffix
uSet = micTiltPairs.getUntilted()
tSet = micTiltPairs.getTilted()
# Create Untilted and Tilted SetOfCoordinates
uCoordSet = self._createSetOfCoordinates(uSet, suffix=uSuffix)
convert.readSetOfCoordinates(coordsDir, uSet, uCoordSet)
uCoordSet.write()
tCoordSet = self._createSetOfCoordinates(tSet, suffix=tSuffix)
convert.readSetOfCoordinates(coordsDir, tSet, tCoordSet)
tCoordSet.write()
boxSize = self._getBoxSize()
if boxSize:
uCoordSet.setBoxSize(boxSize)
tCoordSet.setBoxSize(boxSize)
return uCoordSet, tCoordSet
def _updateOutputCoordSet(self, micList, streamMode):
# Do no proceed if there is not micrograph ready
if not micList:
return []
outputDir = self._getExtraPath('outputCoords')
outputCoords = self.getOutput()
# If there are not outputCoordinates yet, it means that is the first
# time we are updating output coordinates, so we need to first create
# the output set
firstTime = outputCoords is None
if firstTime:
if self.micsSource == SAME_AS_PICKING or self.useOtherScale.get(
) == 1:
boxSize = self.getBoxSize()
micSetPtr = self.getInputMicrographs()
else:
boxSize = self.inputCoordinates.get().getBoxSize()
micSetPtr = self.inputCoordinates.get().getMicrographs()
outputCoords = self._createSetOfCoordinates(
micSetPtr, suffix=self.getAutoSuffix())
outputCoords.copyInfo(self.inputCoordinates.get())
outputCoords.setBoxSize(boxSize)
else:
outputCoords.enableAppend()
self.info("Reading coordinates from mics: %s" %
','.join([mic.strId() for mic in micList]))
readSetOfCoordinates(outputDir,
micList,
outputCoords,
scale=self._getScale())
self.debug(" _updateOutputCoordSet Stream Mode: %s " % streamMode)
self._updateOutputSet(self.getOutputName(), outputCoords, streamMode)
if firstTime:
self._defineSourceRelation(micSetPtr, outputCoords)
return micList
def readSetOfCoordsFromPosFnames(posDir, setOfInputCoords, sqliteOutName,
write=True):
"""
posDir: path where there are .pos files with coordinates
setOfInputCoords. Set to find micrographs
sqliteOutName. Path where sqlite map will be created. Warning, it overwrites
content
"""
inputMics = setOfInputCoords.getMicrographs()
cleanPath(sqliteOutName)
setOfOutputCoordinates= SetOfCoordinates(filename= sqliteOutName)
setOfOutputCoordinates.setMicrographs(inputMics)
setOfOutputCoordinates.setBoxSize(setOfInputCoords.getBoxSize())
readSetOfCoordinates(posDir, micSet=inputMics,
coordSet=setOfOutputCoordinates,
readDiscarded=False)
if write:
setOfOutputCoordinates.write()
return setOfOutputCoordinates
def registerCoords(self, coordsDir):
""" This method is usually inherited by all Pickers
and it is used from the Java picking GUI to register
a new SetOfCoordinates when the user click on +Particles button.
"""
inputset = self.getInputMicrographs()
mySuffix = '_Manual_%s' % coordsDir.split('manualThresholding_')[1]
outputName = 'outputCoordinates' + mySuffix
outputset = self._createSetOfCoordinates(inputset, suffix=mySuffix)
readSetOfCoordinates(coordsDir, outputset.getMicrographs(), outputset)
# summary = self.getSummary(outputset)
# outputset.setObjComment(summary)
outputs = {outputName: outputset}
self._defineOutputs(**outputs)
# Using a pointer to define the relations is more robust to scheduling
# and id changes between the protocol run.db and the main project
# database. The pointer defined below points to the outputset object
self._defineSourceRelation(self.getInputMicrographs(),
Pointer(value=self, extended=outputName))
self._store()
def readCoordsFromMics(self, workingDir, micList, coordSet):
readSetOfCoordinates(workingDir, micList, coordSet)
def readSetOfCoordinates(self, workingDir, coordSet):
readSetOfCoordinates(workingDir, self.getInputMicrographs(), coordSet)