def createOutputStep(self):
micSet = self.getInputMicrographs()
outputCoordinatesName = 'outputCoordinates'
outputSuffix = ''
# If in optimization phase, let's create a subset of the micrographs
if self.isRunOptimize():
outputSuffix = '_subset'
outputCoordinatesName = 'outputCoordinatesSubset'
micSubSet = self._createSetOfMicrographs(suffix=outputSuffix)
micSubSet.copyInfo(micSet)
# Use previously written star file for reading the subset of micrographs,
for row in md.iterRows(self._getPath('input_micrographs.star')):
mic = micSet[row.getValue('rlnImageId')]
micSubSet.append(mic)
self._defineOutputs(outputMicrographsSubset=micSubSet)
self._defineTransformRelation(self.getInputMicrographsPointer(),
micSubSet)
micSet = micSubSet
coordSet = self._createSetOfCoordinates(micSet)
template = self._getExtraPath("%s_autopick.star")
starFiles = [template % pwutils.removeBaseExt(mic.getFileName())
for mic in micSet]
readSetOfCoordinates(coordSet, starFiles, micSet)
self._defineOutputs(**{outputCoordinatesName: coordSet})
self._defineSourceRelation(self.getInputMicrographsPointer(),
coordSet)
def readCoordsFromMics(self, workingDir, micList, coordSet):
""" Parse back the output star files and populate the SetOfCoordinates.
"""
template = self._getExtraPath("%s_autopick.star")
starFiles = [template % pwutils.removeBaseExt(mic.getFileName())
for mic in micList]
readSetOfCoordinates(coordSet, starFiles, micList)
def createOutputStep(self):
micSet = self.getInputMicrographs()
outputCoordinatesName = 'outputCoordinates'
outputSuffix = ''
# If in optimization phase, let's create a subset of the micrographs
if self.isRunOptimize():
outputSuffix = '_subset'
outputCoordinatesName = 'outputCoordinatesSubset'
micSubSet = self._createSetOfMicrographs(suffix=outputSuffix)
micSubSet.copyInfo(micSet)
# Use previously written star file for reading the subset of micrographs,
for row in md.iterRows(self._getPath('input_micrographs.star')):
mic = micSet[row.getValue('rlnImageId')]
micSubSet.append(mic)
self._defineOutputs(outputMicrographsSubset=micSubSet)
self._defineTransformRelation(self.getInputMicrographsPointer(),
micSubSet)
micSet = micSubSet
coordSet = self._createSetOfCoordinates(micSet)
template = self._getExtraPath("%s_autopick.star")
starFiles = [
template % pwutils.removeBaseExt(mic.getFileName())
for mic in micSet
]
readSetOfCoordinates(coordSet, starFiles, micSet)
self._defineOutputs(**{outputCoordinatesName: coordSet})
self._defineSourceRelation(self.getInputMicrographsPointer(), coordSet)
def readRejectedCoordsFromMics(self, micList):
micSet = self.getInputMicrographs()
rejectedCoordSqlite = self._getPath('coordinates_rejected.sqlite')
if not os.path.exists(rejectedCoordSqlite):
coordSetAux = self._createSetOfCoordinates(micSet, suffix='_rejected')
else:
coordSetAux = em.SetOfCoordinates(filename=rejectedCoordSqlite)
coordSetAux.enableAppend()
coordSetAux.setBoxSize(self._getBoxSize())
readSetOfCoordinates(self.getMicrographsDir(), micList,
coordSetAux, suffix='_rejected.star')
coordSetAux.write()
coordSetAux.close()
# debug output
if self.writeCC:
self.createDebugOutput(suffix='_ccmax')
if self.writeFilt:
self.createDebugOutput(suffix='_pref')
if self.writeBg:
self.createDebugOutput(suffix='_bg')
if self.writeBgSub:
self.createDebugOutput(suffix='_bgfree')
if self.writeSigma:
self.createDebugOutput(suffix='_lsigma')
if self.writeMsk:
self.createDebugOutput(suffix='_mask')
def createOutputStep(self):
micSet = self.getInputMicrographs()
ih = em.ImageHandler()
coordSet = self._createSetOfCoordinates(micSet)
if self.boxSize and self.boxSize > 0:
coordSet.setBoxSize(self.boxSize.get())
else:
coordSet.setBoxSize(self.inputReferences.get().getXDim or 100)
readSetOfCoordinates(self.getMicrographsDir(), micSet, coordSet)
coordSetAux = self._createSetOfCoordinates(micSet, suffix='_rejected')
coordSetAux.setBoxSize(coordSet.getBoxSize())
readSetOfCoordinates(self.getMicrographsDir(),
micSet,
coordSetAux,
suffix='_rejected.star')
coordSetAux.write()
# debug output
if self.writeCC:
self.createDebugOutput(suffix='_ccmax')
if self.writeFilt:
self.createDebugOutput(suffix='_pref')
if self.writeBg:
self.createDebugOutput(suffix='_bg')
if self.writeBgSub:
self.createDebugOutput(suffix='_bgfree')
if self.writeSigma:
self.createDebugOutput(suffix='_lsigma')
if self.writeMsk:
self.createDebugOutput(suffix='_mask')
self._defineOutputs(outputCoordinates=coordSet)
self._defineSourceRelation(micSet, coordSet)
def createOutputStep(self):
micSet = self.getInputMicrographs()
# If in optimization phase, let's create a subset of the micrographs
if self.isRunOptimize():
micSubSet = self._createSetOfMicrographs()
micSubSet.copyInfo(micSet)
for mic in self.getMicrographList():
micSubSet.append(mic)
self._defineOutputs(outputMicrographs=micSubSet)
self._defineTransformRelation(self.getInputMicrographsPointer(),
micSubSet)
micSet = micSubSet
else:
# Clean up if previously created the outputMicrographs
if self.hasAttribute('outputMicrographs'):
self._deleteChild('outputMicrographs', self.outputMicrographs)
coordSet = self._createSetOfCoordinates(micSet)
template = self._getExtraPath("%s_autopick.star")
starFiles = [
template % pwutils.removeBaseExt(mic.getFileName())
for mic in micSet
]
readSetOfCoordinates(coordSet, starFiles, micSet)
self._defineOutputs(outputCoordinates=coordSet)
self._defineSourceRelation(self.getInputMicrographsPointer(), coordSet)
def createOutputStep(self):
micSet = self.getInputMicrographs()
coordSet = self._createSetOfCoordinates(micSet)
coordSet.setBoxSize(self.getInputReferences().getDim()[0])
starFiles = [self._getExtraPath(pwutils.removeBaseExt(mic.getFileName()) + "_autopick.star") for mic in micSet]
readSetOfCoordinates(coordSet, starFiles)
self._defineOutputs(outputCoordinates=coordSet)
def readCoordsFromMics(self, workingDir, micDoneList,
outputCoords):
if self.boxSize and self.boxSize > 0:
outputCoords.setBoxSize(self.boxSize.get())
else:
outputCoords.setBoxSize(
self.inputReferences.get().getDim()[0])
readSetOfCoordinates(workingDir, micDoneList, outputCoords)
def createOutputStep(self):
extradir = self._getExtraPath()
inputset = self.tiltpair.get()
uSet = inputset.getUntilted()
tSet = inputset.getTilted()
# Create Untilted and Tilted SetOfCoordinates
uCoordSet = self._createSetOfCoordinates(uSet, suffix='Untilted')
if self.typeOfSet.get() == TYPE_PARTICLES:
# boxsize_u = self.untiltPar.get().getCoordinates().getBoxSize()
# if boxsize_u is None:
aux = self.untiltPar.get()
aux2 = aux[1]
boxsize_u, y_, z_ = aux2.getDim()
else:
boxsize_u = self.untiltCoor.get().getBoxSize()
uCoordSet.setBoxSize(boxsize_u)
tCoordSet = self._createSetOfCoordinates(tSet, suffix='Tilted')
readSetOfCoordinates(extradir, uSet, uCoordSet)
uCoordSet.write()
if self.typeOfSet.get() == TYPE_PARTICLES:
# boxsize_t = self.tiltPar.get().getCoordinates().getBoxSize()
# if boxsize_t is None:
aux = self.tiltPar.get()
aux2 = aux[1]
boxsize_t, y_, z_ = aux2.getDim()
else:
boxsize_t = self.tiltCoor.get().getBoxSize()
tCoordSet.setBoxSize(boxsize_t)
readSetOfCoordinates(extradir, tSet, tCoordSet)
tCoordSet.write()
setAngles = self._createSetOfAngles()
pathangles = self.micsFn + '/input_micrographs.xmd'
readAnglesFromMicrographs(pathangles, setAngles)
setAngles.write()
# Create CoordinatesTiltPair object
outputset = CoordinatesTiltPair(filename=self._getPath('coordinates_pairs.sqlite'))
outputset.setTilted(tCoordSet)
outputset.setUntilted(uCoordSet)
outputset.setAngles(setAngles)
outputset.setMicsPair(inputset)
outputset.setObjComment(self.getSummary(outputset))
# print '-----------------------------'
# print setAngles
# print '-----------------------------'
for coordU, coordT in izip(uCoordSet, tCoordSet):
outputset.append(TiltPair(coordU, coordT))
self._defineOutputs(outputCoordinatesTiltPair=outputset)
self._defineSourceRelation(self.tiltpair, outputset)
def readCoordsFromMics(self, workingDir, micList, coordSet):
""" Parse back the output star files and populate the SetOfCoordinates.
"""
template = self._getExtraPath("%s_autopick.star")
starFiles = [
template % pwutils.removeBaseExt(mic.getFileName())
for mic in micList
]
readSetOfCoordinates(coordSet, starFiles, micList)
def createOutputStep(self):
micSet = self.getInputMicrographs()
coordSet = self._createSetOfCoordinates(micSet)
coordSet.setBoxSize(self.getInputReferences().getDim()[0])
starFiles = [self._getExtraPath(pwutils.removeBaseExt(mic.getFileName()) + '_autopick.star')
for mic in micSet]
readSetOfCoordinates(coordSet, starFiles)
self._defineOutputs(outputCoordinates=coordSet)
self._defineSourceRelation(self.getInputMicrographsPointer(), coordSet)
def writeXmippCoords(self):
""" Write the SetOfCoordinates as expected by Xmipp
to be display with its GUI.
"""
micSet = self.getInputMicrographs()
coordSet = self._createSetOfCoordinates(micSet)
coordSet.setBoxSize(self.getInputReferences().getDim()[0])
starFiles = [self._getExtraPath(pwutils.removeBaseExt(mic.getFileName()) + "_autopick.star") for mic in micSet]
readSetOfCoordinates(coordSet, starFiles)
return self._writeXmippCoords(coordSet)
def writeXmippCoords(self):
""" Write the SetOfCoordinates as expected by Xmipp
to be display with its GUI.
"""
micSet = self.getInputMicrographs()
coordSet = self._createSetOfCoordinates(micSet)
coordSet.setBoxSize(self.getInputReferences().getDim()[0])
starFiles = [self._getExtraPath(pwutils.removeBaseExt(mic.getFileName()) + '_autopick.star')
for mic in micSet]
readSetOfCoordinates(coordSet, starFiles)
return self._writeXmippCoords(coordSet)
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 _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 readRejectedCoordsFromMics(self, micList):
micSet = self.getInputMicrographs()
rejectedCoordSqlite = self._getPath('coordinates_rejected.sqlite')
if not os.path.exists(rejectedCoordSqlite):
coordSetAux = self._createSetOfCoordinates(micSet,
suffix='_rejected')
else:
coordSetAux = em.SetOfCoordinates(filename=rejectedCoordSqlite)
coordSetAux.enableAppend()
coordSetAux.setBoxSize(self._getBoxSize())
readSetOfCoordinates(self.getMicrographsDir(),
micList,
coordSetAux,
suffix='_rejected.star')
coordSetAux.write()
coordSetAux.close()
# debug output
if self.writeCC:
self.createDebugOutput(suffix='_ccmax')
if self.writeFilt:
self.createDebugOutput(suffix='_pref')
if self.writeBg:
self.createDebugOutput(suffix='_bg')
if self.writeBgSub:
self.createDebugOutput(suffix='_bgfree')
if self.writeSigma:
self.createDebugOutput(suffix='_lsigma')
if self.writeMsk:
self.createDebugOutput(suffix='_mask')
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)
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)
def readCoordsFromMics(self, workingDir, micList, coordSet):
coordSet.setBoxSize(self.boxSize.get())
readSetOfCoordinates(workingDir, micList, coordSet)
def readSetOfCoordinates(self, workingDir, coordSet):
readSetOfCoordinates(workingDir, self.inputMicrographs.get(), coordSet)
def readSetOfCoordinates(self, workingDir, coordSet):
readSetOfCoordinates(workingDir, self.inputMics, coordSet)
def readCoordsFromMics(self, workingDir, micList, coordSet):
if coordSet.getBoxSize() is None:
coordSet.setBoxSize(self._getBoxSize())
readSetOfCoordinates(self.getMicrographsDir(), micList, coordSet)
self.readRejectedCoordsFromMics(micList)
def readCoordsFromMics(self, workingDir, micList, coordSet):
readSetOfCoordinates(workingDir, micList, coordSet)
def readSetOfCoordinates(self, workingDir, coordSet):
readSetOfCoordinates(workingDir, self.inputMics, coordSet)
def readCoordsFromMics(self, workingDir, micList, coordSet):
if coordSet.getBoxSize() is None:
coordSet.setBoxSize(self._getBoxSize())
readSetOfCoordinates(self.getMicrographsDir(), micList, coordSet)
self.readRejectedCoordsFromMics(micList)
def readCoordsFromMics(self, workingDir, micList, coordSet):
coordSet.setBoxSize(self.diameter.get())
readSetOfCoordinates(workingDir, micList, coordSet)
def readSetOfCoordinates(self, workingDir, coordSet):
readSetOfCoordinates(workingDir, self.inputMicrographs.get(), coordSet)
