Source code for pwem.protocols.protocol_ctf_assign

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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import pyworkflow.protocol.params as params

import pwem.objects as emobj
from pwem.protocols import ProtCTFMicrographs


[docs]class ProtCTFAssign(ProtCTFMicrographs): """ This protocol assigns a CTF estimation to a particular set of particles producing a new set. """ _label = 'assign ctf' _unionTypes = ['Micrographs', 'Particles'] def __init__(self, **kwargs): ProtCTFMicrographs.__init__(self, **kwargs) # We need to trace the changes of 'inputType' to # dynamically modify the property of pointerClass # of the 'inputSets' parameter def onChangeInputType(): pointerClass = 'SetOf' + self.getEnumText('inputType') self.inputSetsParam.setPointerClass(pointerClass) # Initial update onChangeInputType() # Now keep track of changes and update self.inputType.trace(onChangeInputType) # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputType', params.EnumParam, choices=self._unionTypes, default=0, # Micrographs label='Input type:', help='Select the type of objects that you want to assign' ' the CTF.') self.inputSetsParam = form.addParam('inputSet', params.PointerParam, pointerClass='EMSet', label='Input set', help='Select the images ' '(micrographs or particles) ' 'that you want to update the ' 'CTF parameters.') form.addParam('inputCTF', params.PointerParam, pointerClass='SetOfCTF', label="Input CTF", help='Select the CTF that will be used to update ' 'particles.') form.addParallelSection(threads=0, mpi=0) # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): """for each ctf insert the steps to compare it """ self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -----------------------------
[docs] def createOutputStep(self): inputSet = self.inputSet.get() inputCTF = self.inputCTF.get() if isinstance(inputSet, emobj.SetOfParticles): self._particlesOutputStep(inputSet, inputCTF) else: self._micrographsOutputStep(inputSet, inputCTF)
def _particlesOutputStep(self, inputSet, inputCTF): outputParts = self._createSetOfParticles() outputParts.copyInfo(inputSet) outputParts.setHasCTF(True) ctfDict = {} firstCoord = inputSet.getFirstItem().getCoordinate() hasMicName = firstCoord.getMicName() is not None for ctf in inputCTF: if hasMicName: ctfName = ctf.getMicrograph().getMicName() else: ctfName = ctf.getMicrograph().getObjId() # print("ctf: ", ctf.printAll(), ctfName) ctfDict[ctfName] = ctf.clone() missingSet = set() # Report missing micrographs only once for particle in inputSet: if particle.hasCoordinate(): coord = particle.getCoordinate() micKey = coord.getMicName() if hasMicName else particle.getMicId() else: micKey = particle.getMicId() if micKey not in missingSet: ctf = ctfDict.get(micKey, None) if ctf is None: self.warning("Discarding particles from micrograph with" " micName: %s, CTF not found. " % micKey) missingSet.add(micKey) else: newParticle = particle.clone() newParticle.setCTF(ctf) outputParts.append(newParticle) self._defineOutputs(outputParticles=outputParts) self._defineSourceRelation(self.inputSet, outputParts) self._defineSourceRelation(self.inputCTF, outputParts) def __findCTF(self, inputSet, outputSet, ctfDict, keyFunc): for mic in inputSet: micKey = keyFunc(mic) ctf = ctfDict.get(micKey, None) if ctf is None: self.warning("Discarding micrographs with micName: %s, CTF not found. " % micKey) else: newMic = mic.clone() outputSet.append(newMic) def _micrographsOutputStep(self, inputSet, inputCTF): outputMics = self._createSetOfMicrographs() outputMics.copyInfo(inputSet) ctfDict = {} for ctf in inputCTF: mic = ctf.getMicrograph() ctfDict[mic.getMicName()] = ctf ctfDict[mic.getObjId()] = ctf # Try first to find the ctf by the micrograph micName self.__findCTF(inputSet, outputMics, ctfDict, lambda mic: mic.getMicName()) # Now, if no ctf was found, try using the micId if outputMics.getSize() == 0: self.warning("No CTF found using micName, now trying with micId") self.__findCTF(inputSet, outputMics, ctfDict, lambda mic: mic.getObjId()) self._defineOutputs(outputMicrographs=outputMics) self._defineSourceRelation(self.inputSet, outputMics) self._defineCtfRelation(outputMics, self.inputCTF) # --------------------------- INFO functions ------------------------------ def _summary(self): summary = [] return summary def _methods(self): return [] def _validate(self): """ The function of this hook is to add some validation before the protocol is launched to be executed. It should return a list of errors. If the list is empty the protocol can be executed. """ errors = [] # Add some errors if input is not valid inputSet = self.inputSet.get() if isinstance(inputSet, emobj.SetOfParticles): part = inputSet.getFirstItem() if not part.hasMicId(): errors.append("The input particles doesn't have any micrograph" " assigned.") # same micrographs in both CTF?? return errors # --------------------------- UTILS functions ----------------------------- def _stepsCheck(self): pass