Source code for xmipp3.protocols.protocol_consensus_local_ctf

# coding=utf-8
# **************************************************************************
# *
# * Authors:     Estrella Fernandez Gimenez (me.fernandez@cnb.csic.es)
# *              Carlos Oscar Sanchez Sorzano
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia, CSIC
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# * 02111-1307  USA
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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 numpy as np

from pyworkflow import VERSION_2_0
from pyworkflow.object import Float
from pyworkflow.protocol.params import MultiPointerParam, PointerParam

from pwem.protocols import ProtAnalysis3D
from pwem import emlib

from xmipp3.convert import setXmippAttribute


[docs]class XmippProtConsensusLocalCTF(ProtAnalysis3D): """This protocol compares the estimations of local defocus computed by different protocols for a set of particles""" _label = 'consensus local defocus' _lastUpdateVersion = VERSION_2_0 def __init__(self, **args): ProtAnalysis3D.__init__(self, **args) #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputSet', PointerParam, label="Input particles to assign the consensus defocus", pointerClass='SetOfParticles', help="Particle set of interest to estimate the defocus") form.addParam('inputSets', MultiPointerParam, label="Input defocus estimations", pointerClass='SetOfParticles', help="Sets of particles with different local defocus estimations to compare") #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep("compareDefocus") self._insertFunctionStep("createOutputStep") #--------------------------- STEPS functions ---------------------------------------------------
[docs] def compareDefocus(self): """compare with median, mad and correlation matrix the local defocus value for each pixel estimated by different programs (Xmipp, Relion, gCTF, ...)""" allParticlesDef = {} for defsetP in self.inputSets: defset = defsetP.get() for particle in defset: pIDs = [] pDefAs = [] pIDs.append(particle.getObjId()) defU = particle.getCTF().getDefocusU() defV = particle.getCTF().getDefocusV() pDefAs.append((defU+defV)/2) for pId, pDefA in zip(pIDs,pDefAs): if not pId in allParticlesDef.keys(): allParticlesDef[pId]=[] allParticlesDef[pId].append(pDefA) self.defMatrix = np.full(shape=(len(allParticlesDef.keys()),len(self.inputSets)),fill_value=np.NaN) i=0 self.pMatrixIdx={} for pId,pdefi in allParticlesDef.items(): self.pMatrixIdx[pId]=i for j in enumerate(pdefi): self.defMatrix[i,j[0]]=j[1] i+=1 self.median = np.nanmedian(self.defMatrix, axis=1) self.mad = np.empty_like(self.median) for k in enumerate(self.median): self.mad[k[0]] = np.nanmedian(np.abs(self.defMatrix[k[0],:] - self.median[k[0]])) self.defMatrix = np.hstack((self.defMatrix, self.median.reshape(len(self.median),1))) self.corrMatrix = np.zeros((self.defMatrix.shape[0],self.defMatrix.shape[1])) defMatrixInvalid = np.ma.masked_invalid(self.defMatrix) self.corrMatrix = np.ma.corrcoef(defMatrixInvalid,rowvar=False) np.savetxt(self._getExtraPath("defocusMatrix.txt"),self.defMatrix) np.savetxt(self._getExtraPath("correlationMatrix.txt"),self.corrMatrix)
[docs] def createOutputStep(self): """create as output a setOfParticles with a consensus estimation of local defocus (median) and its median standard deviation (mad)""" imgSet = self.inputSet.get() outputSet = self._createSetOfParticles() outputSet.copyInfo(imgSet) # Loop through input set of for part in imgSet.iterItems(): id = part.getObjId() if id in self.pMatrixIdx: index = self.pMatrixIdx[id] newPart = part.clone() pMedian = Float(self.median[index]) pMad = Float(self.mad[index]) setXmippAttribute(newPart.getCTF(), emlib.MDL_CTF_DEFOCUSA, pMedian) setXmippAttribute(newPart.getCTF(), emlib.MDL_CTF_DEFOCUS_RESIDUAL, pMad) outputSet.append(newPart) self._defineOutputs(outputParticles=outputSet) self._defineSourceRelation(self.inputSet, outputSet)
def _updateItem(self, particle, row): """update each particle in the set with the values computed""" pId = particle.getObjId() setXmippAttribute(particle,emlib.MDL_CTF_DEFOCUSA,self.median[self.pMatrixIdx[pId]]) setXmippAttribute(particle,emlib.MDL_CTF_DEFOCUS_RESIDUAL,self.mad[self.pMatrixIdx[pId]]) #--------------------------- INFO functions -------------------------------------------- def _summary(self): summary = [] summary.append("Consensus local defocus and residual computed for %s particles" % self.getObjectTag('outputParticles')) return summary def _methods(self): methods = [] methods.append("The results obtained when local CTF is estimated by different methods are compared here " "computing the median, MAD and correlation matrix.") return methods