Source code for xmipp3.protocols.protocol_pick_noise

# **************************************************************************
# *
# * Authors:     Ruben Sanchez
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA

# * 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'
# *
# **************************************************************************

import os

from pyworkflow import VERSION_2_0
from pyworkflow.object import Pointer

from pyworkflow.protocol.constants import (STEPS_SERIAL, LEVEL_ADVANCED)
import pyworkflow.protocol.params as params
from pwem.protocols import ProtParticlePicking

import pwem.emlib.metadata as MD
from xmipp3.convert import writeSetOfCoordinates, readSetOfCoordsFromPosFnames
from xmipp3 import XmippProtocol

IN_COORDS_POS_DIR_BASENAME= "pickNoiseInPosCoordinates"
OUT_COORDS_POS_DIR_BASENAME= "pickNoiseOutPosCoordinates"

[docs]class XmippProtPickNoise(ProtParticlePicking, XmippProtocol): """Protocol to pick noise particles""" _label = 'pick noise' _lastUpdateVersion = VERSION_2_0 def __init__(self, **args): ProtParticlePicking.__init__(self, **args) self.stepsExecutionMode = STEPS_SERIAL #--------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputCoordinates', params.PointerParam, pointerClass='SetOfCoordinates', important=True, label="Input coordinates", help='Set of true particle coordinates. ' 'Noise coordinates are chosen so that they are ' 'sufficiently far from particles') form.addParam('extractNoiseNumber', params.IntParam, default=-1, expertLevel=LEVEL_ADVANCED, label='Number of noise particles', help='Number of noise particles to extract from each micrograph. ' 'Set to -1 for extracting the same amount of noise ' 'particles as the number true particles for that micrograph') form.addParallelSection(threads=4, mpi=0) #--------------------------- INSERT steps functions ------------------------ def _insertAllSteps(self): """for each micrograph insert the steps to preprocess it""" #Insert pickNoise steps using function setOfCoords= self.inputCoordinates.get() boxSize = setOfCoords.getBoxSize() inCoordsFname= setOfCoords.getFileName() outPath = self._getExtraPath() inCoordsPosDir= os.path.join(outPath, IN_COORDS_POS_DIR_BASENAME) outCoordsPosDir=os.path.join(outPath, OUT_COORDS_POS_DIR_BASENAME) mics= setOfCoords.getMicrographs() for mic in setOfCoords.getMicrographs(): mic_fname= mic.getFileName() break mics_dir = os.path.split(mic_fname)[0] argTuple=(boxSize, outPath, mics_dir, ) deps=[] deps.append(self._insertFunctionStep("prepareInput")) deps.append(self._insertFunctionStep("pickNoiseStep", mics_dir, inCoordsPosDir, outCoordsPosDir, boxSize, self.extractNoiseNumber.get(), self.numberOfThreads.get()) ) # deps.append(self._insertFunctionStep("loadCoords", mics_dir, outCoordsPosDir, boxSize) self._insertFunctionStep('createOutputStep', outCoordsPosDir, prerequisites=deps) #--------------------------- STEPS functions -------------------------------
[docs] def pickNoiseStep(self, mics_dir, inCoordsPosDir, outCoordsPosDir, boxSize, extractNoiseNumber, nThr): args=" -i %s -c %s -o %s -s %s -n %s -t %s"%(mics_dir, inCoordsPosDir, outCoordsPosDir, boxSize, extractNoiseNumber,nThr) self.runJob('xmipp_pick_noise', args, numberOfMpi=1)
[docs] def prepareInput(self): pickNoise_prepareInput(self.inputCoordinates.get(), self._getExtraPath())
[docs] def createOutputStep( self, outCoordsPosDir): noiseCoords= readSetOfCoordsFromPosFnames(outCoordsPosDir, sqliteOutName=self._getExtraPath('consensus_NOISE.sqlite') , setOfInputCoords=self.inputCoordinates.get()) coordSet = self._createSetOfCoordinates(self.inputCoordinates.get().getMicrographs() ) coordSet.copyInfo(noiseCoords) coordSet.copyItems(noiseCoords, itemDataIterator=MD.iterRows(self._getPath(noiseCoords.getFileName()), sortByLabel=MD.MDL_ITEM_ID)) coordSet.setBoxSize(noiseCoords.getBoxSize()) self._defineOutputs(outputCoordinates=coordSet) self._defineSourceRelation(self.inputCoordinates.get(), coordSet)
[docs] def getInputMicrographs(self): return self.inputCoordinates.get().getMicrographs()
[docs] def getInputMicrographsPointer(self): ptr = Pointer() ptr.set(self.getInputMicrographs()) return ptr
def _summary(self): summary = [] if hasattr(self, 'outputCoordinates'): summary.append('%d noisy particles were picked'%self.outputCoordinates.getSize()) return summary
[docs]def pickNoise_prepareInput(setOfCoords, outPath, outCoordsPosDir=None): boxSize = setOfCoords.getBoxSize() inCoordsFname= setOfCoords.getFileName() inCoordsPosDir= os.path.join(outPath, IN_COORDS_POS_DIR_BASENAME) if not os.path.isdir(inCoordsPosDir): os.mkdir(inCoordsPosDir) if outCoordsPosDir is None: outCoordsPosDir=os.path.join(outPath, OUT_COORDS_POS_DIR_BASENAME) if not os.path.isdir(outCoordsPosDir): os.mkdir(outCoordsPosDir) mics= setOfCoords.getMicrographs() for mic in setOfCoords.getMicrographs(): mic_fname= mic.getFileName() break mics_dir = os.path.split(mic_fname)[0] argTuple=(boxSize, outPath, mics_dir, ) writeSetOfCoordinates(inCoordsPosDir, setOfCoords) return {"boxSize":boxSize, "inCoordsPosDir": inCoordsPosDir, "outCoordsPosDir":outCoordsPosDir, "outPath":outPath, "mics_dir":mics_dir }