# **************************************************************************
# *
# * Authors: Roberto Marabini (roberto@cnb.csic.es)
# *
# * 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
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
from pyworkflow.object import String
from pyworkflow.protocol.params import StringParam
from pwem.protocols import ProtProcessParticles
import pwem.emlib.metadata as md
from pwem.constants import ALIGN_PROJ
from xmipp3.convert import writeSetOfParticles
[docs]class XmippProtAngBreakSymmetry(ProtProcessParticles):
"""
Given an input set of particles with angular assignment, find an
equivalent angular assignment for a given symmetry.
Be aware that input symmetry values follows Xmipp conventions as described in:
http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry
"""
_label = 'break symmetry'
#--------------------------- DEFINE param functions --------------------------------------------
def _defineProcessParams(self, form):
form.addParam('symmetryGroup', StringParam, default="c1",
label='Symmetry group',
help="See http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry"
" for a description of the symmetry groups format in Xmipp.\n"
"If no symmetry is present, use _c1_.")
def _getDefaultParallel(self):
"""This protocol doesn't have mpi version"""
return (0, 0)
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
""" Mainly prepare the command line for call brak symmetry program"""
# Create a metadata with the geometrical information
# as expected by Xmipp
imgsFn = self._getPath('input_particles.xmd')
self._insertFunctionStep('convertInputStep', imgsFn)
self._insertFunctionStep('breakSymmetryStep', imgsFn)
self._insertFunctionStep('createOutputStep')
#--------------------------- STEPS functions --------------------------------------------
#--------------------------- STEPS functions --------------------------------------------
[docs] def breakSymmetryStep(self, imgsFn):
outImagesMd = self._getPath('images.xmd')
args = "-i Particles@%s --sym %s -o %s" % (imgsFn,
self.symmetryGroup.get(),
outImagesMd )
self.runJob("xmipp_angular_break_symmetry", args)
self.outputMd = String(outImagesMd)
[docs] def createOutputStep(self):
imgSet = self.inputParticles.get()
partSet = self._createSetOfParticles()
partSet.copyInfo(imgSet)
partSet.copyItems(imgSet,
updateItemCallback=self._createItemMatrix,
itemDataIterator=md.iterRows(self.outputMd.get(), sortByLabel=md.MDL_ITEM_ID))
self._defineOutputs(outputParticles=partSet)
self._defineSourceRelation(imgSet, partSet)
#--------------------------- INFO functions --------------------------------------------
def _summary(self):
import os
summary = []
if not hasattr(self, 'outputParticles'):
summary.append("Output particles not ready yet.")
else:
summary.append("Symmetry: %s"% self.symmetryGroup.get())
return summary
def _validate(self):
pass
def _citations(self):
return []#['Vargas2013b']
def _methods(self):
methods = []
# if hasattr(self, 'outputParticles'):
# outParticles = len(self.outputParticles) if self.outputParticles is not None else None
# particlesRejected = len(self.inputParticles.get())-outParticles if outParticles is not None else None
# particlesRejectedText = ' ('+str(particlesRejected)+')' if particlesRejected is not None else ''
# rejectionText = [
# '',# REJ_NONE
# ' and removing those not reaching %s%s' % (str(self.maxZscore.get()), particlesRejectedText),# REJ_MAXZSCORE
# ' and removing worst %s percent%s' % (str(self.percentage.get()), particlesRejectedText)# REJ_PERCENTAGE
# ]
# methods.append('Input dataset %s of %s particles was sorted by'
# ' its ZScore using xmipp_image_sort_by_statistics'
# ' program%s. ' % (self.getObjectTag('inputParticles'), len(self.inputParticles.get()), rejectionText[self.autoParRejection.get()]))
# methods.append('Output set is %s.'%self.getObjectTag('outputParticles'))
return methods
#--------------------------- Utils functions --------------------------------------------
def _createItemMatrix(self, item, row):
from xmipp3.convert import createItemMatrix
createItemMatrix(item, row, align=ALIGN_PROJ)