# **************************************************************************
# *
# * Authors: Javier Vargas (jvargas@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'
# *
# **************************************************************************
import pwem.emlib.metadata as md
import pyworkflow.protocol.params as params
from pwem.protocols import ProtProcessParticles
from xmipp3.convert import writeSetOfParticles, xmippToLocation
[docs]class XmippProtCTFCorrectWiener2D(ProtProcessParticles):
"""
Performs CTF correction on images using Wiener filtering in 2D. This method enhances image quality by reducing noise and compensating for the contrast transfer function effects in the micrographs or particle images. Use it with caution, preferably only for visualization purposes or when subsequent methods demand it explicitly.
"""
_label = 'ctf_correct_wiener2d'
def __init__(self, *args, **kwargs):
ProtProcessParticles.__init__(self, *args, **kwargs)
#self.stepsExecutionMode = STEPS_PARALLEL
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputParticles', params.PointerParam, pointerClass='SetOfParticles',
label="Input particles",
help='Select the input projection images .')
form.addParam('isIsotropic', params.BooleanParam, default='True',
label="Isotropic Correction",
help='If true, Consider that there is not astigmatism and then it is performed an isotropic correction.')
form.addParam('padding_factor', params.IntParam, default=2,expertLevel=params.LEVEL_ADVANCED,
label="Padding factor",
help='Padding factor for Wiener correction ')
form.addParam('wiener_constant', params.FloatParam, default=-1,expertLevel=params.LEVEL_ADVANCED,
label="Wiener constant",
help=' Wiener-filter constant (if < 0: use FREALIGN default)')
form.addParam('correctEnvelope', params.BooleanParam, default='False',expertLevel=params.LEVEL_ADVANCED,
label="Correct for CTF envelope",
help=' Only in cases where the envelope is well estimated correct for it')
form.addParallelSection(threads=1, mpi=1)
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('convertInputStep',self.inputParticles.get().getObjId())
self._insertFunctionStep('wienerStep')
self._insertFunctionStep('createOutputStep')
[docs] def wienerStep(self):
params = ' -i %s' % self._getPath('input_particles.xmd')
params += ' -o %s' % self._getPath('corrected_ctf_particles.stk')
params += ' --save_metadata_stack %s' % self._getPath('corrected_ctf_particles.xmd')
params += ' --pad %s' % self.padding_factor.get()
params += ' --wc %s' % self.wiener_constant.get()
params += ' --sampling_rate %s' % self.inputParticles.get().getSamplingRate()
if (self.inputParticles.get().isPhaseFlipped()):
params += ' --phase_flipped '
if (self.correctEnvelope):
params += ' --correct_envelope '
print(params)
nproc = self.numberOfMpi.get()
nT=self.numberOfThreads.get()
self.runJob('xmipp_ctf_correct_wiener2d',
params, numberOfMpi=nproc,numberOfThreads=nT)
[docs] def createOutputStep(self):
imgSet = self.inputParticles.get()
partSet = self._createSetOfParticles()
imgFn = self._getPath('corrected_ctf_particles.xmd')
partSet.copyInfo(imgSet)
partSet.setIsPhaseFlipped(True)
partSet.copyItems(imgSet,
updateItemCallback=self._updateLocation,
itemDataIterator=md.iterRows(imgFn, sortByLabel=md.MDL_ITEM_ID))
self._defineOutputs(outputParticles=partSet)
self._defineSourceRelation(imgSet, partSet)
#--------------------------- INFO functions --------------------------------------------
def _validate(self):
pass
def _summary(self):
pass
def _methods(self):
messages = []
return messages
def _citations(self):
return []
#--------------------------- UTILS functions --------------------------------------------
def _updateLocation(self, item, row):
index, filename = xmippToLocation(row.getValue(md.MDL_IMAGE))
item.setLocation(index, filename)