# **************************************************************************
# *
# * Authors: Carlos Oscar Sorzano (coss@cnb.csic.es)
# * Tomas Majtner (tmajtner@cnb.csic.es) -- streaming version
# *
# * 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 'coss@cnb.csic.es'
# *
# **************************************************************************
"""
Consensus picking protocol
"""
import numpy as np
import pyworkflow.protocol.params as params
from pyworkflow.utils import getFiles, removeBaseExt
from .protocol_particle_pick_consensus import (XmippProtConsensusPicking,
consensusWorker, getReadyMics)
[docs]class XmippProtPickingRemoveDuplicates(XmippProtConsensusPicking):
"""
This protocol removes coordinates that are closer than a given threshold.
The remaining coordinate is the average of the previous ones.
"""
_label = 'remove duplicates'
outputName = 'outputCoordinates'
FN_PREFIX = 'purgedCoords_'
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputCoordinates', params.PointerParam,
pointerClass='SetOfCoordinates',
label="Input coordinates", important=True,
help='Select the set of coordinates to compare')
form.addParam('consensusRadius', params.IntParam, default=10,
label="Radius",
help="All coordinates within this radius (in pixels) "
"are presumed to correspond to the same particle")
# FIXME: It's not using more than one since
# self.stepsExecutionMode = STEPS_SERIAL
# form.addParallelSection(threads=4, mpi=0)
#--------------------------- INSERT steps functions ----------------------------
def _checkNewInput(self):
# If continue from an stopped run, don't repeat what is done
if not self.checkedMics:
for fn in getFiles(self._getExtraPath()):
fn = removeBaseExt(fn)
if fn.startswith(self.FN_PREFIX):
self.checkedMics.update([self.getMicId(fn)])
self.processedMics.update([self.getMicId(fn)])
readyMics, self.streamClosed = getReadyMics(self.inputCoordinates.get())
newMicsIds = readyMics.difference(self.checkedMics)
if newMicsIds:
self.checkedMics.update(newMicsIds)
inMics = self.getMainInput().getMicrographs()
newMics = [inMics[micId].clone() for micId in newMicsIds]
fDeps = self.insertNewCoorsSteps(newMics)
outputStep = self._getFirstJoinStep()
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
[docs] def getMainInput(self):
return self.inputCoordinates.get()
[docs] def defineRelations(self, outputSet):
self._defineTransformRelation(self.getMainInput(), outputSet)
[docs] def removeDuplicatesStep(self, micId, micName):
print("Removing duplicates for micrograph %d: '%s'"
% (micId, micName))
coordArray = np.asarray([x.getPosition() for x in
self.getMainInput().iterCoordinates(micId)],
dtype=int)
consensusWorker([coordArray], 1, self.consensusRadius.get(),
self._getTmpPath('%s%s.txt' % (self.FN_PREFIX, micId)))
self.processedMics.update([micId])
def _validate(self):
errors = []
return errors
def _summary(self):
return ["Radius = %d" % self.consensusRadius]