# **************************************************************************
# *
# * Authors: Yunior C. Fonseca Reyna (cfonseca@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 enum
from pwem.objects import SetOfClasses2D, SetOfParticles
from pwem.protocols import EMProtocol
from pyworkflow import BETA
from pyworkflow.protocol.params import PointerParam
from tomo.objects import SetOfSubTomograms
from tomo.protocols import ProtTomoBase
[docs]class importSubTomograms(enum.Enum):
outputSetOfSubtomograms = SetOfSubTomograms()
[docs]class Prot2DParticlesToSubtomograms(EMProtocol, ProtTomoBase):
""" Protocol to create a set of subtomograms from a selected 2D particles.
"""
_label = '2D particles to subtomograms'
_devStatus = BETA
_possibleOutputs = importSubTomograms
# -------------------------- DEFINE param functions -----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputSubtomogramSet', PointerParam,
pointerClass='SetOfSubTomograms',
label="Set of subtomograms",
help='Select the set of subtomograms ')
form.addParam('inputSet', PointerParam,
pointerClass='SetOfClasses2D, SetOfParticles',
label="Input set",
help='Select the 2D classes or a set of particles')
# -------------------------- INSERT steps functions -----------------------
def _insertAllSteps(self):
self._insertFunctionStep(self.createOutputStep)
# -------------------------- STEPS functions ------------------------------
[docs] def createOutputStep(self):
subtomogramsSet = self.inputSubtomogramSet.get()
inputParticles = self.inputSet.get()
self.outputSubtomograms = 'outputSubtomograms'
self.outputSetOfSubtomograms = subtomogramsSet.createCopy(self._getExtraPath(),
prefix=self.outputSubtomograms,
copyInfo=True)
if isinstance(inputParticles, SetOfClasses2D):
for clazz in inputParticles.iterItems():
self._appendSubtomograms(clazz)
elif isinstance(inputParticles, SetOfParticles):
self._appendSubtomograms(inputParticles)
self._defineOutputs(**{self.outputSubtomograms: self.outputSetOfSubtomograms})
def _appendSubtomograms(self, inputSet):
subTomogramsIds = inputSet.aggregate(["COUNT"], "_subtomogramID", ["_subtomogramID"])
subTomogramsIds = [d['_subtomogramID'] for d in subTomogramsIds]
for item in subTomogramsIds:
subtomogramId = int(item)
subtomogram = self.inputSubtomogramSet.get()[subtomogramId].clone()
self.outputSetOfSubtomograms.append(subtomogram)
def _summary(self):
summary = []
if hasattr(self, 'outputSubtomograms'):
newSize = self.outputSubtomograms.getSize()
excluded = self.inputSubtomogramSet.get().getSize() - newSize
summary.append("Number of subtomogram: %d" % (newSize))
summary.append("Number of excluded subtomogram: %d" % (excluded))
return summary