Source code for xmipp3.protocols.protocol_metaprotocol_create_output
# **************************************************************************
# *
# * Authors: Amaya Jimenez (ajimenez@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.
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# * 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'
# *
# **************************************************************************
from shutil import copy
from pyworkflow import VERSION_2_0
from pyworkflow.protocol.params import MultiPointerParam, PointerParam
from pwem.protocols import EMProtocol
from pwem.objects import Volume, Class3D
[docs]class XmippMetaProtCreateOutput(EMProtocol):
""" Metaprotocol to run together all the protocols to discover discrete
heterogeneity in a set of particles
"""
_label = 'metaprotocol heterogeneity output'
_lastUpdateVersion = VERSION_2_0
#--------------------------- DEFINE param functions ------------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputMetaProt', PointerParam, important=True,
label="Input MetaProtocol", pointerClass='XmippMetaProtDiscreteHeterogeneity',
help='Select the metaprotocol heterogeneity '
'to create the final setOfVolumes and setOfClasses3D.')
form.addParam('inputSignifProts', MultiPointerParam, important=True,
label="Input Significant protocols", pointerClass='XmippProtReconstructHeterogeneous',
help='Select several protocols of significant heterogeneity '
'to create the final setOfVolumes and setOfClasses3D.')
#--------------------------- INSERT steps functions ------------------------
def _insertAllSteps(self):
self._insertFunctionStep('createOutputStep')
#--------------------------- STEPS functions -------------------------------
[docs] def createOutputStep(self):
classListProtocols=[]
classListIds=[]
classListSizes=[]
fnOutFile = self.inputMetaProt.get()._getExtraPath('auxOutputFile.txt')
outFile = open(fnOutFile, 'r')
nameRead = outFile.readline()
while nameRead!='':
nameRead = nameRead[:-1]
for i, item in enumerate(self.inputSignifProts):
if nameRead==self.inputSignifProts[i].get()._objLabel:
classListProtocols.append(self.inputSignifProts[i].get())
idRead = outFile.readline()
classListIds.append(int(idRead))
sizeRead = outFile.readline()
classListSizes.append(int(sizeRead))
break
nameRead = outFile.readline()
# print(classListProtocols)
# print(classListIds)
# print(classListSizes)
inputVolume = self.inputMetaProt.get().inputVolume
myVolList=[]
# outputVolumes = self._createSetOfVolumes('Def')
# outputVolumes.setDim(inputVolume.get().getDim())
# outputVolumes.setSamplingRate(inputVolume.get().getSamplingRate())
origDim = inputVolume.get().getDim()[0]
for i, prot in enumerate(classListProtocols):
# print("createOutputStep ", i)
classItem = prot.outputClasses[classListIds[i]]
volFn = str(classItem._representative._filename)
volFnOut = self._getExtraPath('outVol%d.mrc'%(i+1))
volDim = classItem._representative.getDim()[0]
if volDim!=origDim:
self.runJob("xmipp_image_resize", "-i %s -o %s --fourier %d"
% (volFn, volFnOut, origDim),
numberOfMpi=self.numberOfMpi.get() * self.numberOfThreads.get())
else:
copy(volFn, volFnOut)
vol = Volume()
vol.setLocation(volFnOut)
vol.setSamplingRate(inputVolume.get().getSamplingRate())
myVolList.append(vol)
# outputVolumes.append(vol)
# self._defineOutputs(** {'outputVolumesDef': outputVolumes})
# self._store(outputVolumes)
inputParticles = self.inputMetaProt.get().inputParticles
outputDefClasses = self._createSetOfClasses3D(inputParticles.get(), 'Def')
for i, prot in enumerate(classListProtocols):
classItem = prot.outputClasses[classListIds[i]]
signifInputParts = inputParticles.get()
partIds = classItem.getIdSet()
newClass = Class3D()
newClass.copyInfo(signifInputParts)
newClass.setAcquisition(signifInputParts.getAcquisition())
newClass.setRepresentative(myVolList[i])
outputDefClasses.append(newClass)
enabledClass = outputDefClasses[newClass.getObjId()]
enabledClass.enableAppend()
for itemId in partIds:
enabledClass.append(signifInputParts[itemId])
outputDefClasses.update(enabledClass)
self._defineOutputs(**{'outputClasses3DDef': outputDefClasses})
self._store(outputDefClasses)
#--------------------------- INFO functions --------------------------------
def _validate(self):
errors = []
return errors
def _summary(self):
summary = []
return summary