# **************************************************************************
# *
# * Authors: Estrella Fernandez Gimenez (me.fernandez@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 import BETA
from pyworkflow.protocol.params import PointerParam
from pyworkflow.utils import removeExt
from pwem.protocols import EMProtocol
[docs]class ProtAssignTomo2Subtomo(EMProtocol):
""" This protocol assign tomograms to subtomograms that have been imported before without tomograms.
Subtomograms should contain the name of the original tomogram in their own file name.
"""
_label = 'assign tomos to subtomos'
_devStatus = BETA
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputSubtomos', PointerParam, pointerClass='SetOfSubTomograms', label='Subtomograms',
help='Select the subtomograms that you want to update with original tomograms as precedents.'
'The subtomograms should contain the original tomogram name in their own filename.')
form.addParam('inputTomos', PointerParam, pointerClass='SetOfTomograms', label='Tomograms',
help='Select the tomograms to be assigned to the subtomograms.')
# --------------------------- INSERT steps functions --------------------------
def _insertAllSteps(self):
self._insertFunctionStep('createOutputStep')
# --------------------------- STEPS functions --------------------------------------------
[docs] def createOutputStep(self):
self.tomoDict = {}
inputTomos = self.inputTomos.get()
for tomo in inputTomos:
self.tomoDict[tomo.getBaseName()] = tomo.getObjId()
inputSubtomos = self.inputSubtomos.get()
outputSubtomos = inputSubtomos.create(self._getPath())
outputSubtomos.copyInfo(inputSubtomos)
outputSubtomos.copyItems(inputSubtomos, updateItemCallback=self._updateItem)
self._defineOutputs(outputSubtomograms=outputSubtomos)
self._defineSourceRelation(self.inputSubtomos, outputSubtomos)
self._defineSourceRelation(self.inputTomos, outputSubtomos)
# --------------------------- UTILS functions --------------------------------------------
def _updateItem(self, item, row):
for tomoName in self.tomoDict:
if removeExt(tomoName) in item.getFileName():
item.setVolName(tomoName)
item.setVolId(self.tomoDict.get(tomoName))
break
# --------------------------- INFO functions --------------------------------------------
def _summary(self):
summary = []
if not hasattr(self, 'outputSubtomograms'):
summary.append("Output subtomograms not ready yet.")
else:
summary.append("%s tomograms assigned to %s subtomograms." %
(self.getObjectTag('inputTomos'), self.getObjectTag('inputSubtomos')))
return summary
def _methods(self):
methods = []
if not hasattr(self, 'outputSubtomograms'):
methods.append("Output subtomograms not ready yet.")
else:
methods.append("%d %s tomograms assigned to %d %s subtomograms." %
(self.inputTomos.get().getSize(), self.getObjectTag('inputTomos'),
self.inputSubtomos.get().getSize(), self.getObjectTag('inputSubtomos')))
return methods