# **************************************************************************
# *
# * 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.protocol.params import PointerParam
from pwem.protocols import EMProtocol
[docs]class ProtAlignmentAssignSubtomo(EMProtocol):
""" Assign the alignment calculated for a set of subtomograms to another set.
Both sets should have same pixel size (A/px).
The subtomograms with the alignment can also be a subset of a bigger set.
"""
_label = 'assign alignment subtomo'
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 the new alignment.')
form.addParam('inputAlignment', PointerParam, pointerClass='SetOfSubTomograms', label="Aligned subtomograms",
help='Select the subtomograms with alignment to be apply to the other particles.')
# --------------------------- INSERT steps functions --------------------------
def _insertAllSteps(self):
self._insertFunctionStep('createOutputStep')
# --------------------------- STEPS functions --------------------------------------------
[docs] def createOutputStep(self):
inputSubtomos = self.inputSubtomos.get()
inputAlignment = self.inputAlignment.get()
outputSubtomos = inputSubtomos.create(self._getPath())
outputSubtomos.copyInfo(inputSubtomos)
outputSubtomos.setAlignment(inputAlignment.getAlignment())
outputSubtomos.copyItems(inputSubtomos, updateItemCallback=self._updateItem)
self._defineOutputs(outputSubtomograms=outputSubtomos)
self._defineSourceRelation(self.inputSubtomos, outputSubtomos)
self._defineSourceRelation(self.inputAlignment, outputSubtomos)
# --------------------------- UTILS functions --------------------------------------------
def _updateItem(self, item, row):
# Add alignment info from corresponding item on inputAlignment
inputAlignment = self.inputAlignment.get()
alignedParticle = inputAlignment[item.getObjId()]
# If alignment is found for this particle set the alignment info
# on the output particle, if not do not write that item
if alignedParticle is not None:
alignment = alignedParticle.getTransform()
item.setTransform(alignment)
else:
item._appendItem = False
# --------------------------- INFO functions --------------------------------------------
def _summary(self):
summary = []
if not hasattr(self, 'outputSubtomograms'):
summary.append("Output subtomograms not ready yet.")
else:
summary.append("Assigned alignment to %s subtomograms from a total of %s." % (
self.outputSubtomograms.getSize(), self.inputSubtomos.get().getSize()))
return summary
def _methods(self):
methods = []
if not hasattr(self, 'outputSubtomograms'):
methods.append("Output subtomograms not ready yet.")
else:
methods.append("We assigned alignment to %s subtomograms from %s and produced %s."
% (self.outputSubtomograms.getSize(), self.getObjectTag('inputSubtomos'),
self.getObjectTag('outputSubtomograms')))
return methods
def _validate(self):
validateMsgs = []
for subtomo in self.inputAlignment.get().iterItems():
if not subtomo.hasTransform():
validateMsgs.append('Please provide subtomograms which have transformation matrix in "inputAlignment".')
return validateMsgs