Source code for tomo.protocols.protocol_alignment_assign

# **************************************************************************
# *
# * Authors:     Estrella Fernandez Gimenez (
# *              David Herreros Calero ( (Coordinates3D compatibility)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * You should have received a copy of the GNU General Public License
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# *  All comments concerning this program package may be sent to the
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# **************************************************************************

from pyworkflow import BETA
from pyworkflow.protocol.params import PointerParam
from pwem.protocols import EMProtocol

import tomo.objects as tomoObjs

[docs]class ProtAlignmentAssignSubtomo(EMProtocol): """ Assign the alignment stored in a set of Subtomograms/Coordinates3D to another set. Both sets should have same pixel size (A/px). The Subtomograms/Coordinates3D with the alignment can also be a subset of a bigger set. """ _label = 'assign alignment' _devStatus = BETA def _defineParams(self, form): form.addSection(label='Input') form.addParam('input', PointerParam, pointerClass='SetOfSubTomograms, SetOfCoordinates3D', label='Input', help='Select the Subtomograms/Coordinates3D that you want to update the new alignment.') form.addParam('inputAlignment', PointerParam, pointerClass='SetOfSubTomograms, SetOfCoordinates3D', label="Alignments", help='Select the Subtomograms/Coordinates3D with alignment to be apply to the other object.') # --------------------------- INSERT steps functions -------------------------- def _insertAllSteps(self): self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions --------------------------------------------
[docs] def createOutputStep(self): input = self.input.get() inputAlignment = self.inputAlignment.get() output = input.create(self._getPath()) output.copyInfo(input) if isinstance(output, tomoObjs.SetOfSubTomograms): output.setAlignment(inputAlignment.getAlignment()) output.copyItems(input, updateItemCallback=self._updateItem) self._defineOutputs(outputAligned=output) self._defineSourceRelation(self.input, output) self._defineSourceRelation(self.inputAlignment, output)
# --------------------------- UTILS functions -------------------------------------------- def _updateItem(self, item, row): # Add alignment info from corresponding item on inputAlignment inputAlignment = self.inputAlignment.get() alignedObj = inputAlignment[item.getObjId()] # If alignment is found for this object set the alignment info # on the output object, if not do not write that item if alignedObj is not None: alignment = self._getAlignment(alignedObj) self._setAlignment(item, alignment) else: item._appendItem = False def _getAlignment(self, object): if isinstance(object, tomoObjs.Coordinate3D): return object.getMatrix() elif isinstance(object, tomoObjs.SubTomogram): return object.getTransform() def _setAlignment(self, object, alignment): if isinstance(object, tomoObjs.Coordinate3D): object.setMatrix(alignment) elif isinstance(object, tomoObjs.SubTomogram): return object.setTransform(alignment) # --------------------------- INFO functions -------------------------------------------- def _summary(self): summary = [] if not hasattr(self, 'outputAligned'): summary.append("Output not ready yet.") else: summary.append("Assigned alignment to %s objects from a total of %s." % ( self.outputAligned.getSize(), self.input.get().getSize())) return summary def _methods(self): methods = [] if not hasattr(self, 'outputAligned'): methods.append("Output not ready yet.") else: methods.append("We assigned alignment to %s objects from %s and produced %s." % (self.outputAligned.getSize(), self.getObjectTag('input'), self.getObjectTag('outputAligned'))) return methods def _validate(self): validateMsgs = [] inputAlignment = self.inputAlignment.get().getFirstItem() input = self.input.get().getFirstItem() if type(input) != type(inputAlignment): validateMsgs.append('*Input* and *Alignments* parameters must belong to the same type ' '(SetOfCoordinates3D or SetOfSubtomorgams).') else: if not inputAlignment.hasTransform(): validateMsgs.append('Please provide Subtomograms/Coordinates3D which ' 'have transformation matrix in "inputAlignment".') return validateMsgs