Source code for xmipp3.protocols.protocol_assignment_tilt_pair

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# *
# * Authors:     Jose Luis Vilas (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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    from itertools import izip
except ImportError:
    izip = zip

import pyworkflow.protocol.params as params
from pyworkflow import VERSION_1_1
from pyworkflow.utils.path import makePath, removeBaseExt

from xmipp3.convert import *
from .protocol_particle_pick_pairs import XmippProtParticlePickingPairs


[docs]class XmippProtAssignmentTiltPair(XmippProtParticlePickingPairs): """ From two sets of points (tilted and untilted) the protocol determines the affine transformation between these sets. """ _label = 'assign tiltpairs' _lastUpdateVersion = VERSION_1_1 def __init__(self, *args, **kwargs): XmippProtParticlePickingPairs.__init__(self, *args, **kwargs) self.stepsExecutionMode = params.STEPS_PARALLEL def onChangeInputType(): """ Dynamically change the PointerClass depending on the selected input type (either Coordinates or Particles). """ pointerClass = 'SetOf%s' % self.getEnumText('inputType') self.getParam('untiltedSet').setPointerClass(pointerClass) self.getParam('tiltedSet').setPointerClass(pointerClass) self.inputType.trace(onChangeInputType) # Force callback function onChangeInputType() #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputMicrographsTiltedPair', params.PointerParam, pointerClass='MicrographsTiltPair', important=True, label="Micrograph tilt pair", help='Select micrographs tilt pair.') form.addParam('inputType', params.EnumParam, choices=['Coordinates', 'Particles'], default=0, display=params.EnumParam.DISPLAY_COMBO, label='Input type', help='Select a Set of Coordinates or a Set or Particles.') form.addParam('untiltedSet', params.PointerParam, pointerClass='SetOfCoordinates,SetOfParticles', label="Untilted input", help='Select the untilted input set, it can be either ' 'coordinates or particles (that contains coordinates.') form.addParam('tiltedSet', params.PointerParam, pointerClass='SetOfCoordinates,SetOfParticles', label="Tilted input", help='Select the tilted input set, it can be either ' 'coordinates or particles (that contains coordinates. ' 'It should be of the same type of the input untilted.') form.addParam('tiltAngle', params.FloatParam, default=-1, expertLevel=params.LEVEL_ADVANCED, label="Tilt angle", help='Tilt angle estimation, the method will look for ' 'the assignment in the interval of [tilt_angle-15, ' 'tilt_angle+15].\n By default: tilt angle = -1, if ' 'there is not any information about the tilt angle') form.addParam('threshold', params.FloatParam, default=0.25, expertLevel=params.LEVEL_ADVANCED, label="Threshold value", help='Parameter between 0 and 1 that allows to define if \n' 'a tilt point can be matched with a certain untilt point.\n' 'The matching is performed only if the distance is lesser\n' 'than threshold * particlesize.') form.addParam('maxShift', params.FloatParam, default=1500, expertLevel=params.LEVEL_ADVANCED, label="Maximum shift (pixels)", help='Maximum allowed distance (in pixels) that the tilt ' 'micrograph can be shifted respect to the untilted ' 'micrograph') form.addParallelSection(threads=1, mpi=1) #--------------------------- INSERT steps functions -------------------------------------------- def _particlesPos(self, *parts): return 'particles@%s.pos' % self._getExtraPath(*parts) def _micBaseName(self, mic): return removeBaseExt(mic.getFileName()) def _coordsFromParts(self, micSet, partSet, suffix): """ Create and fill a SetOfCoordinates from a given SetOfParticles. """ coordSet = self._createSetOfCoordinates(micSet, suffix='_untilted') for particle in partSet: coord = particle.getCoordinate().clone() coord.copyObjId(particle) coordSet.append(coord) coordSet.setBoxSize(partSet.getXDim()) return coordSet def _getBoxSize(self): untiltedSet = self.untiltedSet.get() if isinstance(untiltedSet, SetOfParticles): boxSize = untiltedSet.getXDim() else: boxSize = untiltedSet.getBoxSize() # coordinates return boxSize def _insertAllSteps(self): self.micsFn = self._getPath() # Convert input into xmipp Metadata format convertId = self._insertFunctionStep('convertInputStep') deps = [] for tiltPair in self.inputMicrographsTiltedPair.get(): uName = self._micBaseName(tiltPair.getUntilted()) tName = self._micBaseName(tiltPair.getTilted()) stepId = self._insertFunctionStep('assignmentStep', self._particlesPos("untilted", uName), self._particlesPos("tilted", tName), tiltPair.getTilted().getFileName(), self._particlesPos(uName), self._particlesPos(tName), prerequisites=[convertId]) deps.append(stepId) self._insertFunctionStep('createOutputStep', prerequisites=deps)
[docs] def convertInputStep(self): """ Read the input metadatata. """ # Get the converted input micrographs in Xmipp format makePath(self._getExtraPath("untilted")) makePath(self._getExtraPath("tilted")) uSet = self.untiltedSet.get() tSet = self.tiltedSet.get() # Get the untilted and tilted coordinates, depending on the input type if isinstance(uSet, SetOfParticles): uCoords = uSet.getCoordinates() tCoords = tSet.getCoordinates() # If there are not Coordinates associated to particles # we need to create and fill the set of coordinates if uCoords is None or tCoords is None: micTiltedPairs = self.inputMicrographsTiltedPair.get() uCoords = self._coordsFromParts(micTiltedPairs.getUntilted(), uSet, '_untilted') tCoords = self._coordsFromParts(micTiltedPairs.getTilted(), tSet, '_tilted') else: uCoords = uSet tCoords = tSet writeSetOfCoordinates(self._getExtraPath("untilted"), uCoords) writeSetOfCoordinates(self._getExtraPath("tilted"), tCoords)
[docs] def assignmentStep(self, fnuntilt, fntilt, fnmicsize, fnposUntilt, fnposTilt): params = ' --untiltcoor %s' % fnuntilt params += ' --tiltcoor %s' % fntilt params += ' --tiltmicsize %s' % fnmicsize params += ' --maxshift %f' % self.maxShift params += ' --particlesize %d' % self._getBoxSize() params += ' --threshold %f' % self.threshold params += ' --odir %s' % self._getExtraPath() self.runJob('xmipp_image_assignment_tilt_pair', params) # Estimate the tilt axis params = ' --untilted %s' % fnposUntilt params += ' --tilted %s' % fnposTilt params += ' -o %s' % self._getPath('input_micrographs.xmd') self.runJob('xmipp_angular_estimate_tilt_axis', params)
[docs] def createOutputStep(self): self.registerCoords(self._getExtraPath(), store=False)
#--------------------------- INFO functions -------------------------------------------- def _validate(self): errors = [] uSet = self.untiltedSet.get() tSet = self.tiltedSet.get() if (uSet is not None and tSet is not None and uSet.getClassName() != tSet.getClassName()): errors.append('Both untilted and tilted inputs should be of the ' 'same type. ') return errors def _methods(self): messages = [] if hasattr(self,'outputCoordinatesTiltPair'): messages.append('The assignment has been performed using and ' 'affinity transformation [Publication: Vilas2016]') return messages def _citations(self): return ['Vilas2016']