Source code for xmipptomo.protocols.protocol_fit_ellipsoid

# -*- coding: utf-8 -*-
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# *
# * Authors:     Estrella Fernandez Gimenez (me.fernandez@cnb.csic.es)
# *
# *  BCU, Centro Nacional de Biotecnologia, CSIC
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from os.path import basename, dirname, join
import numpy as np
from pyworkflow.protocol.params import PointerParam
import pyworkflow.utils as pwutlis
from pwem.protocols import EMProtocol
from tomo.protocols import ProtTomoBase
from tomo.objects import MeshPoint, Ellipsoid, SubTomogram
from tomo.utils import fit_ellipsoid, generatePointCloud


[docs]class XmippProtFitEllipsoid(EMProtocol, ProtTomoBase): """ This protocol adjust a SetOfSubtomograms with coordinates assigned or a SetOfCoordinates3D, to a vesicle (ellipsoid), defining regions of interest (SetOfMeshes) for each vesicle as output.""" _label = 'fit vesicles' def __init__(self, **args): EMProtocol.__init__(self, **args) # --------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='Input') form.addParam('input', PointerParam, pointerClass="SetOfSubTomograms, SetOfCoordinates3D", label='Subtomograms/Coordinates3D', help='Subtomograms or coordinates3D picked in vesicles. If there are more than one vesicle per ' 'tomogram, input subtomograms or coordinates should have assigned groupId.') form.addParam('inputTomos', PointerParam, label="Tomograms", pointerClass='SetOfTomograms', help='Select tomograms from which subtomograms come.') # --------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('fitEllipsoidStep') self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -------------------------------
[docs] def fitEllipsoidStep(self): input = self.input.get() inputTomos = self.inputTomos.get() self.outSet = self._createSetOfMeshes(inputTomos) totalMeshes = 0 for tomo in inputTomos.iterItems(iterate=False): vesicleList = [] vesicleIdList = [] tomoName = basename(tomo.getFileName()) tomoDim = [float(d) for d in tomo.getDim()] firstItem = input.getFirstItem() if self._getInputisSubtomo(firstItem): dirName = dirname(firstItem.getVolName()) for item in input.iterItems(where="_volName='%s'" % join(dirName, tomoName)): vesicleId = self._getVesicleId(item) if vesicleId not in vesicleIdList: vesicleIdList.append(vesicleId) vesicle = self._createSetOfSubTomograms('_' + pwutlis.removeBaseExt(tomoName) + '_vesicle_' + str(vesicleId)) vesicleList.append(vesicle) idx = vesicleIdList.index(vesicleId) vesicleList[idx].append(item) else: for item in input.iterCoordinates(volume=tomo): vesicleId = self._getVesicleId(item) if vesicleId not in vesicleIdList: vesicleIdList.append(vesicleId) vesicle = self._createSetOfCoordinates3D(inputTomos, '_' + pwutlis.removeBaseExt(tomoName) + '_vesicle_' + str(vesicleId)) vesicleList.append(vesicle) idx = vesicleIdList.index(vesicleId) vesicleList[idx].append(item) totalMeshes += len(vesicleList) for vesicle in vesicleList: x = [] y = [] z = [] if self._getInputisSubtomo(input.getFirstItem()): for item in vesicle.iterItems(): coord = self._getCoor(item) x.append(float(coord.getX()) / tomoDim[0]) y.append(float(coord.getY()) / tomoDim[1]) z.append(float(coord.getZ()) / tomoDim[2]) else: for item in vesicle.iterCoordinates(volume=tomo): coord = self._getCoor(item) x.append(float(coord.getX()) / tomoDim[0]) y.append(float(coord.getY()) / tomoDim[1]) z.append(float(coord.getZ()) / tomoDim[2]) [center, radii, v, _, chi2] = fit_ellipsoid(np.array(x), np.array(y), np.array(z)) algDesc = '%f*x*x + %f*y*y + %f*z*z + 2*%f*x*y + 2*%f*x*z + 2*%f*y*z + 2*%f*x + 2*%f*y + 2*%f*z + %f ' \ '= 0' % (v[0], v[1], v[2], v[3], v[4], v[5], v[6], v[7], v[8], v[9]) adjEllipsoid = Ellipsoid() adjEllipsoid.setAlgebraicDesc(algDesc) adjEllipsoid.setCenter(str(center)) adjEllipsoid.setRadii(str(radii)) print(algDesc) print('Chi2: ', chi2) pointCloud = generatePointCloud(v, tomo.getDim()) if not pointCloud: raise Exception("It does not seem like any output is produced!") for point in pointCloud: meshPoint = MeshPoint() meshPoint.setX(point[0]) meshPoint.setY(point[1]) meshPoint.setZ(point[2]) meshPoint.setGroupId(self._getVesicleId(item)) meshPoint.setDescription(adjEllipsoid) meshPoint.setVolume(tomo.clone()) meshPoint.setVolumeName(basename(tomo.getFileName())) self.outSet.append(meshPoint) self.outSet.setPrecedents(inputTomos) self.outSet.setNumberOfMeshes(totalMeshes)
[docs] def createOutputStep(self): self._defineOutputs(outputMeshes=self.outSet) self._defineSourceRelation(self.inputTomos.get(), self.outSet)
# --------------------------- INFO functions -------------------------------- def _validate(self): validateMsgs = [] input = self.input.get() if input.getSize() < 9: validateMsgs.append('At least 9 subtomograms/coordinates are required to fit a unique ellipsoid') if self._getInputisSubtomo(self.input.get().getFirstItem()): if not input.getFirstItem().hasCoordinate3D(): validateMsgs.append('Subtomograms should have coordinates') return validateMsgs def _summary(self): summary = [] if not self.isFinished(): summary.append("Output vesicles not ready yet.") else: summary.append("%d subtomograms/coordinates3D from %d tomograms\n%d vesicles adjusted" % (self.input.get().getSize(), self.inputTomos.get().getSize(), self.outputMeshes.getNumberOfMeshes())) return summary def _methods(self): if not self.isFinished(): return ["Protocol not finished yet"] else: return ["Fit an ellipsoid and compute a 3D set of points (mesh) for each of the %d vesicles adjusted." % self.outputMeshes.getNumberOfMeshes()] # --------------------------- UTILS functions -------------------------------------------- def _getInputisSubtomo(self, item): if isinstance(item, SubTomogram): return True else: return False def _getCoor(self, item): if self._getInputisSubtomo(item): coor = item.getCoordinate3D() else: coor = item return coor def _getVesicleId(self, item): coor = self._getCoor(item) if coor.hasGroupId(): vesicleId = coor.getGroupId() else: vesicleId = '1' # For now it works with several vesicles in the same tomo just for subtomos with groupId return vesicleId def _evaluateQuadric(self, v, x, y, z): return v[0]*x*x + v[1]*y*y + v[2]*z*z + 2*v[3]*x*y + 2*v[4]*x*z + 2*v[5]*y*z + 2*v[6]*x + 2*v[7]*y + 2*v[8]*z +\ v[9]