Source code for xmipptomo.protocols.protocol_coords_roi

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# * Authors:     Estrella Fernandez Gimenez (
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# *  BCU, Centro Nacional de Biotecnologia, CSIC
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import os
import numpy as np
from pyworkflow.protocol.params import IntParam, PointerParam, EnumParam
from pwem.protocols import EMProtocol
from tomo.protocols import ProtTomoBase

[docs]class XmippProtCCroi(EMProtocol, ProtTomoBase): """ This protocol adjust a SetOfCoordinates (which usually will come from a connected componnent) to a ROI (region of interest) previously defined""" _label = 'connected components to ROIs' def __init__(self, **args): EMProtocol.__init__(self, **args) # --------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputCoordinates', PointerParam, label="Connected components", pointerClass='SetOfCoordinates3D', help='Select the Connected components (SetOfCoordinates3D).') form.addParam('inputMeshes', PointerParam, label="ROIs", pointerClass='SetOfMeshes', help='Select the ROIs (Regions Of Interest) they are SetOfMeshes') form.addParam('selection', EnumParam, choices=['Connected component', 'Points'], default=0, label='Selection', display=EnumParam.DISPLAY_HLIST, help='Selection options:\n*Connected component*: It takes the whole connected component (cc) if ' 'a percentage of the points (introduced in the next field) in the cc belongs to the ROI. ' '\n*Points*: It takes just the points of the cc which belongs to the roi') form.addParam('points', IntParam, label="Percentage of coordinates in ROI", default=80, condition='selection == 0', allowsNull=True, help='Percentage of coordinates from a connected component that should be inside' ' the ROI to consider that connected component.') form.addParam('distance', IntParam, label='Distance', default=50, help='Maximum euclidean distance (in pixels) between ROI vertex and a coordinate to consider that' ' it belongs to the ROI.') # --------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('computeDistances') self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -------------------------------
[docs] def computeDistances(self): """Compare all connected components with all meshes; a connected component can be just in one mesh (first one found)""" inputSetCoor = self.inputCoordinates.get() inputSetMeshes = self.inputMeshes.get() # group connected components by groupId listOfCCs = [] listOfgroupIdCCs = [] for coor in inputSetCoor.iterCoordinates(): tomoNameC = coor.getVolName() groupIdC = coor.getGroupId() tupleC = (groupIdC, tomoNameC) if tupleC not in listOfgroupIdCCs: listOfgroupIdCCs.append(tupleC) listOfCCs.append(self._createSetOfCoordinates3D(inputSetCoor.getPrecedents(), groupIdC)) coorLoc = listOfCCs[listOfgroupIdCCs.index(tupleC)] if not coorLoc: coorLoc.append(coor) else: if coorLoc.getFirstItem().getVolName() == tomoNameC: coorLoc.append(coor) # group meshes by groupId and tomoName listOfMeshes = [] listOfgroupIdMeshes = [] for meshPoint in inputSetMeshes.iterCoordinates(): tomoNameM = meshPoint.getVolName() tomoId = meshPoint.getVolume().getObjId() groupIdM = meshPoint.getGroupId() tupleM = (groupIdM, tomoNameM) if tupleM not in listOfgroupIdMeshes: listOfgroupIdMeshes.append(tupleM) listOfMeshes.append(self._createSetOfMeshes(inputSetMeshes.getPrecedents(), '%d_%d' % (tomoId,groupIdM))) meshPointLoc = listOfMeshes[listOfgroupIdMeshes.index(tupleM)] if not meshPointLoc: meshPointLoc.append(meshPoint) else: if meshPointLoc.getFirstItem().getVolName() == tomoNameM: meshPointLoc.append(meshPoint) sel = self.selection.get() self.outputSet = self._createSetOfCoordinates3D(inputSetCoor.getPrecedents()) self.outputSet.copyInfo(inputSetCoor) self.outputSet.setBoxSize(inputSetCoor.getBoxSize()) self.outputSet.setSamplingRate(inputSetCoor.getSamplingRate()) for cc in listOfCCs: for mesh in listOfMeshes: if os.path.basename(cc.getFirstItem().getVolName()) == os.path.basename(mesh.getFirstItem().getVolName()): if sel == 0: i = 0 else: outputSetList = [] for coorcc in cc: for meshPoint in mesh: if self._euclideanDistance(coorcc, meshPoint) <= self.distance.get(): if sel == 0: i += 1 else: outputSetList.append(coorcc.getObjId()) break if sel == 0: perc = self._percentage(cc) if i >= perc: self.groupIdCoorCC = coorcc.getGroupId() self.outputSet.copyItems(inputSetCoor, updateItemCallback=self._updateItem) else: if len(outputSetList) != 0: for coor3D in inputSetCoor.iterItems(): if coor3D.getObjId() in outputSetList: self.outputSet.append(coor3D) break
[docs] def createOutputStep(self): self._defineOutputs(outputSet=self.outputSet) self._defineSourceRelation(self.inputCoordinates, self.outputSet)
# --------------------------- INFO functions -------------------------------- def _summary(self): summary = [] if self.selection.get() == 0: summary.append("Percentage of coordinates in ROI: %d" % self.points.get()) if self.selection.get() == 0: sel = 'complete connected components' else: sel = 'points in connected components' summary.append("Max distance to ROI: %d\nSelect: %s" % (self.distance.get(), sel)) return summary def _methods(self): methods = "Connected components detected" if self.selection.get() == 0: methods.append("with at least %d percent of points" % self.points.get()) methods.append("at a maximun distance of %d pixels of a ROI." % self.distance.get()) return methods # --------------------------- UTILS functions -------------------------------------------- def _percentage(self, inputSetCoor): return (self.points.get()*inputSetCoor.getSize())/100 def _euclideanDistance(self, coorcc, cm): return np.sqrt((coorcc.getX() - int(cm.getX())) + (coorcc.getY() - int(cm.getY())) + (coorcc.getZ() - int(cm.getZ()))) def _updateItem(self, item, row): if item.getGroupId() != self.groupIdCoorCC: setattr(item, "_appendItem", False)