Commit 2026524b authored by JosefBrandt's avatar JosefBrandt
Browse files

rejection of invalid particles already during particle detection

parent ca1b48a0

analysis/particleAndMeasurement.py

+1 −0
Original line number Diff line number Diff line
@@ -32,6 +32,7 @@ class Particle(object): 
        self.measurements = []

        self.color = None

        self.shape = None

        self.wasManuallyEdited = False   #useful tag for extracting data that can now be considered reliable and obviously was classfiied wrong before by the algorithms

    

    def addMeasurement(self, refToMeasurement):

        refToMeasurement.assignedParticle = self

analysis/particleCharacterization.py

+8 −5
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ from copy import deepcopy 
from .particleClassification.colorClassification import ColorClassifier

from .particleClassification.shapeClassification import ShapeClassifier

from segmentation import closeHolesOfSubImage

from errors import NotConnectedContoursError, InvalidParticleError

from errors import InvalidParticleError



class ParticleStats(object):

    longSize = None
@@ -46,16 +46,19 @@ def particleIsValid(particle): 
    return True

    



def getParticleStatsWithPixelScale(cnt, pixelscale, fullimage, dataset):

    newStats = ParticleStats()

def getParticleStatsWithPixelScale(cnt, fullimage, dataset):

    pixelscale = dataset.getPixelScale()

    

    newStats = ParticleStats()

    newStats.longSize, newStats.shortSize, newStats.area = getContourStats(cnt)

    newStats.longSize *= pixelscale

    newStats.shortSize *= pixelscale

    newStats.area *= (pixelscale**2)

    

    if 0 in [newStats.longSize, newStats.shortSize, newStats.area]:

        raise InvalidParticleError

    

    newStats.height = getParticleHeight(cnt, dataset)    

    print('newHeight =', newStats.height)

    newStats.shape = getParticleShape(cnt, newStats.height)

    

    partImg = getParticleImageFromFullimage(cnt, fullimage)

analysis/particleContainer.py

+16 −12
Original line number Diff line number Diff line
@@ -98,13 +98,8 @@ class ParticleContainer(object): 
        

    def setParticleStats(self, particlestats):

        assert len(self.particles) == len(particlestats)

        #particlestats is list of [long, short, longellipse, shortellipse, cv2.contourArea(cnt)]

        for index, particle in enumerate(self.particles):

            particle.longSize_box = float(particlestats[index][0])

            particle.shortSize_box = float(particlestats[index][1])

            particle.longSize_ellipse = float(particlestats[index][2])

            particle.shortSize_ellipse = float(particlestats[index][3])

            particle.area = float(particlestats[index][4])

            particle.__dict__.update(particlestats[index].__dict__)

            

    def testForInconsistentParticles(self): #i.e., particles that have multiple measurements with different assignments

        self.inconsistentParticles = []
@@ -146,10 +141,6 @@ class ParticleContainer(object): 
            scanIndex = meas.getScanIndex()

            meas.setHQI(hqiList[scanIndex])

    

    def reassignParticleToAssignment(self, particleIndex, newAssignment):

        particle = self.getParticleOfIndex(particleIndex)

        particle.setAllSpectraToNewAssignment(newAssignment)

    

    def getParticleOfIndex(self, index):

        try:

            particle = self.particles[index]
@@ -248,6 +239,12 @@ class ParticleContainer(object): 
            colors.append(particle.color)

        return colors

    

    def getShapesOfAllParticles(self):

        shapes = []

        for particle in self.particles:

            shapes.append(particle.shape)

        return shapes

    

    def getParticleColorByIndex(self, particleIndex):

        particle = self.getParticleOfIndex(particleIndex)

        return particle.color
@@ -289,13 +286,20 @@ class ParticleContainer(object): 
        final_typehistogram = {i[0]: i[1] for i in sorted_typehistogram}

        return final_typehistogram

    

    def reassignParticleToAssignment(self, particleIndex, newAssignment):

        particle = self.getParticleOfIndex(particleIndex)

        particle.setAllSpectraToNewAssignment(newAssignment)

        particle.wasManuallyEdited = True

    

    def changeParticleColor(self, index, newColor):

        particle = self.getParticleOfIndex(index)

        particle.color = newColor

        particle.wasManuallyEdited = True

    

    def changeParticleShape(self, index, newShape):

        particle = self.getParticleOfIndex(index)

        particle.shape = newShape

        particle.wasManuallyEdited = True

    

    def addMergedParticle(self, particleIndices, newContour, newStats, newAssignment=None):

        newParticle = Particle()
@@ -310,7 +314,7 @@ class ParticleContainer(object): 
                newParticle.addMeasurement(meas)



        newParticle.__dict__.update(newStats.__dict__)



        newParticle.wasManuallyEdited = True

        self.particles.append(newParticle)

        print('added new particle')

analysis/particleEditor.py

+1 −3
Original line number Diff line number Diff line
@@ -227,8 +227,7 @@ class ParticleEditor(QtCore.QObject): 
            self.particlePainter = None

    

    def mergeParticlesInParticleContainerAndSampleView(self, indices, newContour, assignment):

        pixelscale = self.viewparent.dataset.getPixelScale()

        stats = pc.getParticleStatsWithPixelScale(newContour, pixelscale, self.viewparent.imgdata, self.viewparent.dataset)

        stats = pc.getParticleStatsWithPixelScale(newContour, self.viewparent.imgdata, self.viewparent.dataset)

        

        self.viewparent.addParticleContourToIndex(newContour, len(self.viewparent.contourItems)-1)

        self.particleContainer.addMergedParticle(indices, newContour, stats, newAssignment=assignment)
@@ -240,7 +239,6 @@ class ParticleEditor(QtCore.QObject): 
        self.viewparent.resetContourIndices()

        self.particleContainer.resetParticleIndices()

        self.particleAssignmentChanged.emit()

        #TODO: INCLUDE SANITY CHECK!!!!!!!!!

    

    @QtCore.pyqtSlot(list, str)

    def changeParticleColors(self, contourIndices, newColor):

analysis/sqlexport.py

+2 −0
Original line number Diff line number Diff line
@@ -42,6 +42,7 @@ class SQLExport(QtWidgets.QDialog): 
        self.longSizes = np.round(self.particleContainer.getSizesOfAllParticles())

        self.shortSize = np.round(self.particleContainer.getShortSizesOfAllParticles())

        self.colors = self.particleContainer.getColorsOfAllParticles()

        self.shapes = self.particleContainer.getShapesOfAllParticles()

        self.spectra = self.particleContainer.getSpectraFromDisk()

        

        self.particleImages = None
@@ -219,6 +220,7 @@ class SQLExport(QtWidgets.QDialog): 
                        usedCols['Analyst'] = str(self.analystIndices[self.analystSelector.currentIndex()])

                        usedCols['Size_fraction'] = self.getSizeFraction(sizeCategories, self.longSizes[polymInd])

                        usedCols['Colour'] = self.colors[polymInd]

                        usedCols['Shape'] = self.shapes[polymInd]

                        usedCols[sizeCols[0]] = str(self.longSizes[polymInd])

                        usedCols[sizeCols[1]] = str(self.shortSize[polymInd])

                        if self.particleImages is not None: