Commit a974f0be authored by JosefBrandt's avatar JosefBrandt
Browse files

Bugfix in selection

parent fcca6561

analysis/analysisview.py

+2 −5
Original line number Diff line number Diff line
@@ -149,7 +149,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        navigationLayout.addWidget(QtWidgets.QLabel('Select Spectrum'))

        navigationLayout.addWidget(self.spectrumSelector)

        navigationLayout.addWidget(self.spectrumNumberLabel)

#        navigationLayout.addStretch()

        

        self.navigationGroup.setLayout(navigationLayout)
@@ -579,14 +578,12 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        self.currentSpectrumIndex = self.specNumberSelector.value()-1

        self.currentParticleIndex = self.particleContainer.getParticleIndexContainingSpecIndex(self.currentSpectrumIndex)

        self.centerOnSpecIndex(self.currentSpectrumIndex)

        self.highLightContour(self.currentParticleIndex)

        self.viewparent.highLightContour(self.currentParticleIndex)

        self.updateSpecPlot()

    

    def centerOnSpecIndex(self, index):

        self.viewparent.centerOnRamanIndex(index)

    

    def highLightContour(self, index):

        self.viewparent.highLightContour(index)

    

    def darkenBackground(self):

        self.viewparent.darkenPixmap = self.darkenAct.isChecked()

analysis/analysiswidgets.py

+4 −5
Original line number Diff line number Diff line
@@ -37,7 +37,6 @@ class ExpExcelDialog(QtWidgets.QDialog): 
        

        self.dataset = dataset

        self.particleContainer = particleContainer

#        self.particles = self.datastats.getParticleStats()

        self.polymers = self.particleContainer.getListOfParticleAssignments

#        self.additives = self.datastats.currentAdditives

        self.hqis = self.particleContainer.getListOfHighestHQIs
@@ -62,10 +61,10 @@ class ExpExcelDialog(QtWidgets.QDialog): 
            if option == 'Polymer Type (mandatory)':

                self.checkBoxes[-1].setEnabled(False)           #is mandatory!!!

            

            if option == 'Additives':

                if self.additives is None:

                    self.checkBoxes[-1].setEnabled(False)

                    self.checkBoxes[-1].setChecked(False)

#            if option == 'Additives':

#                if self.additives is None:

#                    self.checkBoxes[-1].setEnabled(False)

#                    self.checkBoxes[-1].setChecked(False)

                    

            excelvbox.addWidget(self.checkBoxes[-1])

analysis/particleInfo.py

+10 −20
Original line number Diff line number Diff line
@@ -18,21 +18,13 @@ You should have received a copy of the GNU General Public License 
along with this program, see COPYING.  

If not, see <https://www.gnu.org/licenses/>.

"""

#import os

import numpy as np

import operator

#from PyQt5 import QtWidgets, QtCore



#try:

#    from dataset import loadData, recursiveDictCompare

#    print('exported dataset methods from datastats')

#except:

#    print('failed exported dataset methods from datastats')



class ParticleContainer(object):

    def __init__(self, parent):

    def __init__(self, datasetParent):

        super(ParticleContainer, self).__init__()

        self.parent = parent

        self.datasetParent = datasetParent

        self.particles = []

        self.spectra = None

        self.inconsistentParticles = []
@@ -223,7 +215,7 @@ class ParticleContainer(object): 
        final_typehistogram = {i[0]: i[1] for i in sorted_typehistogram}

        return final_typehistogram

    

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

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

        newParticle = Particle()

        #copy Measurements

        for index in particleIndices:
@@ -243,15 +235,10 @@ class ParticleContainer(object): 
        newParticle.area = area

        newParticle.contour = newContour

        

        self.removeParticles(particleIndices)

        print('removed particles')

        self.particles.append(newParticle)

        print('added new particle')

        self.resetParticleIndices()

        print('resetted indices')

        

    def removeParticles(self, indexList):

        for index in sorted(indexList, reverse=True):

    def removeParticle(self, index):

        particle = self.getParticleOfIndex(index)   #just for asserting to have the correct particle!

        del self.particles[index]
@@ -259,7 +246,6 @@ class ParticleContainer(object): 
        for newIndex, particle in enumerate(self.particles):

            particle.index = newIndex





class Particle(object):

    def __init__(self):

        super(Particle, self).__init__()
@@ -271,6 +257,7 @@ class Particle(object): 
        self.area = None

        self.contour = None

        self.measurements = []

        self.viewItem = None

        

    def addExistingMeasurement(self, meas):

        self.measurements.append(meas)
@@ -362,6 +349,9 @@ class Particle(object): 
        for measurement in self.measurements:

            measurement.applyHQIThreshold(minHQI)

    

#    def recreateViewItem(self):

#        pass

            

    

class Measurement(object):

    def __init__(self):

analysis/particleeditor.py

+56 −43
Original line number Diff line number Diff line
@@ -29,7 +29,27 @@ import numpy as np 
import cv2

from PyQt5 import QtWidgets, QtCore



from analysis.particlePainter import ParticlePainter

from .particlePainter import ParticlePainter



def getContourStatsWithPixelScale(contours, pixelscale):

        ##characterize particle

        longellipse, shortellipse = np.nan, np.nan

        

        cnt = contours

        

        if cnt.shape[0] >= 5:       ##at least 5 points required for ellipse fitting...

            ellipse = cv2.fitEllipse(cnt)

            shortellipse, longellipse = ellipse[1]



        rect = cv2.minAreaRect(cnt)

        long, short = rect[1]

        if short>long:

            long, short = short, long

        

        area = cv2.contourArea(cnt)

    

        return long*pixelscale, short*pixelscale, longellipse*pixelscale, shortellipse*pixelscale, area*pixelscale**2





class ParticleContextMenu(QtWidgets.QMenu):

    combineParticlesSignal = QtCore.pyqtSignal(list, str)
@@ -110,7 +130,6 @@ class ParticleContextMenu(QtWidgets.QMenu): 




class ParticleEditor(QtCore.QObject):

#    particleContoursChanged = QtCore.pyqtSignal()

    particleAssignmentChanged = QtCore.pyqtSignal()

    def __init__(self, viewparent, particleContainer):

        super(ParticleEditor, self).__init__()
@@ -142,19 +161,15 @@ class ParticleEditor(QtCore.QObject): 
        self.createSafetyBackup()

        print(f'Combining particles {contourIndices} into {newAssignment}')

        contours = self.particleContainer.getParticleContoursByIndex(contourIndices)

        try:

            newContour = self.mergeContours(contours.copy()) 

        pixelscale = self.viewparent.dataset.getPixelScale()

        stats = self.characterizeParticle(newContour, pixelscale)



        self.particleContainer.mergeParticles(contourIndices, newContour, stats, newAssignment=newAssignment)

        for ind in contourIndices:

            self.viewparent.removeParticleContour(ind)

        except NotConnectedContoursError:

            return

        

        self.viewparent.resetContourIndices()

        self.viewparent.addParticleContour(newContour, len(self.viewparent.contourItems))

        pixelscale = self.viewparent.dataset.getPixelScale()

        stats = getContourStatsWithPixelScale(newContour, pixelscale)



        self.particleAssignmentChanged.emit()

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

        self.mergeParticlesInParticleContainerAndSampleView(contourIndices,newContour, stats, newAssignment)

    

    @QtCore.pyqtSlot(list, str)

    def reassignParticles(self, contourindices, newAssignment):
@@ -167,7 +182,8 @@ class ParticleEditor(QtCore.QObject): 
     

    @QtCore.pyqtSlot(list, str)

    def paintParticles(self, contourIndices, newAssignment):

        self.createSafetyBackup

        print(f'painting indices {contourIndices} into {newAssignment}')

        self.createSafetyBackup()

        self.storedIndices = contourIndices

        self.storedAssignmend = newAssignment

        contours = self.particleContainer.getParticleContoursByIndex(contourIndices)
@@ -178,19 +194,19 @@ class ParticleEditor(QtCore.QObject): 
        self.viewparent.update()

        

    def acceptPaintedResult(self):

        try:

            newContour = self.mergeContours(self.particlePainter.contours.copy())

        pixelscale = self.viewparent.dataset.getPixelScale()

        stats = self.characterizeParticle(newContour, pixelscale)

        except NotConnectedContoursError:

            self.storedIndices = []

            self.storedAssignmend = None

            self.destroyParticlePainter()

            return

        

        self.particleContainer.mergeParticles(self.storedIndices, newContour, stats, newAssignment=self.storedAssignmend)

        for ind in self.storedIndices:

            self.viewparent.removeParticleContour(ind)

        pixelscale = self.viewparent.dataset.getPixelScale()

        stats = getContourStatsWithPixelScale(newContour, pixelscale)

        

        self.particleAssignmentChanged.emit()

        self.viewparent.resetContourIndices()

        self.viewparent.addParticleContour(newContour, len(self.viewparent.contourItems))

        self.mergeParticlesInParticleContainerAndSampleView(self.storedIndices, newContour, stats, self.storedAssignmend)

        

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

        self.storedIndices = []

        self.storedAssignmend = None

        self.destroyParticlePainter()
@@ -230,7 +246,7 @@ class ParticleEditor(QtCore.QObject): 
        if len(contours)>1:

            QtWidgets.QMessageBox.critical(self.viewparent, 'ERROR!', 

                                           'Particle contours are not connected and cannot be combined!')

            return

            raise NotConnectedContoursError

        

        newContour = contours[0]

        for i in range(len(newContour)):
@@ -239,24 +255,18 @@ class ParticleEditor(QtCore.QObject): 
            

        return newContour

    

    def characterizeParticle(self, contours, pixelscale):

        ##characterize particle

        longellipse, shortellipse = np.nan, np.nan

        

        cnt = contours

        

        if cnt.shape[0] >= 5:       ##at least 5 points required for ellipse fitting...

            ellipse = cv2.fitEllipse(cnt)

            shortellipse, longellipse = ellipse[1]



        rect = cv2.minAreaRect(cnt)

        long, short = rect[1]

        if short>long:

            long, short = short, long

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

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

        self.particleContainer.addMergedParticle(indices, newContour, stats, newAssignment=assignment)

        

        area = cv2.contourArea(cnt)

        for ind in sorted(indices, reverse=True):

            self.viewparent.removeParticleContour(ind)

            self.particleContainer.removeParticle(ind)

        

        return long*pixelscale, short*pixelscale, longellipse*pixelscale, shortellipse*pixelscale, area*pixelscale**2

        self.viewparent.resetContourIndices()

        self.particleContainer.resetParticleIndices()

        self.particleAssignmentChanged.emit()

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

    

    @QtCore.pyqtSlot(list)

    def deleteParticles(self, contourIndices):
@@ -274,4 +284,7 @@ class ParticleEditor(QtCore.QObject): 
            self.viewparent.analysiswidget.updateHistogramsAndContours()





class NotConnectedContoursError(Exception):

    pass

        

    
 No newline at end of file

sampleview.py

+9 −7
Original line number Diff line number Diff line
@@ -422,9 +422,11 @@ class SampleView(QtWidgets.QGraphicsView): 
                        removeContourFromSelection(cnt)

            

            else:    #not clicked on particle

                

                if event.modifiers()!=QtCore.Qt.ShiftModifier and cnt.particleIndex in self.selectedParticleIndices:

                    removeContourFromSelection(cnt)

                if event.modifiers()!=QtCore.Qt.ShiftModifier:

                    cnt.isSelected = False

                    cnt.update()

                    if cnt.particleIndex in self.selectedParticleIndices:

                        self.selectedParticleIndices.remove(cnt.particleIndex)

                    

        self.update()
@@ -584,11 +586,11 @@ class SampleView(QtWidgets.QGraphicsView): 
        self.contourItems = []

        if self.dataset is not None:

            for particleIndex, contour in enumerate(self.dataset.particleContainer.getParticleContours()):

                self.addParticleContour(contour, particleIndex)

                self.addParticleContourToIndex(contour, particleIndex)

            self.update()

        print('resetted contours: {} ms'.format(round((time.time()-t0)*1000)))

        

    def addParticleContour(self, contour, index):

    def addParticleContourToIndex(self, contour, index):

        newCnt = SegmentationContour(self, contour)

        newCnt.setIndex(index)

        assignment = self.dataset.particleContainer.getParticleAssignmentByIndex(index)
@@ -616,10 +618,10 @@ class SampleView(QtWidgets.QGraphicsView): 
            self.ramanscanitems[index].setHighLight(True)

    

    def highLightContour(self, index):

        print('highlighting contour', index)

        for contour in self.contourItems:

            contour.isSelected = False

        self.contourItems[index].isSelected = True

        self.selectedParticleIndices =[index]

    

    def centerOnRamanIndex(self, index, centerOn=True, highlightIndex=True):

        if centerOn: