Commit 92775bcc authored by JosefBrandt's avatar JosefBrandt
Browse files 

Bugfix in contour selection
parent 83cdeb70

analysis/analysisview.py

+92 −102
Original line number Diff line number Diff line
@@ -116,16 +116,21 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        self.specNumberSelector = QtWidgets.QSpinBox()

        self.specNumberSelector.setMinimumWidth(100)

        self.specNumberSelector.setMinimum(1)

        self.specNumberSelector.setMaximum(1E6)

        numParticles = self.particleContainer.getNumberOfParticles()

        self.specNumberSelector.setMaximum(numParticles)

        

        self.jumpToSpecBtn = QtWidgets.QPushButton('Jump To Spectrum of Number:')

        self.jumpToSpecBtn.released.connect(self.jumpToIndicatedSpectrum)

        

        self.typeSelectorCombo = QtWidgets.QComboBox()

        self.typeSelectorCombo.setMinimumWidth(150)

        self.typeSelectorCombo.currentIndexChanged.connect(self.setTypeSelector)

        self.particleSelector = QtWidgets.QSpinBox()

        self.particleSelector.valueChanged.connect(self.setParticleSelector)

        self.particleNumberLabel = QtWidgets.QLabel('of xx particles; ')

        

        self.spectrumSelector = QtWidgets.QSpinBox()

        self.spectrumSelector.valueChanged.connect(self.setSpecSelector)

        self.spectrumNumberLabel = QtWidgets.QLabel('of xx spectra')

        for spinbox in [self.particleSelector, self.spectrumSelector]:

            spinbox.setMinimum(1)
@@ -218,8 +223,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        self.applyHQIThresholdToResults()

        self.createHistogramData()

        self.initializeSpecPlot()

        self.displayNewPolymerType()

        self.updateSpecPlotToSelectedParticle()

        self.setTypeSelector()

        self.updateHistogramsAndContours()

    

    def createActions(self):
@@ -330,7 +334,25 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        self.createHistogramData()

        self.updateHistogramsAndContours()

     

    def updateHistogramsAndContours(self):  

        self.createHistogramData()

        t0 = time.time()

        self.updateTypeHistogram()

        print('update type hist: {} ms'.format(round((time.time()-t0)*1000)))

        t0 = time.time()

        self.updateSizeHistogram()

        print('update size hist: {} ms'.format(round((time.time()-t0)*1000)))

        t0 = time.time()

        self.updateContourColors()

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

        t0 = time.time()

        self.updateLegend()

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

        self.dataset.save()

        

    def createHistogramData(self):

        self.lastSelectedCheckBoxNames = self.getSelectedPolymers()

        

        ###Handle Checkboxes for all polymers...

        self.menuLayout.removeWidget(self.resultScrollarea)

        for i in [self.resultCheckBoxes, self.resultCheckBoxesLayout, self.resultScrollarea, self.layout_SArea]:
@@ -381,12 +403,14 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
            self.expSQLAct.setDisabled(False)

        

        self.navigationGroup.setEnabled(True)

#        self.typeSelectorCombo.currentIndexChanged.disconnect()

        self.typeSelectorCombo.currentIndexChanged.disconnect()

        self.typeSelectorCombo.clear()

        self.typeSelectorCombo.addItems(uniquePolymers)

#        self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)

        self.typeSelectorCombo.currentIndexChanged.connect(self.setTypeSelector)

        

        numParticles = self.particleContainer.getNumberOfParticles()

        self.specNumberSelector.setMaximum(numParticles)

        

        self.polymerIndex = self.typeSelectorCombo.currentIndex()

#        if self.lastSpectrumInFocus is not None:

#            self.currentSpectrumIndex = self.lastSpectrumInFocus

#            self.displayNewPolymerType(resetCurrentIndex=False)
@@ -395,22 +419,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
#            print('displaying new type with resetting index')

#            self.displayNewPolymerType()

        

    def updateHistogramsAndContours(self):  

        self.createHistogramData()

        t0 = time.time()

        self.updateTypeHistogram()

        print('update type hist: {} ms'.format(round((time.time()-t0)*1000)))

        t0 = time.time()

        self.updateSizeHistogram()

        print('update size hist: {} ms'.format(round((time.time()-t0)*1000)))

        t0 = time.time()

        self.updateContourColors()

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

        t0 = time.time()

        self.updateLegend()

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

        self.dataset.save()

    

    def initializeSpecPlot(self):

        self.specPlot.loadSpectraAndInitializeSpecPlot()

        self.updateSpecPlot()
@@ -466,8 +474,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
            self.sizeHist_ax.set_xlim(3, 1100)        

            self.sizeHist_ax.figure.canvas.draw()

    

            self.lastSelectedCheckBoxNames = self.getSelectedPolymers()

    

    def updateSpecPlot(self):

        particleSize = self.particleContainer.getSizeOfParticleByIndex(self.currentParticleIndex)

        hqi = self.particleContainer.getHQIOfSpectrumIndex(self.currentSpectrumIndex)
@@ -505,102 +511,81 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
                    legendItems.append((polymer, color))

            self.viewparent.updateLegend(legendItems)



                        

    def getSelectedPolymers(self):

        return [checkbox.text() for checkbox in self.polymerCheckBoxes if checkbox.isChecked()]

     

    def getSpecIndexFromBoxesAndJumpThere(self):

        self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()

    def setTypeSelector(self):

        assignment = self.typeSelectorCombo.currentText()

        partIndices = self.particleContainer.getIndicesOfParticleType(assignment)

        self.particleSelector.setMaximum(len(partIndices))

        self.particleNumberLabel.setText(f'of {len(partIndices)} particles; ')

        self.particleSelector.setValue(1)

        self.setParticleSelector()

    

    def setParticleSelector(self):

        assignment = self.typeSelectorCombo.currentText()

        if assignment != '':

            partIndices = self.particleContainer.getIndicesOfParticleType(assignment)

            self.currentParticleIndex = partIndices[self.particleSelector.value()-1]

            

            specIndices = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)

            self.spectrumSelector.setValue(1)

            self.spectrumSelector.setMaximum(len(specIndices))        

            self.spectrumNumberLabel.setText(f'of {len(specIndices)} spectra')

            self.setSpecSelector()

        

    def setSpecSelector(self):

        specIndices = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)

        self.currentSpectrumIndex = specIndices[self.spectrumSelector.value()-1]

        self.specNumberSelector.setValue(self.currentSpectrumIndex+1)

        

        self.updateSpecPlot()

        self.jumpToIndicatedSpectrum()

    

    def jumpToIndicatedSpectrum(self, centerOn=True):

        print('jumping to spec index with centerOn', centerOn)

        ###disconnect Boxes

    def setWidgetsToNewParticleIndex(self, particleIndex):   #TODO: Probably refactor. Its basically a combination of the above methods... Just a bit different to avoid directly jumping to the particle in sampleview

        try:

            self.typeSelectorCombo.currentIndexChanged.disconnect()

            self.particleSelector.valueChanged.disconnect()

            self.spectrumSelector.valueChanged.disconnect()

            self.typeSelectorCombo.currentIndexChanged.disconnect()

        except TypeError:

            pass   #i.e., there was no connection

            pass #signals were not connected...

        

        

        specIndex = self.specNumberSelector.value()-1

        print('specIndex', specIndex)

        partIndex = self.particleContainer.getParticleIndexContainingSpecIndex(specIndex)

        print('partIndex', partIndex)

        assignment = self.particleContainer.getParticleAssignmentByIndex(partIndex)

        assignment = self.particleContainer.getParticleAssignmentByIndex(particleIndex)

        self.typeSelectorCombo.setCurrentText(assignment)

        

        self.currentParticleIndex = particleIndex

        partIndices = self.particleContainer.getIndicesOfParticleType(assignment)

        self.particleSelector.setValue(partIndices.index(partIndex)+1)

        

        specIndices = self.particleContainer.getSpectraIndicesOfParticle(partIndex)

        self.spectrumSelector.setValue(specIndices.index(specIndex)+1)

        

        if centerOn:

            self.viewparent.centerOnRamanIndex(self.currentSpectrumIndex, centerOn=True, highlightContour=True)

        self.viewparent.highLightContour(self.getParticleIndexFromParticleSelector())

            

        ###connect Boxes

        self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)

        self.typeSelectorCombo.currentIndexChanged.connect(self.getSpecIndexFromBoxesAndJumpThere)

#        self.particleSelector.valueChanged.connect(self.updateSpecPlotToSelectedParticle)

        self.particleSelector.valueChanged.connect(self.getSpecIndexFromBoxesAndJumpThere)

#        self.spectrumSelector.valueChanged.connect(self.selectSpectrum)

        self.spectrumSelector.valueChanged.connect(self.getSpecIndexFromBoxesAndJumpThere)

        self.displayNewPolymerType()

        self.updateSpecPlotToSelectedParticle()

        self.updateHistogramsAndContours()

        self.particleSelector.setMaximum(len(partIndices))

        

        

    def selectParticleOfIndex(self, particleIndex, centerOn=False):

        specIndices = self.particleContainer.getSpectraIndicesOfParticle(particleIndex)

        self.specNumberSelector.setValue(specIndices[0]+1)

        self.jumpToIndicatedSpectrum(centerOn=centerOn)

        self.particleSelector.setValue(partIndices.index(particleIndex)+1)

        

    def displayNewPolymerType(self, resetCurrentIndex=True):

        polymerName = self.typeSelectorCombo.currentText()

        numParticles = self.particleContainer.getNumberOfParticlesOfAssignment(polymerName)

        self.particleSelector.setMaximum(numParticles)

        self.particleNumberLabel.setText(f'of {numParticles} Particles; ')

        

        self.particleSelector.setValue(1)

        specIndices = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)

        self.spectrumSelector.setValue(1)

        self.spectrumSelector.setMaximum(len(specIndices))        

        self.spectrumNumberLabel.setText(f'of {len(specIndices)} spectra')

        

        self.currentParticleIndex = self.getParticleIndexFromParticleSelector()

        numSpectra = self.particleContainer.getNumberOfSpectraOfParticle(self.currentParticleIndex)

        self.spectrumSelector.setMaximum(numSpectra)

        self.spectrumNumberLabel.setText(f'of {numSpectra} Spectra')

        self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()

        self.currentSpectrumIndex = specIndices[self.spectrumSelector.value()-1]

        self.specNumberSelector.setValue(self.currentSpectrumIndex+1)

        self.updateSpecPlot()

        

    def updateSpecPlotToSelectedParticle(self, resetSpectrumCount=True):

        polymerName = self.typeSelectorCombo.currentText()

        if polymerName != '':

            self.currentParticleIndex = self.getParticleIndexFromParticleSelector()

            numSpectra = self.particleContainer.getNumberOfSpectraOfParticle(self.currentParticleIndex)

            self.spectrumSelector.setMaximum(numSpectra)

            self.spectrumNumberLabel.setText(f'of {numSpectra} Spectra')

            if resetSpectrumCount:

                self.spectrumSelector.setValue(1)

        self.typeSelectorCombo.currentIndexChanged.connect(self.setTypeSelector)

        self.spectrumSelector.valueChanged.connect(self.setSpecSelector)

        self.particleSelector.valueChanged.connect(self.setParticleSelector)

        

            self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()

            self.updateSpecPlot()

    def jumpToIndicatedSpectrum(self):   #TODO: This should be transferred to sampleview...

        self.currentSpectrumIndex = self.specNumberSelector.value()-1

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

        self.centerOnSpecIndex(self.currentSpectrumIndex)

        self.highLightContour(self.currentParticleIndex)

    

#    def selectSpectrum(self):

#        self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()

#        self.updateSpecPlot()

    def centerOnSpecIndex(self, index):

        self.viewparent.centerOnRamanIndex(index)

    

    def getSpectrumIndexFromSpectrumSelector(self):

        specIndicesOfParticle = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)

        try:

            return specIndicesOfParticle[self.spectrumSelector.value()-1]

        except IndexError:

            print(f'requested specIndex {self.spectrumSelector.value()-1} for particle Index {self.currentParticleIndex} of specIndices: {specIndicesOfParticle}')

    

    def getParticleIndexFromParticleSelector(self):

        particleIndicesOfType = self.particleContainer.getIndicesOfParticleType(self.typeSelectorCombo.currentText())

        return particleIndicesOfType[self.particleSelector.value()-1]

    def highLightContour(self, index):

        self.viewparent.highLightContour(index)

    

    def darkenBackground(self):

        self.viewparent.darkenPixmap = self.darkenAct.isChecked()
@@ -628,9 +613,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        numIndices = len(indices)

        

        for index, partIndex in enumerate(indices):

            self.selectParticleOfIndex(partIndex, centerOn=True)

            self.setWidgetsToNewParticleIndex(partIndex)

            assignment = self.dataset.particleContainer.getParticleAssignmentByIndex(partIndex)

            specIndices = self.dataset.particleContainer.getSpectraIndicesOfParticle(partIndex)

            self.viewparent.highLightContour(partIndex)

            self.viewparent.centerOnRamanIndex(specIndices[0])

            reply = QtWidgets.QMessageBox.question(self, f'Particle {index+1} of {numIndices}',

                                "Do you want to remove that particle?",

                                f"Do you want to remove that particle? Type = {assignment}",

                                QtWidgets.QMessageBox.Yes | 

                                QtWidgets.QMessageBox.No | QtWidgets.QMessageBox.Cancel, QtWidgets.QMessageBox.No)
@@ -645,6 +634,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        

        self.particleContainer.resetParticleIndices()

        self.viewparent.resetContourIndices()

        self.updateHistogramsAndContours()

                

    

    def show_hide_labels(self):

analysis/particleInfo.py

+2 −2
Original line number Diff line number Diff line
@@ -337,9 +337,9 @@ class Particle(object): 
    

    def getShortParticleSize(self):

        if not np.isnan(self.shortSize_ellipse):

            return round(self.shortSize_ellipse)

            return self.shortSize_ellipse

        elif not np.isnan(self.shortSize_box):

            return round(self.shortSize_box)

            return self.shortSize_box

        else:

            print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')

            raise ValueError

sampleview.py

+7 −8
Original line number Diff line number Diff line
@@ -397,7 +397,8 @@ class SampleView(QtWidgets.QGraphicsView): 
        I would prefer having it in the viewitems themselves, but somehow the sampleview has to check

        for already selected indices and also check when nothing is hit...

        '''

        def addContourToSelection(cnt):

        def acceptSelection(cnt):

            self.analysiswidget.setWidgetsToNewParticleIndex(cnt.particleIndex)

            cnt.isSelected = True

            cnt.update()

            self.selectedParticleIndices.append(cnt.particleIndex)
@@ -413,12 +414,10 @@ class SampleView(QtWidgets.QGraphicsView): 
        for index, cnt in enumerate(self.contourItems):

            if cnt.polygon.containsPoint(p, QtCore.Qt.OddEvenFill):   #clicked on particle

                if not event.modifiers()==QtCore.Qt.ShiftModifier:

                    addContourToSelection(cnt)

                    self.analysiswidget.selectParticleOfIndex(cnt.particleIndex)

                    acceptSelection(cnt)

                else:

                    if cnt.particleIndex not in self.selectedParticleIndices:

                        addContourToSelection(cnt)

                        self.analysiswidget.selectParticleOfIndex(cnt.particleIndex)

                        acceptSelection(cnt)

                    elif cnt.particleIndex in self.selectedParticleIndices:

                        removeContourFromSelection(cnt)
@@ -617,15 +616,15 @@ 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

    

    

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

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

        if centerOn:

            self.centerOn(self.ramanscanitems[index])

        if highlightContour:

        if highlightIndex:

            self.highLightRamanIndex(index)

        

    def clearItems(self):