Commit 48dddf1d authored by Lars Bittrich's avatar Lars Bittrich
Browse files

bugfixes in particle analysis

parent 545f462e

analysis/analysisview.py

+5 −4
Original line number Diff line number Diff line
@@ -456,6 +456,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        #draw Sample Spectrum

        specIndex = self.currentSpectrumIndex

        spectra = self.datastats.spectra

        particlestats = self.datastats.getParticleStats()

        self.spec_ax.axis("on")

        self.spec_ax.clear()

        self.spec_ax.plot(spectra[:, 0], spectra[:, specIndex+1])
@@ -463,7 +464,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        self.spec_ax.set_xlabel('Wavenumber (cm-1)', fontsize = 15)

        self.spec_ax.set_ylabel('Counts', fontsize = 15)

        self.spec_ax.set_title('ScanPoint Number {}, Size = {} µm'.format(specIndex+1, 

                               np.round(self.datastats.particlestats[self.currentParticleIndex][2], 1)))

                               np.round(particlestats[self.currentParticleIndex][2], 1)))

        self.spec_ax.set_xbound(100, (3400 if spectra[-1, 0] > 3400 else spectra[-1, 0]))

        wavenumber_diff = list(spectra[:, 0]-100)

        y_start = wavenumber_diff.index(min(wavenumber_diff))
@@ -498,8 +499,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        if uniquePolymers is not None:

            #the index is the contour index, find particle index:

            specIndex = self.datastats.particles2spectra[index][0]  #select first spectrum of partoicle

            self.datastats.currentParticleIndex = index

            self.datastats.currentSpectrumIndex = specIndex

            self.currentParticleIndex = index

            self.currentSpectrumIndex = specIndex

            

            selectedPolymer = self.datastats.currentPolymers[specIndex]

            try:
@@ -649,7 +650,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow): 
        

        #general size histogram

        self.bins = np.logspace(0.1, 3, 20)

        self.sizes = [i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.particlestats]      #extract long size (if ellipse fit is nan -> box fit)

        self.sizes = [i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.getParticleStats()]      #extract long size (if ellipse fit is nan -> box fit)

        sizehist = np.histogram(self.sizes, self.bins)

        self.totalhistx = []

        for i in range(19):

analysis/analysiswidgets.py

+1 −1
Original line number Diff line number Diff line
@@ -36,7 +36,7 @@ class ExpExcelDialog(QtWidgets.QDialog): 
        self.setGeometry(200,200, 300, 300)

        

        self.datastats = datastats

        self.particles = self.datastats.particlestats

        self.particles = self.datastats.getParticleStats()

        self.polymers = self.datastats.particleResults

        self.additives = self.datastats.currentAdditives

        self.hqis = self.datastats.hqis

analysis/datastats.py

+11 −12
Original line number Diff line number Diff line
@@ -41,7 +41,6 @@ class DataStats(object): 
        

        self.spectraResults = None                  #entire List of all spectra assignments

        self.additiveResults = None                 #entire List of all additives

        self.particlestats = None

        self.particleResults = None                 #final assignment for each particle

        

        self.currentPolymers = None                 #list of polymers after setting entries with low hqi to unknown
@@ -113,15 +112,6 @@ class DataStats(object): 
        return specs

    

    def loadParticleData(self):

        self.particlestats = np.array(self.dataset.particlestats)

        pixelscale = self.dataset.getPixelScale()

        #convert to mikrometer scale

        for index in range(len(self.particlestats)):

            for subindex in range(5):

                self.particlestats[index][subindex] = self.particlestats[index][subindex] * pixelscale    #multiply by pixelscale

                if subindex == 4:

                    self.particlestats[index][subindex] = self.particlestats[index][subindex] * pixelscale  #again for the area...

        

        self.particles2spectra = self.dataset.particles2spectra

        

        sortindices = self.dataset.ramanscansortindex
@@ -161,12 +151,21 @@ class DataStats(object): 
            return None

        return self.uniquePolymers

    

    def getParticleStats(self):

        particlestats = np.array(self.dataset.particlestats)

        pixelscale = self.dataset.getPixelScale()

        #convert to mikrometer scale

        particlestats[:,:5] *= pixelscale

        particlestats[:,4] *= pixelscale   #again for the area...

        return particlestats

    

    def createHistogramData(self):

        particlestats = self.getParticleStats()

        self.uniquePolymers = np.unique(self.currentPolymers)

        self.particleResults = [None]*len(self.particlestats)

        self.particleResults = [None]*len(particlestats)

        self.typehistogram = {i: 0 for i in self.uniquePolymers}

        

        if len(self.particles2spectra) != len(self.particlestats):

        if len(self.particles2spectra) != len(particlestats):

            return False

        

        for particleID, specList in enumerate(self.particles2spectra):

analysis/particleeditor.py

+14 −8
Original line number Diff line number Diff line
@@ -57,8 +57,6 @@ class ParticleEditor(object): 
            return

        

        contourIndices = sorted(contourIndices)   #we want to keep the contour with lowest index

        print('merging contours:', contourIndices)

        self.createSafetyBackup()

        #get contours:

        contours = [self.datastats.dataset.particlecontours[i] for i in contourIndices]

        cnt = np.vstack(tuple(contours))  #combine contous
@@ -73,7 +71,7 @@ class ParticleEditor(object): 


        img = np.zeros((rangey, rangex))

        for i in contourIndices:

            curCnt = self.datastats.dataset.particlecontours[i]

            curCnt = self.datastats.dataset.particlecontours[i].copy()

            for i in range(len(curCnt)):

                curCnt[i][0][0] -= xmin-padding

                curCnt[i][0][1] -= ymin-padding
@@ -88,6 +86,11 @@ class ParticleEditor(object): 
        else:

            temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)



        if len(contours)>1:

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

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

            return

        

        newContour = contours[0]

        stats = self.characterizeParticle(newContour)
@@ -95,6 +98,8 @@ class ParticleEditor(object): 
            newContour[i][0][0] += xmin-padding

            newContour[i][0][1] += ymin-padding

        

        print('merging contours:', contourIndices)

        self.createSafetyBackup()

        

        #check, if dataset contains (already modified) particle2spectra, otherwise create new.

        if self.datastats.dataset.particles2spectra is None:  #create default assignment
@@ -134,6 +139,9 @@ class ParticleEditor(object): 
            print('removing index from particles2spectra:', index)

            del self.datastats.dataset.particles2spectra[index]



        #update contours in sampleview

        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)

        self.parent.loadParticleData()

        #save data

        minHQI = self.parent.hqiSpinBox.value()

        compHQI = self.parent.compHqiSpinBox.value()
@@ -142,9 +150,6 @@ class ParticleEditor(object): 
                    'Data inconsistency after saving!', QtWidgets.QMessageBox.Ok, 

                    QtWidgets.QMessageBox.Ok)

        

        #update contours in sampleview

        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)

        self.parent.loadParticleData()

       

    

    def reassignParticles(self, contourindices, new_assignment):
@@ -161,6 +166,9 @@ class ParticleEditor(object): 
                self.datastats.spectraResults[specIndex] = new_assignment

                self.datastats.hqis[specIndex] = 100



        #update contours in sampleview

        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)

        self.parent.loadParticleData()

        #save data

        minHQI = self.parent.hqiSpinBox.value()

        compHQI = self.parent.compHqiSpinBox.value()
@@ -169,8 +177,6 @@ class ParticleEditor(object): 
                                'Data inconsistency after saving!',

                                QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)

            

        self.parent.loadParticleData()

            

    

    def deleteParticles(self):

        self.createSafetyBackup()

analysis/sqlexport.py

+7 −4
Original line number Diff line number Diff line
@@ -21,16 +21,16 @@ class SQLExport(QtWidgets.QDialog): 
        

        self.datastats = datastats

        self.polymerList = self.datastats.particleResults

        self.longSizes = np.round(np.array([i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.particlestats]), 1)

        self.shortSize = np.round(np.array([i[1] if np.isnan(i[3]) else i[3] for i in self.datastats.particlestats]), 1)

        particlestats = self.datastats.getParticleStats()

        self.longSizes = np.round(np.array([i[0] if np.isnan(i[2]) else i[2] for i in particlestats]), 1)

        self.shortSize = np.round(np.array([i[1] if np.isnan(i[3]) else i[3] for i in particlestats]), 1)

        

        #spectra can be quite some data size, they are not copied here but referenced later on...

        

        self.particleImages = None

        self.log = []

        

        configfilename = os.path.join(os.path.dirname(os.path.split(__file__)[0]), 

                                      'database_config.txt')

        configfilename = os.path.join(os.path.split(__file__)[0], 'database_config.txt')

        

        if not os.path.exists(configfilename):

            QtWidgets.QMessageBox.warning(self, 'Warning!',
@@ -338,6 +338,9 @@ class SQLExport(QtWidgets.QDialog): 
            self.cnx = mysql.connector.connect(**self.config)  #port: 3306

        except mysql.connector.Error as err:

            print(err)

            QtWidgets.QMessageBox.warning(self, 'Error!',

                                str(err),

                                QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)

            self.cnx = None

    

    def getEntireTable(self, tablename):