Commit c90f7b26 authored by JosefBrandt's avatar JosefBrandt
Browse files

Several Bugfixes

parent 2026524b

analysis/analysisplots.py

+1 −1
Original line number Diff line number Diff line
@@ -113,7 +113,7 @@ class SpectraPlot(QtWidgets.QGroupBox): 
        layout = QtWidgets.QHBoxLayout()

        self.canvas = FigureCanvas(Figure())

        self.spec_axis = self.canvas.figure.subplots()

        self.reference_ax = self.spec_axis.twinx()

        self.reference_axis = self.spec_axis.twinx()

        self.canvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.9)

        specNavigation = NavigationToolbar(self.canvas, self)

        specNavigation.setOrientation(QtCore.Qt.Vertical)

analysis/particleCharacterization.py

+13 −1
Original line number Diff line number Diff line
@@ -60,12 +60,24 @@ def getParticleStatsWithPixelScale(cnt, fullimage, dataset): 
    

    newStats.height = getParticleHeight(cnt, dataset)    

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

    if newStats.shape == 'fibre':

        newStats.longSize, newStats.shortSize = getFibreDimension(cnt)

        newStats.longSize *= pixelscale

        newStats.shortSize *= pixelscale

    

    partImg = getParticleImageFromFullimage(cnt, fullimage)

    newStats.color = getParticleColor(partImg)

    

    return newStats



def getFibreDimension(contour):

    longSize = cv2.arcLength(contour, True)/2

    img = contoursToImg([contour])[0]

    dist = cv2.distanceTransform(img, cv2.DIST_L2, 3)

    maxThickness = np.max(dist)*2

    return longSize, maxThickness

    

    



def getParticleColor(imgRGB, colorClassifier=None):

    img = cv2.cvtColor(imgRGB, cv2.COLOR_RGB2HSV_FULL)

    meanHSV = cv2.mean(img)

analysis/particleEditor.py

+8 −2
Original line number Diff line number Diff line
@@ -180,12 +180,14 @@ class ParticleEditor(QtCore.QObject): 
        for partIndex in contourindices:

            self.particleContainer.reassignParticleToAssignment(partIndex, newAssignment)

        

        self.viewparent.updateParticleInfoBox(partIndex)

        self.particleAssignmentChanged.emit()

     

    @QtCore.pyqtSlot(list, str)

    def paintParticles(self, contourIndices, newAssignment):

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

        self.createSafetyBackup()

        self.viewparent.removeParticleInfoBox()

        self.storedIndices = contourIndices

        self.storedAssignmend = newAssignment
@@ -208,6 +210,7 @@ class ParticleEditor(QtCore.QObject): 
        except NotConnectedContoursError:

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

                                       'Particle contours are not connected.\nThat is currently not supported!')

            self.viewparent.updateParticleInfoBox(self.storedIndices[-1])

            self.storedIndices = []

            self.storedAssignmend = None

            self.destroyParticlePainter()
@@ -238,6 +241,7 @@ class ParticleEditor(QtCore.QObject): 
        

        self.viewparent.resetContourIndices()

        self.particleContainer.resetParticleIndices()

        self.viewparent.updateParticleInfoBox(self.particleContainer.getNumberOfParticles()-1)

        self.particleAssignmentChanged.emit()

    

    @QtCore.pyqtSlot(list, str)
@@ -245,12 +249,14 @@ class ParticleEditor(QtCore.QObject): 
        print(f'changing color of particles {contourIndices} into {newColor}')

        for partIndex in contourIndices:

            self.particleContainer.changeParticleColor(partIndex, newColor)

        self.viewparent.updateParticleInfoBox(partIndex)

            

    @QtCore.pyqtSlot(list, str)

    def changeParticleShapes(self, contourIndices, newShape):

        print(f'changing shape of particles {contourIndices} into {newShape}')

        for partIndex in contourIndices:

            self.particleContainer.changeParticleShape(partIndex, newShape)

        self.viewparent.updateParticleInfoBox(partIndex)

    

    @QtCore.pyqtSlot(list)

    def deleteParticles(self, contourIndices):

gepard.py

+2 −2
Original line number Diff line number Diff line
@@ -352,8 +352,8 @@ if __name__ == '__main__': 
        logname = os.path.join(logpath, 'logfile.txt')



        fp = open(logname, "a")

#        sys.stderr = fp

#        sys.stdout = fp

        sys.stderr = fp

        sys.stdout = fp

    print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), flush=True)

    

    gepard = GEPARDMainWindow(logpath)

legacyConvert.py

+5 −0
Original line number Diff line number Diff line
@@ -191,6 +191,11 @@ def updateParticleStats(dset): 
            except InvalidParticleError:

                markForDeletion(particle)

            

            if particle.shape == 'fibre':

                particle.longSize, particle.shortSize = pc.getFibreDimension(particle.contour)

                particle.longSize *= dset.getPixelScale()

                particle.shortSize *= dset.getPixelScale()

            

    print(f'deleting {len(deleteIndices)} particles')

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

        dset.particleContainer.removeParticle(index)