Commit 92f24fb4 authored by Josef Brandt's avatar Josef Brandt
Browse files

Particle Painting seems to be stable

parent 156ef9b8

analysis/particleContainer.py

+1 −3
Original line number Diff line number Diff line
@@ -178,8 +178,6 @@ class ParticleContainer(object): 
    

    def getMeasurementPixelCoords(self):

        coords = []

#        for particle in self.particles:

#            for measurement in particle.getMeasurements():

        for meas in self.measurements:

            coords.append([meas.pixelcoord_x, meas.pixelcoord_y])

        return coords

analysis/particlePainter.py

+53 −40
Original line number Diff line number Diff line
@@ -23,7 +23,6 @@ from PyQt5 import QtWidgets, QtCore, QtGui 
import numpy as np

import cv2





class ParticlePainter(QtWidgets.QGraphicsItem):

    def __init__(self, editorParent, img, topLeft):

        super(ParticlePainter, self).__init__()
@@ -38,22 +37,20 @@ class ParticlePainter(QtWidgets.QGraphicsItem): 
        self.painting = False

        self.erasing = False

        

        self.minRadius = 10

        self.minRadius = 5

        self.maxRadius = 500

        self.radius = 30

        self.brect = QtCore.QRectF(0,0,1,1)

        

        self.imgToPixmap()

        self.setPixmap()

        self.setBrect()



    def imgToPixmap(self):

    def setPixmap(self):

        img = self.img.repeat(3).reshape(self.img.shape[0], self.img.shape[1], 3)

        height, width, channel = img.shape

        assert channel==3

        bytesPerLine = 3 * width

        pix = QtGui.QPixmap()

        pix.convertFromImage(QtGui.QImage(img.data, width, height, bytesPerLine, QtGui.QImage.Format_RGB888))

        self.pixmap = pix

        self.pixmap = QtGui.QPixmap()

        self.pixmap.convertFromImage(QtGui.QImage(img.data, width, height, bytesPerLine, QtGui.QImage.Format_RGB888))



    def setBrect(self):

        x0 = self.topLeft[1]
@@ -101,48 +98,64 @@ class ParticlePainter(QtWidgets.QGraphicsItem): 
        elif event.key() == QtCore.Qt.Key_Return:

            self.editorParent.acceptPaintedResult()

    

    def drawParticle(self, pos):

        pixelPos = round(pos.y()-self.topLeft[0]), round(pos.x()-self.topLeft[1])

        x_min, x_max = round(pixelPos[1]-self.radius/2), round(pixelPos[1]+self.radius/2)

        y_min, y_max = round(pixelPos[0]-self.radius/2), round(pixelPos[0]+self.radius/2)

    def drawParticle(self, pixelPos):

        x_min, x_max = round(pixelPos.x()-self.radius), round(pixelPos.x()+self.radius)

        y_min, y_max = round(pixelPos.y()-self.radius), round(pixelPos.y()+self.radius)

        

        x_shift = y_shift = 0

        x_shift = y_shift = int(0)

        

        if x_min < 0:

            x_shift = x_min

        elif x_min >= self.img.shape[1]:

            x_shift = x_min + 1 - self.img.shape[1]

            x_shift = int(x_min)

            self.topLeft[1] -= abs(x_min)

        elif x_max >= self.img.shape[1]:

            x_shift = int(x_max + 1 - self.img.shape[1])

        

        if y_min < 0:

            y_shift = y_min

        elif y_min >= self.img.shape[0]:

            y_shift = y_min + 1 - self.img.shape[0]

            self.topLeft[0] -= abs(y_min)

            y_shift = int(y_min)

        elif y_max >= self.img.shape[0]:

            y_shift = int(y_max + 1 - self.img.shape[0])

        

        if x_shift != 0 or y_shift != 0:

            x_range = self.img.shape[1] + abs(x_shift)

            y_range = self.img.shape[0] + abs(y_shift)

            

            x_range = int(self.img.shape[1] + abs(x_shift))

            y_range = int(self.img.shape[0] + abs(y_shift))

            newImg = np.zeros((y_range, x_range))

            if x_shift < 0:

                if y_shift == 0:

                    newImg[abs(x_shift):, :] = self.img

                elif y_shift < 0:

                

        

                if y_shift < 0:

                    newImg[abs(y_shift):, abs(x_shift):] = self.img

                elif y_shift == 0:

                    newImg[:, abs(x_shift):] = self.img

                elif y_shift > 0:

                    newImg[:self.img.shape[0], abs(x_shift):] = self.img

        

            elif x_shift == 0:

                if y_shift < 0:

                    newImg[abs(y_shift):, :] = self.img

                elif y_shift == 0:

                    newImg[:, :] = self.img

                elif y_shift > 0:

                    newImg[:self.img.shape[0], :] = self.img

                

            elif x_shift > 0:

                if y_shift < 0:

                    newImg[abs(y_shift):, :self.img.shape[1]] = self.img

                elif y_shift == 0:

                    newImg[:, :self.img.shape[1]] = self.img

                elif y_shift > 0:

                    newImg[:y_shift, :self.img.shape[1]] = self.img

            

            self.img = np.uint8(newImg)

            self.setBrect()

        

        center = (int(pixelPos.x()), int(pixelPos.y()))

        

        if self.painting:

            cv2.circle(self.img, center, self.radius, 255, -1)

        elif self.erasing:

            cv2.circle(self.img, center, self.radius, 0, -1)

            

#        img, xmin, ymin, padding = self.contoursToImg(self.contours)

#        center = (int(pos.x()+self.radius), int(pos.y()+self.radius))

#        if self.painting:

#            cv2.circle(img, center, self.radius, 255, -1)

#        elif self.erasing:

#            cv2.circle(img, center, self.radius, 0, -1)

#            

#        img = np.uint8(img)

#        self.contours = self.imgToCnt(img, xmin, ymin, padding)

#        self.getBrectAndPolygon()

#        self.update()

        self.setPixmap()

        self.update()



    def paint(self, painter, option, widget):   

        painter.setPen(QtCore.Qt.white)

analysis/particleeditor.py

+10 −6
Original line number Diff line number Diff line
@@ -189,9 +189,10 @@ class ParticleEditor(QtCore.QObject): 
        self.storedAssignmend = newAssignment

        

        contours = self.particleContainer.getParticleContoursByIndex(contourIndices)

        topLeft = self.getTopLeft(contours)

        img, self.xmin, self.ymin, self.padding = self.contoursToImg(contours)

        

#        topLeft = self.getTopLeft(contours)

#        img, self.xmin, self.ymin, self.padding = self.contoursToImg(contours, padding=0)

        img, xmin, ymin, self.padding = self.contoursToImg(contours, padding=0)

        topLeft = [ymin, xmin]

        self.particlePainter = ParticlePainter(self, img, topLeft)

        

        self.viewparent.normalSize()
@@ -201,7 +202,10 @@ class ParticleEditor(QtCore.QObject): 
        

    def acceptPaintedResult(self):

        try:

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

            img = self.particlePainter.img

            xmin = self.particlePainter.topLeft[1]

            ymin = self.particlePainter.topLeft[0]

            newContour = self.imgToCnt(img, xmin, ymin, 0)

        except NotConnectedContoursError:

            self.storedIndices = []

            self.storedAssignmend = None
@@ -258,7 +262,7 @@ class ParticleEditor(QtCore.QObject): 


        if len(contours)>1:

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

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

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

            raise NotConnectedContoursError

        

        newContour = contours[0]
@@ -273,7 +277,7 @@ class ParticleEditor(QtCore.QObject): 
        #draw contours

        xmin = cnt[:,0,:][:, 0].min()

        ymin= cnt[:,0,:][:, 1].min()

        return ymin, xmin

        return [ymin, xmin]

    

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

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

gepard.py

+5 −6
Original line number Diff line number Diff line
@@ -326,12 +326,11 @@ if __name__ == '__main__': 
        if not os.path.exists(logpath):

            os.mkdir(logpath)

        logname = os.path.join(logpath, 'logfile.txt')

#

#        fp = open(logname, "a")

#        sys.stderr = fp

#        sys.stdout = fp

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

          flush=True)



        fp = open(logname, "a")

        sys.stderr = fp

        sys.stdout = fp

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

    

    gepard = GEPARDMainWindow(logpath)

    gepard.showMaximized()

sampleview.py

+2 −9
Original line number Diff line number Diff line
@@ -268,14 +268,9 @@ class SampleView(QtWidgets.QGraphicsView): 
            

        if self.particleEditor is None:

            self.particleEditor = ParticleEditor(self, self.dataset.particleContainer)

        #try disconnecting the signals. If they are connected multiple times, the functions will run accordingly...

#        tryDisconnectingSignal(self.particleEditor.particleContoursChanged)

        tryDisconnectingSignal(self.particleEditor.particleAssignmentChanged)

        

#        self.particleEditor.particleContoursChanged.connect(self.resetParticleContours)

            

        tryDisconnectingSignal(self.particleEditor.particleAssignmentChanged)

        if self.analysiswidget is not None:

#            self.particleEditor.particleContoursChanged.connect(self.analysiswidget.updateHistogramsAndContours)

            self.particleEditor.particleAssignmentChanged.connect(self.analysiswidget.updateHistogramsAndContours)



    def setMicroscopeMode(self):
@@ -381,9 +376,7 @@ class SampleView(QtWidgets.QGraphicsView): 
                    self.dataset.readin = False

                else:

                    return

#                x, y, z = self.dataset.mapToLengthRaman([p0.x(), p0.y()], 

#                                                         microscopeMode=self.microscopeMode,

#                                                         noz=(False if self.mode=="RamanScan" else True))



            noz = (self.mode in ['OpticalScan', 'RamanScan'])

            x, y, z = self.dataset.mapToLengthRaman([pos.x(), pos.y()], microscopeMode=self.microscopeMode, noz=noz)

            if z is not None: