Commit 48537f7f authored by Josef Brandt's avatar Josef Brandt
Browse files 

Added the following features:
In optical scan: BackgroundManager for subtraction of background images
In segmentation: CLAHE and multiple thresholding
parent 8fc15b1e

dataset.py

+3 −0
Original line number Diff line number Diff line
@@ -347,6 +347,9 @@ class DataSet(object): 
    def getLegacyDetectImageName(self):

        return os.path.join(self.path, "detectimage.png")

    

    def getBackgroundImageName(self):

        return os.path.join(self.path, "background.bmp")

    

    def getDetectImageName(self):

        raise NotImplementedError("No longer implemented due to change in API")

gepard.py

+13 −2
Original line number Diff line number Diff line
@@ -101,12 +101,23 @@ class MeasureParticleWindow(QtWidgets.QMainWindow): 
            fileName = QtWidgets.QFileDialog.getSaveFileName(self, "Create New Project",

                                        defaultPath, "*.pkl")[0]

        if fileName:

            if fileName.find(' ') < 0:

            isValid, msg = self.testFilename(fileName)

            if isValid:

                self.fname = str(fileName)

                self.view.new(self.fname)  

                self.scalingChanged(1.)

            else:

                QtWidgets.QMessageBox.critical(self, "Error", "File path must not contain spaces.")

                QtWidgets.QMessageBox.critical(self, "Error", msg)

            

    @QtCore.pyqtSlot()  

    def testFilename(self, fileName):

        if self.view.ramanctrl.name == 'RenishawCOM':   #the renishawCom does not allow Spaces within filePath

            if fileName.find(' ') == 0:

                return False, "File path must not contain spaces."

            else:

                return True, ""

        else:

            return True, ""

    

    @QtCore.pyqtSlot() 

    def about(self):

imagestitch.py

+5 −2
Original line number Diff line number Diff line
@@ -48,15 +48,17 @@ def imageStacking(colimgs): 
    return im, zval



def combineImages(path, nx, ny, nk, width, height, angle):

    imgs = []

    full = None

    for i in range(nx):

        for j in range(ny):

            if nk > 1:

                colimgs = []

                for k in range(nk):

                    colimgs.append(cv2.imread(path + f'test_{i}_{j}_{k}.bmp'))

                img = imageStacking(colimgs)

            imgs.append(img)

            else:

                img = cv2.imread(path + f'test_{i}_{j}_1.bmp')



            dx = i*.9*img.shape[1]

            dy = j*.8*img.shape[0]

            c, s = np.cos(np.radians(angle)), np.sin(np.radians(angle))
@@ -67,6 +69,7 @@ def combineImages(path, nx, ny, nk, width, height, angle): 
                full = dst

            else:

                full = cv2.max(full,dst)



    cv2.imwrite("full_dunkel.png", full)

opticalbackground.py

0 → 100644
+251 −0
Original line number Diff line number Diff line 
# -*- coding: utf-8 -*-

"""

GEPARD - Gepard-Enabled PARticle Detection

Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 

Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    



This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.



This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.



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/>.

"""



from PyQt5 import QtCore, QtWidgets, QtGui

import cv2

import numpy as np

import os



from helperfunctions import cv2imread_fix



class BackGroundManager(QtWidgets.QWidget):

    managerClosed = QtCore.pyqtSignal()

    readBackground = QtCore.pyqtSignal(int)

    

    def __init__(self, parentOSwidget):

        super(BackGroundManager, self).__init__()

        self.setFixedSize(1500, 900)

        self.setWindowTitle('Optical Background Manager')

        self.parentOSwidget = parentOSwidget

        self.parentOSwidget.backGroundSavedToPath.connect(self.updateChildImage)

        self.ramanctrl = self.parentOSwidget.ramanctrl

        

        layout = QtWidgets.QHBoxLayout()

        self.setLayout(layout)

        

        self.imagesGroup = QtWidgets.QGroupBox('Current Background Images')

        self.imagesLayout = QtWidgets.QGridLayout()        

        

        self.imgContainers = []

        self.avgImg = None

        self.presetIndividualImages()

        

        self.previewImage = QtWidgets.QGraphicsView()

        self.setupGraphicsView(self.previewImage, scaleFactor=0.8)

        

        previewGroup = QtWidgets.QGroupBox()

        previewLayout = QtWidgets.QVBoxLayout()

        self.blurspinbox = QtWidgets.QSpinBox(self)

        self.blurspinbox.setMinimum(3)

        self.blurspinbox.setMaximum(99)

        self.blurspinbox.setSingleStep(2)

        self.blurspinbox.setValue(5)

        self.blurspinbox.valueChanged.connect(self.calculateAverageImage)

        self.blurspinbox.setMaximumWidth(150)

        

        self.previewCurrentViewBtn = QtWidgets.QPushButton('Acquire 3x3 area and preview subtracted result')

        self.previewCurrentViewBtn.clicked.connect(self.previewStitchedArea)

        self.previewArea = QtWidgets.QGraphicsView()

        self.setupGraphicsView(self.previewArea, scaleFactor=0.5)

        

        previewLayout.addWidget(QtWidgets.QLabel('Radius for blur'))

        previewLayout.addWidget(self.blurspinbox)

        previewLayout.addWidget(QtWidgets.QLabel('Preview of averaged and smoothed image'))

        previewLayout.addWidget(self.previewImage)

        previewLayout.addWidget(self.previewCurrentViewBtn)

        previewLayout.addWidget(self.previewArea)

        

        previewGroup.setLayout(previewLayout)

        

        layout.addWidget(self.imagesGroup)

        layout.addWidget(previewGroup)

        

    def presetIndividualImages(self, nrows=3, ncols=2):

        index = 0

        for row in range(nrows):

            for col in range(ncols):

                self.imgContainers.append(SingleImageContainer(self, index))

                self.imagesLayout.addWidget(self.imgContainers[-1], row, col)

                index += 1

                

        self.imagesGroup.setLayout(self.imagesLayout)

    

    def previewStitchedArea(self):

        if self.avgImg is None:

            QtWidgets.QMessageBox.about(self, 'Warning', 'No Background Image is aquired')

            return

        else:

            from opticalscan import loadAndPasteImage

            self.dataset = self.parentOSwidget.dataset

            

            #acquire images in 3x3 area to preview quality of background subtraction

            x, y, z = self.ramanctrl.getPosition()

            micMode = self.parentOSwidget.view.microscopeMode

            width, height, angle = self.ramanctrl.getImageDimensions(micMode)

            startPoint = [x-width, y-height]

            endPoint = [x+width, y+height]

            points = np.concatenate(([startPoint], [endPoint]), axis=0)

            p0 = [points[:,0].min(), points[:,1].max()]

            p1 = [points[:,0].max(), points[:,1].min()]

            

            reply = QtWidgets.QMessageBox.question(self, 'Message',f"The stage will move {round(3*width)} in x and {round(3*height)} in y.\nContinue?", 

                                                   QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)

            if reply == QtWidgets.QMessageBox.Yes:

                fullimg = None

                zimg = None

         

                for row in range(3):

                    for col in range(3):

                        curPoint = [startPoint[0] + row*width, startPoint[1] + col*height]

                        self.ramanctrl.moveToAbsolutePosition(curPoint[0], curPoint[1])

                        self.ramanctrl.saveImage(self.dataset.getTmpImageName())

                        

                        fullimg, zimg = loadAndPasteImage([self.dataset.getTmpImageName()], fullimg, zimg, width, height, angle, p0, p1, curPoint, background=self.avgImg)

                        self.updateGraphicsView(self.previewArea, fullimg, convertColors=True)





    def setupGraphicsView(self, graphView, scaleFactor=1.):

        graphView.item = QtWidgets.QGraphicsPixmapItem()

        scene = QtWidgets.QGraphicsScene(graphView)

        scene.addItem(graphView.item)

        graphView.setScene(scene)

        graphView.scale(scaleFactor, scaleFactor)

    

    def updateGraphicsView(self, graphView, img, convertColors=False):

        if img is not None:

            prevImg = img

        else:

            prevImg = np.zeros((300, 300))

        

        if convertColors:

            prevImg = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)

            

        height, width = prevImg.shape[:2]

        bytesPerLine = 3 * width

        pix = QtGui.QPixmap()

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

        graphView.item.setPixmap(pix)

    

    @QtCore.pyqtSlot(int, str) 

    def updateChildImage(self, index, path):

        self.imgContainers[index].updateImage(path)

        self.calculateAverageImage()

    

    def calculateAverageImage(self):

        curImgs = [i.getImage() for i in self.imgContainers if i.getImage() is not None]

                

        if len(curImgs) > 0:

            curImgs = np.array(curImgs)

            self.avgImg = np.sum(curImgs, axis=0)/len(curImgs)

            radius = self.blurspinbox.value()

            if radius %2 == 0:

                radius += 1

            if radius < 0:

                radius = 1    

            self.avgImg = cv2.GaussianBlur(self.avgImg, (radius, radius), 0)

            self.avgImg = np.uint8(self.avgImg)

            self.parentOSwidget.writeBackGroundImage(self.avgImg)

        else:

            self.avgImg = None

            self.parentOSwidget.deleteBackGroundImage()

            

        self.updateGraphicsView(self.previewImage, self.avgImg)

        

    def closeEvent(self, event):

        self.managerClosed.emit()

        event.accept()

    

    

class SingleImageContainer(QtWidgets.QGroupBox):

    def __init__(self, parent, index):

        super(SingleImageContainer, self).__init__()

        self.index = index

        self.parent = parent

        

        layout = QtWidgets.QVBoxLayout()

        layout.addWidget(QtWidgets.QLabel(f'Background {index+1}'))

        

        readBtn = QtWidgets.QPushButton('ReadImage')

        readBtn.clicked.connect(self.readImage)

        

        self.image = ImagePixmap()

        

        delBtn = QtWidgets.QPushButton('Delete Image')

        delBtn.clicked.connect(self.clearImage)

        

        layout.addWidget(readBtn)

        layout.addWidget(self.image)

        layout.addWidget(delBtn)

        

        self.setLayout(layout)

    

    def readImage(self):

        self.parent.readBackground.emit(self.index)

    

    def updateImage(self, path):

        self.image.updateImage(path)

    

    def clearImage(self):

        self.image.clearImage()

        self.parent.calculateAverageImage()

        

    def getImage(self):

        return self.image.imgdata





class ImagePixmap(QtWidgets.QGraphicsView):

    def __init__(self):

        super(ImagePixmap, self).__init__()

        self.item = QtWidgets.QGraphicsPixmapItem()

        self.item.setPos(0, 0)

        self.item.setAcceptedMouseButtons(QtCore.Qt.NoButton)

        self.imgdata = None

        

        scene = QtWidgets.QGraphicsScene(self)

        scene.addItem(self.item)

        self.setScene(scene)

        

        self.scale(0.4, 0.4)

        self.updateImage()

        

    def updateImage(self, img_path=None):

        if img_path is None:

            self.loadImageIntoPixmap(self.createBlancImage())

            

        elif os.path.exists(img_path):

            self.imgdata = cv2.cvtColor(cv2imread_fix(img_path), cv2.COLOR_BGR2RGB)

            self.loadImageIntoPixmap(self.imgdata)



    def createBlancImage(self):

        blancImg = np.zeros((300, 500, 3))

        cv2.putText(blancImg, 'None selected', (150, 150), cv2.FONT_HERSHEY_COMPLEX, 1, (255, 255, 255), 2)

        return blancImg

    

    def loadImageIntoPixmap(self, img):

        height, width = img.shape[:2]

        bytesPerLine = 3 * width

        pix = QtGui.QPixmap()

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

        self.item.setPixmap(pix)

    

    def clearImage(self):

        self.imgdata = None

        self.updateImage()

opticalscan.py

+121 −35
Original line number Diff line number Diff line
@@ -30,6 +30,7 @@ from helperfunctions import cv2imread_fix, cv2imwrite_fix 
from time import time

import datetime

import sys

from opticalbackground import BackGroundManager



def scan(path, sol, zpositions, grid, controlclass, dataqueue, 

         stopevent, logpath='', ishdr=False):
@@ -81,17 +82,24 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue, 
    if fp is not None:

        fp.close()



def subtractBackground(image, background):

    avg = np.mean(background)

    subtracted = np.clip(np.array(image - background + avg, dtype = np.uint8), 0, 255)

    return subtracted

    

def loadAndPasteImage(srcnames, fullimage, fullzval, width, height, 

                      rotationvalue, p0, p1, p, halfResolution = False):

                      rotationvalue, p0, p1, p, background=None):

    colimgs = []

    for name in srcnames:

        colimgs.append(cv2.cvtColor(cv2imread_fix(name), cv2.COLOR_BGR2RGB))

        curImg = cv2imread_fix(name)

        if background is not None:

            curImg = subtractBackground(curImg, background)

        colimgs.append(cv2.cvtColor(curImg, cv2.COLOR_BGR2RGB))

    img, zval = imageStacking(colimgs)



    if halfResolution:              #halve resolution, if fullimage would become too large otherwise

        img = cv2.resize(img, None, fx = 0.5, fy = 0.5, interpolation = cv2.INTER_CUBIC)

        zval= cv2.resize(zval, None, fx = 0.5, fy = 0.5, interpolation = cv2.INTER_CUBIC)

#    if halfResolution:              #halve resolution, if fullimage would become too large otherwise

#        img = cv2.resize(img, None, fx = 0.5, fy = 0.5, interpolation = cv2.INTER_CUBIC)

#        zval= cv2.resize(zval, None, fx = 0.5, fy = 0.5, interpolation = cv2.INTER_CUBIC)



    x, y = p

    Nx, Ny = int((p1[0]-p0[0]+width)/width*img.shape[1]), int((p0[1]-p1[1]+height)/height*img.shape[0]) + 10  # + 10 because of rotation and hopefully it will be small
@@ -179,18 +187,20 @@ class PointCoordinates(QtWidgets.QGridLayout): 
            self.itemAtPosition(i+1,5).setVisible(False)

            self.itemAtPosition(i+1,6).setVisible(False)

        self.N = N

        for i, p in pointsgiven:

            wx, wy, wz = self.dswidgets[i]

            x, y, z = p

            wx.setValue(x)

            wy.setValue(y)        

            wz.setValue(z)

            self.validpoints[i] = True

        for i in range(len(pointsgiven), N):

            wx, wy, wz = self.dswidgets[i]

            wx.setValue(0)

            wy.setValue(0)        

            wz.setValue(0)

        

        self.setGivenPoints(pointsgiven, N)

#        for i, p in pointsgiven:

#            wx, wy, wz = self.dswidgets[i]

#            x, y, z = p

#            wx.setValue(x)

#            wy.setValue(y)        

#            wz.setValue(z)

#            self.validpoints[i] = True

#        for i in range(len(pointsgiven), N):

#            wx, wy, wz = self.dswidgets[i]

#            wx.setValue(0)

#            wy.setValue(0)        

#            wz.setValue(0)

        

        self.update()
@@ -217,9 +227,25 @@ class PointCoordinates(QtWidgets.QGridLayout): 
                points[i,:] = np.nan

        return points

    

    def setGivenPoints(self, pointsgiven, N):

        for i, p in pointsgiven:

            wx, wy, wz = self.dswidgets[i]

            x, y, z = p

            wx.setValue(x)

            wy.setValue(y)        

            wz.setValue(z)

            self.validpoints[i] = True

        for i in range(len(pointsgiven), N):

            wx, wy, wz = self.dswidgets[i]

            wx.setValue(0)

            wy.setValue(0)        

            wz.setValue(0)

    



class OpticalScan(QtWidgets.QWidget):

    imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate')    #str = 'df' (= darkfield) or 'bf' (=bright field)

    boundaryUpdate = QtCore.pyqtSignal()

    backGroundSavedToPath = QtCore.pyqtSignal(int, str)

    

    def __init__(self, ramanctrl, dataset, logpath='', parent=None):

        super().__init__(parent, QtCore.Qt.Window)
@@ -235,6 +261,22 @@ class OpticalScan(QtWidgets.QWidget): 
        pointgroup.setLayout(self.points)

        self.points.readPoint.connect(self.takePoint)

        

        bkggroup = QtWidgets.QGroupBox('Manage Background Images')

        self.enableBackGround = QtWidgets.QCheckBox('Enable BackgroundSubtraction')

        self.enableBackGround.setChecked(False)

        self.enableBackGround.stateChanged.connect(self.enableDisableBackground)

        self.backGroundManager = BackGroundManager(self)

        self.backGroundManager.managerClosed.connect(self.managerWasClosed)

        self.backGroundManager.readBackground.connect(self.readBackground)

        self.showBgkManagerBtn = QtWidgets.QPushButton('Show Background Manager Window')

        self.showBgkManagerBtn.setDisabled(True)

        self.showBgkManagerBtn.clicked.connect(self.showHideBackgroundWindow)

        

        bkglayout = QtWidgets.QVBoxLayout()

        bkglayout.addWidget(self.enableBackGround)

        bkglayout.addWidget(self.showBgkManagerBtn)

        bkggroup.setLayout(bkglayout)

        

        self.pareaselect = QtWidgets.QPushButton("Area select", self)

        label = QtWidgets.QLabel("Size increase:", self)

        self.radiusincreaseedit = QtWidgets.QDoubleSpinBox(self)
@@ -253,7 +295,7 @@ class OpticalScan(QtWidgets.QWidget): 
        self.zmaxedit.setMaximumWidth(100)

        label3 = QtWidgets.QLabel("Focus steps:", self)

        self.nzedit = QtWidgets.QSpinBox(self)

        self.nzedit.setRange(2,10)

        self.nzedit.setRange(2,20)

        self.nzedit.setValue(3)

        self.nzedit.setMaximumWidth(100)

        self.hdrcheck = QtWidgets.QCheckBox("High dynamic range", self)
@@ -294,9 +336,9 @@ class OpticalScan(QtWidgets.QWidget): 
        micModeLayout.addWidget(self.bf_btn)

        micModeGroup.setLayout(micModeLayout)

        

        self.halfResChecker = QtWidgets.QCheckBox('Half resolution')

        self.halfResChecker.setChecked(False)

        self.halfResChecker.setToolTip('Enable for very high resolution images.\nFull resolution slows down the scan too much..')

#        self.halfResChecker = QtWidgets.QCheckBox('Half resolution')  #TODO: Consider removing, as soon as tiling works

#        self.halfResChecker.setChecked(False)

#        self.halfResChecker.setToolTip('Enable for very high resolution images.\nFull resolution slows down the scan too much..')

        

        self.deleteImgChecker = QtWidgets.QCheckBox('Delete image files after run')

        self.deleteImgChecker.setChecked(True)
@@ -318,16 +360,16 @@ class OpticalScan(QtWidgets.QWidget): 
        furtherOptionsLayout.addRow(label3, self.nzedit)

        furtherOptionsLayout.addRow(self.hdrcheck)

        furtherOptionsLayout.addRow(self.deleteImgChecker)

        furtherOptionsLayout.addRow(self.halfResChecker)

#        furtherOptionsLayout.addRow(self.halfResChecker)    #TODO: Consider removing, as soon as tiling works

        furtherOptionsGroup.setLayout(furtherOptionsLayout)

        

        

        btnLayout = QtWidgets.QHBoxLayout()

        btnLayout.addWidget(self.prun)

        btnLayout.addWidget(self.pexit)

        btnLayout.addStretch()

        

        vbox.addWidget(pointgroup)

        vbox.addWidget(bkggroup)

        vbox.addWidget(self.areaOptionsGroup)

        vbox.addWidget(furtherOptionsGroup)

        vbox.addLayout(btnLayout)
@@ -335,9 +377,27 @@ class OpticalScan(QtWidgets.QWidget): 
        vbox.addWidget(self.progressbar)

        

        self.setLayout(vbox)

        #self.show()

        self.setVisible(False)



    def enableDisableBackground(self):

        self.showBgkManagerBtn.setEnabled(self.enableBackGround.isChecked())

        if self.enableBackGround.isChecked():

            self.backGroundManager.calculateAverageImage()

        else:

            self.deleteBackGroundImage()

        

    

    def showHideBackgroundWindow(self):

        if self.backGroundManager.isHidden():

            self.backGroundManager.show()

            self.showBgkManagerBtn.setText('Hide Background Manager Window')

        else:

            self.backGroundManager.hide()

            self.showBgkManagerBtn.setText('Show Background Manager Window')

        

    def managerWasClosed(self):

        self.showBgkManagerBtn.setText('Show Background Manager Window')

    

    @QtCore.pyqtSlot()

    def stopScan(self):

        if self.process is not None and self.process.is_alive():
@@ -418,16 +478,14 @@ class OpticalScan(QtWidgets.QWidget): 
        pshift = self.ramanctrl.getRamanPositionShift()

        self.dataset.pshift = pshift

        img = cv2.cvtColor(cv2imread_fix(self.dataset.getTmpImageName()), cv2.COLOR_BGR2RGB)

        if self.halfResChecker.isChecked():

            img = cv2.resize(img, None, fx = 0.5, fy = 0.5, interpolation = cv2.INTER_CUBIC)

#        if self.halfResChecker.isChecked():

#            img = cv2.resize(img, None, fx = 0.5, fy = 0.5, interpolation = cv2.INTER_CUBIC)

        

        self.dataset.imagedim_bf = self.ramanctrl.getImageDimensions('bf')

        self.dataset.pixelscale_bf = self.dataset.imagedim_bf[0]/img.shape[1]          #=imagedim_width/shape[1]

        self.dataset.imagedim_df = self.ramanctrl.getImageDimensions('df')

        self.dataset.pixelscale_df = self.dataset.imagedim_df[0]/img.shape[1]          #=imagedim_width/shape[1]

        



        

        points = self.points.getPoints()

        ind = np.isfinite(points[:,0])

        self.dataset.fitindices = np.arange(points.shape[0])[ind]
@@ -457,7 +515,8 @@ class OpticalScan(QtWidgets.QWidget): 
                full = cv2.warpAffine(full, M, (Nx, Ny))            #fails, if image dimensions are >32767x32767px...

                dst = cv2.max(full, dst)

            except:

                QtWidgets.QMessageBox.critical(self, 'Error', 'Image is too large\nPlease repeat with "scale image" checked.')

                QtWidgets.QMessageBox.critical(self, 'Error', 'Image is too large\nSelect smaller region.')

                raise

                return

        

        self.view.imgdata = dst
@@ -466,6 +525,19 @@ class OpticalScan(QtWidgets.QWidget): 
        self.dataset.readin = False

        self.imageUpdate.emit(self.view.microscopeMode)

    

    @QtCore.pyqtSlot(int) 

    def readBackground(self, indexOfCallingImage):

        tmp_path = self.dataset.getTmpImageName()

        self.ramanctrl.saveImage(tmp_path)

        self.backGroundSavedToPath.emit(indexOfCallingImage, tmp_path)

    

    def writeBackGroundImage(self, backgroundImg):

        cv2imwrite_fix(self.dataset.getBackgroundImageName(), cv2.cvtColor(backgroundImg, cv2.COLOR_RGB2BGR))

    

    def deleteBackGroundImage(self):

        if os.path.exists(self.dataset.getBackgroundImageName()):

            os.remove(self.dataset.getBackgroundImageName())

        

    @QtCore.pyqtSlot() 

    def run(self):

        if self.dataset.ramanscansortindex is not None:
@@ -485,6 +557,14 @@ class OpticalScan(QtWidgets.QWidget): 
            else:

                return

        

        if os.path.exists(self.dataset.getBackgroundImageName()):

            reply = QtWidgets.QMessageBox.critical(self, 'Background correction info.',

                "A background image was saved. All acquired images will be corrected. Continue?\nOtherwise delete images in background manager", 

                QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.Yes)



            if reply != QtWidgets.QMessageBox.Yes:

                return

        

        self.view.imparent.ramanSwitch.df_btn.setChecked(self.df_btn.isChecked())

        self.view.imparent.ramanSwitch.setDisabled(True)

        self.view.setMicroscopeMode()
@@ -544,11 +624,6 @@ class OpticalScan(QtWidgets.QWidget): 
            QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)



        if reply == QtWidgets.QMessageBox.Yes:

#            if self.halfResChecker.isChecked():

#                #reset pixelscales!!!

#                self.dataset.pixelscale_df /= 2

#                self.dataset.pixelscale_bf /= 2

            

            self.prun.setEnabled(False)

            self.ramanctrl.disconnect()

            self.processstopevent = Event()
@@ -593,8 +668,15 @@ class OpticalScan(QtWidgets.QWidget): 
            width, height, rotationvalue = (self.dataset.imagedim_df if self.view.imparent.ramanSwitch.df_btn.isChecked() else self.dataset.imagedim_bf)

            p = self.dataset.grid[i]

            p0, p1 = self.dataset.maxdim[:2], self.dataset.maxdim[2:]

            

            if os.path.exists(self.dataset.getBackgroundImageName()):

                background_img = cv2imread_fix(self.dataset.getBackgroundImageName())

            else:

                background_img = None

            

            

            self.view.imgdata, self.dataset.zvalimg = loadAndPasteImage(names, self.view.imgdata, self.dataset.zvalimg, width, height, 

                                                                        rotationvalue, p0, p1, p, halfResolution = self.halfResChecker.isChecked())

                                                                        rotationvalue, p0, p1, p, background=background_img)

            self.progressbar.setValue(i+1)

            if i>3:

                timerunning = time()-self.starttime
@@ -628,6 +710,10 @@ class OpticalScan(QtWidgets.QWidget): 
                return

        self.timer.start(100.)

        

    def closeEvent(self, event):

        self.backGroundManager.close()

        event.accept()

            

if __name__ == "__main__":

    from ramancom.simulatedraman import SimulatedRaman

    from dataset import DataSet