sampleview.py 31.1 KB
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# -*- 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, QtGui, QtWidgets
import numpy as np
import os
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import cv2
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import time
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from .dataset import DataSet, loadData
from .ramancom.ramancontrol import RamanControl, simulatedRaman
from .opticalscan import OpticalScan
from .ramanscanui import RamanScanUI
from .detectionview import ParticleDetectionView
from .analysis.analysisview import ParticleAnalysis
from .zeissimporter import ZeissImporter
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from .viewitems import FitPosIndicator, Node, Edge, ScanIndicator, RamanScanIndicator, SegmentationContour, ParticleInfo
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from .helperfunctions import polygoncovering, cv2imread_fix
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from .analysis.colorlegend import getColorFromNameWithSeed
from .analysis.particleEditor import ParticleEditor
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from .ramancom.configRaman import RamanConfigWin
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class SampleView(QtWidgets.QGraphicsView):
    ScalingChanged = QtCore.pyqtSignal(float)
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    ParticleOfIndexSelected = QtCore.pyqtSignal(int)
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    def __init__(self, logpath):
        super(SampleView, self).__init__()
        
        self.logpath = logpath
        self.item = QtWidgets.QGraphicsPixmapItem()
        self.item.setPos(0, 0)
        self.item.setAcceptedMouseButtons(QtCore.Qt.NoButton)
        self.scaleFactor = 1.0
        scene = QtWidgets.QGraphicsScene(self)
        scene.setItemIndexMethod(QtWidgets.QGraphicsScene.NoIndex)
        scene.addItem(self.item)
        scene.setBackgroundBrush(QtCore.Qt.darkGray)
        self.setScene(scene)
        self.setCacheMode(QtWidgets.QGraphicsView.CacheBackground)
        self.setViewportUpdateMode(QtWidgets.QGraphicsView.BoundingRectViewportUpdate)
        self.setRenderHint(QtGui.QPainter.Antialiasing)
        self.setTransformationAnchor(QtWidgets.QGraphicsView.AnchorUnderMouse)
        self.setResizeAnchor(QtWidgets.QGraphicsView.AnchorViewCenter)
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        self.ramanctrl = RamanControl()
        self.simulatedRaman = simulatedRaman        
        #determine, if ramanSwitch is needed:
        self.ramanctrl.connect()
        if not self.ramanctrl.connected:
            QtWidgets.QMessageBox.warning(self, 'Error', 'Please enable Raman Connection')
            return
        if self.ramanctrl.getImageDimensions(mode='bf')[0] == self.ramanctrl.getImageDimensions(mode='df')[0]:
            self.ramanSwitchNeeded = False
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        else:
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            self.ramanSwitchNeeded = True
        self.ramanctrl.disconnect()
        
        self.drag = None
        self.mode = None
        self.dataset = None
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        self.particleEditor = None
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        self.fititems = []
        self.boundaryitems = [[],[]]
        self.scanitems = []
        self.ramanscanitems = []
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        self.particleInfoBox = None
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        self.imgdata = None
        self.isblocked = False
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        self.contourItems = []
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        self.selectedParticleIndices = []
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        self.particlePainter = None
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        self.detectionwidget = None
        self.ramanwidget = RamanScanUI(self.ramanctrl, None, self.logpath, self)
        self.ramanwidget.imageUpdate.connect(self.loadPixmap)
        self.oscanwidget = OpticalScan(self.ramanctrl, None, self.logpath, self)
        self.oscanwidget.imageUpdate.connect(self.loadPixmap)
        self.oscanwidget.boundaryUpdate.connect(self.resetBoundary)
        self.analysiswidget = None
        self.setMinimumSize(600, 600)
        self.darkenPixmap = False
        self.microscopeMode = None
        
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        self.update()
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    def takeScreenshot(self):
        #TODO:
        #LIMIT SCREENSHOT TO ACTUAL VIEWSIZE OF LOADED IMAGE...
        #hide scrollbars
        self.setHorizontalScrollBarPolicy(1)
        self.setVerticalScrollBarPolicy(1)
        #capture screen
        screen = QtWidgets.QApplication.primaryScreen()
        self.repaint()
        screenshot = screen.grabWindow(self.winId())
        #unhide scrollbars
        self.setHorizontalScrollBarPolicy(0)
        self.setVerticalScrollBarPolicy(0)
        
        fname = self.dataset.path + '/screenshot.png'
        validFileName = False
        incr = 1
        while not validFileName:
            if not os.path.exists(fname):
                validFileName = True
            else:
                fname = self.dataset.path + '/screenshot ({}).png'.format(incr)
                incr += 1
        screenshot.save(fname , 'png')
        QtWidgets.QMessageBox.about(self, 'Message', 'Saved as {} to project directory.'.format(fname.split('/')[-1]))
                    
    def closeEvent(self, event):
        reply = QtWidgets.QMessageBox.question(self, 'Message',
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            "Do you really want to quit?", QtWidgets.QMessageBox.Yes | 
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            QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)

        if reply == QtWidgets.QMessageBox.Yes:
            self.disconnectRaman()
            self.saveDataSet()
            event.accept()
            self.oscanwidget.close()
            if self.detectionwidget is not None:
                self.detectionwidget.close()
            if self.analysiswidget is not None:
                self.analysiswidget.close()
            self.ramanwidget.close()
        else:
            event.ignore()
    
    def configureRamanControl(self):
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        """
        Launches a window for updating Raman instrument configuration.
        :return:
        """
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        self.configWin = RamanConfigWin(self)
        self.configWin.show()
    
    def saveDataSet(self):
        if self.dataset is not None:
            self.dataset.save()
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    @QtCore.pyqtSlot() 
    def zoomIn(self):
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        self.zoomDisplay(1.25)
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    @QtCore.pyqtSlot() 
    def zoomOut(self):
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        self.zoomDisplay(0.8)
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    @QtCore.pyqtSlot() 
    def normalSize(self):
        self.scaleFactor = 1.0
        self.setTransform(QtGui.QTransform.fromScale(1., 1.))
        self.announceScaling()

    @QtCore.pyqtSlot() 
    def fitToWindow(self):
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        """
        Fits the window to show the entire sample.
        :return:
        """
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        brect = self.item.sceneBoundingRect()
        self.fitInView(0, 0, brect.width(), brect.height(), QtCore.Qt.KeepAspectRatio)
        self.scaleFactor = self.transform().m11()
        self.announceScaling()
        
    def switchMode(self, mode, loadnew=False):
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        """
        Switch the gepard to another module
        :return:
        """
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        if mode is None:
            return
        assert mode in ["OpticalScan", "ParticleDetection", "RamanScan", "ParticleAnalysis"]
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        print("switching to mode:", mode, flush=True)
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        self.oscanwidget.setVisible(False)
        if self.detectionwidget is not None:
            self.detectionwidget.close()
            self.detectionwidget.destroy()
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            self.detectionwidget = None
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        self.ramanwidget.setVisible(False)
        self.mode = mode
        self.loadPixmap(self.microscopeMode)
        if mode == "OpticalScan":
            self.oscanwidget.setVisible(True)
            self.oscanwidget.resetDataset(self.dataset)
            
        elif mode == "ParticleDetection":
            if self.detectionwidget is None:
                self.detectionwidget = ParticleDetectionView(self.imgdata, self.dataset, self)
                self.detectionwidget.imageUpdate.connect(self.detectionUpdate)
                self.detectionwidget.detectionFinished.connect(self.activateMaxMode)
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            self.detectionwidget.show()
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        elif mode == "RamanScan":
            self.ramanwidget.resetDataset(self.dataset)
            self.ramanwidget.setVisible(True)
            
        elif mode == "ParticleAnalysis":
            if self.ramanwidget.isVisible():
                self.ramanwidget.setVisible(False)
            if self.analysiswidget is None:
                print('creating new analysiswidget')
                self.analysiswidget = ParticleAnalysis(self.dataset, self)
                self.analysiswidget.showMaximized()
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                self.setupParticleEditor()
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            else:
                print('show maximized already exisiting analysiswidget')
                self.analysiswidget.showMaximized()
            
            if self.detectionwidget is not None:
                self.detectionwidget.setVisible(False)
            
            #show legend:
            self.imparent.legend.show()    
        
        if loadnew:
            self.fitToWindow()
        self.imparent.updateModes(mode, self.getMaxMode())
        
    def open(self, fname):       
        self.saveDataSet()
        
        #close all widgets
        for widget in [self.detectionwidget, self.ramanwidget, self.oscanwidget, self.analysiswidget]:
            if widget is not None:
                widget.close()
                widget.destroy()
                del widget
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        self.dataset = loadData(fname)
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        self.setupParticleEditor()
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        self.setMicroscopeMode()
        self.imparent.setWindowTitle(self.dataset.name + (" SIMULATION" if simulatedRaman else ""))
        self.imgdata = None
        self.activateMaxMode(loadnew=True)
        self.imparent.snapshotAct.setEnabled(True)
        
    def importProject(self, fname):
        zimp = ZeissImporter(fname, self.ramanctrl, self)
        if zimp.validimport:
            zimp.exec()
            if zimp.result() == QtWidgets.QDialog.Accepted:
                self.open(zimp.gepardname)
        
    def new(self, fname):
        self.saveDataSet()
        if self.dataset is not None:
            self.dataset.save()
        self.dataset = DataSet(fname, newProject=True)
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        self.setupParticleEditor()
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        self.setMicroscopeMode()
        self.imparent.setWindowTitle(self.dataset.name + (" SIMULATION" if simulatedRaman else ""))
        self.imgdata = None
        self.activateMaxMode(loadnew=True)
        self.imparent.snapshotAct.setEnabled(True)
    
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    def setupParticleEditor(self):
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        """
        Setting up the particle editor for editing properties or contours of particles. 
        It needs some connections to sampleview and analysisview.
        """
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        def tryDisconnectingSignal(signal):
            try: 
                signal.disconnect()
            except TypeError:
                pass
            
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        if self.particleEditor is None:
            self.particleEditor = ParticleEditor(self, self.dataset.particleContainer)
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        tryDisconnectingSignal(self.particleEditor.particleAssignmentChanged)
        if self.analysiswidget is not None:
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            self.particleEditor.particleAssignmentChanged.connect(self.analysiswidget.updatePlotsAndContours)
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    def setMicroscopeMode(self):
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        """
        The opical microscope can be in either Brightfield (bf) or Darkfield (df) mode. In the case of the Renishaw instrument
        this mode affects the current image size in µm. Hence, gepard needs to be aware of the current mode
        :return:
        """
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        if self.ramanSwitchNeeded:
            self.imparent.ramanSwitch.connectToSampleView()
            self.imparent.ramanSwitch.show()
        self.microscopeMode = ('df' if self.imparent.ramanSwitch.df_btn.isChecked() else 'bf')
    
    @QtCore.pyqtSlot()    
    def activateMaxMode(self, loadnew=False):
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        """
        Activates the "highest" available mode of gepard. The modes follow gepard's operation workflow: 
            OpticalScan, ParticleDetection, RamanScan, ParticleAnalysis
        :return:
        """
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        mode = self.getMaxMode()
        self.imparent.updateModes(self.mode, self.getMaxMode())
        self.switchMode(mode, loadnew=loadnew)
        
    def getMaxMode(self):
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        """
        Determines the "highest" available mode of gepard. The modes follow gepard's operation workflow: 
            OpticalScan, ParticleDetection, RamanScan, ParticleAnalysis
        :return:
        """
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        if self.dataset is None:
            return None
        if not self.ramanctrl.connected:
            self.connectRaman()
        if not self.ramanctrl.connected:
            return None
        maxmode = "OpticalScan"
        if os.path.exists(self.dataset.getImageName()):
            maxmode = "ParticleDetection"
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            if self.dataset.particleDetectionDone:
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                maxmode = "RamanScan"
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            if self.dataset.ramanscandone:  
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                maxmode = "ParticleAnalysis"
        return maxmode
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    def blockUI(self):
        self.isblocked = True
        self.imparent.blockUI()
        
    def unblockUI(self):
        self.isblocked = False
        self.imparent.unblockUI(self.ramanctrl.connected)
        self.imparent.updateModes(self.mode, self.getMaxMode())
        
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    def mousePressEvent(self, event):
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        if event.button()==QtCore.Qt.MiddleButton:
            self.drag = event.pos()
        
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        if self.particlePainter is None:
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            if event.button()==QtCore.Qt.LeftButton:
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                if self.analysiswidget is not None:
                    self.checkForContourSelection(event)
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                if self.mode in ["OpticalScan", "RamanScan"] and event.modifiers()==QtCore.Qt.ControlModifier:
                    p0 = self.mapToScene(event.pos())
                    self.moveStageToPosition(p0)
                    
                elif self.mode=="ParticleDetection":
                    p0 = self.mapToScene(event.pos())
                    self.detectionwidget.setImageCenter([p0.x(), p0.y()])
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                else:
                    p0 = self.mapToScene(event.pos())
                    super(SampleView, self).mousePressEvent(event)
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        else:
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            self.particlePainter.mousePressEvent(event)

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    def mouseMoveEvent(self, event):
        if self.drag is not None:
            p0 = event.pos()
            move = self.drag-p0
            self.horizontalScrollBar().setValue(move.x() + self.horizontalScrollBar().value())
            self.verticalScrollBar().setValue(move.y() + self.verticalScrollBar().value())
            
            self.drag = p0
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        elif self.particlePainter is None:
            p0 = self.mapToScene(event.pos())
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            super(SampleView, self).mouseMoveEvent(event)
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        else:
            self.particlePainter.mouseMoveEvent(event)
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    def mouseReleaseEvent(self, event):
        self.drag = None
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        if self.particlePainter is None:
            super(SampleView, self).mouseReleaseEvent(event)
        else:
            self.particlePainter.mouseReleaseEvent(event)
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    def wheelEvent(self, event):
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        if self.particlePainter is None:
            factor = 1.01**(event.angleDelta().y()/8)
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            self.zoomDisplay(factor)
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        else:
            self.particlePainter.wheelEvent(event)
            
    def keyPressEvent(self, event):
        if self.particlePainter is not None:
            self.particlePainter.keyPressEvent(event)
    
    def moveStageToPosition(self, pos):
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        """
        Sends a command to the ramancontrol to move the microscope stage to the position of the click event.
        :return:
        """
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        if self.dataset is not None and self.dataset.pshift is not None:
            if self.dataset.readin:
                reply = QtWidgets.QMessageBox.critical(self, 'Dataset is newly read from disk!',
                    "Coordinate systems might have changed since. Do you want to continue with saved coordinates?", 
                    QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
        
                if reply == QtWidgets.QMessageBox.Yes:
                    self.dataset.readin = False
                else:
                    return
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            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:
                assert z>-100.
            self.ramanctrl.moveToAbsolutePosition(x, y, z)
    
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    def checkForContourSelection(self, event):
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        """
        Checks, if at the given event position any contour is selected.
        :return:
        """
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        def acceptSelection(cnt):
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            self.ParticleOfIndexSelected.emit(cnt.particleIndex)
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            cnt.isSelected = True
            cnt.update()
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            if cnt.particleIndex not in self.selectedParticleIndices:
                self.selectedParticleIndices.append(cnt.particleIndex)
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        def removeContourFromSelection(cnt):
            cnt.isSelected = False
            cnt.update()
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            self.selectedParticleIndices.remove(cnt.particleIndex)
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        p = self.mapToScene(event.pos())
        p = QtCore.QPointF(p.x(), p.y())
        
        for index, cnt in enumerate(self.contourItems):
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            if cnt.polygon.containsPoint(p, QtCore.Qt.OddEvenFill):   #clicked on particle
                if not event.modifiers()==QtCore.Qt.ShiftModifier:
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                    acceptSelection(cnt)
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                else:
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                    if cnt.particleIndex not in self.selectedParticleIndices:
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                        acceptSelection(cnt)
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                    elif cnt.particleIndex in self.selectedParticleIndices:
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                        removeContourFromSelection(cnt)
            
            else:    #not clicked on particle
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                if event.modifiers()!=QtCore.Qt.ShiftModifier:
                    cnt.isSelected = False
                    cnt.update()
                    if cnt.particleIndex in self.selectedParticleIndices:
                        self.selectedParticleIndices.remove(cnt.particleIndex)
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        if len(self.selectedParticleIndices) > 0:
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            self.updateParticleInfoBox(self.selectedParticleIndices[-1])
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        else:
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            self.removeParticleInfoBox()
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        self.update()
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    def zoomDisplay(self, factor):
        """
        Zooms the GraphicsView in or out, according to the given factor.
        :return:
        """
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        if factor<1 and not self.imparent.zoomOutAct.isEnabled():
            return
        if factor>1 and not self.imparent.zoomInAct.isEnabled():
            return
        self.scaleFactor *= factor      
        self.scale(factor, factor)
        self.announceScaling()
        
    def announceScaling(self):
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        """
        Processes a new scaling of the GraphicsView.
        :return:
        """
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        pixelscale = self.dataset.getPixelScale(self.microscopeMode)
        if self.dataset is None or pixelscale is None:
            self.ScalingChanged.emit(-1.0)
        else:
            self.ScalingChanged.emit(pixelscale/self.scaleFactor)           ##CURRENTLY ONLY DARKFIELD!!! FIX NEEDED!!!
        
    def connectRaman(self):
        if not self.ramanctrl.connect():
            msg = QtWidgets.QMessageBox()
            msg.setText("Connection failed! Please enable remote control.")
            msg.exec()
        else:
            mode = self.getMaxMode()
            self.switchMode(mode)
        self.imparent.updateConnected(self.ramanctrl.connected)
    
    def disconnectRaman(self):
        self.ramanctrl.disconnect()
        self.imparent.updateConnected(self.ramanctrl.connected)

    @QtCore.pyqtSlot(str)
    def detectionUpdate(self):
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        """
        Is connected to particle detection. When a new segmentation result was obtained, the sampleview has to update here.
        :return:
        """
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        self.resetParticleContours()
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        self.prepareAnalysis()
        self.update()

    @QtCore.pyqtSlot(str) 
    def loadPixmap(self, microscope_mode='df'):
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        """
        Loads the pixmap image as background for the GraphicsView.
        It is stored in self.imgdata
        :return:
        """
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        self.clearItems()
        if self.dataset is None:
            self.item.setPixmap(QtGui.QPixmap())
        else:
            data = self.imgdata
            fname = self.dataset.getImageName()
            if self.mode == "ParticleDetection" or self.mode == "ParticleAnalysis":
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                self.resetParticleContours()
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            if data is None and os.path.exists(fname):
                data = cv2.cvtColor(cv2imread_fix(fname), cv2.COLOR_BGR2RGB)
                self.imgdata = data
            if data is not None:
                height, width, channel = data.shape
                bytesPerLine = 3 * width
                pix = QtGui.QPixmap()
                pix.convertFromImage(QtGui.QImage(data.data, 
                                width, height, bytesPerLine, QtGui.QImage.Format_RGB888))
                self.item.setPixmap(pix)
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                if self.darkenPixmap:
                    self.scene().setBackgroundBrush(QtGui.QColor(5, 5, 5))
                    self.item.setOpacity(0.2)
                else:
                    self.scene().setBackgroundBrush(QtCore.Qt.darkGray)
                    self.item.setOpacity(1)
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            else:
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                self.item.setPixmap(QtGui.QPixmap())
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            if self.mode == "OpticalScan":
                for i, p in zip(self.dataset.fitindices, self.dataset.fitpoints):
                    p = self.dataset.mapToPixel(p, mode=microscope_mode, force=True)
                    fititem = FitPosIndicator(i+1, pos=p)
                    self.scene().addItem(fititem)
                    self.fititems.append(fititem)                    
            if self.mode == "ParticleDetection" or self.mode == "ParticleAnalysis":
                self.prepareAnalysis()
            else:
                self.fitToWindow()
    
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    def prepareAnalysis(self):
        """
        Is called after final particle detection. Raman Scan Indicators are added.
        """
        self.clearItems()
        if self.dataset.particleDetectionDone:
            for meas in self.dataset.particleContainer.measurements:
                if meas.ramanScanIndex is not None:
                    number = meas.ramanScanIndex+1
                    item = RamanScanIndicator(self, number, 20, (meas.pixelcoord_x, meas.pixelcoord_y))
                    self.scene().addItem(item)
                    self.ramanscanitems.append(item)
    
    def clearItems(self):
        """
        Removes items from the GraphicsScene. ContourItems remain, however..
        :return:
        """
        for itemList in [self.fititems, self.scanitems, self.ramanscanitems]:
            for item in itemList:
                self.scene().removeItem(item)
            itemList = []
        
        edges, nodes = self.boundaryitems
        for item in edges:
            self.scene().removeItem(item)
        for item in nodes:
            self.scene().removeItem(item)
        self.boundaryitems = [], []

    
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    @QtCore.pyqtSlot()        
    def resetScanPositions(self):
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        """
        Calculates position of scan tiles for the optical scan, according to the boundary and the polygoncovering method.
        The corresponding graphic items are added to the scene.
        :return:
        """
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        micMode = ('df' if self.oscanwidget.df_btn.isChecked() else 'bf')
        for item in self.scanitems:
            self.scene().removeItem(item)
        edges, nodes = self.boundaryitems
        boundary = []
        for n in nodes:
            p = n.pos().x(), n.pos().y()
            boundary.append(self.dataset.mapToLength(p, self.microscopeMode, force=True))
        boundary = np.array(boundary)
        self.dataset.boundary = boundary
        if micMode == 'df':
            width, height, angle = self.dataset.imagedim_df
        else:
            width, height, angle = self.dataset.imagedim_bf
        
        margin = min(width, height)*0.02
        wx, wy = width-margin, height-margin
        print(wx,wy)
        p1 = polygoncovering(boundary, wx, wy)
        b2 = boundary.copy()
        b2 = b2[:,[1,0]]
        p2 = polygoncovering(b2, wy, wx)
        if len(p2)<len(p1):
            p1 = [[pi[1],pi[0]] for pi in p2]
        self.dataset.grid = p1
        pixelscale = self.dataset.getPixelScale(self.microscopeMode)
        wxs, wys = width/pixelscale, height/pixelscale
        
        self.scanitems = []
        for i, p in enumerate(p1):
            p = self.dataset.mapToPixel(p, self.microscopeMode, force=True)
            s = ScanIndicator(i+1, wxs, wys, p)
            self.scene().addItem(s)
            self.scanitems.append(s)
    
    @QtCore.pyqtSlot()        
    def resetBoundary(self):
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        """
        Resets the Boundary Items in the GraphicsView.
        :return:
        """
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        micMode = self.microscopeMode
        edges, nodes = self.boundaryitems
        for item in edges:
            self.scene().removeItem(item)
        for item in nodes:
            self.scene().removeItem(item)
        edges, nodes = [], []
        for p in self.dataset.boundary:
            p = self.dataset.mapToPixel(p, micMode, force=True)
            n = Node(p, self)
            nodes.append(n)
            self.scene().addItem(n)
        for i in range(len(nodes)):
            e = Edge(nodes[i-1], nodes[i])
            edges.append(e)
            self.scene().addItem(e)
        self.boundaryitems = edges, nodes
        self.resetScanPositions()
    
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    def resetParticleContours(self):
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        """
        Resets the Contour Indicator Items in the GraphicsView.
        :return:
        """
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        t0 = time.time()
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        for cnt in self.contourItems:
            self.scene().removeItem(cnt)
        self.contourItems = []
        if self.dataset is not None:
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            for particle in self.dataset.particleContainer.particles:
                self.addParticleContourToIndex(particle.contour, particle.index)
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            self.update()
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        print('resetted contours: {} ms'.format(round((time.time()-t0)*1000)))
        
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    def addParticleContourToIndex(self, contour, index):
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        """
        Creates and adds a new ContourItem to the particle of a given index.
        :return:
        """
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        newCnt = SegmentationContour(self, contour)
        newCnt.setIndex(index)
        assignment = self.dataset.particleContainer.getParticleAssignmentByIndex(index)
        color = getColorFromNameWithSeed(assignment, self.dataset.colorSeed)
        newCnt.setColor(QtGui.QColor(color[0], color[1], color[2], 255))
        self.contourItems.append(newCnt)
        self.scene().addItem(newCnt)
    
    def removeParticleContour(self, contourIndex):
        correspondingParticle = self.dataset.particleContainer.getParticleOfIndex(contourIndex)   #this checks validity of contourIndex
        self.scene().removeItem(self.contourItems[contourIndex])
        del self.contourItems[contourIndex]
    
    def resetContourIndices(self):
        for index, contour in enumerate(self.contourItems):
            contour.setIndex(index)    
    
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    def updateLegend(self, legendItems):
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        """
        Updates the color legend in the graphics view.
        :return:
        """
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        self.imparent.legend.setTextColorItems(legendItems)
    
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    def highLightContour(self, index):
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        """
        Highlights a contour and fits the GraphicsView to the particle and its infobox.
        :return:
        """
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        for contour in self.contourItems:
            contour.isSelected = False
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        contour = self.contourItems[index]
        contour.isSelected = True
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        self.selectedParticleIndices =[index]
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        self.updateParticleInfoBox(index)
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        self.fitToParticleAndInfoBox()
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        self.update()
    
    def updateParticleInfoBox(self, particleIndex):
        self.removeParticleInfoBox()
        self.addParticleInfoBox(particleIndex)
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    def removeParticleInfoBox(self):
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        if self.particleInfoBox is not None:
            self.scene().removeItem(self.particleInfoBox)
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            self.particleInfoBox = None
    
    def addParticleInfoBox(self, particleIndex):
        self.particleInfoBox = ParticleInfo(self.dataset.particleContainer.getParticleOfIndex(particleIndex))
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        self.scene().addItem(self.particleInfoBox)
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    def fitToParticleAndInfoBox(self):
        """
        Fits the view to display the current particleInfoBox and its associated particle
        ;return:
        """
        def getGlobalBrect(graphItem):
            """
            Calculates bounding rect relative to scene origin (0,0)
            :return:
            """
            top = graphItem.pos().y() + graphItem.brect.top()
            left = graphItem.pos().x() + graphItem.brect.left()
            width = graphItem.brect.width()
            height = graphItem.brect.height()
            return QtCore.QRectF(left, top, width, height)
        
        def combineRects(rect1, rect2, margin=20):
            """
            Calculates a combined bounding rect.
            :return:
            """
            top = min(rect1.top(), rect2.top()) - margin/2
            left = min(rect1.left(), rect2.left()) - margin/2
            bottom = max((rect1.top()+rect1.height()), (rect2.top()+rect2.height())) + margin/2
            right = max((rect1.left()+rect1.width()), (rect2.left()+rect2.width())) + margin/2
            return QtCore.QRectF(left, top, (right-left), (bottom-top))
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        infoBoxRect = getGlobalBrect(self.particleInfoBox)
        particleIndex = self.particleInfoBox.particle.index
        selectedContour = self.contourItems[particleIndex]
        contourRect = getGlobalBrect(selectedContour)
        viewRect = combineRects(infoBoxRect, contourRect)
        self.fitInView(viewRect, QtCore.Qt.KeepAspectRatio)
        self.scaleFactor = self.transform().m11()
        self.announceScaling()
    
    def centerOnRamanIndex(self, index):
        """
        Centers the graphicsView to a given ScanIndicator Item.
        :return:
        """
        for scanItem in self.ramanscanitems:
            if scanItem.number == index+1:
                self.centerOn(scanItem)
                return
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    def highLightRamanIndex(self, index):
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        """
        Sets highlight parameter of a given ScanIndicator Item.
        :return:
        """
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        if index < len(self.ramanscanitems):
            for item in self.ramanscanitems:
                if item.number == index+1:
                    item.setHighLight(True)
                else:
                    item.setHighLight(False)
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