detectionview.py 27.9 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/>.
"""
import numpy as np
from PyQt5 import QtCore, QtWidgets, QtGui
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from segmentation import Segmentation, MeasurementPoint
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from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
import matplotlib.pyplot as plt
from threading import Thread

Nscreen = 1000

class HistWidget(QtWidgets.QWidget):
    def __init__(self, histcallback, curvecallback, parent=None):
        super().__init__(parent)
        
        self.updateCallbacks(histcallback, curvecallback)
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        if parent.dataset is None:
            self.points = np.array([[50,0],[100,220],[200,255]])
        else:
            self.points = parent.dataset.detectParams['points']
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        self.fig = plt.Figure()
        self.canvas = FigureCanvasQTAgg(self.fig)
        self.canvas.setParent(self)
        
        self.ax = self.fig.add_subplot(111, autoscale_on=False)
        self.ax.axis("off")
        self.fig.subplots_adjust(left=0.05, top=0.98, bottom=0.05, right=0.995)
        self.canvas.mpl_connect('pick_event', self.moveControlPoint)
        self.canvas.mpl_connect('button_release_event', self.releaseAxes)
        self.canvas.mpl_connect('motion_notify_event', self.moveAxes)
        
        self.moveind = None
        
        self.plot()
        self.setMaximumSize(200,200)
        
        vbox = QtWidgets.QVBoxLayout()
        vbox.addWidget(self.canvas)
        self.setLayout(vbox)
        
    def value(self):
        return self.points
        
    def moveAxes(self, event):
        if (event.inaxes==self.ax) and self.moveind is not None:
            x = event.xdata
            y = event.ydata
            if self.moveind == 0:
                self.points[0,0] = max(0,min(x, self.points[1,0]))
            elif self.moveind == 1:
                self.points[1,0] = max(self.points[0,0]+1, min(x, self.points[2,0]-1))
                self.points[1,1] = max(0, min(y, 255))
            else:
                self.points[2,0] = max(self.points[1,0]+1, min(x, 255))
            self.plot()
                
    def releaseAxes(self, event):
        self.moveind = None
        
    def plot(self):
        self.ax.lines = []
        self.ax.collections = []
        self.ax.artists = []
        
        hist = self.histcallback()[:,0]
        hist /= hist.max()
        hist *= 255
        hist[0] = 0
        hist[-1] = 0
        xarr, arr = self.curvecallback(self.points)
        
        self.ax.fill(xarr, hist, color=(.7,.7,.7))
        self.ax.plot([0,0], [255,255], "k-")
        self.ax.plot(xarr, arr, "b-")
        self.ax.plot(self.points[:,0], self.points[:,1], "go", picker=5)
        self.ax.set_xlim(0,255)
        self.ax.set_ylim(0,255)
        
        self.canvas.draw()        
        self.repaint()
        
    def updateCallbacks(self, histcallback, curvecallback):
        self.histcallback = histcallback
        self.curvecallback = curvecallback
                
    def moveControlPoint(self, event):
        if self.moveind is None:
            self.moveind = event.ind
    

class ImageView(QtWidgets.QLabel):
    seedChanged = QtCore.pyqtSignal()
    
    def __init__(self, parent=None):
        super().__init__(parent)
        self.overlay = None
        self.drag = False
        self.alpha = .8
        self.contours = []
        self.seedradius = 3
        self.showseedpoints = True
        self.measpoints = []
        self.seedpoints = []
        self.seeddeletepoints = []
        
    @QtCore.pyqtSlot(int)
    def resetAlpha(self, num):
        self.alpha = num/100.
        self.update()
    
    @QtCore.pyqtSlot(int)
    def setSeedRadius(self, num):
        self.seedradius = num
        self.update()
        
    @QtCore.pyqtSlot(int)
    def changeSeedDisplay(self, state):
        self.showseedpoints = (state==QtCore.Qt.Checked)
        self.update()
        
    def showStep(self, img, imgtype):
        self.overlay = None
        if imgtype==0:
            img = img.repeat(3).reshape(img.shape[0],img.shape[1],3)
            self.setOverlay(img)
        elif imgtype==1:
            levels = img
            img = np.zeros(tuple(levels.shape)+(3,), dtype=np.uint8)
            img[:,:,0][np.nonzero(levels&1)] = 255.
            img[:,:,1][np.nonzero(levels&2)] = 255.
            self.setOverlay(img)
        self.update()
        
    def removeSeeds(self,p0):
        p0 = np.array([p0])
        if len(self.seedpoints)>0:
            arr = np.array(self.seedpoints)
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            d = np.linalg.norm(arr[:, :2]-p0, axis=1)
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            ind = d>self.seedradius
            self.seedpoints = arr[ind,:].tolist()
        if len(self.seeddeletepoints)>0:
            arr = np.array(self.seeddeletepoints)
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            d = np.linalg.norm(arr[:, :2]-p0, axis=1)
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            ind = d>self.seedradius
            self.seeddeletepoints = arr[ind,:].tolist()
        
    def mousePressEvent(self, event):
        if event.button()==QtCore.Qt.LeftButton and event.modifiers() & QtCore.Qt.ControlModifier:
            if event.modifiers()&QtCore.Qt.ShiftModifier:
                self.drag = "delete"
            elif event.modifiers()&QtCore.Qt.AltModifier:
                self.drag = "remove"
            else:
                self.drag = "add"
            p0 = event.pos()
            if self.drag=="add":
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                self.seedpoints.append([p0.x(),p0.y(),self.seedradius])
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            elif self.drag=="delete":
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                self.seeddeletepoints.append([p0.x(),p0.y(),self.seedradius])
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            else:
                self.removeSeeds([p0.x(),p0.y()])
                
            self.update()
        super().mousePressEvent(event)
        
    def mouseMoveEvent(self, event):
        if self.drag:
            p0 = event.pos()
            if self.drag=="add":
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                self.seedpoints.append([p0.x(),p0.y(),self.seedradius])
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            elif self.drag=="delete":
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                self.seeddeletepoints.append([p0.x(),p0.y(),self.seedradius])
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            else:
                self.removeSeeds([p0.x(),p0.y()])
            self.update()
        super().mouseMoveEvent(event)
        
    def mouseReleaseEvent(self, event):
        if self.drag:
            self.seedChanged.emit()
        self.drag = False
        super().mouseReleaseEvent(event)
        
    def clearData(self):
        self.contours = []
        self.measpoints = []
        self.seedpoints = []
        self.seeddeletepoints = []
        self.overlay = None
        
    def updateSeedPoints(self, seedpoints=[], seeddeletepoints=[]):
        self.seedpoints = seedpoints
        self.seeddeletepoints = seeddeletepoints
        
    def updateDetectionResults(self, contours, measpoints):
        self.overlay = None
        cp = []
        for c in contours:
            polygon = QtGui.QPolygonF()
            for ci in c:
                polygon.append(QtCore.QPointF(ci[0,0],ci[0,1]))
            cp.append(polygon)
        
        self.contours = cp
        self.measpoints = measpoints
        self.update()
        
    def setOverlay(self, img):
        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.overlay = pix
        
    def paintEvent(self, event):
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        painter = QtGui.QPainter(self)
        painter.drawPixmap(0, 0, self.pixmap())
        painter.setOpacity(self.alpha)
        if self.overlay is not None:
            painter.drawPixmap(0, 0, self.overlay)
        else:
            painter.setPen(QtCore.Qt.blue)
            painter.setBrush(QtCore.Qt.green)
            for c in self.contours:
                painter.drawPolygon(c)
            painter.setPen(QtCore.Qt.red)
            painter.setBrush(QtCore.Qt.red)
            for p in self.measpoints:
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                for point in self.measpoints[p]:
#                painter.drawEllipse(p[0]-2, p[1]-2, 5, 5)
                    painter.drawEllipse(point.x-2, point.y-2, 5, 5)
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        if self.showseedpoints:
            painter.setPen(QtCore.Qt.white)
            painter.setBrush(QtCore.Qt.white)
            for p in self.seedpoints:
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                painter.drawEllipse(p[0]-p[2], p[1]-p[2], 2*p[2], 2*p[2])
            
            painter.setPen(QtCore.Qt.magenta)           #I think it is more useful when the deletpoints override the seedpoints
            painter.setBrush(QtCore.Qt.magenta)
            
            for p in self.seeddeletepoints:
                painter.drawEllipse(p[0]-p[2], p[1]-p[2], 2*p[2], 2*p[2])
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class ParticleDetectionView(QtWidgets.QWidget):
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    imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate')    #str = 'df' (= darkfield) or 'bf' (=bright field)
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    detectionFinished = QtCore.pyqtSignal(name='detectionFinished')
    
    def __init__(self, img, dataset, parent=None):
        super().__init__(parent, QtCore.Qt.Window)
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        self.dataset = self.verifySeedpoints(dataset)
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        self.img = img
        self.imgclip = 0,0,0,0
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        self.seg = Segmentation(self.dataset, self)
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        self.thread = None
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        self.view = parent
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        vbox = QtWidgets.QVBoxLayout()
        hbox = QtWidgets.QHBoxLayout()
        
        def makeShowLambda(name):
            def f(): return self.detectShow(name)
            return QtCore.pyqtSlot()(f)
        def makeValueLambda(objmethod):
            return lambda : objmethod()
        
        self.imglabel = ImageView(self)
        self.imglabel.seedChanged.connect(self.seedChanged)
        self.drag = False
        self.seedradiusedit = QtWidgets.QSpinBox(self)
        self.seedradiusedit.setMinimum(1)
        self.seedradiusedit.valueChanged.connect(self.imglabel.setSeedRadius)
        self.seedradiusedit.valueChanged.connect(self.updateImageSeeds)
        self.seedradiusedit.setValue(3)
        self.showseedpoints = QtWidgets.QCheckBox("Show manual seed points", self)
        self.showseedpoints.stateChanged.connect(self.imglabel.changeSeedDisplay)
        self.showseedpoints.setChecked(True)
        self.setImageCenter()
        group = QtWidgets.QGroupBox("Detection settings", self)
        grid = QtWidgets.QGridLayout()
        self.parameters = []
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        checkBoxesToLink = {}
        
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        # create editable parameters:
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        for i, p in enumerate(self.seg.parlist):
            label, colstretch = None, 1
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            if p.name == "contrastCurve":
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                paramui = HistWidget(lambda : self.seg.calculateHist(self.seg.convert2Gray(self.subimg)),
                                     self.seg.calculateHistFunction, self)
                valuefunc = makeValueLambda(paramui.value)
                colstretch = 2
            if p.dtype == np.bool:
                paramui = QtWidgets.QCheckBox(p.helptext, self)
                paramui.setChecked(p.value)
                valuefunc = makeValueLambda(paramui.isChecked)
                colstretch = 2
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                if p.linkedParameter is not None:
                    checkBoxesToLink[paramui] = p.linkedParameter
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            elif p.dtype == int or p.dtype == float:
                label = QtWidgets.QLabel(p.helptext, self)
                if p.dtype == int:
                    paramui = QtWidgets.QSpinBox(self)
                else:
                    paramui = QtWidgets.QDoubleSpinBox(self)
                    paramui.setDecimals(p.decimals)
                if p.valrange[0] is not None:
                    paramui.setMinimum(p.valrange[0])
                if p.valrange[1] is not None:
                    paramui.setMaximum(p.valrange[1])
                paramui.setSingleStep(p.stepsize)
                paramui.setValue(p.value)
                paramui.setMinimumWidth(70)
                valuefunc = makeValueLambda(paramui.value)
            elif p.dtype is None:
                label = QtWidgets.QLabel(p.helptext, self)
                paramui = None
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            if paramui is not None:
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                self.parameters.append([paramui, p.name, valuefunc, None])
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                if colstretch == 1:
                    grid.addWidget(paramui, i, 1, QtCore.Qt.AlignLeft)
                else:
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                    grid.addWidget(paramui, i, 0, 1, 2, QtCore.Qt.AlignLeft) 
                    
                
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            if label is not None:
                grid.addWidget(label, i, 0, QtCore.Qt.AlignLeft)
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            if p.show is True:
                pshow = QtWidgets.QPushButton(">", self)
                pshow.released.connect(makeShowLambda(p.name))
                grid.addWidget(pshow, i, 2, QtCore.Qt.AlignRight)
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                if paramui is not None:
                    self.parameters[-1][3] = pshow
                
                    
            
        
        #link checkboxes to other parameters:
        def makeEnableLambda(checkbox, parameter):
            return lambda: parameter.setEnabled(checkbox.isChecked())
        
        for box in checkBoxesToLink:
            linkedName = checkBoxesToLink[box]
            for p in self.parameters:
                if p[1] == linkedName:
                    p[0].setEnabled(box.isChecked())
                    box.stateChanged.connect(makeEnableLambda(box, p[0]))   #the actual control element
                    if p[3] is not None: #the "show" box, if present
                        box.stateChanged.connect(makeEnableLambda(box, p[3]))   
                        p[3].setEnabled(box.isChecked())
        
        
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        label = QtWidgets.QLabel("Seed radius", self)
        grid.addWidget(label, i+1, 0, QtCore.Qt.AlignLeft)
        grid.addWidget(self.seedradiusedit, i+1, 1, QtCore.Qt.AlignLeft)
        grid.addWidget(self.showseedpoints, i+2, 0, 1, 2, QtCore.Qt.AlignLeft) 
        grid.addWidget(QtWidgets.QLabel("Use Ctrl for seeds and Ctrl+Shift for delete points"), i+3, 0, 1, 2, QtCore.Qt.AlignLeft) 
        grid.addWidget(QtWidgets.QLabel("Ctrl+Alt removes seeds near cursor"), i+4, 0, 1, 2, QtCore.Qt.AlignLeft) 
        group.setLayout(grid)
        vbox.addWidget(group)
            
        self.slider = QtWidgets.QSlider(self)
        self.slider.setRange(0,100)
        self.slider.setValue(80)
        self.slider.setOrientation(QtCore.Qt.Horizontal)
        self.slider.sliderMoved.connect(self.imglabel.resetAlpha)
        vbox.addWidget(self.slider)
        hbox2 = QtWidgets.QHBoxLayout()
        self.pdetectsub = QtWidgets.QPushButton("Detect", self)
        self.pdetectall = QtWidgets.QPushButton("Detect all", self)
        self.pclear = QtWidgets.QPushButton("Clear detection", self)
        self.pdetectsub.released.connect(makeShowLambda(None))
        self.pdetectall.released.connect(self.detectParticles)
        self.pclear.released.connect(self.clearDetection)
        hbox2.addWidget(self.pdetectsub)
        hbox2.addWidget(self.pdetectall)
        hbox2.addWidget(self.pclear)
        vbox.addLayout(hbox2)

        vbox.addStretch()
        hbox.addLayout(vbox,0)
        hbox.addWidget(self.imglabel,1)
        
        self.setLayout(hbox)
        self.setWindowTitle("Particle Detection")
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    def saveDetectParams(self, ds=None):
        if ds is not None:
            for param in self.parameters:
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                if param[1] == 'contrastCurve':
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                    print(param[0].value())
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                try:                # is it a spinbox or the histWidget? Read out the value
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                    ds.detectParams[param[1]] = param[0].value()
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                except:             # otherwise checkbox -> take its state
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                    ds.detectParams[param[1]] = param[0].isChecked()
            ds.detectParams['seedRad'] = self.seedradiusedit.value()
            ds.save()

    def verifySeedpoints(self, dataset):
        seedpoints = dataset.seedpoints
        seeddeletepoints = dataset.seeddeletepoints
        
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        if len(seedpoints) > 0:     # points are present
            if seedpoints.shape[1] == 2:    # old entries with only x,y coordinates
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                radii = np.ones((seedpoints.shape[0], 1))*3
                dataset.seedpoints = np.hstack((seedpoints, radii))
        else:
            dataset.seedpoints = np.array([])
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        if len(seeddeletepoints) > 0:     # points are present
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            if seeddeletepoints.shape[1] == 2:    #old entries with only x,y coordinates
                radii = np.ones((seeddeletepoints.shape[0], 1))*3
                dataset.seeddeletepoints = np.hstack((seeddeletepoints, radii))
        else:
            dataset.seeddeletepoints = np.array([])
        return dataset
    
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    @QtCore.pyqtSlot()
    def seedChanged(self):
        seedradius = self.seedradiusedit.value()
        def clipdata(arr0, arr1, p0, n1, n2, m1, m2):
            if arr0.shape[0]>0:
                ind = (arr0[:,0]>m1-seedradius)&(arr0[:,0]<=m2+seedradius) 
                ind &= (arr0[:,1]>n1-seedradius)&(arr0[:,1]<=n2+seedradius)
                arr0 = arr0[~ind,:]
            else:
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                arr0 = arr0.reshape(0,3)

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            if arr1.shape[0]>0:
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                arr1[:,:2] += p0
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            else:
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                arr1 = arr1.reshape(0,3)
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            return np.concatenate((arr0, arr1), axis=0)
        
        if self.dataset is not None:
            n1,n2,m1,m2 = self.imgclip
            p0 = np.array([[m1,n1]], dtype=np.int32)
            self.dataset.seedpoints = clipdata(self.dataset.seedpoints,
                                               np.array(self.imglabel.seedpoints, dtype=np.int32),
                                               p0, n1, n2, m1, m2)
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            self.dataset.seeddeletepoints = clipdata(self.dataset.seeddeletepoints,
                                                     np.array(self.imglabel.seeddeletepoints, dtype=np.int32),
                                                     p0, n1, n2, m1, m2)
            self.dataset.save()
            
    @QtCore.pyqtSlot()
    def updateImageSeeds(self):
        if self.dataset is not None:
            n1,n2,m1,m2 = self.imgclip
            p0 = np.array([[m1,n1]], dtype=np.int32)
            seedpoints = []
            seeddeletepoints = []
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            arr1 = self.dataset.seedpoints
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            # what seeds are actually in image view?
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            for point in arr1:                  #Josef says: I replaced the commented logic with the one right here below, as the old one somehow did not work.... The for-loop might become slow at some point??
                if point[0] > (m1-point[2]) and point[0] <= (m2+point[2]) and point[1] > (n1-point[2]) and point[1] <= (n2+point[2]):
                    seedpoints.append([point[0] - p0[0][0], point[1] - p0[0][1], point[2]])
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            arr2 = self.dataset.seeddeletepoints
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            for point in arr2:                  #Josef says: I replaced the commented logic with the one right here below, as the old one somehow did not work.... The for-loop might become slow at some point??
                if point[0] > (m1-point[2]) and point[0] <= (m2+point[2]) and point[1] > (n1-point[2]) and point[1] <= (n2+point[2]):
                    seeddeletepoints.append([point[0] - p0[0][0], point[1] - p0[0][1], point[2]])

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            self.imglabel.updateSeedPoints(seedpoints, seeddeletepoints)
        
    def closeEvent(self, event):
        self.detectionFinished.emit()
        
    def mousePressEvent(self, event):
        if event.button()==QtCore.Qt.RightButton:
            self.drag = True
            self.p0 = event.pos()
        
    def mouseMoveEvent(self, event):
        if self.drag:
            dp = self.p0-event.pos()
            self.lastmove = (self.lastcenter[0]+dp.x(),self.lastcenter[1]+dp.y())
            self.setImageCenter(self.lastmove)
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    def wheelEvent(self, event):
        if event.angleDelta().y() > 0:
            self.seedradiusedit.setValue(self.seedradiusedit.value()+1)
        else:
            self.seedradiusedit.setValue(self.seedradiusedit.value()-1)
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    def mouseReleaseEvent(self, event):
        if self.drag:
            self.lastcenter = self.lastmove
        self.drag = False
        
    def setDataSet(self, ds):
        self.dataset = ds
        self.updateImageSeeds()
        
    def setImageCenter(self, center=None):
        if center is None:
            centerx = self.img.shape[1]//2
            centery = self.img.shape[0]//2
        else:
            centerx, centery = center
        if self.img.shape[0]<Nscreen:
            centery = self.img.shape[0]//2
        if self.img.shape[1]<Nscreen:
            centerx = self.img.shape[1]//2
        if not self.drag:  
            self.lastcenter = centerx, centery
        n1, n2 = int(centery-Nscreen//2),int(centery+Nscreen//2+1)
        m1, m2 = int(centerx-Nscreen//2),int(centerx+Nscreen//2+1)
        if n1<0: 
            n2 -= n1
            n1 = 0
        if n2>self.img.shape[0]: 
            n1 -= n2-self.img.shape[0]
            if n1<0: n1 = 0
            n2 = self.img.shape[0]
        if m1<0: 
            m2 -= m1
            m1 = 0
        if m2>self.img.shape[1]: 
            m1 -= m2-self.img.shape[1]
            if m1<0: m1 = 0
            m2 = self.img.shape[1]
        sub = self.img[n1:n2,m1:m2,:].copy()
        self.imgclip = n1,n2,m1,m2
        self.subimg = sub
        height, width, channel = sub.shape
        bytesPerLine = 3 * width
        pix = QtGui.QPixmap()
        pix.convertFromImage(QtGui.QImage(sub.data, width, height, 
                                          bytesPerLine, QtGui.QImage.Format_RGB888))
        self.imglabel.clearData()
        self.imglabel.setPixmap(pix)
        self.updateImageSeeds()
        
    def detectShow(self, showname):
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        self.saveDetectParams(self.dataset)
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        img = self.subimg.copy()
        kwargs = {}
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        for ui, name, valuefunc, showbtn in self.parameters:
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            kwargs[name] = valuefunc()
        self.seg.setParameters(**kwargs)
        seedradius = self.seedradiusedit.value()
        if showname is not None:
            stepImg, imgtype = self.seg.apply2Image(img, self.imglabel.seedpoints,
                                                    self.imglabel.seeddeletepoints,
                                                    seedradius,
                                                    return_step=showname)
            self.imglabel.showStep(stepImg, imgtype)
        else:
            measurementpoints, contours, particlestats = self.seg.apply2Image(img,
                                                  self.imglabel.seedpoints,
                                                  self.imglabel.seeddeletepoints,
                                                  seedradius)
            self.imglabel.updateDetectionResults(contours, measurementpoints)
            
    @QtCore.pyqtSlot()
    def clearDetection(self):
        if self.dataset is not None:
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            self.dataset.particleContainer.clearParticles()
            self.dataset.particleContainer.clearMeasurements()
            self.dataset.particleDetectionDone = False
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            self.dataset.ramanscandone = False
            self.dataset.mode = "opticalscan"
            self.dataset.save()
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            self.imageUpdate.emit(self.view.microscopeMode)
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    @QtCore.pyqtSlot()
    def cancelThread(self):
        self.seg.cancelcomputation = True
        self.thread.join()
        self.seg.cancelcomputation = False
        self.threadrunning = False
        
    def blockUI(self):
        self.pdetectsub.setEnabled(False)
        self.pclear.setEnabled(False)
    
    def unBlockUI(self):
        self.pdetectsub.setEnabled(True)
        self.pclear.setEnabled(True)
    
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    def raiseWarning(self, warning):
        QtWidgets.QMessageBox.critical(self, "Warning", warning)
    
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    @QtCore.pyqtSlot()
    def detectParticles(self):
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        self.saveDetectParams(self.dataset)
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        if self.thread is not None and self.thread.is_alive():
            self.cancelThread()
            return
        self.blockUI()
        self.pdetectall.setText("Cancel")
        self.threadrunning = True
        self.thread = Thread(target=self._worker)
        self.thread.start()
        self.timer = QtCore.QTimer(self)
        self.timer.timeout.connect(self.checkOnComputation)
        self.timer.setSingleShot(True)
        self.timer.start(100.)
        
    @QtCore.pyqtSlot()      
    def checkOnComputation(self):
        if self.thread is not None:
            if not self.threadrunning:
                #self.thread.join()
                self.thread = None
                self.unBlockUI()
                self.pdetectall.setText("Detect all")
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                self.imageUpdate.emit(self.view.microscopeMode)
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                if self.dataset is not None:
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                    self.setWindowTitle(str(self.dataset.particleContainer.getNumberOfParticles()) + " Particles")
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            else:
                self.timer.start(100.)    
        
    def _worker(self):
        kwargs = {}
        seedpoints, deletepoints = [], []
        if self.dataset is not None:
            seedpoints = self.dataset.seedpoints
            deletepoints = self.dataset.seeddeletepoints
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        for ui, name, valuefunc, showbtn in self.parameters:
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            kwargs[name] = valuefunc()
        seedradius = self.seedradiusedit.value()
        self.seg.setParameters(**kwargs)
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        measurementPoints, contours, particlestats = self.seg.apply2Image(self.img,
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                                                                          seedpoints,
                                                                          deletepoints,
                                                                          seedradius)
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        if measurementPoints is None: # computation was canceled
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            return
        if self.dataset is not None:
            self.dataset.ramanscandone = False
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            numParticles = len(contours)
            particleContainer = self.dataset.particleContainer
            
            particleContainer.initializeParticles(numParticles)
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            particleContainer.setParticleContours(contours)
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            particleContainer.setParticleStats(particlestats)
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            particleContainer.applyPixelScaleToParticleStats(self.dataset.getPixelScale())
            
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            for particleIndex in measurementPoints.keys():
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                measPoints = measurementPoints[particleIndex]
                for index, point in enumerate(measPoints):
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                    curParticle = particleContainer.getParticleOfIndex(particleIndex)
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                    indexOfNewMeas = particleContainer.addEmptyMeasurement()
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                    particleContainer.setMeasurementPixelCoords(indexOfNewMeas, point.x, point.y)
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                    curParticle.addMeasurement(particleContainer.measurements[indexOfNewMeas])
                    
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            self.dataset.ramanpoints = measurementPoints
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            self.dataset.particleDetectionDone = True
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            self.dataset.mode = "prepareraman"
            self.dataset.save()
        
        self.threadrunning = False
        
        
if __name__ == "__main__":
    import cv2
    import sys
    from helperfunctions import cv2imread_fix
    from dataset import DataSet
    from time import time
    
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    fname = r"C:\Users\brandt\Desktop\20180723DemoTZW\fullimage.tif"
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    app = QtWidgets.QApplication(sys.argv)
    
    t2 = time()
    img = cv2imread_fix(fname)
    t3 = time()
    print("OpenCV read:", t3-t2)
    img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
    
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    ds = DataSet("dummy")    
    view = ParticleDetectionView(img, ds, None)    
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    view.setDataSet(ds)
    view.show()
    app.exec_()