KaptureControlGui/KCG/widgets/TimescanWidget.py

from __future__ import print_function 

from PyQt4 import QtGui, QtCore
from PyQt4.QtCore import pyqtSlot
import pyqtgraph as pg
from PyQt4.QtGui import QFont, QTableWidget

from scipy.optimize import curve_fit
from scipy.stats import chisquare
from scipy.stats import chi2_contingency
from scipy.special import erfc, erf

import copy

from ..base import kcgwidget as kcgw
from ..base.backend import board
from ..base.backend.DataSet import DataSet
from ..base.backend.TimeScan import TimeScan
from ..base.backend.board import available_boards
from ..base import backendinterface as bif
from ..base.groupedelements import Elements, live_plot_windows
from ..base.globals import glob as global_objects
from .. import config
from ..config import colours, coloursTrans
from ..base import storage
from ..base.backend.CalibrationHandle import theCalibration
from . import UpdateCalibrationWidget
from . import CorrelationWidget
import logging

import time
from time import sleep
import h5py
import traceback

import numpy as np
import os

__widget_id__ = None

MODE_ALL = 0
MODE_THREASHOLD = 1
MODE_AUTOBUCKET = 2
MODE_AUTOBUCKET_TMP_THRESHOLD = 3
MODE_BUCKET = 4
MODE_BUCKET_THRESHOLD = 5
MODE_ALL_BUCKETS = 6


class ScanThread(QtCore.QObject):
    '''Timescan Thread class'''
    pbarSignal = QtCore.pyqtSignal(object, float)
    stopSignal = QtCore.pyqtSignal(object, str)
    plotSignal = QtCore.pyqtSignal(object)


    def __init__(self, c_min, c_max, f_min, f_max, board_id, index, info, outdir="", threshold=0, saveraw=False, c25_min=-1, c25_max=-1, step4=False, meanMode=MODE_ALL, fastMode=False, calibScan=False):
        super(ScanThread, self).__init__()
        self.c_min = c_min
        self.c_max = c_max
        self.f_min = f_min
        self.f_max = f_max
        self.c25_min = c25_min
        self.c25_max = c25_max
        self.step4 = step4
        self.board_id = board_id
        self.threshold = threshold
        self.index = index
        self.info = info
        self.saveraw = saveraw
        self.rawdir = ""
        self.outdir = outdir
        self.adc_number = board.get_board_config(self.board_id).get('adc_number')
        self.board_config =  board.get_board_config(self.board_id)
        
        self.timescan = TimeScan()
        self.stop = False
        self.timestamp = 0
        self.meanMode = meanMode
        self.buckets = None
        self.fastMode = fastMode
        self.calibrationScan = calibScan
        

    def setDelay(self, value):
        board.get_board_config(self.board_id).update('delay_330_th', value)
        board.get_board_config(self.board_id).update('delay_330_th_2', value)

    def setDelay25(self, value):
        board.get_board_config(self.board_id).update('delay_25_th', value)
        board.get_board_config(self.board_id).update('delay_25_th_2', value)

    def setDelayB(self, value):
        board.get_board_config(self.board_id).update('delay_330_th_2', value)

    def setDelayB25(self, value):
        board.get_board_config(self.board_id).update('delay_25_th_2', value)

    def setFineDelay(self, value):
        board.get_board_config(self.board_id).update('chip_delay', [value,value,value,value,value,value,value,value])

    def scan(self):
        print('##################################################################')
        self.stop = False
        self.timestamp = time.time()

        self.timescan.prepare(self.adc_number, self.meanMode==MODE_ALL_BUCKETS)

        if self.fastMode:
            print('fastMode')     
            self.board_config.update('chip_delay', [0,10,20,30,0,10,20,30])     

        if self.saveraw or self.meanMode in [MODE_AUTOBUCKET_TMP_THRESHOLD, MODE_AUTOBUCKET]:
            self.saveraw = True
            self.rawdir  = os.path.join(self.outdir, 'raw')#, '{:02d}_{:.3f}'.format(self.index, self.timestamp))
            self.rawfilename = os.path.join(self.rawdir, '{:02d}_{:.3f}.hdf'.format(self.index, self.timestamp))
            if not os.path.isdir(self.rawdir):
                os.makedirs(self.rawdir)
            self.rawFile = h5py.File(self.rawfilename, 'w')
            self.dataGroup = self.rawFile.create_group('data')

        for c_step in range(self.c_min, self.c_max+1):
            self.setDelay(c_step)
            sleep(0.1)
            step = 1
            if self.step4:
                step=4
            for c25_step in range(self.c25_min, self.c25_max+1, step):
                if board.get_board_config(self.board_id).is_KAPTURE2():
                    self.setDelay25(c25_step)

                    if self.calibrationScan:
                        #self.setDelayB(0)
                        self.setDelayB25(4)
                        c25_step_b = 4
                        pass
                    c25_step_b = board.get_board_config(self.board_id).get('delay_25_th_2')
            
                for f_step in range(self.f_min, self.f_max+1):
                    if not self.fastMode:
                        self.setFineDelay(f_step)
                    self.startTime = time.time()
                    print('--------------------------------------------------------')
                    print('{:4.3f} step'.format(time.time()))
                    if not kcgw.testing:
                        sleep(0.25)
                    else:
                        sleep(0.05)

                    if self.stop:
                        self.finished(c_step, c25_step, f_step)
                        return
                    
                    self.readData(c_step, c25_step, f_step, 0, c25_step_b)

                #for f_step 

                if self.calibrationScan:
                    self.setFineDelay(0)
                    f_step = 0
                    self.setDelayB(0)
                    c_step_b = 0
                    for c25_step_b in range(1, 8+1):
                        self.setDelayB25(c25_step_b)
                        print('--------------------------------------------------------')
                        print('{:4.3f} step'.format(time.time()))

                        if not kcgw.testing:
                            sleep(0.25)
                        else:
                            sleep(0.05)

                        if self.stop:
                            self.finished(c_step, c25_step, f_step)
                            return
                        self.readData(c_step, c25_step, f_step, c_step_b, c25_step_b)
                #if calibrationScan
            #for c25_step
        #for c_step

        self.finished(c_step, c25_step, f_step)

    def readData(self, c_step, c25_step, f_step, c_step_b=0, c25_step_b=0):
        try:
            # -----------[ IMPORTANT ]---------------------
            if not kcgw.testing:
                data_raw =  np.fromstring(bif._bif_read_data(self.board_id, True), dtype=np.uint32)
                if data_raw is None:
                    print('no data returned')
                    self.stop = True
                    self.finished(c_step, c25_step, f_step)
                    return
            # ----------------------------------------------
            else:
                f_name = "t/1544038883.603.out"#1529502127.686.out"
                data_raw = np.memmap(f_name, dtype='uint32')
            
        
            data = DataSet(rawData=data_raw, tRev=config.tRev, bunchesPerTurn=config.bunches_per_turn, shiftFMC2=config.shiftFMC2)
            
            #print('{:4.3f} emit Plot'.format(time.time()-self.startTime))
            self.plotSignal.emit(data)
            #print('{:4.3f} emit Plot done'.format(time.time()-self.startTime))

        except Exception as e:
            print(e)
            self.stop = True
            self.finished(c_step, c25_step, f_step)    
            return


        if self.saveraw:
            self.dataGroup.create_dataset(
                "{:02d}_{:02d}_{:02d}_{:02d}_{:02d}".format(c_step, c25_step, f_step, c_step_b, c25_step_b),
                data=data_raw, dtype='uint32',
                shuffle=False, chunks=(2**8,4),
                compression='lzf'
            )

        baseline = 2048

        tmpmeans=[0,0,0,0,0,0,0,0]

        for adc in range(self.adc_number):
            try:
                tmp = data.array[:,adc]
            except Exception as e:
                print(e)
                self.stop = True
                self.finished(c_step, c25_step, f_step)  
                return
            #print('{:4.3f} Calc ADC {} '.format(time.time()-self.startTime, adc))
            
            if self.meanMode in [MODE_THREASHOLD]:
                if self.threshold > 0:
                    tmp = tmp[np.where((tmp > (baseline)+self.threshold))]# | (tmp < baseline-self.threshold))]
                else:
                    tmp = tmp[np.where((tmp < (baseline)+self.threshold))]# | (tmp < baseline-self.threshold))]
                #print('{:4.3f} MODE_THREASHOLD done'.format(time.time()-self.startTime))

            elif self.meanMode in [MODE_BUCKET]:
                tmp = tmp[self.threshold::184]
                #print('{:4.3f} MODE_BUCKET done'.format(time.time()-self.startTime))
                
            elif self.meanMode in [MODE_ALL_BUCKETS]:
                tmp = np.reshape(tmp, (-1,184))

            if len(tmp) < 5:
                tmp=[baseline,baseline]

            mean = np.mean(tmp,0)
            std  = np.std(tmp,0)
            

            self.timescan.appendData(mean,std,adc, c_step, c25_step, f_step, c25_step_b)

            
        #print('{:4.3f} emit pbar'.format(time.time()-self.startTime))
        tmpScan = copy.deepcopy(self.timescan)
        self.pbarSignal.emit(tmpScan, 
                             ((c_step-self.c_min)*(self.c25_max-self.c25_min+1.0) * (self.f_max-self.f_min+1.0) + (c25_step-self.c25_min)*(self.f_max-self.f_min+1.0) + (f_step-self.f_min))/
                             ((self.c_max-self.c_min+1.0) * (self.c25_max-self.c25_min+1.0) * (self.f_max-self.f_min+1.0))
                            )
        #print('{:4.3f} emit pbar done'.format(time.time()-self.startTime))

    def finished(self, c_step=0, c25_step=0, f_step=0):
        '''Method to handle the end of the thread'''
        
        if self.saveraw:
            grp = self.rawFile.create_group('info')
            grp['Nr']        =  self.index
            grp['Info']      =  '{}'.format(self.info)
            grp['Threshold'] =  self.threshold
            grp['T/H']       = [self.c_min, self.c_max]
            grp['25ps']      = [self.c25_min, self.c25_max]
            grp['fine']      = [self.f_min, self.f_max]
            grp['Step4']     =  self.step4
            grp['Mode']      =  self.meanMode
            grp['stop']      = [c_step, c25_step, f_step]
            grp['fastMode']  =  self.fastMode
            grp['Calibration']  =  self.calibrationScan
            self.rawFile.close()

        
        file= '{:02d}_{:0.3f}.scan'.format(self.index, self.timestamp)
        filename = os.path.join(self.outdir, file)

        self.timescan.saveScan(filename, self.index, self.info, self.threshold,
                               self.c_min, self.c_max, self.c25_min, self.c25_max,
                               self.f_min, self.f_max, self.stop, c_step, c25_step, f_step,
                               self.step4, self.meanMode, self.fastMode, self.calibrationScan)
        


        board.get_board_status(self.board_id).time_scan = False

        self.stop = True
        self.stopSignal.emit(self.timescan, filename)
        return

    


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#                                                                    888
#                                                               Y8b d88P
#                                                                "Y88P"

LINEAR = 0
GAUSS  = 1
EGAUSS = 2
EGAUSSB= 3
SKEW   = 4
SINUS  = 5


__timing_plot_widget_id__ = {}
__timing_plot_widget__ = None
__datastorage__ = None

##################################################################################
class ScanPlotWidget(kcgw.KCGWidgets):
    """
    The Timescan result plot subwindow.
    """
    def __init__(self, unique_id, board_id, parent=None):
        """
        Initialises the timing plot window
        :param unique_id: the id for this window
        :param parent: parent object
        :return: -
        """
        super(ScanPlotWidget, self).__init__()

        self.id = unique_id
        self.par = parent
        self.board_id = board_id
        self.timeScan = None
        #self.block = False

        # ------[ Variable declaration ]------------
        self.xrange = (0, 1) #T/H
        self.yrange = (0, 1) #fine
        self.zrange = (0, 1) #25ps
        self.x = 1  # Number of Ticks in the x-direction     This is set by the gui programmatically
        self.y = 1  # Number of Ticks in the y-direction     This is set by the gui programmatically
        self.z = 1
        self.data = None  # Data to plot
        self.levels = None  # Levels for colors
        self.step4 = False
        self.type=0
        self.board_config = board.get_board_config(self.board_id)
        self.adc_number = self.board_config.get('adc_number')
        
        self.plotList = []
        self.scanyAll = []
        self.delays = np.zeros(self.adc_number)

        # -------[ Create structure ]----------
        self.outerLayout = QtGui.QVBoxLayout()  # Outermost layout of this window
        self.setLayout(self.outerLayout)

        self.plotWidget1 = QtGui.QWidget()
        self.plotlayout1 = QtGui.QGridLayout()
        self.adc_plot_widgets = []
        for i in range(self.adc_number):
            self.adc_plot_widgets.append(pg.PlotWidget(title="ADC {}".format(i+1)))
        
        for i,item in enumerate(self.adc_plot_widgets):
            self.plotlayout1.addWidget(item, i//(self.adc_number//2), i%(self.adc_number//2))
        self.plotWidget1.setLayout(self.plotlayout1)
        
        self.plotWidget2 = QtGui.QWidget()
        self.plotlayout2 = QtGui.QGridLayout()  # Main Layout to hold the most elements in this window      
        self.all_plot_widget = pg.PlotWidget(title="over Time")
        self.plotlayout2.addWidget(self.all_plot_widget, 0, 0)
        self.plotWidget2.setLayout(self.plotlayout2)

        self.layout = QtGui.QGridLayout()  # Main Layout to hold the most elements in this window
        lineindex = 0
        self.adccb = []
        for adc in range(self.adc_number):
            self.adccb.append(self.createCheckbox('ADC{}'.format(adc+1), checked=True, connect=self.plot, color=colours[adc]))
            self.layout.addWidget(self.adccb[adc],lineindex,adc)
        lineindex +=1

        self.layout.addWidget(self.createLabel('Plot Type:'), lineindex,0)
        self.plotSelect = QtGui.QComboBox(self)
        self.plotSelect.addItem("default") #0
        self.plotSelect.addItem("timecorreted") #1
        self.plotSelect.currentIndexChanged.connect(self.changePlotType)
        self.layout.addWidget(self.plotSelect, lineindex, 1)

        self.showError=self.createCheckbox('show Error', connect=self.plot)
        self.layout.addWidget(self.showError, lineindex,2)
        self.useCalib=self.createCheckbox('use Calib', connect=self.plot)
        self.layout.addWidget(self.useCalib, lineindex,3)
        self.showADC=self.createCheckbox('show ADCs', connect=self.plot)
        self.layout.addWidget(self.showADC, lineindex,4)
        self.updateCalib = self.createButton('Update Calibration', connect=self.onUpdateCalibration)
        self.layout.addWidget(self.updateCalib, lineindex, 5)
        self.correlationTest = self.createButton('Correlation Test', connect=self.onCorrelation)
        self.layout.addWidget(self.correlationTest, lineindex, 6)

        lineindex += 1

        self.multiBunchSelector = self.createSpinbox(0,184, start_value=0, interval=1, connect=self.plot)
        self.multiBunchSelectorLabel = self.createLabel('Bunch Selection:')
        self.layout.addWidget(self.multiBunchSelectorLabel, lineindex, 0)
        self.layout.addWidget(self.multiBunchSelector, lineindex, 1)
        self.multiBunchSelector.hide()
        self.multiBunchSelectorLabel.hide()

        lineindex += 1

        self.fitSin=self.createCheckbox('plot Fit', connect=self.plot)
        self.layout.addWidget(self.fitSin, lineindex,0)

        self.fitSelect = QtGui.QComboBox(self)
        self.fitSelect.addItem("Linear") #0
        self.fitSelect.addItem("Gauss") #1
        self.fitSelect.addItem("Exponential mod Gauss") #2
        self.fitSelect.addItem("Exponential mod Gauss V2") #3
        self.fitSelect.addItem("skew Gauss") #4
        self.fitSelect.addItem("Sinus") #5
        self.fitSelect.currentIndexChanged.connect(self.plot)
        self.layout.addWidget(self.fitSelect, lineindex, 1)
        self.fitoffset = self.createSpinbox(-1000,1100, start_value=-1, interval=1, connect=self.plot)
        self.layout.addWidget(self.fitoffset, lineindex,2)
        self.fitInfoLable = self.createLabel()
        self.layout.addWidget(self.fitInfoLable, lineindex, 4)
        
        self.invertFit=self.createCheckbox('invert Fit', connect=self.plot)
        self.layout.addWidget(self.invertFit, lineindex, 3)
        lineindex += 1

        
        
        self.outerLayout.addWidget(self.plotWidget1)
        self.outerLayout.addWidget(self.plotWidget2)
        self.plotWidget2.hide()
        self.outerLayout.addLayout(self.layout)
        self.setWindowTitle("Scan Results")


        Elements.addButton(['timescan', 'acquire_{}'.format(self.board_id)], [
                                                self.updateCalib,
                                                self.correlationTest,
                                                self.useCalib,
                                                self.showError,
                                                self.showADC,
                                                self.fitSin
                                             ])

        # Initially show the plot
        self.line_plot()  

       

        self.board_config.observe(self, self.setADCdelays, 'chip_delay')
        self.board_config.observe(self, self.setADCdelays, 'delay_330_th')
        self.board_config.observe(self, self.setADCdelays, 'delay_25_th')
        self.board_config.observe(self, self.setADCdelays, 'delay_25_th_2')


    def setADCdelays(self, value):
        #print('set ADC Delays')
        self.delays = np.zeros(self.adc_number)
        id = 'None'
        if self.useCalib.isChecked():
            id = 'current'
        for i in range(self.adc_number):
            value = theCalibration.calibrateX(i, self.board_config.get('delay_330_th'), self.board_config.get('delay_25_th'), self.board_config.get('chip_delay')[i], self.board_config.get("delay_25_th_2"), id=id)
            self.delays[i] = value

        self.plotADCPositions()
        



    def setPlotParams(self, c_min, c_max, c25_min, c25_max, f_min, f_max, step4):
        self.xrange = (c_min, c_max)
        self.zrange = (c25_min, c25_max)
        self.yrange = (f_min, f_max)
        self.step4 = step4
        
    @pyqtSlot(object)
    def new_data(self, timeScan):
        #while self.block:
        #    pass

        self.block = True
        self.timeScan = timeScan
        if self.timeScan.multibunch:
            self.multiBunchSelector.show()
            self.multiBunchSelectorLabel.show()
        else:
            self.multiBunchSelector.hide()
            self.multiBunchSelectorLabel.hide()
        self.plot(True)
        self.block = False

    def changePlotType(self, type):
        self.type=type
        if type == 0:
            self.plotWidget2.hide()
            self.plotWidget1.show()
            self.plot()
        else:
            self.plotWidget1.hide()
            self.plotWidget2.show()
            self.plot()

    def onUpdateCalibration(self):
        if self.timeScan is not None:
            calibrationUpdater = UpdateCalibrationWidget.addUpdateCalibrationWidget()
            calibrationUpdater.openWith(self.timeScan, bunch=self.multiBunchSelector.value())

    def onCorrelation(self):
        if self.timeScan is not None:
            w = CorrelationWidget.addCorrelationWidget()
            w.updateTimeScan(self.timeScan)

    ##################################################################################
    def line_plot_axis_strings(self, values, scale, spacing):
        """
        Plot to format the strings for the line plot
        This is used to override the default tickStrings method of pyqtgraph.AxisItem
        :param values: See pyqtgraph.AxisItem.tickStrings
        :param scale: See pyqtgraph.AxisItem.tickStrings
        :param spacing: See pyqtgraph.AxisItem.tickStrings
        :return: See pyqtgraph.AxisItem.tickStrings
        """
        #print(values)
        mult = 1
        if self.step4:
            mult = 4
        coarses = [self.xrange[0] + i//(self.x) for i in values]
        c25     = [self.zrange[0] + (i//(self.y))%(self.z) for i in values]
        fines   = [self.yrange[0] + i%(self.y) for i in values]
        
        if board.get_board_config(self.board_id).is_KAPTURE2():
            return [str(int(c))+"\n"+str(int(c25*mult))+"\n"+str(int(f)) for c, c25, f in zip(coarses, c25, fines)]
        else:
            return [str(int(c))+"\n"+str(int(f)) for c, f in zip(coarses, fines)]

    ##################################################################################
    def spacing(self, minVal, maxVal, size):
        """
        Calculate spacing between ticks
        This is used to override the default tickSpacing method of pyqtgraph.AxisItem
        :param minVal: See pyqtgraph.AxisItem.tickSpacing
        :param maxVal: See pyqtgraph.AxisItem.tickSpacing
        :param size: See pyqtgraph.AxisItem.tickSpacing
        :return: See pyqtgraph.AxisItem.tickSpacing
        """
        if maxVal - minVal < 10.:
            return [(1, 0),]
        else:
            return [(round((maxVal-minVal)/10.), 0),]

    ##################################################################################
    def y_axis_strings(self, values, scale, spacing):
        """
        Sets the strings for the y axis
        :param values:
        :param scale:
        :param spacing:
        :return:
        """
        if np.mean(values) > 3:
            return [str(int(v)) for v in values]
        return [str(v) for v in values]

    ##################################################################################
    def line_plot(self):
        """
        Initialise the Line Plot
        :return: -
        """
        self.plot_type = "line"
        for item in self.adc_plot_widgets:
            item.enableAutoRange()
            item.plotItem.setLabel("left", "Intensity")
            item.plotItem.setLabel("bottom", "Coarse over Fine")
            bax = item.plotItem.getAxis('bottom')
            lax = item.plotItem.getAxis('left')

            bax.setTickSpacing()
            bax.tickSpacing = self.spacing
            bax.tickStrings = self.line_plot_axis_strings
            lax.setTickSpacing()


        def setAxis(axis, lable, unit="", setSpace=False):
            labelStyle = {'color': '#000', 'font-size': '14pt'}
            axis.setLabel(lable, units=unit, **labelStyle)
                
            font=QtGui.QFont()
            font.setPixelSize(15)
            axis.tickFont = font
            axis.setStyle(tickTextOffset = 20)
            if unit != "":
                axis.enableAutoSIPrefix()
            if setSpace:
                axis.setWidth(int(80))

        setAxis(self.all_plot_widget.plotItem.getAxis('bottom'), 't', 's')
        setAxis(self.all_plot_widget.plotItem.getAxis('left'), 'ADC counts', '', True)


    ##################################################################################
    def plot(self, nonblock=False):
        """
        Plot Data
        :return: -
        """
        """
        if self.block:
            if nonblock == False:
                return 
        else:
            self.block = True
        """
        try:
            #print('plot')
            if self.timeScan is None:
                return

            if self.type == 0:
                self.z = 1
                if board.get_board_config(self.board_id).is_KAPTURE2():
                    self.z = (self.zrange[1]-self.zrange[0]+1)
                    if self.step4:
                        self.z = self.z//4+1

                self.y = (self.yrange[1]-self.yrange[0]+1)
                self.x = self.z*self.y

                for i, item in enumerate(self.adc_plot_widgets):
                    item.plotItem.clear()
                    #item.plotItem.plot(np.array(self.timeScan.scanData[i]).T[0])
                    scanx, scany, scane = self.timeScan.getScanOverDelay(i, bunch=self.multiBunchSelector.value())
                    item.plotItem.plot(scany)

            else:    
                self.all_plot_widget.plotItem.clear()
                #if self.useCalib.isChecked():
                #    self.calibrationFile = h5py.File(config.config_path('calibration.hdf'), 'r')
                dt = []
                self.scanyAll = []
                text = ""
                for i in range(self.adc_number):
                    if self.adccb[i].isChecked():
                        scanx, scany, scane = self.timeScan.getScanOverTime(i, calibrateX=self.useCalib.isChecked(), calibrateY=self.useCalib.isChecked(), bunch=self.multiBunchSelector.value())
                        #scanx, scany = self.calibrate(self.data[i], i)
                        self.scanyAll.append(scany)
                        self.all_plot_widget.plotItem.plot(scanx, scany, pen=None, symbolPen=pg.mkPen(colours[i]), symbolSize=2, pxMode=True, symbolBrush=pg.mkBrush(colours[i]), downsample=200)
                        
                        if self.showError.isChecked():
                            self.all_plot_widget.plotItem.addItem(pg.ErrorBarItem(x=scanx, y=scany, height=scane, pen=pg.mkPen(coloursTrans[i], width=2), autoDownsample=True, clipToView=True ))
                        
                        if self.fitSin.isChecked():
                            # display fit
                            try:
                                type = self.fitSelect.currentIndex()
                                popt, perr, fitFun, pcov, label, x = self.doFit(scanx, scany, type)
                                
                                fitx = np.linspace(np.min(scanx), np.max(scanx), 100000)
                                fity = fitFun(fitx, *popt)
                                self.plot_widget.plotItem.plot(fitx, fity, pen=pg.mkPen(colours[i]),  downsample=200)
                  
                                if type == SINUS:
                                    dt.append(popt[3]/(2*np.pi)/popt[1]*1e12)
                                elif type in [GAUSS, EGAUSS, SKEW, EGAUSSB, GAUSSB]:
                                    try:
                                        dt.append(fitx[np.where(fity==np.min(fity))][0]*1e12)
                                    except:
                                        pass
                            except:
                                pass


                if self.fitSin.isChecked():
                    if type in [SINUS, GAUSS, EGAUSS, SKEW, EGAUSSB, GAUSSB]:
                        text += 'delta T '
                        for i in range(len(dt)):
                            text +=  '| {:.3f}ps '.format(dt[0]-dt[i])
                    

                    self.fitInfoLable.setText(text)

                self.plotADCPositions()
                #if self.useCalib.isChecked():
                #    self.calibrationFile.close()
            # ---[ Show this window and set focus to it ]------
            self.parent().show()
            self.show()
        except:
            pass
        self.block = False
        #self.setFocus()

    def plotADCPositions(self):
        if self.type != 1:
            return
        if not self.showADC.isChecked():
            return

        #print('plot delays')
        if self.scanyAll == []:
            self.scanyAll.extend([0,1])
        i=1
        font = QtGui.QFont()
        font.setPixelSize(14)
        if self.plotList != []:
            for item in self.plotList:
                self.all_plot_widget.plotItem.removeItem(item)
            self.plotList = []
        
        for x in self.delays:
            if self.adccb[i-1].isChecked():
                self.plotList.append(self.all_plot_widget.plotItem.plot([x,x], [np.min(self.scanyAll)-10, np.max(self.scanyAll)+20], pen=pg.mkPen(colours[0]), downsample=200))
                text = pg.TextItem(str(i), anchor=(0.5,1), color=colours[i-1])
                text.setFont(font)
                text.setPos(x,np.max(self.scanyAll)+24)
                self.all_plot_widget.addItem(text)
                self.plotList.append(text)
            i += 1

    def doFit(self, x,y, type, p0=None):
        def linear(x,a,b):
            return a + b*x

        def gauss(x, sigma, mu, A, b):
            return A*np.exp(-0.5*((x-mu)/sigma)**2) + b

        def expgauss(x, s, m, a ,l, b):
            return a*l/2*np.exp(l/2*(2*m + l*s**2 - 2*x)) * erfc((m +l*s**2 -x)/(np.sqrt(2)*s)) + b

        def expgauss2(x, s, m, a, t, b):
            return a*s/t*np.sqrt(np.pi/2) * np.exp(0.5 * (s/t)**2 - (x-m)/t) * erfc(1/np.sqrt(2)*(s/t - (x-m)/s)) + b

        def sinus(x,a,b,c,d):
            return a*np.sin(b*x*(2*np.pi)+d)+c

        def skewnorm(x, s, m, a, l, b):
            def p(x):
                return 1/np.sqrt(2*np.pi) * np.exp(- x**2/2)
            def g(x):
                return 0.5*(1+erf(x/np.sqrt(2)))

            return a*2/s*p((x-m)/s)*g(l*(x-m)/s) +b
        
        if self.invertFit.isChecked():
            startx = x[np.where(y==np.min(y))]
        else:    
            startx = x[np.where(y==np.max(y))]

        y = y[np.argsort(x)]
        x = x[np.argsort(x)]
        if type == LINEAR:
            fitFun = linear
            label = ['a' , 'b']
        elif type == GAUSS:
            fitFun = gauss
            p0 = (90e-12, startx, 500, 2000)
            label = ['sigma', '  mu ', '  A  ', '  b  ']
            if self.invertFit.isChecked():
                p0 = (90e-12, startx, -500, 2000)
            end = np.argmax(y)+self.fitoffset.value()
            x = x[:end]
            y = y[:end]
        elif type == EGAUSS:
            fitFun = expgauss
            p0 = (23e-12, startx, 7e-8, 0.02e12, 2040)
            if self.invertFit.isChecked():
                p0 = (23e-12, startx, -7e-8, 0.02e12, 2040)
            label = ['  s  ', '  m  ', '  a  ', '  l  ', '  b  ']
        elif type == EGAUSSB:
            fitFun = expgauss2
            p0 = (22e-12, startx, 1200, 70e-12, 2040)
            if self.invertFit.isChecked():
                p0 = (22e-12, startx, -1200, 70e-12, 2040)
            end = self.fitoffset.value()
            x = x[:end]
            y = y[:end]
            label = ['  s  ', '  m  ', '  a  ', '  l  ', '  b  ']
        elif type == SKEW:
            fitFun = skewnorm
            end = self.fitoffset.value()
            x = x[:end]
            y = y[:end]
            p0 = (80e-12, startx, 6e-8, 3, 2040) # 220e-12
            label = ['  s  ', '  m  ', '  a  ', '  l  ', '  b  ']
            if self.invertFit.isChecked():
                p0 = (80e-12, startx, -6e-8, 3, 2040) # 220e-12
        elif type == SINUS:
            fitFun = sinus
            if p0 == None:
                p0 = (-700, 500e6, 2048, 0.5)
            label = ['  A  ', '  f  ', '  b  ', '  phi']
        else:
            print('Fit type unknown ', type)
            return 0,0, lambda x: x , 0
        if p0 is not None:
            popt, pcov = curve_fit(fitFun, x, y, p0=p0)
        else:
            popt, pcov = curve_fit(fitFun, x, y)
        #popt = p0
        perr = np.sqrt(np.absolute(np.diag(pcov)))

        #print(popt)
        return popt, perr, fitFun, pcov, label, x

    ##################################################################################
    def closeEvent(self, event):
        """
        Event handler for closing this window
        """
        self.board_config.unobserve(self, 'chip_delay')
        self.board_config.unobserve(self, 'delay_330_th')
        self.board_config.unobserve(self, 'delay_25_th')
        self.board_config.unobserve(self, 'delay_25_th_2')


        global __timing_plot_widget_id__
        __timing_plot_widget_id__ = {}
        global __timing_plot_widget__
        __timing_plot_widget__ = None
    
        del self.par.widgets[self.id]





#        d8888          888                                    888    d8b
#       d88888          888                                    888    Y8P
#      d88P888          888                                    888
#     d88P 888 888  888 888888  .d88b.  88888b.d88b.   8888b.  888888 888  .d88b.  88888b.
#    d88P  888 888  888 888    d88""88b 888 "888 "88b     "88b 888    888 d88""88b 888 "88b
#   d88P   888 888  888 888    888  888 888  888  888 .d888888 888    888 888  888 888  888
#  d8888888888 Y88b 888 Y88b.  Y88..88P 888  888  888 888  888 Y88b.  888 Y88..88P 888  888
# d88P     888  "Y88888  "Y888  "Y88P"  888  888  888 "Y888888  "Y888 888  "Y88P"  888  888
#
#
#

class AutomationThread(QtCore.QObject):
    '''Automation Thread class'''
    updateSignal = QtCore.pyqtSignal(int)
    stopSignal = QtCore.pyqtSignal()
    startScan  = QtCore.pyqtSignal()
    poststartScan  = QtCore.pyqtSignal()
    running = False

    def __init__(self, start, stop, step, board_id):
        super(AutomationThread, self).__init__()
        self.start = start
        self.stop  = stop
        self.step  = step
        self.board_id = board_id


    def scan(self):
        self.running = True
        for v in range(self.start, self.stop+self.step, self.step):
            self.updateSignal.emit(v)
            sleep(0.5)
            print('startScan')
            self.startScan.emit()

            while not board.get_board_status(self.board_id).time_scan:
                #wait for Scan to start
                sleep(0.05)
                if not self.running:
                    self.stopSignal.emit()
                    return
            
            self.poststartScan.emit()   
            
            while board.get_board_status(self.board_id).time_scan:
                #wait for Scan to stop
                sleep(0.05)
                if not self.running:
                    self.stopSignal.emit()
                    return
            
            
            if not self.running:
                self.stopSignal.emit()
                return

        self.running = False
        self.stopSignal.emit()

from ..extensions import deltaPower
class Automation(kcgw.KCGWidgets):
    def __init__(self, layout, startScan, info, abortScan):
        super(Automation, self).__init__()
        self.layout = layout
        self.startScan = startScan
        self.abortScan = abortScan
        self.info = info
        self.outdir = os.path.join(storage.storage.save_location, storage.storage.subdirname, 'CalibrationScan')
        self.running = False
        self.power = None #deltaPower.DeltaPower("192.1.1.1")
        lineindex = 0
        self.layout.addWidget(self.createLabel("Automated Voltage Scan"), lineindex, 0,1,3)
        lineindex +=1
        self.layout.addWidget(self.createLabel("Power Supply IP"), lineindex, 0)
        self.input = self.createInput('10.1.0.101')
        self.layout.addWidget(self.input, lineindex, 1,1,2)
        self.buttonConnect = self.createButton('connect', connect=self.connect)
        self.layout.addWidget(self.buttonConnect, lineindex, 3)
        lineindex += 1

        self.layout.addWidget(self.createLabel("Spannung (mV)"), lineindex, 0)
        self.vin  = self.createSpinbox(0,1000, start_value=0)
        self.layout.addWidget(self.vin, lineindex, 1)
        self.buttonSetV = self.createButton('set', connect=lambda: self.setV(self.vin.value()))
        self.layout.addWidget(self.buttonSetV, lineindex, 2)
        lineindex += 1

        self.layout.addWidget(self.createLabel("Start"), lineindex, 1)
        self.layout.addWidget(self.createLabel("Stop"), lineindex, 2)
        self.layout.addWidget(self.createLabel("Schritt"), lineindex, 3)
        lineindex += 1

        self.layout.addWidget(self.createLabel("Spannung (mV)"), lineindex, 0)
        self.vmin  = self.createSpinbox(0,1000, start_value=0)
        self.vmax  = self.createSpinbox(0,1000, start_value=800)
        self.vstep = self.createSpinbox(0,500, start_value=20)
        self.layout.addWidget(self.vmin, lineindex, 1)
        self.layout.addWidget(self.vmax, lineindex, 2)
        self.layout.addWidget(self.vstep, lineindex, 3)
        lineindex += 1
        self.button = self.createButton('start', connect=self.start)
        self.layout.addWidget(self.button, lineindex, 0)
        Elements.addButton(['timescan','acquire_0', 'automation'], [self.button, self.buttonConnect, self.buttonSetV])
        Elements.addButton(['automation'], [self.input, self.vin, self.vmin, self.vmax, self.vstep])
        
        lineindex += 1
        self.progressbar = QtGui.QProgressBar()
        self.layout.addWidget(self.progressbar, lineindex,0,1,4)
        self.progressbar.setRange(0,1000)
        lineindex += 1

        self.tst = None
        
    def connect(self):
        try:
            self.power = deltaPower.DeltaPower(str(self.input.text()))
        except Exception as e:
            logging.error('Not connected to Powersupply - ' + str(e))
            self.power = None 


    def setV(self, value):
        if self.power is not None:
            self.power.write_Voltage(value/1000.0)
        else:
            logging.error('no Powersupply')
            

    def start(self):
        self.thread = storage.get_board_specific_storage(available_boards[0]).setdefault("AutoScanThread", storage.ThreadStorage())

        if self.thread.running:
            logging.info("Time scan already running")
            self.tst.running = False
            
            return
        start = self.vmin.value()
        stop  = self.vmax.value()
        step  = self.vstep.value()

        fileinfo = os.path.join(self.outdir, 'scan.info')
        f = open(fileinfo, 'a')
        f.write('##########################\n')
        f.write('#Automated Voltage Scan\n')
        f.write('#Range: {:4d} - {:4d}\n'.format(start,stop))
        f.write('#Step: {:4d}\n'.format(step))
        f.write('\n')
        f.close()


        self.tst = AutomationThread(start, stop, step, available_boards[0])
        self.thread.register(self.tst)
        self.thread.connect('updateSignal', self.update)
        self.thread.connect('stopSignal', self.stop)
        self.thread.connect('startScan', self.startScan)
        self.thread.connect('poststartScan', self.reactivateButton)


        self.progressbar.setRange(start, stop+step)

        self.thread.start('scan')
        self.scaning = True
        self.button.setText('stop')
        Elements.setEnabled('automation', False, exclude=[self.button])
        Elements.setEnabled('timescan', False)
            

    def stop(self):
        if board.get_board_status(available_boards[0]).time_scan:
            self.abortScan()
            while board.get_board_status(available_boards[0]).time_scan:
                sleep(0.05)

        self.thread.stop()
        self.scaning = False
        print('Automation Stop')
        self.progressbar.setValue(self.vmax.value()+self.vstep.value())
        self.button.setText('start')
        Elements.setEnabled('automation', True)
        Elements.setEnabled('timescan', True)

        fileinfo = os.path.join(self.outdir, 'scan.info')
        f = open(fileinfo, 'a')
        f.write('#End\n')
        f.write('##########################\n')
        f.write('\n')
        f.close()
        pass


    def update(self, value):
        self.setV(value)
        self.progressbar.setValue(value)
        self.info.setText("Auto: {:4d} mV".format(value))
        print('Automation update')
        pass

    def reactivateButton(self):
        self.button.setEnabled(True)





# 88888888888 d8b                         .d8888b.                                 888       888 d8b      888                   888
#     888     Y8P                        d88P  Y88b                                888   o   888 Y8P      888                   888
#     888                                Y88b.                                     888  d8b  888          888                   888
#     888     888 88888b.d88b.   .d88b.   "Y888b.    .d8888b  8888b.  88888b.      888 d888b 888 888  .d88888  .d88b.   .d88b.  888888
#     888     888 888 "888 "88b d8P  Y8b     "Y88b. d88P"        "88b 888 "88b     888d88888b888 888 d88" 888 d88P"88b d8P  Y8b 888
#     888     888 888  888  888 88888888       "888 888      .d888888 888  888     88888P Y88888 888 888  888 888  888 88888888 888
#     888     888 888  888  888 Y8b.     Y88b  d88P Y88b.    888  888 888  888     8888P   Y8888 888 Y88b 888 Y88b 888 Y8b.     Y88b.
#     888     888 888  888  888  "Y8888   "Y8888P"   "Y8888P "Y888888 888  888     888P     Y888 888  "Y88888  "Y88888  "Y8888   "Y888
#                                                                                                                  888
#                                                                                                             Y8b d88P
#                                                                                                              "Y88P"     



class TimeScanWidget(kcgw.KCGWidgets):
    def __init__(self, unique_id, parent):
        super(TimeScanWidget, self).__init__()

        self.scaning = False
        self.id = unique_id
        self.par = parent
        self.scanNumber = 0

        #self.layout = QtGui.QHBoxLayout()
        self.board_id = available_boards[0]
        self.board_config =  board.get_board_config(self.board_id)
        
        self.layout = QtGui.QGridLayout()
        self.outerLayout = QtGui.QVBoxLayout()
        self.outerLayout.addLayout(self.layout)
        self.setLayout(self.outerLayout)
        lineindex = 0
        

        if self.board_config.is_KAPTURE2():
            #KAPTURE 2#########################################
            self.layout.addWidget(self.createLabel("330 ps Delay"), lineindex, 0)
            self.delaythmin = self.createSpinbox(0,6, start_value=0)
            self.delaythmax = self.createSpinbox(0,12, start_value=6)
            self.layout.addWidget(self.delaythmin, lineindex, 1)
            self.layout.addWidget(self.delaythmax, lineindex, 2)
            lineindex += 1

            self.layout.addWidget(self.createLabel("25 ps Delay"), lineindex, 0)
            self.delay25min = self.createSpinbox(0,23, start_value=0)
            self.delay25max = self.createSpinbox(0,23, start_value=12)
            self.layout.addWidget(self.delay25min, lineindex, 1)
            self.layout.addWidget(self.delay25max, lineindex, 2)
            lineindex += 1

            self.stepSwitcher = self.createSwitch(startRight=True)
            self.layout.addWidget(self.createLabel("25ps Step 1"), lineindex, 0)
            self.layout.addWidget(self.stepSwitcher, lineindex, 1)
            self.layout.addWidget(self.createLabel("25ps Step 4"), lineindex, 2)
            lineindex += 1

            Elements.addButton(['timescan'], [
                                                self.delaythmin,
                                                self.delaythmax,
                                                self.delay25max,
                                                self.delay25min,
                                                self.stepSwitcher
                                             ])
            

        else:
            #KAPTURE 1#########################################
            self.layout.addWidget(self.createLabel("ADC to T/H Delay"), lineindex, 0)
            self.delayADCTH = self.createSpinbox(0,15, start_value=self.board_config.get('th_to_adc_cycles'), connect=lambda x: self.board_config.update('th_to_adc_cycles', x))
            self.layout.addWidget(self.delayADCTH, lineindex, 1)
            lineindex += 1

            line = QtGui.QFrame()
            line.setFrameStyle(QtGui.QFrame.HLine)
            self.layout.addWidget(line, lineindex, 0, 1, 10)
            lineindex += 1

            self.layout.addWidget(self.createLabel("T/H Delay"), lineindex, 0)
            self.delaythmin = self.createSpinbox(0,15, start_value=0)
            self.delaythmax = self.createSpinbox(0,15, start_value=15)
            self.layout.addWidget(self.delaythmin, lineindex, 1)
            self.layout.addWidget(self.delaythmax, lineindex, 2)
            lineindex += 1
            Elements.addButton(['timescan'], [
                                                self.delaythmin,
                                                self.delaythmax,
                                                self.delayADCTH
                                             ])

        self.layout.addWidget(self.createLabel("Fine Delay"), lineindex, 0)
        self.delayfinemin = self.createSpinbox(0,31, start_value=0)
        self.delayfinemax = self.createSpinbox(0,31, start_value=31)
        self.layout.addWidget(self.delayfinemin, lineindex, 1)
        self.layout.addWidget(self.delayfinemax, lineindex, 2)
        lineindex += 1

        self.layout.addWidget(self.createLabel("Number of turns"), lineindex, 0)
        self.numofturns = self.createSpinbox(0,1e6, start_value=1000)
        self.layout.addWidget(self.numofturns, lineindex, 1)
        lineindex += 1

        self.layout.addWidget(self.createLabel("Turns to skip"), lineindex, 0)
        self.numofturnsSkip = self.createSpinbox(0,1e6, start_value=0)
        self.layout.addWidget(self.numofturnsSkip, lineindex, 1)
        lineindex += 1
        
        self.layout.addWidget(self.createLabel("Identifyer"), lineindex, 0)
        self.input = self.createInput()
        self.layout.addWidget(self.input, lineindex, 1)
        lineindex += 1


        self.comboBox = QtGui.QComboBox(self)
        self.comboBox.addItem("Mean over Everything", MODE_ALL) #0
        self.comboBox.addItem("Use Threshold", MODE_THREASHOLD) #1
        #self.comboBox.addItem("Use Bucket Detection - processed after scan", MODE_AUTOBUCKET) #2
        #self.comboBox.addItem("Use Bucket Detection and Threshold for live", MODE_AUTOBUCKET_TMP_THRESHOLD) #3
        self.comboBox.addItem("Use Bucket", MODE_BUCKET) #4
        #self.comboBox.addItem("Use TDS Mode", MOD) #5
        self.comboBox.addItem("Use All Buckets", MODE_ALL_BUCKETS) #6
        self.layout.addWidget(self.comboBox, lineindex, 0,1,3)
        lineindex += 1

        self.layout.addWidget(self.createLabel("Threshold / Bucket"), lineindex, 0)
        self.threshold = self.createSpinbox(-2000,2000, start_value=15)
        self.layout.addWidget(self.threshold, lineindex, 1)
        lineindex += 1
        Elements.addButton(['timescan'], [
                                            self.delayfinemin,
                                            self.delayfinemax,
                                            self.numofturns,
                                            self.numofturnsSkip,
                                            self.input,
                                            self.comboBox,
                                            self.threshold
                                         ])

        self.layout.addWidget(self.createLabel("Fast Mode"), lineindex, 0)
        self.fastModeSelector = self.createSwitch('Fast Mode', connect=self.setFastMode)
        self.fastModeSelector.setState(False)
        self.layout.addWidget(self.fastModeSelector, lineindex, 1)
        lineindex +=1
        if self.board_config.is_KAPTURE2():
            self.layout.addWidget(self.createLabel("Calibration Scan"), lineindex, 0)
            self.calibSelector = self.createSwitch('Calibration Scan')
            self.calibSelector.setState(False)
            self.layout.addWidget(self.calibSelector, lineindex, 1)
            lineindex +=1

        self.button = self.createButton('start', connect=self.startScan)
        self.layout.addWidget(self.button, lineindex, 1,1,2)
        
        Elements.addButton(['timescan','acquire_0'], self.button)
        self.saverawCB = self.createCheckbox('save Raw', checked=False)
        self.layout.addWidget(self.saverawCB, lineindex, 0)
        lineindex += 1

        self.labelBucket = self.createLabel("")
        self.layout.addWidget(self.labelBucket, lineindex, 0,1,3)
        lineindex += 1

        self.progressbar = QtGui.QProgressBar()
        self.layout.addWidget(self.progressbar, lineindex,0,1,3)
        self.progressbar.setRange(0,1000)
        lineindex += 1

        line = QtGui.QFrame()
        line.setFrameStyle(QtGui.QFrame.HLine)
        self.layout.addWidget(line, lineindex, 0, 1, 3)
        lineindex += 1
        

        ###########################################################
        ### Automation
        #self.automationLayout = QtGui.QGridLayout()
        #self.outerLayout.addLayout(self.automationLayout)
        #self.auto = Automation(self.automationLayout, self.startScan, self.input, self.abort)  
        ###########################################################

        self.outerLayout.addStretch(1)
        self.adjustSize()
        #self.layout.addStretch(1)
        self.setWindowTitle("Time Scan Widget")


        self.openPlotWidget()

        self.tst = None

    def setFastMode(self):
        if self.fastModeSelector.state:
            self.delaythmin.setValue(0)
            self.delaythmax.setValue(6)
            self.delay25min.setValue(0)
            self.delay25max.setValue(12)
            self.delayfinemax.setValue(0)
            self.delayfinemin.setValue(0)
            self.threshold.setValue(15)
            self.comboBox.setCurrentIndex(1)
            self.stepSwitcher.setState(False)
            self.calibSelector.setState(False)
            self.stepSwitcher.setEnabled(False)
            self.calibSelector.setEnabled(False)
            self.delayfinemin.setEnabled(False)
            self.delayfinemax.setEnabled(False)
            self.saverawCB.setChecked(False)
        else:
            self.delaythmin.setValue(0)
            self.delaythmax.setValue(6)
            self.delay25min.setValue(0)
            self.delay25max.setValue(12)
            self.delayfinemax.setValue(32)
            self.delayfinemin.setValue(0)
            self.threshold.setValue(3)
            self.comboBox.setCurrentIndex(3)
            self.stepSwitcher.setState(True)
            self.stepSwitcher.setEnabled(True)
            self.calibSelector.setEnabled(True)
            self.delayfinemin.setEnabled(True)
            self.delayfinemax.setEnabled(True)
            #self.saverawCB.setChecked(True)

    def openPlotWidget(self):
        global __timing_plot_widget_id__
        global __timing_plot_widget__
        if __timing_plot_widget__ == None:
            nid = kcgw.idg.genid()
            __timing_plot_widget_id__[self.board_id] = nid
            self.plotWidget = ScanPlotWidget(nid, self.board_id, global_objects.get_global('area'))
            __timing_plot_widget__ = self.plotWidget
            global_objects.get_global('area').newWidget(self.plotWidget, "Timing result", nid, widget_type=5)
            


    def startScan(self):
        if not self.scaning:
            Elements.setEnabled('acquire_{}'.format(self.board_id), False, exclude=[self.button])
            Elements.setEnabled("acquireTrigger_{}".format(self.board_id), False)

            if __timing_plot_widget__ == None:
                __timing_plot_widget__.showError.setChecked(False)
                __timing_plot_widget__.useCalib.setChecked(False)
                __timing_plot_widget__.fitSin.setChecked(False)
                __timing_plot_widget__.showADC.setChecked(False)

            outdir = os.path.join(storage.storage.save_location, storage.storage.subdirname, 'TimeScan')
            if not os.path.isdir(outdir):
                bif._bif_update_working_dir()
                os.makedirs(outdir)

            self.scanNumber = 0
            filelist = np.sort(os.listdir(outdir))
            for file in filelist:
                if '.scan' in file:
                    self.scanNumber += 1
            

            saveraw = self.saverawCB.isChecked()
            #print(saveraw)
            
            self.board_config.update('turns_observe', self.numofturns.value())
            self.board_config.update('turns_skip', self.numofturnsSkip.value())

            if self.board_config.is_KAPTURE2():
                self.start(self.delaythmin.value(), self.delaythmax.value(), self.delayfinemin.value(), self.delayfinemax.value(), 
                        self.input.text(), outdir, self.threshold.value(), saveraw, 
                        c25_min=self.delay25min.value(), c25_max=self.delay25max.value(), step4=self.stepSwitcher.state, 
                        meanMode =self.comboBox.itemData(self.comboBox.currentIndex()), fastMode=self.fastModeSelector.state, calibScan=self.calibSelector.state)

            else:
                self.start(self.delaythmin.value(), self.delaythmax.value(), self.delayfinemin.value(), self.delayfinemax.value(), 
                        self.input.text(), outdir, self.threshold.value(), saveraw, meanMode =self.comboBox.itemData(self.comboBox.currentIndex()))

        else:
            self.abort()
            #self.stop()



    def start(self, c_min, c_max, f_min, f_max, ident, outdir, threshold, saveraw, c25_min=-1, c25_max=-1, step4=False, meanMode=MODE_ALL, fastMode=False, calibScan=False):
        try:
            self.progressbar.setValue(0)
            board.get_board_status(self.board_id).time_scan = True
            self.openPlotWidget()
            self.plotWidget.setPlotParams(c_min, c_max, c25_min, c25_max, f_min, f_max, step4)
            self.thread = storage.get_board_specific_storage(self.board_id).setdefault("TimeScanThread", storage.ThreadStorage())

            if self.thread.running:
                logging.info("Time scan already running")
                return

            self.tst = ScanThread(c_min, c_max, f_min, f_max, available_boards[0], self.scanNumber, ident, outdir, threshold, saveraw, c25_min, c25_max, step4, meanMode, fastMode, calibScan)
            self.thread.register(self.tst)
            self.thread.connect('pbarSignal', self.update)
            self.thread.connect('stopSignal', self.stop)
            self.thread.connect('plotSignal', self.plot)
            self.thread.start('scan')
            self.scaning = True
            self.button.setText('stop')

        except Exception as e:
            logging.error('Start Calibrationscan: ' + str(e))

    def abort(self):
        if self.tst is not None:
            self.tst.stop = True
        #board.get_board_status(self.board_id).time_scan = False
                            

    def stop(self, timeScan, file):
        self.thread.stop()
        self.openPlotWidget()
        self.plotWidget.new_data(timeScan)
        #self.labelBucket.setText('Signal in Buckets: {}'.format(self.tst.buckets))
        self.scaning = False
        board.get_board_status(self.board_id).time_scan = False
        self.scanNumber +=1
        self.button.setText('start')
        self.progressbar.setValue(1000)
        #self.plotWidget.giveFilename(file)
        Elements.setEnabled('acquire_{}'.format(self.board_id), True)
        Elements.setEnabled("acquireTrigger_{}".format(self.board_id), True)

        print('fine')

    def update(self, timescan, prozent):
        #   print(c_step, f_step, data, prozent)
        #print('update')
        self.openPlotWidget()
        self.plotWidget.new_data(timescan)
        self.progressbar.setValue(prozent*1000)

    def plot(self, data):
        #print('plot', len(data_raw))
        #bif._bif_read_and_update_data_from_string(self.board_id, data_raw)
        if live_plot_windows.hasWindows(self.board_id):
            for plotwin in live_plot_windows.getWindows(self.board_id):
                plotwin.plot_live(data=data)
                QtGui.qApp.processEvents()


    def closeEvent(self, event):
        self.abort()
        global __widget_id__
        __widget_id__ = None
        global updateData
        updateData = None

        del self.par.widgets[self.id]


def addCalibrationWidget():
    global __widget_id__
    if __widget_id__:
        global_objects.get_global('area').widgets[__widget_id__].setFocus()
    else:
        nid = kcgw.idg.genid()
        __widget_id__ = nid
        w = TimeScanWidget(nid, global_objects.get_global('area'))
        global_objects.get_global('area').newWidget(w, "Time Scan Widget", nid, widget_type=4, minSize=True)

kcgw.register_widget(QtGui.QIcon(config.icon_path("timescan.png")), "Time Scan Widget", addCalibrationWidget, "Ctrl+Shift+T")