analysisview.py 29.7 KB
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# -*- coding: utf-8 -*-
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#!/usr/bin/env python3
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"""
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
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import numpy as np
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import sys

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from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar

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from .analysiswidgets import ExpExcelDialog
from .analysisplots import TypeHistogramView, SpectraPlot
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from .loadresults import LoadTrueMatchResults
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from .particleeditor import ParticleEditor
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from .database import DataBaseWindow
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from .colorlegend import ColorHandler

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try:
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    from .sqlexport import SQLExport
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    sqlEnabled = True
except:
    sqlEnabled = False
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class ParticleAnalysis(QtWidgets.QMainWindow):
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    def __init__(self, dataset, parent=None):
        super(ParticleAnalysis, self).__init__(parent)
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        self.setGeometry(100, 100, 1680, 1050)
        self.setWindowTitle('Results of polymer analysis')
        self.layout = QtWidgets.QHBoxLayout()
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        self.widget = QtWidgets.QWidget()
        self.widget.setLayout(self.layout)
        self.setCentralWidget(self.widget)
        
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        self.parent = parent
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        self.dataset = dataset
        self.particleContainer = dataset.particleContainer
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        self.editor = ParticleEditor(self.particleContainer, self)
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        self.colorHandler = ColorHandler()
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#        self.additivePlot = None
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        self.importWindow = None
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        self.polymerCheckBoxes = []
        self.lastSelectedCheckBoxNames = []
        
        self.currentParticleIndex = 0
        self.currentSpectrumIndex = 0
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#        self.lastSpectrumInFocus = None
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        self.typeHistogramPlot = TypeHistogramView(self)
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#        self.typeHistogramPlot.indexClicked.connect(self.getAdditivePlot)
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        self.sizeHistogramCanvas = FigureCanvas(Figure())
       
        sizeHistGroup = QtWidgets.QGroupBox()
        sizeHistLayout = QtWidgets.QHBoxLayout()
        self.sizeHist_ax = self.sizeHistogramCanvas.figure.subplots()
        self.sizeHist_ax.axis('off')
        self.sizeHistogramCanvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.995)
        histNavigation = NavigationToolbar(self.sizeHistogramCanvas, self)
        histNavigation.setOrientation(QtCore.Qt.Vertical)
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        histNavigation.setFixedWidth(50)
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        sizeHistLayout.addWidget(histNavigation)
        sizeHistLayout.addWidget(self.sizeHistogramCanvas)
        sizeHistGroup.setLayout(sizeHistLayout)
        
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        self.specPlot = SpectraPlot(self.dataset)
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        splitter1 = QtWidgets.QSplitter(QtCore.Qt.Vertical)
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        splitter1.addWidget(self.specPlot)
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        splitter1.addWidget(sizeHistGroup)
        splitter2 = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
        splitter2.addWidget(splitter1)
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        splitter2.addWidget(self.typeHistogramPlot)
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        splitter2.setSizes([300, 150])
       
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        referenceGroup = QtWidgets.QGroupBox('Reference Spectra')
        referenceLayout = QtWidgets.QHBoxLayout()
        
        self.refSelector = QtWidgets.QComboBox()
        self.refSelector.setMinimumWidth(200)
        self.refSelector.setDisabled(True)
        self.dbWin = DataBaseWindow(self)
        self.dbWin.selectDataBase(refreshParent=True)  #this includes updating the refSelector
        
        self.refSelector.currentIndexChanged.connect(self.updateSpecPlot)
        referenceLayout.addWidget(QtWidgets.QLabel('Select Reference'))
        referenceLayout.addWidget(self.refSelector)
        referenceLayout.addStretch()
        referenceGroup.setLayout(referenceLayout)
        

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        self.navigationGroup = QtWidgets.QGroupBox('Navigate through polymers')
        self.navigationGroup.setDisabled(True)
        navigationLayout = QtWidgets.QHBoxLayout()
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        self.typeSelectorCombo = QtWidgets.QComboBox()
        self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
        self.typeSelectorCombo.setMinimumWidth(150)
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        self.particleSelector = QtWidgets.QSpinBox()
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        self.particleSelector.valueChanged.connect(self.updateParticleSelection)
        self.particleNumberLabel = QtWidgets.QLabel('of xx particles; ')
        
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        self.spectrumSelector = QtWidgets.QSpinBox()
        self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
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        self.spectrumNumberLabel = QtWidgets.QLabel('of xx spectra')
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        for spinbox in [self.particleSelector, self.spectrumSelector]:
            spinbox.setMinimum(1)
            spinbox.setSingleStep(1)
            spinbox.setValue(1)
        
        navigationLayout.addWidget(QtWidgets.QLabel('Select Polymer Type:'))
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        navigationLayout.addWidget(self.typeSelectorCombo)
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        navigationLayout.addStretch()
        navigationLayout.addWidget(QtWidgets.QLabel('Select Particle'))
        navigationLayout.addWidget(self.particleSelector)
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        navigationLayout.addWidget(self.particleNumberLabel)
        navigationLayout.addStretch()
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        navigationLayout.addWidget(QtWidgets.QLabel('Select Spectrum'))
        navigationLayout.addWidget(self.spectrumSelector)
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        navigationLayout.addWidget(self.spectrumNumberLabel)
#        navigationLayout.addStretch()
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        self.navigationGroup.setLayout(navigationLayout)
        
        topLayout = QtWidgets.QHBoxLayout()
        topLayout.addWidget(self.navigationGroup)
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        topLayout.addWidget(referenceGroup)
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        viewLayout = QtWidgets.QVBoxLayout()
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        viewLayout.addLayout(topLayout)
        viewLayout.addWidget(splitter2)
        viewLayout.setStretch(1, 1)

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        self.optionsGroup = QtWidgets.QGroupBox('Set HQI Threshold')
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        optionsLayout = QtWidgets.QFormLayout()
        
        self.hqiSpinBox = QtWidgets.QDoubleSpinBox()
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        self.hqiSpinBox.setValue(self.dataset.resultParams['minHQI'])
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        self.hqiSpinBox.setDecimals(1)
        self.hqiSpinBox.setMinimum(0)
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        self.hqiSpinBox.setMaximum(100)
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        self.hqiSpinBox.setMaximumWidth(100)
        self.hqiSpinBox.valueChanged.connect(self.applyHQIThresholdToResults)
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        optionsLayout.addRow(QtWidgets.QLabel('minimum HQI:'), self.hqiSpinBox)
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#        self.compHqiSpinBox = QtWidgets.QDoubleSpinBox()
#        self.compHqiSpinBox.setValue(30.0)
#        self.compHqiSpinBox.setDecimals(1)
#        self.compHqiSpinBox.setMinimum(0)
#        self.compHqiSpinBox.setDisabled(True)
#        optionsLayout.addRow(QtWidgets.QLabel('min component HQI'), self.compHqiSpinBox)
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        self.optionsGroup.setLayout(optionsLayout)
        self.optionsGroup.setMinimumWidth(175)
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#        self.optionsGroup.setDisabled(True)
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        self.resultScrollarea = QtWidgets.QScrollArea(self)
        self.resultScrollarea.setFixedWidth(250)
        self.resultScrollarea.setWidgetResizable(True)

        widget = QtWidgets.QWidget()
        self.resultScrollarea.setWidget(widget)
        self.layout_SArea = QtWidgets.QVBoxLayout(widget)

        self.resultCheckBoxes = QtWidgets.QGroupBox('Display Polymer Types:')
        self.resultCheckBoxesLayout = QtWidgets.QVBoxLayout()
        self.showTotalSelector = QtWidgets.QCheckBox('Show Total Distribution')
        self.showTotalSelector.setChecked(True)
        self.showTotalSelector.setDisabled(True)
        self.resultCheckBoxesLayout.addWidget(self.showTotalSelector)
       
        self.resultCheckBoxesLayout.addStretch()
        self.resultCheckBoxes.setLayout(self.resultCheckBoxesLayout)

        self.layout_SArea.addWidget(self.resultCheckBoxes)
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        self.menuLayout = QtWidgets.QVBoxLayout()
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        self.menuLayout.addWidget(self.optionsGroup)
        self.menuLayout.addWidget(self.resultScrollarea)
        
        self.layout.addLayout(self.menuLayout)
        self.layout.addLayout(viewLayout)
        
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        minHQI = self.dataset.resultParams['minHQI']
#        compHQI = self.dataset.resultParams['compHQI']
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        if minHQI is not None:
            self.hqiSpinBox.setValue(minHQI)
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#            self.compHqiSpinBox.setValue(compHQI)
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        self.createActions()
        self.createMenus()
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        self.applyHQIThresholdToResults()
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        self.createHistogramData()
        self.updateHistograms()
        self.initializeSpecPlot()
        self.displayNewPolymerType()
        self.updateParticleSelection()
#        self.createPolymerOverlay()
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    def createActions(self):
        self.loadTrueMatchAct = QtWidgets.QAction("Load &TrueMatch Results", self)
        self.loadTrueMatchAct.triggered.connect(self.importTrueMatchResults)
        
        self.loadTextFileAct = QtWidgets.QAction("Load &ordered Text File", self)
        self.loadTextFileAct.setDisabled(True)
        
        self.noOverlayAct = QtWidgets.QAction("&No Overlay", self)
        self.selOverlayAct = QtWidgets.QAction("&Selected Overlay", self)
        self.fullOverlayAct = QtWidgets.QAction("&Full Overlay", self)
        
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        self.transpAct = QtWidgets.QAction("&Transparent Overlay", self)
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        self.transpAct.triggered.connect(self.createPolymerOverlay)
            
        self.hideLabelAct = QtWidgets.QAction('&Hide Polymer Numbers', self)
        self.hideLabelAct.triggered.connect(self.show_hide_labels)
        
        self.darkenAct = QtWidgets.QAction("&Darken Image", self)
        self.darkenAct.triggered.connect(self.darkenBackground)
        
        for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct, self.hideLabelAct, self.transpAct, self.darkenAct]:
            act.setCheckable(True)
        self.fullOverlayAct.setChecked(True)
        
        self.seedAct = QtWidgets.QAction("&Set Color Seed", self)
        self.seedAct.triggered.connect(self.updateColorSeed)

        self.databaseAct = QtWidgets.QAction("&ManageDatabase", self)
        self.databaseAct.triggered.connect(self.launchDBManager)
        
        self.expExcelAct= QtWidgets.QAction("Export &Excel List", self)
        self.expExcelAct.setDisabled(True)
        self.expExcelAct.triggered.connect(self.exportToExcel)
        
        self.expSQLAct = QtWidgets.QAction("Export to &SQL Database", self)
        self.expSQLAct.setDisabled(True)
        self.expSQLAct.triggered.connect(self.exportToSQL)
    
    def createMenus(self):
        self.importMenu = QtWidgets.QMenu("&Import Results")
        self.importMenu.addActions([self.loadTrueMatchAct, self.loadTextFileAct])
        
        self.dispMenu = QtWidgets.QMenu("&Display", self)
        self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
        self.overlayActGroup.setExclusive(True)
        self.overlayActGroup.triggered.connect(self.createPolymerOverlay)
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        self.overlayActGroup.triggered.connect(self.updateHistograms)
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        for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct]:
            self.dispMenu.addAction(act)
            self.overlayActGroup.addAction(act)
        
        self.dispMenu.addSeparator()
        self.dispMenu.addActions([self.transpAct, self.hideLabelAct, self.darkenAct, self.seedAct])
        
        self.refMenu = QtWidgets.QMenu("&References")
        self.refMenu.addAction(self.databaseAct)
        
        self.exportMenu = QtWidgets.QMenu("&Export", self)
        self.exportMenu.addAction(self.expExcelAct)
        self.exportMenu.addAction(self.expSQLAct)
        
        self.menuBar().addMenu(self.importMenu)
        self.menuBar().addMenu(self.dispMenu)
        self.menuBar().addMenu(self.refMenu)
        self.menuBar().addMenu(self.exportMenu)
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    def launchDBManager(self):
        if self.dbWin.isHidden():
            self.dbWin.show()
    
    def populateRefSelector(self):
        #delete all present entries:
        self.refSelector.clear()
        
        if self.dbWin.activeDatabase is None:
            self.refSelector.setDisabled(True)
        else:
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            self.refSelector.addItem('')
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            self.refSelector.addItems(self.dbWin.activeDatabase.spectraNames)
            self.refSelector.setDisabled(False)
            
    def importTrueMatchResults(self):
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        self.importWindow = LoadTrueMatchResults(self.particleContainer, self)
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        self.importWindow.exec()
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#    @QtCore.pyqtSlot(int)
#    def getAdditivePlot(self, clickedindex):
#        polymer = self.datastats.typehistogram[clickedindex][0]        #get the polymer name, that was clicked on
#      
#        if self.datastats.sorted_additives is not None and \
#           len(self.datastats.sorted_additives[clickedindex]) > 0:            
#            self.additivePlot = AdditiveViewer(polymer, self.datastats.sorted_additives[clickedindex])
#            self.additivePlot.show()
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    @QtCore.pyqtSlot()
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    def applyHQIThresholdToResults(self):
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        hqi = self.hqiSpinBox.value()
        self.particleContainer.applyHQITresholdToParticles(hqi)
        self.dataset.resultParams['minHQI'] = hqi
        self.dataset.save()
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        self.createHistogramData()
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        self.updateHistograms()
        
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#    def formatResults(self):
#        if self.datastats.spectraResults is not None:
#            print('formatResults')
#            self.optionsGroup.setDisabled(False)
#            
#            self.datastats.formatResults(self.hqiSpinBox.value(), self.compHqiSpinBox.value())
#            
#            if self.datastats.additiveResults is not None:
#                self.compHqiSpinBox.setDisabled(False)
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    def createHistogramData(self):
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#        if not self.datastats.createHistogramData():
#            QtWidgets.QMessageBox.critical(self, 'Error', 'Inconsistent particle data. Please restore backup!')
#            return
#        self.particleContainer.updateTypeHistogram()
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        ###Handle Checkboxes for all polymers...
        self.menuLayout.removeWidget(self.resultScrollarea)
        for i in [self.resultCheckBoxes, self.resultCheckBoxesLayout, self.resultScrollarea, self.layout_SArea]:
            i.setParent(None)
            del i

        for i in self.polymerCheckBoxes:        #remove present boxlabels
            i.setParent(None)
            del i
        self.showTotalSelector.setParent(None)
        self.showTotalSelector.setDisabled(False)
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        self.showTotalSelector.stateChanged.connect(self.updateHistograms)
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        del self.resultCheckBoxes
        del self.resultCheckBoxesLayout
        del self.resultScrollarea
        del self.layout_SArea
        
        self.resultScrollarea = QtWidgets.QScrollArea(self)
        self.resultScrollarea.setFixedWidth(250)
        self.resultScrollarea.setWidgetResizable(True)
        widget = QtWidgets.QWidget()
        self.resultScrollarea.setWidget(widget)
        self.layout_SArea = QtWidgets.QVBoxLayout(widget)
        self.resultCheckBoxes = QtWidgets.QGroupBox('Show Polymer Types:')
        self.resultCheckBoxesLayout = QtWidgets.QVBoxLayout()
        self.resultCheckBoxesLayout.addWidget(self.showTotalSelector)
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        #generate new checkboxes 
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        self.polymerCheckBoxes = []#
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        uniquePolymers = self.particleContainer.getUniquePolymers()
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        for index, polymer in enumerate(uniquePolymers):
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            self.polymerCheckBoxes.append(QtWidgets.QCheckBox(self))
            self.polymerCheckBoxes[index].setText(polymer)
            self.resultCheckBoxesLayout.addWidget(self.polymerCheckBoxes[index])
            if polymer in self.lastSelectedCheckBoxNames:
                self.polymerCheckBoxes[index].setChecked(True)
            
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            self.polymerCheckBoxes[index].stateChanged.connect(self.updateHistograms)
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            self.polymerCheckBoxes[index].stateChanged.connect(self.createPolymerOverlay)

        self.resultCheckBoxesLayout.addStretch()
        self.resultCheckBoxes.setLayout(self.resultCheckBoxesLayout)
        self.layout_SArea.addWidget(self.resultCheckBoxes)
        self.menuLayout.addWidget(self.resultScrollarea)
        
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        self.expExcelAct.setDisabled(False)
        if sqlEnabled:
            self.expSQLAct.setDisabled(False)
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        self.navigationGroup.setEnabled(True)
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        self.typeSelectorCombo.currentIndexChanged.disconnect()
        self.typeSelectorCombo.clear()
        self.typeSelectorCombo.addItems(uniquePolymers)
        self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
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        self.polymerIndex = self.typeSelectorCombo.currentIndex()
#        if self.lastSpectrumInFocus is not None:
#            self.currentSpectrumIndex = self.lastSpectrumInFocus
#            self.displayNewPolymerType(resetCurrentIndex=False)
#            print('displaying new type without resetting index')
#        else:
#            print('displaying new type with resetting index')
#            self.displayNewPolymerType()
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    def updateHistograms(self):  
        self.updateTypeHistogram()
        self.updateSizeHistogram()
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    def initializeSpecPlot(self):
        self.specPlot.loadSpectraAndInitializeSpecPlot()
        self.updateSpecPlot()
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    def updateSpecPlot(self, centerOn=True, highlightContour=True):
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        particleSize = self.particleContainer.getSizeOfParticleByIndex(self.currentParticleIndex)
        hqi = self.particleContainer.getHQIOfSpectrumIndex(self.currentSpectrumIndex)
        self.specPlot.updateParticleSpectrum(self.currentSpectrumIndex, particleSize, hqi)
        self.parent.centerOnRamanIndex(self.currentSpectrumIndex, centerOn=centerOn, highlightContour=highlightContour)  #TODO: is this reasonable to do in that way???
        self.parent.highLightRamanIndex(self.currentSpectrumIndex)
#        self.lastSpectrumInFocus = self.currentSpectrumIndex
            
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        if self.refSelector.isEnabled() and self.refSelector.currentText() != '':
            refID = self.dbWin.activeDatabase.spectraNames.index(self.refSelector.currentText())
            ref = self.dbWin.activeDatabase.spectra[refID]
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            self.specPlot.updateReferenceSpectrum(ref[:, 0], ref[:, 1])
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    def selectContour(self, index, centerOn=True):
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        print('select Contour in analysisview not yet refactored')
#        uniquePolymers = self.particleContainer.getUniquePolymers()
#        if uniquePolymers is not None:
#            #the index is the contour index, find particle index:
#            specIndex = self.datastats.particles2spectra[index][0]  #select first spectrum of partoicle
#            self.currentParticleIndex = index
#            self.currentSpectrumIndex = specIndex
#            
#            selectedPolymer = self.datastats.currentPolymers[specIndex]
#            try:
#                self.polymerIndex = uniquePolymers.index(selectedPolymer)
#            except:
#                print(selectedPolymer)
#                raise
#            
#            #subparticleIndex
#            partIndicesOfThatPolymer = self.datastats.indices[self.polymerIndex]
#            subPartInd = partIndicesOfThatPolymer.index(index)
#            
#            #disconnect analysis widgets:
#            self.particleSelector.valueChanged.disconnect()
#            self.spectrumSelector.valueChanged.disconnect()
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#            self.typeSelectorCombo.currentIndexChanged.disconnect()
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#            
#            #set widgets...
#            self.particleSelector.setValue(subPartInd+1)
#            self.particleSelector.setMaximum(len(partIndicesOfThatPolymer))
#            
#            self.spectrumSelector.setValue(1)
#            self.spectrumSelector.setMaximum(len(self.datastats.particles2spectra[index]))
#            
#            selectedPolymer = self.datastats.currentPolymers[specIndex]
#            self.polymerIndex = uniquePolymers.index(selectedPolymer)
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#            self.typeSelectorCombo.setCurrentIndex(self.polymerIndex)
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#           
#            #reconnect all widgets:
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#            self.particleSelector.valueChanged.connect(self.updateParticleSelection)
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#            self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
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#            self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
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#            
#            self.updateSpecPlot(centerOn=centerOn)
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    def displayNewPolymerType(self, resetCurrentIndex=True):
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        polymerName = self.typeSelectorCombo.currentText()
        numParticles = self.particleContainer.getNumberOfParticlesOfAssignment(polymerName)
        self.particleSelector.setMaximum(numParticles)
        self.particleNumberLabel.setText(f'of {numParticles} Particles; ')
        
        self.particleSelector.setValue(1)
        self.spectrumSelector.setValue(1)
        
        self.currentParticleIndex = self.getParticleIndexFromParticleSelector()
        self.spectrumSelector.setMaximum(self.particleContainer.getNumberOfSpectraOfParticle(self.currentParticleIndex))
        self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()
        self.updateSpecPlot(centerOn=False)
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    def updateParticleSelection(self, resetSpectrumCount=True):
        polymerName = self.typeSelectorCombo.currentText()
        if polymerName != '':
            self.currentParticleIndex = self.getParticleIndexFromParticleSelector()
            numSpectra = self.particleContainer.getNumberOfSpectraOfParticle(self.currentParticleIndex)
            self.spectrumSelector.setMaximum(numSpectra)
            self.spectrumNumberLabel.setText(f'of {numSpectra} Spectra')
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            if resetSpectrumCount:
                self.spectrumSelector.setValue(1)
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            self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()
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            self.updateSpecPlot()
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    def selectSpectrum(self):
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        self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()
        self.updateSpecPlot()
        
    def getSpectrumIndexFromSpectrumSelector(self):
        specIndicesOfParticle = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)
        try:
            return specIndicesOfParticle[self.spectrumSelector.value()-1]
        except IndexError:
            print(f'requested specIndex {self.spectrumSelector.value()-1} for particle Index {self.currentParticleIndex} of specIndices: {specIndicesOfParticle}')
    
    def getParticleIndexFromParticleSelector(self):
        particleIndicesOfType = self.particleContainer.getIndicesOfParticleType(self.typeSelectorCombo.currentText())
        return particleIndicesOfType[self.particleSelector.value()-1]
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    def updateTypeHistogram(self):
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        #draw the general histogram
        colorList = []
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        abundancyList = []
        labelList = []
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        typeHistogram = self.particleContainer.getTypeHistogram()
        for index, polymType in enumerate(typeHistogram):
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            if not self.selOverlayAct.isChecked() or self.polymerCheckBoxes[index].isChecked():
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                text = f'{typeHistogram[polymType]} x {polymType}'
                labelList.append(text)
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                abundancyList.append(typeHistogram[polymType])
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                curColor = self.colorHandler.getColorFromName(self.dataset.colorSeed, polymType)
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                colorList.append(QtGui.QColor(*curColor))
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#        print("abundancyList:", abundancyList)
#        print("labelList:", labelList)
#        print("colorList:", colorList)
        self.typeHistogramPlot.updateTypeHistogram(list(zip(abundancyList, labelList, colorList)))
    
    def updateSizeHistogram(self):
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        if self.particleContainer.getNumberOfParticles() > 0:
            #general size histogram
            self.sizeHist_ax.clear()
            self.sizeHist_ax.axis('on')
    
            self.bins = np.logspace(0.1, 3, 20)
            self.sizes = self.particleContainer.getSizesOfAllParticles()
                
    #        self.sizes = [i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.getParticleStats()]      #extract long size (if ellipse fit is nan -> box fit)
            sizehist = np.histogram(self.sizes, self.bins)
            self.totalhistx = []
            for i in range(19):
                self.totalhistx.append(np.mean((sizehist[1][i], sizehist[1][i+1])))
            self.totalhisty = sizehist[0]
            
            self.sizeHist_ax.tick_params(axis='both', which='both', labelsize=15)
            self.sizeHist_ax.set_xlabel('Size (µm)', fontsize = 15)
            self.sizeHist_ax.set_ylabel('Number', fontsize = 15)
            self.sizeHist_ax.set_xlim(3, 1100)        
            self.sizeHist_ax.figure.canvas.draw()
            
            if self.showTotalSelector.isChecked():
                self.sizeHist_ax.semilogx(self.totalhistx, self.totalhisty, label = 'total')
                
            #get selected boxes
            selectedTypes = []
            for checkbox in self.polymerCheckBoxes:
                if checkbox.isChecked() == True:
                    selectedTypes.append(checkbox.text())
            
            for polymType in selectedTypes:
                sizes = self.particleContainer.getSizesOfParticleType(polymType)
    #            sizes = [self.sizes[index] for index in range(len(self.sizes)) 
    #                        if self.datastats.currentPolymers[index] == i]
                sizehist = np.histogram(sizes, self.bins)
                color = self.colorHandler.getColorFromName(self.dataset.colorSeed, polymType, base255=False)
                self.sizeHist_ax.semilogx(self.totalhistx, sizehist[0], label=polymType, color=color)    
            
            self.sizeHist_ax.legend(prop = {'size': 15})
            self.sizeHist_ax.tick_params(axis='both', which='both', labelsize=15)
            self.sizeHist_ax.set_xlabel('Size (µm)', fontsize = 15)
            self.sizeHist_ax.set_ylabel('Number', fontsize = 15)
            self.sizeHist_ax.set_xlim(3, 1100)        
            self.sizeHist_ax.figure.canvas.draw()
            
            self.lastSelectedCheckBoxNames = [checkbox.text() for checkbox in self.polymerCheckBoxes if checkbox.isChecked()]
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    def darkenBackground(self):
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        self.parent.darkenPixmap = self.darkenAct.isChecked()
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        if self.darkenAct.isChecked():
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            self.parent.scene().setBackgroundBrush(QtGui.QColor(5, 5, 5))
            self.parent.item.setOpacity(0.2)
        else:
            self.parent.scene().setBackgroundBrush(QtCore.Qt.darkGray)
            self.parent.item.setOpacity(1)

    def updateColorSeed(self):
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        text, ok = QtWidgets.QInputDialog.getText(self, 'Color Seed', 'Enter New Seed here', text=self.dataset.colorSeed)
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        if ok:
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            self.dataset.colorSeed = text
#            self.datastats.dataset.colorSeed = text
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            self.updateHistograms()
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            self.createPolymerOverlay()
    
    def createPolymerOverlay(self):  
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        pass   #REFACTOR TO INDIVIDUAL CONTOUR ITEMS
##        uniquePolymers = self.datastats.getUniquePolymers()
#        uniquePolymers = self.particleContainer.getUniquePolymers()
##        if not self.noOverlayAct.isChecked() and self.datastats.indices is not None:
#        if not self.noOverlayAct.isChecked():
##            if len(self.datastats.indices) > 0:
#            
#            alpha = (128 if self.transpAct.isChecked() else 255)
#            #get colors for each polymer type
#            colorList = [QtGui.QColor(255, 255, 255, alpha=50)]*len(self.datastats.particleResults)
#            legendItems = []
#                
#            for index, indexList in enumerate(self.datastats.indices):
#                if self.fullOverlayAct.isChecked() or (self.selOverlayAct.isChecked() and self.polymerCheckBoxes[index].isChecked()):
#                    
#                    color = self.colorHandler.getColorFromName(self.dataset.colorSeed, uniquePolymers[index])
##                        color = self.getColorFromName(uniquePolymers[index], base255=True)
#                    color = QtGui.QColor(color[0], color[1], color[2], alpha=alpha)
#                    legendItems.append((uniquePolymers[index], color))
#                    for i in indexList:
#                        colorList[i] = color
#            
#            self.parent.contouritem.colorList = colorList
#            self.parent.contouritem.update()
#            
#            self.parent.imparent.legend.setTextColorItems(legendItems)
#            self.parent.imparent.legend.show()
#            
#        else:
#            self.parent.contouritem.colorList = []
#            self.parent.contouritem.update()
#            self.parent.imparent.legend.setTextColorItems([])
#            self.parent.imparent.legend.hide()
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    def show_hide_labels(self):
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        hidden = self.hideLabelAct.isChecked()
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        for scanIndicator in self.parent.ramanscanitems:
            scanIndicator.hidden = hidden
            scanIndicator.update()
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    def exportToExcel(self):
        expWin = ExpExcelDialog(self.particleContainer, self)
        expWin.exec()
            
    def exportToSQL(self):
        sqlexp = SQLExport(self.particleContainer, self)
        sqlexp.exec()
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    def closeEvent(self, event):
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        for window in [self.importWindow, self.dbWin]:
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            try: window.close()
            except: pass
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        self.parent.imparent.particelAnalysisAct.setChecked(False)
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        event.accept()


if __name__ == '__main__':
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    from ..dataset import DataSet
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    def run():
        app = QtWidgets.QApplication(sys.argv)
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        meas = ParticleAnalysis(DataSet("dummydata"))
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        meas.showMaximized()
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        return app.exec_()
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    run()