Basic plots working, proceeding to contours

analysis/analysisplots.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+GEPARD - Gepard-Enabled PARticle Detection
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program, see COPYING.  
+If not, see <https://www.gnu.org/licenses/>.
+"""
+from PyQt5 import QtWidgets, QtGui, QtCore
+from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
+import os
+import numpy as np
+
+from analysis import importSpectra
+
+
+class ParticleIndicator(QtWidgets.QPushButton):
+    def __init__(self, number, numtotal, color, text, parent=None):
+        super().__init__(parent)
+        self.number = number
+        self.numtotal = numtotal
+        self.color = color
+        self.text = text
+        self.setFixedHeight(30)
+        
+    def paintEvent(self, event):
+        r = self.number/self.numtotal
+        width = self.width()
+        height = self.height()
+        
+        qp = QtGui.QPainter()
+        qp.begin(self)
+        #qp.fillRect(self.rect(), QtCore.Qt.white)
+        qp.setBrush(QtCore.Qt.white)
+        qp.drawRoundedRect(0, 0, width, height, 5. ,5.)
+        qp.setPen(self.color)
+        qp.setBrush(self.color)
+        qp.drawRoundedRect(0, 0, int(width*r), height, 5. ,5.)
+        qp.setPen(QtCore.Qt.black)
+        qp.setBrush(QtCore.Qt.NoBrush)
+        qp.drawRoundedRect(0, 0, width, height, 5. ,5.)
+        font = qp.font()
+        font.setPointSize(13)
+        font.setStyleStrategy(QtGui.QFont.NoAntialias)
+        font.setWeight(0)
+        qp.setFont(font)
+        qp.setCompositionMode(QtGui.QPainter.RasterOp_SourceXorDestination)
+        qp.setPen(QtCore.Qt.white)
+        qp.drawText(5, 0, width-10, height, QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter, 
+                    self.text)
+        qp.end()
+        
+        
+class TypeHistogramView(QtWidgets.QScrollArea):
+    indexClicked = QtCore.pyqtSignal(int)
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.view = QtWidgets.QWidget(self)
+        self.view.setCursor(QtGui.QCursor(QtCore.Qt.WhatsThisCursor))
+        self.view.setMinimumWidth(250)
+        
+        group = QtWidgets.QGroupBox('Polymer Type Distribution', self.view)
+        self.indicatorbox = QtWidgets.QVBoxLayout()
+        self.indicatorbox.setContentsMargins(5,5,5,5)
+        group.setLayout(self.indicatorbox)
+        
+        hbox = QtWidgets.QHBoxLayout()
+        hbox.addWidget(group)
+        self.view.setLayout(hbox)
+        self.setWidgetResizable(True)
+        self.setWidget(self.view)
+        self.setAlignment(QtCore.Qt.AlignHCenter)
+        self.widgets = []
+        
+    def updateTypeHistogram(self, types):
+#        print("Updating polymer type view", flush=True)
+        for pi in self.widgets:
+            self.indicatorbox.removeWidget(pi)
+            pi.setParent(None)
+            pi.destroy()
+        self.indicatorbox.takeAt(0)
+        self.widgets = []
+        numtotal = sum([num for num, text, color in types])
+        
+        def getIndexFunction(index):
+            return lambda : self.indexClicked.emit(index)
+        
+        for index, entry in enumerate(types):
+            num, text, color = entry
+#            print("num, text, color:", num, text, color, flush=True)
+            pi = ParticleIndicator(num, numtotal, color, text)
+            self.indicatorbox.addWidget(pi)
+            pi.clicked.connect(getIndexFunction(index))
+            self.widgets.append(pi)
+        self.indicatorbox.addStretch()
+        self.view.update()
+
+
+class SpectraPlot(QtWidgets.QGroupBox):
+    def __init__(self, dataset):
+        super(SpectraPlot, self).__init__()
+        self.dataset = dataset
+        self.spectra = None
+        
+        layout = QtWidgets.QHBoxLayout()
+        self.canvas = FigureCanvas(Figure())
+        self.spec_axis = self.canvas.figure.subplots()
+        self.spec_axis.axis("off")
+        self.reference_ax = self.spec_axis.twinx()
+        self.canvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.9)
+        specNavigation = NavigationToolbar(self.canvas, self)
+        specNavigation.setOrientation(QtCore.Qt.Vertical)
+        specNavigation.setFixedWidth(50)
+        
+        layout.addWidget(specNavigation)
+        layout.addWidget(self.canvas)
+        self.setLayout(layout)
+        
+    def loadSpectraAndInitializeSpecPlot(self):  #formerly updateData(self)....
+        def tryLoadingNumpySpecFile():
+            specPath = self.dataset.getSpectraFileName()
+            if os.path.exists(specPath):
+                return np.load(specPath)
+            else:
+                raise ImportError
+        try:
+            self.spectra = tryLoadingNumpySpecFile()
+        except ImportError:
+            
+            fname = QtWidgets.QFileDialog.getOpenFileName(QtWidgets.QWidget(), 'Select Spectra File', self.dataset.path, 'text file (*.txt)')[0]
+    
+            try:
+                self.spectra, spectraNames = importSpectra.importWITecSpectra(fname)
+            except ImportError:
+                try:
+                    self.spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
+                except ImportError:
+                    self.spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)
+                
+            if self.spectra is None:
+                raise ImportError
+            else:
+                np.save(self.dataset.getSpectraFileName(), self.spectra)
+ 
+        self.canvas.draw()
+        
+    def updateParticleSpectrum(self, specIndex, particleSize, hqi):
+        if self.spectra is not None:
+            #draw Sample Spectrum
+            self.spec_axis.axis("on")
+            self.spec_axis.clear()
+            self.spec_axis.plot(self.spectra[:, 0], self.spectra[:, specIndex+1])
+            self.spec_axis.tick_params(axis='both', which='both', labelsize=15)
+            self.spec_axis.set_xlabel('Wavenumber (cm-1)', fontsize = 15)
+            self.spec_axis.set_ylabel('Counts', fontsize = 15)
+            self.spec_axis.set_title('ScanPoint Number {}, Size = {} µm, HQI = {}'.format(specIndex+1, particleSize, hqi))
+            self.spec_axis.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
+            wavenumber_diff = list(self.spectra[:, 0]-100)
+            y_start = wavenumber_diff.index(min(wavenumber_diff))
+            y_min = min(self.spectra[y_start:, specIndex+1])
+            y_max = max(self.spectra[y_start:, specIndex+1])
+            self.spec_axis.set_ybound(0.9*y_min, 1.1*y_max)
+            
+        self.canvas.draw()
+    
+    def updateReferenceSpectrum(self, ref_wavenumber, ref_intensity):
+        #draw Reference
+        self.reference_axis.clear()
+        self.reference_axis.tick_params(axis='both', which='both', labelsize=15)
+        self.reference_axis.plot(ref_wavenumber, ref_intensity, color = 'r')
+        self.reference_axis.set_ylabel('Ref. Intensity', fontsize = 15, color = 'r')
+        self.reference_axis.tick_params('y', colors = 'r')
+        self.reference_axis.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
+#        wavenumber_diff = list(ref[:, 0]-100)
+#        y_start = wavenumber_diff.index(min(wavenumber_diff))
+#        y_min = min(ref[y_start:, specIndex+1])
+#        y_max = max(ref[y_start:, specIndex+1])
+        
+        self.canvas.draw()
+
+        
+        
\ No newline at end of file

analysis/analysisview.py

@@ -22,20 +22,20 @@ If not, see <https://www.gnu.org/licenses/>.
 
 from PyQt5 import QtCore, QtGui, QtWidgets
 import numpy as np
-import sys, os
-import random
-import colorsys
+import sys
+
 
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
 
-from .analysiswidgets import ExpExcelDialog, AdditiveViewer, ParticleTypeView
+from .analysiswidgets import ExpExcelDialog
+from .analysisplots import TypeHistogramView, SpectraPlot
 from .loadresults import LoadWITecResults
 from .particleeditor import ParticleEditor
 from .database import DataBaseWindow
-#from .datastats import DataStats
-from analysis import importSpectra
+from .colorlegend import ColorHandler
+
 try:
     from .sqlexport import SQLExport
     sqlEnabled = True
@@ -56,8 +56,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.parent = parent
         self.dataset = dataset
         self.particleContainer = dataset.particleContainer
-#        self.datastats = DataStats(dataset)
         self.editor = ParticleEditor(self.particleContainer, self)
+        self.colorHandler = ColorHandler()
         
 #        self.additivePlot = None
         self.importWindow = None
@@ -67,9 +67,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         
         self.currentParticleIndex = 0
         self.currentSpectrumIndex = 0
-        self.lastSpectrumInFocus = None
+#        self.lastSpectrumInFocus = None
         
-        self.typeHistogramPlot = ParticleTypeView(self)
+        self.typeHistogramPlot = TypeHistogramView(self)
 #        self.typeHistogramPlot.indexClicked.connect(self.getAdditivePlot)
         self.sizeHistogramCanvas = FigureCanvas(Figure())
        
@@ -85,76 +85,69 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         sizeHistLayout.addWidget(self.sizeHistogramCanvas)
         sizeHistGroup.setLayout(sizeHistLayout)
         
-        specGroup = QtWidgets.QGroupBox()
-        specLayout = QtWidgets.QHBoxLayout()
-        self.specCanvas = FigureCanvas(Figure())
-        self.spec_ax = self.specCanvas.figure.subplots()
-        self.spec_ax.axis("off")
-        self.ref_ax = self.spec_ax.twinx()
-        self.specCanvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.9)
-        specNavigation = NavigationToolbar(self.specCanvas, self)
-        specNavigation.setOrientation(QtCore.Qt.Vertical)
-        specNavigation.setFixedWidth(50)
-        
-        specLayout.addWidget(specNavigation)
-        specLayout.addWidget(self.specCanvas)
-        specGroup.setLayout(specLayout)
-        
-        viewLayout = QtWidgets.QVBoxLayout()
-        self.menuLayout = QtWidgets.QVBoxLayout()
+        self.specPlot = SpectraPlot(self.dataset)
         
         splitter1 = QtWidgets.QSplitter(QtCore.Qt.Vertical)
-        splitter1.addWidget(specGroup)
+        splitter1.addWidget(self.specPlot)
         splitter1.addWidget(sizeHistGroup)
         splitter2 = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
         splitter2.addWidget(splitter1)
         splitter2.addWidget(self.typeHistogramPlot)
         splitter2.setSizes([300, 150])
        
+        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)
+        
+
         self.navigationGroup = QtWidgets.QGroupBox('Navigate through polymers')
         self.navigationGroup.setDisabled(True)
         navigationLayout = QtWidgets.QHBoxLayout()
-        self.polymerComboBox = QtWidgets.QComboBox()
-        self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)
-        self.polymerComboBox.setMinimumWidth(150)
+        self.typeSelectorCombo = QtWidgets.QComboBox()
+        self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
+        self.typeSelectorCombo.setMinimumWidth(150)
         self.particleSelector = QtWidgets.QSpinBox()
-        self.particleSelector.valueChanged.connect(self.selectParticle)
+        self.particleSelector.valueChanged.connect(self.updateParticleSelection)
+        self.particleNumberLabel = QtWidgets.QLabel('of xx particles; ')
+        
         self.spectrumSelector = QtWidgets.QSpinBox()
         self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
+        self.spectrumNumberLabel = QtWidgets.QLabel('of xx spectra')
         for spinbox in [self.particleSelector, self.spectrumSelector]:
             spinbox.setMinimum(1)
             spinbox.setSingleStep(1)
             spinbox.setValue(1)
         
         navigationLayout.addWidget(QtWidgets.QLabel('Select Polymer Type:'))
-        navigationLayout.addWidget(self.polymerComboBox)
+        navigationLayout.addWidget(self.typeSelectorCombo)
         navigationLayout.addStretch()
         navigationLayout.addWidget(QtWidgets.QLabel('Select Particle'))
         navigationLayout.addWidget(self.particleSelector)
+        navigationLayout.addWidget(self.particleNumberLabel)
+        navigationLayout.addStretch()
         navigationLayout.addWidget(QtWidgets.QLabel('Select Spectrum'))
         navigationLayout.addWidget(self.spectrumSelector)
-        navigationLayout.addStretch()
+        navigationLayout.addWidget(self.spectrumNumberLabel)
+#        navigationLayout.addStretch()
         
         self.navigationGroup.setLayout(navigationLayout)
         
-        referenceGroup = QtWidgets.QGroupBox('Reference Spectra')
-        referenceLayout = QtWidgets.QHBoxLayout()
-        
-        self.refSelector = QtWidgets.QComboBox()
-        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)
-        referenceGroup.setLayout(referenceLayout)
-        
         topLayout = QtWidgets.QHBoxLayout()
         topLayout.addWidget(self.navigationGroup)
         topLayout.addWidget(referenceGroup)
-        topLayout.addStretch()
         
+        viewLayout = QtWidgets.QVBoxLayout()
         viewLayout.addLayout(topLayout)
         viewLayout.addWidget(splitter2)
         viewLayout.setStretch(1, 1)
@@ -163,11 +156,12 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         optionsLayout = QtWidgets.QFormLayout()
         
         self.hqiSpinBox = QtWidgets.QDoubleSpinBox()
-        self.hqiSpinBox.setValue(75.0)
+        self.hqiSpinBox.setValue(self.dataset.resultParams['minHQI'])
         self.hqiSpinBox.setDecimals(1)
         self.hqiSpinBox.setMinimum(0)
         self.hqiSpinBox.setMaximum(100)
-        self.hqiSpinBox.setMaximumWidth(45)
+        self.hqiSpinBox.setMaximumWidth(100)
+        self.hqiSpinBox.valueChanged.connect(self.applyHQIThresholdToResults)
         optionsLayout.addRow(QtWidgets.QLabel('min HQI:'), self.hqiSpinBox)
         
 #        self.compHqiSpinBox = QtWidgets.QDoubleSpinBox()
@@ -180,13 +174,10 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.dispResultSpinBox = QtWidgets.QSpinBox()
         self.dispResultSpinBox.setValue(20)
         self.dispResultSpinBox.setMinimum(1)
+        self.dispResultSpinBox.setMaximumWidth(100)
         self.dispResultSpinBox.valueChanged.connect(self.updateHistograms)
         optionsLayout.addRow(QtWidgets.QLabel('Max. items in display:'), self.dispResultSpinBox)
         
-        self.updateBtn = QtWidgets.QPushButton('Update Results')
-        self.updateBtn.clicked.connect(self.applyHQIThresholdToResults)
-#        self.updateBtn.setDisabled(True)
-        optionsLayout.addRow(self.updateBtn)
         
         self.optionsGroup.setLayout(optionsLayout)
         self.optionsGroup.setMinimumWidth(175)
@@ -211,7 +202,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.resultCheckBoxes.setLayout(self.resultCheckBoxesLayout)
 
         self.layout_SArea.addWidget(self.resultCheckBoxes)
-
+        
+        self.menuLayout = QtWidgets.QVBoxLayout()
         self.menuLayout.addWidget(self.optionsGroup)
         self.menuLayout.addWidget(self.resultScrollarea)
         
@@ -226,9 +218,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
          
         self.createActions()
         self.createMenus()
-        
-        self.loadSpectraAndInitializeSpecPlot()
         self.applyHQIThresholdToResults()
+        self.createHistogramData()
+        self.updateHistograms()
+        self.initializeSpecPlot()
+        self.displayNewPolymerType()
+        self.updateParticleSelection()
+#        self.createPolymerOverlay()
     
     def createActions(self):
         self.loadTrueMatchAct = QtWidgets.QAction("Load &TrueMatch Results", self)
@@ -312,50 +308,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
             self.refSelector.addItems(self.dbWin.activeDatabase.spectraNames)
             self.refSelector.setDisabled(False)
             
-    def loadSpectraAndInitializeSpecPlot(self):  #formerly updateData(self)....
-        def tryLoadingNumpySpecFile():
-            specPath = self.dataset.getSpectraFileName()
-            if os.path.exists(specPath):
-                return np.load(specPath)
-            else:
-                raise ImportError
-        try:
-            self.spectra = tryLoadingNumpySpecFile()
-        except ImportError:
-            
-            fname = QtWidgets.QFileDialog.getOpenFileName(QtWidgets.QWidget(), 'Select Spectra File', self.dataset.path, 'text file (*.txt)')[0]
-    
-            try:
-                self.spectra, spectraNames = importSpectra.importWITecSpectra(fname)
-            except ImportError:
-                try:
-                    self.spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
-                except ImportError:
-                    self.spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)
-                
-            if self.spectra is None:
-                raise ImportError
-            else:
-                np.save(self.dataset.getSpectraFileName(), self.spectra)
- 
-        self.specCanvas.draw()
-#        self.loadParticleData()
-        
-#    def loadParticleData(self):
-#        #check, if dataset already contains results. Otherwise load them...
-#        if not self.datastats.loadParticleData():
-#            self.show()
-#            answer = QtWidgets.QMessageBox.question(self, 'Warning', 'No (or inconsistent) spectra results found, please run import dialog.\nPress OK to import or cancel to set to empty.', QtWidgets.QMessageBox.Ok | QtWidgets.QMessageBox.Cancel)
-#            if answer == QtWidgets.QMessageBox.Ok:
-#                self.importTrueMatchResults()
-#            elif answer == QtWidgets.QMessageBox.Cancel:
-#                self.datastats.invalidateSpectra()
-#                self.updateBtn.clicked.connect(self.formatResults)
-#                self.formatResults()
-#        else:
-#            self.updateBtn.clicked.connect(self.formatResults)
-#            self.formatResults()
-        
     def importTrueMatchResults(self):
         self.importWindow = LoadWITecResults(self.particleContainer, self)
         self.importWindow.exec()
@@ -371,13 +323,17 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
     
     @QtCore.pyqtSlot()
     def applyHQIThresholdToResults(self):
-        self.particleContainer.applyHQITresholdToParticles(self.hqiSpinBox.value())
+        hqi = self.hqiSpinBox.value()
+        self.particleContainer.applyHQITresholdToParticles(hqi)
+        self.dataset.resultParams['minHQI'] = hqi
+        self.dataset.save()
         self.createHistogramData()
+        self.updateHistograms()
+        
         
 #    def formatResults(self):
 #        if self.datastats.spectraResults is not None:
 #            print('formatResults')
-#            self.updateBtn.setDisabled(False)
 #            self.optionsGroup.setDisabled(False)
 #            
 #            self.datastats.formatResults(self.hqiSpinBox.value(), self.compHqiSpinBox.value())
@@ -422,7 +378,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.resultCheckBoxesLayout.addWidget(self.showTotalSelector)
         
         #generate new checkboxes 
-        self.polymerCheckBoxes = []
+        self.polymerCheckBoxes = []#
         uniquePolymers = self.particleContainer.getUniquePolymers()
         for index, polymer in enumerate(uniquePolymers):
             self.polymerCheckBoxes.append(QtWidgets.QCheckBox(self))
@@ -444,20 +400,20 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
             self.expSQLAct.setDisabled(False)
         
         self.navigationGroup.setEnabled(True)
-        self.polymerComboBox.currentIndexChanged.disconnect()
-        self.polymerComboBox.clear()
-        self.polymerComboBox.addItems(uniquePolymers)
-        self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)
+        self.typeSelectorCombo.currentIndexChanged.disconnect()
+        self.typeSelectorCombo.clear()
+        self.typeSelectorCombo.addItems(uniquePolymers)
+        self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
                 
-        self.polymerIndex = self.polymerComboBox.currentIndex()
-        if self.lastSpectrumInFocus is not None:
-            self.currentSpectrumIndex = self.lastSpectrumInFocus
-            self.displayNewPolymerType(resetCurrentIndex=False)
-        else:
-            self.displayNewPolymerType()
+        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()
             
-        self.updateHistograms()
-        self.createPolymerOverlay()
     
     def exportToExcel(self):
         expWin = ExpExcelDialog(self.particleContainer, self)
@@ -466,47 +422,23 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
     def exportToSQL(self):
         sqlexp = SQLExport(self.particleContainer, self)
         sqlexp.exec()
-        
+    
+    def initializeSpecPlot(self):
+        self.specPlot.loadSpectraAndInitializeSpecPlot()
+        self.updateSpecPlot()
     
     def updateSpecPlot(self, centerOn=True, highlightContour=True):
-        #draw Sample Spectrum
-        specIndex = self.currentSpectrumIndex
-        self.spec_ax.axis("on")
-        self.spec_ax.clear()
-        self.spec_ax.plot(self.spectra[:, 0], self.spectra[:, specIndex+1])
-        self.spec_ax.tick_params(axis='both', which='both', labelsize=15)
-        self.spec_ax.set_xlabel('Wavenumber (cm-1)', fontsize = 15)
-        self.spec_ax.set_ylabel('Counts', fontsize = 15)
-        self.spec_ax.set_title('ScanPoint Number {}, Size = {} µm'.format(specIndex+1, 
-                               self.particleContainer.getSizeOfParticleByIndex(self.currentParticleIndex)))
-        self.spec_ax.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
-        wavenumber_diff = list(self.spectra[:, 0]-100)
-        y_start = wavenumber_diff.index(min(wavenumber_diff))
-        y_min = min(self.spectra[y_start:, specIndex+1])
-        y_max = max(self.spectra[y_start:, specIndex+1])
-        self.spec_ax.set_ybound(0.9*y_min, 1.1*y_max)
-        
-        #draw Reference
-        self.ref_ax.clear()
+        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
+            
         if self.refSelector.isEnabled() and self.refSelector.currentText() != '':
-            self.ref_ax.tick_params(axis='both', which='both', labelsize=15)
             refID = self.dbWin.activeDatabase.spectraNames.index(self.refSelector.currentText())
             ref = self.dbWin.activeDatabase.spectra[refID]
-            self.ref_ax.plot(ref[:, 0], ref[:, 1], color = 'r')
-            self.ref_ax.set_ylabel('Ref. Intensity', fontsize = 15, color = 'r')
-            self.ref_ax.tick_params('y', colors = 'r')
-            self.ref_ax.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
-#            wavenumber_diff = list(ref[:, 0]-100)
-#            y_start = wavenumber_diff.index(min(wavenumber_diff))
-#            y_min = min(ref[y_start:, specIndex+1])
-#            y_max = max(ref[y_start:, specIndex+1])
-            
-            
-        
-        self.spec_ax.figure.canvas.draw()
-        self.parent.centerOnRamanIndex(specIndex, centerOn=centerOn, highlightContour=highlightContour)
-        self.parent.highLightRamanIndex(specIndex)
-        self.lastSpectrumInFocus = specIndex
+            self.specPlot.updateReferenceSpectrum(ref[:, 0], ref[:, 1])
         
     def selectContour(self, index, centerOn=True):
         print('select Contour in analysisview not yet refactored')
@@ -531,7 +463,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
 #            #disconnect analysis widgets:
 #            self.particleSelector.valueChanged.disconnect()
 #            self.spectrumSelector.valueChanged.disconnect()
-#            self.polymerComboBox.currentIndexChanged.disconnect()
+#            self.typeSelectorCombo.currentIndexChanged.disconnect()
 #            
 #            #set widgets...
 #            self.particleSelector.setValue(subPartInd+1)
@@ -542,53 +474,61 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
 #            
 #            selectedPolymer = self.datastats.currentPolymers[specIndex]
 #            self.polymerIndex = uniquePolymers.index(selectedPolymer)
-#            self.polymerComboBox.setCurrentIndex(self.polymerIndex)
+#            self.typeSelectorCombo.setCurrentIndex(self.polymerIndex)
 #           
 #            #reconnect all widgets:
-#            self.particleSelector.valueChanged.connect(self.selectParticle)
+#            self.particleSelector.valueChanged.connect(self.updateParticleSelection)
 #            self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
-#            self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)
+#            self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
 #            
 #            self.updateSpecPlot(centerOn=centerOn)