Merge branch 'RefactoringAnalysisModules'

.gitignore

+
+__pycache__/
+
+gepard\.cfg
+
+analysis/database_config\.txt
+
+*.so
+
+*.c
+
+external/build/
+
+.idea/

gepard.py → __main__.py

@@ -18,18 +18,17 @@ 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, QtWidgets, QtGui
-from sampleview import SampleView
-from scalebar import ScaleBar
-from ramancom.ramancontrol import defaultPath
-from ramancom.ramanSwitch import RamanSwitch
-from colorlegend import ColorLegend
 import os
+from PyQt5 import QtCore, QtWidgets, QtGui
+from .sampleview import SampleView
+from .scalebar import ScaleBar
+from .ramancom.ramancontrol import defaultPath
+from .ramancom.ramanSwitch import RamanSwitch
+from .analysis.colorlegend import ColorLegend
             
-class MeasureParticleWindow(QtWidgets.QMainWindow):
-    
+class GEPARDMainWindow(QtWidgets.QMainWindow):
     def __init__(self, logpath):
-        super(MeasureParticleWindow, self).__init__()
+        super(GEPARDMainWindow, self).__init__()
 
         self.setWindowTitle("GEPARD")
         self.resize(900, 700)
@@ -101,13 +100,24 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
             fileName = QtWidgets.QFileDialog.getSaveFileName(self, "Create New Project",
                                         defaultPath, "*.pkl")[0]
         if fileName:
-            if fileName.find(' ') < 0:
+            isValid, msg = self.testFilename(fileName)
+            if isValid:
                 self.fname = str(fileName)
                 self.view.new(self.fname)  
                 self.scalingChanged(1.)
             else:
-                QtWidgets.QMessageBox.critical(self, "Error", "File path must not contain spaces.")
-     
+                QtWidgets.QMessageBox.critical(self, "Error", msg)
+            
+    @QtCore.pyqtSlot()  
+    def testFilename(self, fileName):
+        if self.view.ramanctrl.name == 'RenishawCOM':   #the renishawCom does not allow Spaces within filePath
+            if fileName.find(' ') == 0:
+                return False, "File path must not contain spaces."
+            else:
+                return True, ""
+        else:
+            return True, ""
+    
     @QtCore.pyqtSlot() 
     def about(self):
         QtWidgets.QMessageBox.about(self, 'GEPARD',
@@ -116,7 +126,7 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
 
     def createActions(self):
         fname = os.path.join(os.path.split(__file__)[0],
-                             os.path.join("data","brand.png"))
+                             os.path.join('data', 'brand.png'))
         self.aboutAct = QtWidgets.QAction(QtGui.QIcon(fname),
                                           "About Particle Measurment", self)
         self.aboutAct.triggered.connect(self.about)
@@ -125,7 +135,7 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.openAct.setShortcut("Ctrl+O")
         self.openAct.triggered.connect(self.open)
         
-        self.importAct = QtWidgets.QAction("&Import Project...", self)
+        self.importAct = QtWidgets.QAction("&Import Zeiss Project...", self)
         self.importAct.setShortcut("Ctrl+I")
         self.importAct.triggered.connect(self.importProject)
         
@@ -188,12 +198,23 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.snapshotAct = QtWidgets.QAction("Save Screenshot", self)
         self.snapshotAct.triggered.connect(self.view.takeScreenshot)
         self.snapshotAct.setDisabled(True)
-        
+
         self.configRamanCtrlAct = QtWidgets.QAction("Configure Raman Control", self)
         self.configRamanCtrlAct.triggered.connect(self.view.configureRamanControl)
         if self.view.simulatedRaman:
             self.configRamanCtrlAct.setDisabled(True)
-    
+            
+        self.noOverlayAct = QtWidgets.QAction("&No Overlay", self)
+        self.selOverlayAct = QtWidgets.QAction("&Selected Overlay", self)
+        self.fullOverlayAct = QtWidgets.QAction("&Full Overlay", self)
+        self.transpAct = QtWidgets.QAction("&Transparent Overlay", self)
+        self.hideLabelAct = QtWidgets.QAction('&Hide Spectra Numbers', self)
+        self.darkenAct = QtWidgets.QAction("&Darken Image", self)
+        self.seedAct = QtWidgets.QAction("&Set Color Seed", self)
+        
+        for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct, self.hideLabelAct, self.transpAct, self.darkenAct, self.seedAct]:
+            act.setDisabled(True)
+            
     def updateModes(self, active=None, maxenabled=None):
         ose, osc, pde, pdc, rse, rsc, pae, pac = [False]*8
         if maxenabled=="OpticalScan":
@@ -273,6 +294,17 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.toolsMenu = QtWidgets.QMenu("&Tools")
         self.toolsMenu.addAction(self.snapshotAct)
         self.toolsMenu.addAction(self.configRamanCtrlAct)
+
+        self.dispMenu = QtWidgets.QMenu("&Display", self)
+        self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
+        self.overlayActGroup.setExclusive(True)
+        
+        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.helpMenu = QtWidgets.QMenu("&Help", self)
         self.helpMenu.addAction(self.aboutAct)
@@ -281,9 +313,9 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.menuBar().addMenu(self.viewMenu)
         self.menuBar().addMenu(self.modeMenu)
         self.menuBar().addMenu(self.toolsMenu)
+        self.menuBar().addMenu(self.dispMenu)
         self.menuBar().addMenu(self.helpMenu)
 
-
     def createToolBar(self):
         self.toolbar = QtWidgets.QToolBar("Tools")
         self.toolbar.setIconSize(QtCore.QSize(100,50))
@@ -322,12 +354,10 @@ if __name__ == '__main__':
         fp = open(logname, "a")
         sys.stderr = fp
         sys.stdout = fp
+    print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), flush=True)
     
-    print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), 
-          flush=True)
-    
-    meas = MeasureParticleWindow(logpath)
-    meas.showMaximized()
+    gepard = GEPARDMainWindow(logpath)
+    gepard.showMaximized()
     ret = app.exec_()
     if fp is not None:
-        fp.close()
\ No newline at end of file
+        fp.close()

analysis/DBAssignments.py

+# -*- coding: utf-8 -*-
+"""
+GEPARD - Gepard-Enabled PARticle Detection
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program, see COPYING.  
+If not, see <https://www.gnu.org/licenses/>.
+"""
+
+import pickle
+
+def loadAssigments(fname):
+    with open(fname, "rb") as fp:
+        assignment = pickle.load(fp)
+    return assignment
+
+def saveAssignments(assignment, fname):
+    with open(fname, "wb") as fp:
+        pickle.dump(assignment, fp, protocol=-1)
+
+
+class DBAssignment(object):
+    def __init__(self):
+        self.filename = None
+        self.assignments = []
+    
+    def setFileName(self, fname):
+        self.filename = fname
+    
+    def save(self):
+        saveAssignments(self, self.filename)
+        
+    def hasAssignment(self, polymerName):
+        polymIsPresent = False
+        for assignment in self.assignments:
+            if assignment.polymerName == polymerName:
+                polymIsPresent = True
+                break
+        return polymIsPresent
+    
+    def getAssignment(self, polymerName):
+        for assignment in self.assignments:
+            if assignment.polymerName == polymerName:
+                return assignment
+    
+    def createNewAssignment(self, polymerName):
+        self.assignments.append(Assignment(polymerName))
+    
+    def updateAssignment(self, polymerName, result, catRes, indic_paint):
+        for assignment in self.assignments:
+            if assignment.polymerName == polymerName:
+                assignment.update(result, catRes, indic_paint)
+                return
+
+
+class Assignment(object):
+    def __init__(self, polymerName):
+        self.polymerName = polymerName
+        self.result = None
+        self.categorizedResult = None
+        self.indication_paint = None
+    
+    def update(self, result, catRes, indic_paint):
+        self.result = result
+        self.categorizedResult = catRes
+        self.indication_paint = indic_paint
+    

colorlegend.py → analysis/colorlegend.py

@@ -20,10 +20,25 @@ If not, see <https://www.gnu.org/licenses/>.
 """
 from PyQt5 import QtCore, QtWidgets, QtGui
 import numpy as np
+import random
+import colorsys
 
+def getColorFromNameWithSeed(name, seed, base255=True):
+    random.seed(seed + name)
+    hue = random.random()
+    random.seed((seed + name)*2)
+    saturation = random.random()/4 + 0.75      #i.e., between 0.75 and 1
+    random.seed((seed + name)*3)
+    value = random.random()/5 + 0.8     #i.e., between 0.8 and 1
+    color = colorsys.hsv_to_rgb(hue, saturation, value)
+    if base255:
+        color = list(color)
+        for i in range(3):
+            color[i] = np.round(color[i]*255)
+        color = tuple(color)
+    return color
 
-WX, WY = 1024, 200
-        
+  
 class ColorLegend(QtWidgets.QMdiSubWindow):
     def __init__(self, parent=None):
         super().__init__(parent)
@@ -40,7 +55,6 @@ class ColorLegend(QtWidgets.QMdiSubWindow):
         
     def setTextColorItems(self, items):
         for text, color in items:
-            print(text, color)
             assert type(text)==str or type(text)==np.str_, "items must be tuples of text and QColor"
             assert type(color)==QtGui.QColor or type(color)==QtCore.Qt.GlobalColor, "items must be tuples of text and QColor"
         self.items = items
@@ -109,6 +123,4 @@ class ColorLegend(QtWidgets.QMdiSubWindow):
                 y0 = index*(fontSize+spacer) + (fontSize - tileSize)/2 +spacer/2
                 qp.drawRect(x0, y0, tileSize, tileSize)
             
-            qp.end()
-        
-        
\ No newline at end of file
+            qp.end()
\ No newline at end of file

analysis/database.py

@@ -27,24 +27,26 @@ with permission from github user CJ Carey (perimosocordiae)
 
 from PyQt5 import QtWidgets, QtCore
 import numpy as np
-import sys
-import dill
+import dill   #TODO: Make it run with pickle... Having two different methods is not so sensefull...
 import os
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
 from matplotlib.figure import Figure
 import functools
 from scipy.linalg import solveh_banded
-from pathlib import Path
 
 class DataBaseWindow(QtWidgets.QMainWindow):
     def __init__(self, parent):
         super(DataBaseWindow, self).__init__()
         self.parent = parent
-        self.path = os.path.join(Path.home(), 'gepard', 'databases')
+        
+        logpath = QtCore.QStandardPaths.writableLocation(
+              QtCore.QStandardPaths.AppLocalDataLocation)
+        
+        self.path = os.path.join(logpath, 'databases')
         self.importPath = self.path
         if not os.path.exists(self.path):
-            os.mkdir(self.path)
+            os.makedirs(self.path)
         self.activeDatabase = None
         self.activeSpectrum = None
         self.activeSpectrumName = None
@@ -314,16 +316,14 @@ class DataBaseWindow(QtWidgets.QMainWindow):
         self.removeSpecBtn.setText('Remove {}'.format(self.activeSpectrumName))
         self.removeSpecBtn.setDisabled(False)
     
-    def save(self):
+    def save(self, showMessage=True):
         for index, db in enumerate(self.databases):
-#            pickling_on = open(db.title+'.dbpkl', 'wb')
-#            pickle.dump(db, pickling_on)
-#            pickling_on.close()
             savename = os.path.join(self.path, db.title+'.db')
             with open(savename, 'wb') as f:
                 dill.dump(db, f)
-            
-        QtWidgets.QMessageBox.about(self, 'Done.', 'Saved {} database(s)'.format(len(self.databases)))
+        
+        if showMessage:
+            QtWidgets.QMessageBox.about(self, 'Done.', 'Saved {} database(s)'.format(len(self.databases)))
     
     def updateDBSelectorList(self):
         self.db_selector.clear()
@@ -336,7 +336,6 @@ class DataBaseWindow(QtWidgets.QMainWindow):
                 self.db_selector.setCurrentText(self.activeDatabase.title)
     
     def selectDataBase(self, refreshParent=False):
-#        if not self.noDBFound:
         if len(self.databases) > 0:
             self.activeDatabaseIndex = self.db_selector.currentIndex()
             self.activeDatabase = self.databases[self.activeDatabaseIndex]
@@ -349,13 +348,7 @@ class DataBaseWindow(QtWidgets.QMainWindow):
                 self.parent.populateRefSelector()
     
     def closeEvent(self, event):
-#        response = QtWidgets.QMessageBox.question(self, 'Warning', 'Exit without saving?', QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
-#        if response == QtWidgets.QMessageBox.Yes:
-#            if self.parent is not None:
-#                self.parent.setDisabled(False)
-#            event.accept()
-#        else:
-#            event.ignore()
+        self.save(showMessage=False)
         if self.parent is not None:
             self.parent.setDisabled(False)
 
@@ -423,8 +416,6 @@ class BaseLineCorrect(QtWidgets.QDialog):
         for i in range(len(spectra)):
             spectra[i][:, 1] = self.origspectra[i][:, 1].copy() - self.als_baseline(self.origspectra[i][:, 1].copy(), asymmetry_param=self.asymSpinBox.value(), 
                                     smoothness_param=self.smoothSpinBox.value(), max_iters = self.iterSpinBox.value())
-#        self.newSpectra = spectra.copy()
-#        self.parent.drawSpectrum(spectra[self.parent.activeSpectrumIndex], self.parent.activeSpectrumName)
         self.saveBtn.setDisabled(False)
     
     def als_baseline(self, intensities, asymmetry_param=0.05, smoothness_param=1e4,
@@ -450,27 +441,17 @@ class BaseLineCorrect(QtWidgets.QDialog):
         if conv < conv_thresh:
           break
         w = new_w
-    #  else:
-    #    print( 'ALS did not converge in %d iterations' % max_iters)
+      else:
+        print( 'ALS did not converge in %d iterations' % max_iters)
       return z
     
-    def save(self):
-#        self.parent.databases[self.parent.activeDatabaseIndex].spectra = self.spectra
-#        self.parent.activeDatabase = self.parent.databases[self.parent.activeDatabaseIndex]
-#        self.parent.activeSpectrum = self.parent.activeDatabase.spectra[self.parent.activeSpectrumIndex]
-#        self.parent.drawSpectrum(self.parent.activeSpectrum, self.parent.activeSpectrumName)
-        self.close()
-    
     def cancel(self):
         self.close()
     
     def closeEvent(self, event):
         if self.parent is not None:
             self.parent.setDisabled(False)
-#            self.parent.drawSpectrum(self.parent.activeSpectrum, self.parent.activeSpectrumName)
-            
-            
-            
+
 
 class WhittakerSmoother(object):
   def __init__(self, signal, smoothness_param, deriv_order=1):
@@ -546,18 +527,4 @@ class CropSpectra(QtWidgets.QDialog):
     def closeEvent(self, event):
         if self.parent is not None:
             self.parent.setDisabled(False)
-        event.accept()
-        
-
-
-def main():
-    global dbWin
-    #start Application
-    app = QtWidgets.QApplication(sys.argv)
-    dbWin = DataBaseWindow(None)
-    app.exec_()
-    
-
-if __name__ == '__main__':
-    main()
-    
\ No newline at end of file
+        event.accept()
\ No newline at end of file

analysis/excelexport.py

+# -*- 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
+import numpy as np
+import pandas as pd
+import os
+import sys
+
+class ExpExcelDialog(QtWidgets.QDialog):
+    def __init__(self, dataset):
+        super(ExpExcelDialog, self).__init__()
+        self.setWindowTitle('Export Options')
+        self.setGeometry(200, 200, 300, 300)
+        self.layout = QtWidgets.QHBoxLayout()
+        self.setLayout(self.layout)
+        
+        self.dataset = dataset
+        self.particleContainer = dataset.particleContainer
+        
+        excelvbox = QtWidgets.QVBoxLayout()
+        excelvbox.addWidget(QtWidgets.QLabel('Select Parameters for Export'))
+        excelgroup = QtWidgets.QGroupBox("Export to Excel", self)
+        
+        self.exportOptions = ['Polymer Type (mandatory)', 'Long Size (µm)', 'Short Size (µm)', 'Area (µm²)', 'HQI', 'Size Classes']
+        self.checkBoxes = []
+        self.sizeClasses = [5, 10, 20, 50, 100, 1e6]
+        
+        for index, option in enumerate(self.exportOptions):
+            self.checkBoxes.append(QtWidgets.QCheckBox(self))
+            self.checkBoxes[-1].setText(option)
+            self.checkBoxes[-1].setChecked(True)
+            
+            if option == 'Polymer Type (mandatory)':
+                self.checkBoxes[-1].setEnabled(False)           #is mandatory!!!
+                    
+            excelvbox.addWidget(self.checkBoxes[-1])
+        
+        self.xlsFileName = QtWidgets.QLineEdit()
+        self.xlsFileName.setText('{}_Particle_List'.format(self.dataset.name))
+        excelvbox.addWidget(QtWidgets.QLabel('Filename:'))
+        excelvbox.addWidget(self.xlsFileName)
+        
+        self.exlbtn = QtWidgets.QPushButton('Export to Excel')
+        self.exlbtn.resize(self.exlbtn.sizeHint())
+        self.exlbtn.clicked.connect(self.toExcel)
+        
+        excelvbox.addWidget(self.exlbtn)
+        excelgroup.setLayout(excelvbox)
+        
+        self.layout.addWidget(excelgroup)
+
+        self.show()
+    
+    def toExcel(self):
+        requiredcolumns = []       
+        uniquePolymers = self.particleContainer.getUniquePolymers()
+        polymers = np.array(self.particleContainer.getListOfParticleAssignments())
+        sizes = np.array(self.particleContainer.getSizesOfAllParticles())
+        
+
+        for box in self.checkBoxes:
+            if box.isChecked() == True:
+                if box.text() != 'Size Classes':
+                    requiredcolumns.append(box.text())
+                    if box.text() == 'Long Size (µm)':
+                        longSizes = np.round(sizes)
+                    elif box.text() == 'Short Size (µm)':
+                        shortSizes = np.round(np.array(self.particleContainer.getShortSizesOfAllParticles()))
+                    elif box.text() == 'HQI':
+                        hqis = np.array(self.particleContainer.getListOfHighestHQIs())
+                    elif box.text() == 'Area (µm²)':
+                        areas = np.array(self.particleContainer.getAreasOfAllParticles())
+                    
+                else:
+                    requiredcolumns.append('0 - 5 µm')
+                    requiredcolumns.append('5 - 10 µm')
+                    requiredcolumns.append('10 - 20 µm')
+                    requiredcolumns.append('20 - 50 µm')
+                    requiredcolumns.append('50 - 100 µm')
+                    requiredcolumns.append('> 100 µm')
+        
+        finalData = np.zeros((len(polymers),len(requiredcolumns)-1))
+        polymertypes = [""]*len(polymers)
+        rowindex = 0
+        for polymer in uniquePolymers:
+            indices = polymers == polymer
+            numentries = int(np.sum(indices))
+            sys.stdout.flush()
+            
+            for colindex, column in enumerate(requiredcolumns):
+                if column == 'Polymer Type (mandatory)':
+                    polymertypes[rowindex:rowindex+numentries] = polymers[indices]              
+                if column == 'Long Size (µm)':
+                    finalData[rowindex:rowindex+numentries, colindex-1] = longSizes[indices]
+                if column == 'Short Size (µm)':
+                    finalData[rowindex:rowindex+numentries, colindex-1] = shortSizes[indices]
+                if column == 'Area (µm²)':
+                    finalData[rowindex:rowindex+numentries, colindex-1] = areas[indices]
+                if column == 'HQI':
+                    finalData[rowindex:rowindex+numentries, colindex-1] = hqis[indices]
+            
+            if '> 100 µm' in requiredcolumns:
+                ##append size classes
+                numPrevCols = len(requiredcolumns) - 1 - len(self.sizeClasses)      #number of previous columns
+                for tableindex, dataindex in enumerate(np.arange(len(indices))[indices]):    
+                    for classindex in range(len(self.sizeClasses)):
+                        upLimit = self.sizeClasses[classindex]
+                        if classindex == 0: lowLimit = 0
+                        else: lowLimit = self.sizeClasses[classindex-1]
+                        curSize = sizes[dataindex]
+                        
+                        if  curSize > lowLimit and curSize <= upLimit:
+                            finalData[rowindex+tableindex, numPrevCols + classindex] = np.int(1)
+                        else:
+                            finalData[rowindex+tableindex, numPrevCols + classindex] = np.int(0)               
+            
+            rowindex = rowindex + numentries
+            
+        #dump into excel file
+        xlsname = os.path.join(self.dataset.path, f'{self.xlsFileName.text()}.xlsx')
+        print('exporting excel to:\n file name:  {} in directory: {}'.format(self.xlsFileName.text(), self.dataset.path))
+        incr = 1
+        while os.path.exists(xlsname):
+            xlsname = os.path.join(self.dataset.path, f'{self.xlsFileName.text()} {incr}.xlsx')
+            incr += 1
+    
+        writer = pd.ExcelWriter(xlsname, engine = 'xlsxwriter')
+        
+        df = pd.DataFrame(finalData, columns=requiredcolumns[1:])
+        df.insert(0, 'Polymer Type', polymertypes)
+        df.to_excel(writer, sheet_name = 'Individual Particles', index = False)
+        if  '> 100 µm' in requiredcolumns:
+            #generate particle statistics report
+            header = ['0 - 5 µm', '5 - 10 µm', '10 - 20 µm', '20 - 50 µm', '50 - 100 µm', '> 100 µm']
+            particleclasses = []
+            
+            for polymer in uniquePolymers:
+                indices = self.particleContainer.getIndicesOfParticleType(polymer)
+                sortind = np.searchsorted([5,10,20,50,100], sizes[indices], 'right')
+                classes = np.bincount(sortind, minlength=6)
+                particleclasses.append(classes)
+            
+            particleclasses = np.array(particleclasses)
+            report = pd.DataFrame(np.array(particleclasses), columns=header,
+                                  dtype=int)
+            report.insert(0, 'Polymer Type', uniquePolymers)
+            report.insert(len(report.columns), 'Sum total', particleclasses.sum(axis=1))
+            report.to_excel(writer, sheet_name = 'Particle Statistics', index=False)
+        writer.save()
+        self.accept()
+        QtWidgets.QMessageBox.about(self, 'Particles succesfully exported', 'List saved to\n' + str(xlsname))
\ No newline at end of file

analysis/importSpectra.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue May 28 20:33:14 2019
+
+@author: brandt
+"""
+import numpy as np
+
+'''Return Spectra array (First column: Wavenumbers, all other columns, intensities)
+and names for all in file contained spectra'''
+
+
+#TODO: Include sanity checks for correct file format?
+
+def importWITecSpectra(fname):
+    def firstColumnOnlyHasUniqueNumbers(data):
+        #this is the case for WITec Spectra sets, but not for Renishaw
+        if len(np.unique(data[:, 0])) == len(data[:, 0]):
+            return True
+        else:
+            return False
+        
+    data = np.loadtxt(fname)
+    names = [f'Spectrum {i+1}' for i in range(data.shape[1]-1)]
+    
+    if firstColumnOnlyHasUniqueNumbers(data):
+        return data, names
+    else:
+        raise ImportError
+    
+def importRenishawSpectra(fname):
+    data = np.loadtxt(fname)
+    rawSpectra = data[:, 2:4]
+    spectraIndices = np.where(rawSpectra[:, 0] == rawSpectra[0, 0])[0]
+    positions = np.zeros((len(spectraIndices), 2))
+    spectra = []
+    names = []
+    
+    spectra = np.zeros((spectraIndices[1], len(spectraIndices)+1))
+    spectra[:, 0] = rawSpectra[0:spectraIndices[1], 0]
+    for i in range(len(spectraIndices)):
+        names.append(f'Spectrum {i+1}')
+        positions[i, :] = [data[spectraIndices[i], 0], data[spectraIndices[i], 1]]
+        if i < len(spectraIndices)-1:
+            spectra[:, i+1] = rawSpectra[spectraIndices[i]:spectraIndices[i+1], 1]
+        else:
+            spectra[:, i+1] = rawSpectra[spectraIndices[i]:, 1]
+    
+    spectra = np.flipud(spectra)
+    wavenumbers = spectra[:, 0]
+    spectra = spectra[:, 1:]
+    
+    return np.transpose(np.vstack((wavenumbers, spectra))), names
+
+def importPerkinElmerSpectra(fname):
+    names = []
+    spectra = []
+    with open(fname) as fp:
+        for index, line in enumerate(fp.readlines()):
+            if index == 0:
+                for name in line.split(';'):
+                    names.append(name.split('.sp')[0])
+                    
+            elif index > 1:
+                spectra.append(line.split(';'))
+    
+    return np.array(spectra, dtype=np.float), names[1:]

analysis/particleAndMeasurement.py

+# -*- coding: utf-8 -*-
+"""
+GEPARD - Gepard-Enabled PARticle Detection
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program, see COPYING.  
+If not, see <https://www.gnu.org/licenses/>.
+"""
+import numpy as np
+
+class Particle(object):
+    def __init__(self):
+        super(Particle, self).__init__()
+        self.index = None
+        self.longSize = np.nan
+        self.shortSize = np.nan
+        self.height = None
+        self.area = None
+        self.contour = None
+        self.measurements = []
+        self.color = None
+        self.shape = None
+        self.wasManuallyEdited = False   #useful tag for extracting data that can now be considered reliable and obviously was classfiied wrong before by the algorithms
+    
+    def addMeasurement(self, refToMeasurement):
+        refToMeasurement.assignedParticle = self
+        self.measurements.append(refToMeasurement)
+