Load TrueMatchResult Works

analysis/analysisview.py

@@ -31,7 +31,7 @@ from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as Navigatio
 
 from .analysiswidgets import ExpExcelDialog
 from .analysisplots import TypeHistogramView, SpectraPlot
-from .loadresults import LoadWITecResults
+from .loadresults import LoadTrueMatchResults
 from .particleeditor import ParticleEditor
 from .database import DataBaseWindow
 from .colorlegend import ColorHandler
@@ -152,7 +152,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         viewLayout.addWidget(splitter2)
         viewLayout.setStretch(1, 1)
 
-        self.optionsGroup = QtWidgets.QGroupBox('Further Options')
+        self.optionsGroup = QtWidgets.QGroupBox('Set HQI Threshold')
         optionsLayout = QtWidgets.QFormLayout()
         
         self.hqiSpinBox = QtWidgets.QDoubleSpinBox()
@@ -162,7 +162,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.hqiSpinBox.setMaximum(100)
         self.hqiSpinBox.setMaximumWidth(100)
         self.hqiSpinBox.valueChanged.connect(self.applyHQIThresholdToResults)
-        optionsLayout.addRow(QtWidgets.QLabel('min HQI:'), self.hqiSpinBox)
+        optionsLayout.addRow(QtWidgets.QLabel('minimum HQI:'), self.hqiSpinBox)
         
 #        self.compHqiSpinBox = QtWidgets.QDoubleSpinBox()
 #        self.compHqiSpinBox.setValue(30.0)
@@ -171,14 +171,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
 #        self.compHqiSpinBox.setDisabled(True)
 #        optionsLayout.addRow(QtWidgets.QLabel('min component HQI'), self.compHqiSpinBox)
         
-        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.optionsGroup.setLayout(optionsLayout)
         self.optionsGroup.setMinimumWidth(175)
 #        self.optionsGroup.setDisabled(True)
@@ -309,7 +301,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
             self.refSelector.setDisabled(False)
             
     def importTrueMatchResults(self):
-        self.importWindow = LoadWITecResults(self.particleContainer, self)
+        self.importWindow = LoadTrueMatchResults(self.particleContainer, self)
         self.importWindow.exec()
     
 #    @QtCore.pyqtSlot(int)
@@ -414,14 +406,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
 #            print('displaying new type with resetting index')
 #            self.displayNewPolymerType()
             
-    
-    def exportToExcel(self):
-        expWin = ExpExcelDialog(self.particleContainer, self)
-        expWin.exec()
-            
-    def exportToSQL(self):
-        sqlexp = SQLExport(self.particleContainer, self)
-        sqlexp.exec()
+    def updateHistograms(self):  
+        self.updateTypeHistogram()
+        self.updateSizeHistogram()
     
     def initializeSpecPlot(self):
         self.specPlot.loadSpectraAndInitializeSpecPlot()
@@ -525,10 +512,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         particleIndicesOfType = self.particleContainer.getIndicesOfParticleType(self.typeSelectorCombo.currentText())
         return particleIndicesOfType[self.particleSelector.value()-1]
     
-    def updateHistograms(self):  
-        self.updateTypeHistogram()
-        self.updateSizeHistogram()
-        
     def updateTypeHistogram(self):
         #draw the general histogram
         colorList = []
@@ -655,7 +638,14 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         for scanIndicator in self.parent.ramanscanitems:
             scanIndicator.hidden = hidden
             scanIndicator.update()
-
+    
+    def exportToExcel(self):
+        expWin = ExpExcelDialog(self.particleContainer, self)
+        expWin.exec()
+            
+    def exportToSQL(self):
+        sqlexp = SQLExport(self.particleContainer, self)
+        sqlexp.exec()
     
     def closeEvent(self, event):
         for window in [self.importWindow, self.dbWin]:

analysis/loadresults.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Created on Thu May 31 10:07:45 2018
+GEPARD - Gepard-Enabled PARticle Detection
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    
 
-@author: brandt
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program, see COPYING.  
+If not, see <https://www.gnu.org/licenses/>.
 """
 
 import numpy as np
 from PyQt5 import QtWidgets
-import sys
-from os import chdir, getcwd
 
 class LoadWITecResults(QtWidgets.QDialog):
     def __init__(self, particleContainer, parent):
@@ -28,43 +40,34 @@ class LoadWITecResults(QtWidgets.QDialog):
         self.hqis = None
         self.addhqis = None
         
-        self.btn1 = QtWidgets.QPushButton('LoadTrueMatchResults')
-        self.btn1.resize(self.btn1.sizeHint()) 
-        self.btn1.clicked.connect(self.loadFileManually)
+        self.loadBtn = QtWidgets.QPushButton('LoadTrueMatchResults')
+        self.loadBtn.resize(self.loadBtn.sizeHint()) 
+        self.loadBtn.clicked.connect(self.loadFileManually)
 
-        optionsLayout = QtWidgets.QFormLayout()
-        self.optionsGroup = QtWidgets.QGroupBox('Compute Options')
-        self.optionsGroup.setDisabled(True)
-        self.btn3 = QtWidgets.QPushButton('Compute')
-        self.btn3.clicked.connect(self.runCalculations)
-        
-        self.label1 = QtWidgets.QLabel('HQI-Threshold:')
-        self.spinbox1 = QtWidgets.QDoubleSpinBox(self)
-        self.spinbox1.valueChanged.connect(self.updateParentSpinboxes)
-        optionsLayout.addRow(self.label1, self.spinbox1)
+#        optionsLayout = QtWidgets.QFormLayout()
+#        self.optionsGroup = QtWidgets.QGroupBox('Compute Options')
+#        self.optionsGroup.setDisabled(True)
+#        
+#        self.label1 = QtWidgets.QLabel('HQI-Threshold:')
+#        self.spinbox1 = QtWidgets.QDoubleSpinBox(self)
+#        self.spinbox1.valueChanged.connect(self.runCalculations)
+#        optionsLayout.addRow(self.label1, self.spinbox1)
         
-        self.label2 = QtWidgets.QLabel('ComponentThreshold:')
-        self.spinbox2 = QtWidgets.QDoubleSpinBox(self)
-        self.spinbox2.valueChanged.connect(self.updateParentSpinboxes)
-        optionsLayout.addRow(self.label2, self.spinbox2)
-        self.label3 = QtWidgets.QLabel('Max Items in Display:')
-        self.numDispSpinbox = QtWidgets.QSpinBox(self)
-        self.numDispSpinbox.setValue(20)
-        self.numDispSpinbox.setMinimum(1)
-        self.numDispSpinbox.setMaximum(40)
-        self.numDispSpinbox.valueChanged.connect(self.updateParentSpinboxes)
-        optionsLayout.addRow(self.label3, self.numDispSpinbox)
-        optionsLayout.addRow(self.btn3)
+#        self.label2 = QtWidgets.QLabel('ComponentThreshold:')
+#        self.spinbox2 = QtWidgets.QDoubleSpinBox(self)
+#        self.spinbox2.valueChanged.connect(self.updateParentSpinboxes)
+#        optionsLayout.addRow(self.label2, self.spinbox2)
         
-        for box in [self.spinbox1, self.spinbox2]:
-            box.setValue(50)
-            box.setDecimals(1)
-            box.setSingleStep(5)
-            box.setMinimum(0)
-            box.setMaximum(100)
-        self.spinbox2.setValue(30)          #more reasonable...
-        
-        self.optionsGroup.setLayout(optionsLayout)
+#        for box in [self.spinbox1, self.spinbox2]:
+#        for box in [self.spinbox1]:
+#            box.setValue(50)
+#            box.setDecimals(1)
+#            box.setSingleStep(5)
+#            box.setMinimum(0)
+#            box.setMaximum(100)
+##        self.spinbox2.setValue(30)          #more reasonable...
+#        
+#        self.optionsGroup.setLayout(optionsLayout)
         
         self.reviewGroup = QtWidgets.QGroupBox('Review Changes')
         self.reviewGroup.setDisabled(True)
@@ -76,8 +79,8 @@ class LoadWITecResults(QtWidgets.QDialog):
         reviewLayout.addStretch()
         self.reviewGroup.setLayout(reviewLayout)
 
-        self.layout.addWidget(self.btn1, 0, 0)
-        self.layout.addWidget(self.optionsGroup, 1, 0)
+        self.layout.addWidget(self.loadBtn, 0, 0)
+#        self.layout.addWidget(self.optionsGroup, 1, 0)
         self.layout.addWidget(self.reviewGroup, 2, 0)
         
         self.manualPolymers = {}
@@ -90,11 +93,6 @@ class LoadWITecResults(QtWidgets.QDialog):
         self.numFlagForSetUnknown = 2
         self.numFlagForPrompt = 3
     
-    def updateParentSpinboxes(self):
-        self.parent.hqiSpinBox.setValue(self.spinbox1.value())
-        self.parent.compHqiSpinBox.setValue(self.spinbox2.value())
-        self.parent.dispResultSpinBox.setValue(self.numDispSpinbox.value())
-    
     def show3FlagsReview(self):
         self.editEntryWindow = ModifyManualEdits(self, self.manualPolymers, self.manualAdditives)        
         self.editEntryWindow.show()
@@ -114,18 +112,14 @@ class LoadWITecResults(QtWidgets.QDialog):
                     for lineindex, line in enumerate(file):
                         if lineindex > 0:
                             self.trueMatchResults.append(line)
-
-        self.btn1.setText('Data loaded')
-        self.optionsGroup.setDisabled(False)
+        self.runCalculations()                            
     
     def formatResults(self, rawResults):   #get rid of header line, first data interpretation
         results = []
-        for index,line in enumerate(rawResults):
+        for index, line in enumerate(rawResults):
             if index == 0:
                 line = line.strip().split(';')[:-1]         #disregard the last entry of each line, as each line ends with ; <- that produces an empty entry...
-                if line[0] != 'Search Spectrum Name':
-                    print('incompatible data format')
-                    break 
+                assert line[0] == 'Search Spectrum Name', 'Assertion Error in loadTrueMatchResults'
                 #detect, whether one- or multicomponent-search was done
                 if line[-1] == 'IsMarked':
                     numhits = np.int(line[-2].split(' ')[-1])
@@ -142,38 +136,29 @@ class LoadWITecResults(QtWidgets.QDialog):
         
         return results, numspectra, numcomps, numhits
     
-    def interpretEntry(self, index, entry, numhits, numcomps):
+    def interpretEntry(self, entry, numhits, numcomps):
         entry = entry.split(';')
-        polymertype, additive, hqi, addhqi = None, None, None, None   #assign default None
-
+        specIndex, polymertype, additive, hqi, addhqi = None, None, None, None, 0   #assign defaults
+        
+        #specNameFormat is: SampleName_000_Spec.Data 1 (SpecIndex)
+        specName = entry[0]
+        indexOpenBracket = specName.find('(')
+        indexCloseBracket = specName.find(')')
+        specIndex = int(specName[indexOpenBracket+1:indexCloseBracket])
+        
         #find yes-flags
         flags = np.where(np.array(entry) == 'yes')[0]
         if len(flags) == 0:
             #take highest HQI entry
             if numcomps == 1:
-                if float(entry[1]) > self.spinbox1.value():
-                    polymertype = entry[2]
-                    hqi = entry[1]
-                else:
-                    polymertype = 'unknown'
-                    hqi = 0
+                polymertype = entry[2]
+                hqi = entry[1]
             else:
-                if float(entry[1]) > self.spinbox1.value():
-                    polymertype = entry[5]
-                    hqi = entry[1]
-                    if float(entry[6]) > self.spinbox2.value(): 
-                        additive = entry[7]
-                        addhqi = entry[6]
-                    else: 
-                        additive = 'none'
-                        addhqi = 0
-                        
-                else:
-                    polymertype = 'unknown'
-                    additive = 'none'
-                    hqi = 0
-                    addhqi = 0
-                    
+                polymertype = entry[5]
+                hqi = entry[1]
+                additive = entry[7]
+                addhqi = entry[6]
+
         elif len(flags) == 1:
             #exactly one flag was placed, take this entry
             if numcomps == 1:
@@ -193,78 +178,68 @@ class LoadWITecResults(QtWidgets.QDialog):
                 addhqi = 0
                 
         elif len(flags) == 3:
-            
             hqi = 100
-            if index not in self.manualPolymers:
-                polymertype, ok = QtWidgets.QInputDialog.getText(self, 'Name of main component', 'Spectrum at index {} is:'.format(index))
-                self.manualPolymers[index] = polymertype
+            if specIndex not in self.manualPolymers:
+                polymertype, ok = QtWidgets.QInputDialog.getText(self, 'Name of main component', 'Spectrum at index {} is:'.format(specIndex))
+                self.manualPolymers[specIndex] = polymertype
             else:
-                polymertype = self.manualPolymers[index]
+                polymertype = self.manualPolymers[specIndex]
             if numcomps > 1:
                 addhqi = 100
                 if entry[0] not in self.manualAdditives:
-                    additive, ok = QtWidgets.QInputDialog.getText(self, 'Name of additive', 'Additive at index {} is:'.format(index))
-                    self.manualAdditives[index] = additive
+                    additive, ok = QtWidgets.QInputDialog.getText(self, 'Name of additive', 'Additive at index {} is:'.format(specIndex))
+                    self.manualAdditives[specIndex] = additive
                 else:
-                    additive = self.manualAdditives[index]
+                    additive = self.manualAdditives[specIndex]
         else: 
-            QtWidgets.QMessageBox.about(self, 'Error!', 'No rule for {} flags, found at spectrum index {}'.format(len(flags), index))
+            QtWidgets.QMessageBox.about(self, 'Error!', 'No rule for {} flags, found at spectrum index {}'.format(len(flags), specIndex))
             
-        if addhqi is None:
-            addhqi = 0
-        
-        return polymertype, additive, float(hqi), float(addhqi)
+        return specIndex, polymertype, additive, float(hqi), float(addhqi)
 
-    def runCalculations(self):        
+    def runCalculations(self):     
         self.resultList, numspectra, numcomps, numhits = self.formatResults(self.trueMatchResults)
-        self.dispresults = self.numDispSpinbox.value()
-        
-        self.polymertypes =[]
-        self.hqis = []        
+        self.polymertypes = [None]*numspectra
+        self.hqis = [None]*numspectra        
         
         if numcomps == 1:               #####SINGLE COMPONENT SEARCH
             self.additives = None
             self.addhqis = None
-            self.spinbox2.setEnabled(False)
+#            self.spinbox2.setEnabled(False)
             for index, entry in enumerate(self.resultList):
                 if len(entry) == 0:
                     del self.resultList[index]
                 else:
-                    polymertype, additive, hqi, addhqi = self.interpretEntry(index, entry, numhits, numcomps)
-                    self.polymertypes.append(polymertype)
-                    self.hqis.append(hqi)
+                    specIndex, polymertype, additive, hqi, addhqi = self.interpretEntry(entry, numhits, numcomps)
+                    self.polymertypes[specIndex] = polymertype
+                    self.hqis[specIndex] = hqi
 
         else:                   #####MULTI-COMPONENT SEARCH
-            self.additives = []
-            self.addhqis = []
+            self.additives = [None]*numspectra
+            self.addhqis = [None]*numspectra
 
             for index, entry in enumerate(self.resultList):
                 if len(entry) > 0:
-                    polymertype, additive, hqi = self.interpretEntry(index, entry, numhits, numcomps)
-                    self.polymertypes.append(polymertype)
-                    self.hqis.append(hqi)
-                    self.additives.append(additive)
-                    self.addhqis.append(addhqi)
+                    specIndex, polymertype, additive, hqi = self.interpretEntry(entry, numhits, numcomps)
+                    self.polymertypes[specIndex] = polymertype
+                    self.hqis[specIndex] = hqi
+                    self.additives[specIndex] = additive
+                    self.addhqis[specIndex] = addhqi
     
         assert len(self.polymertypes) == len(self.resultList), 'incorrect number of polymer types added...'
+        assert not None in self.polymertypes, 'wrong assignments in loadResults'
+        assert not None in self.hqis, 'wrong assignments in loadResults'
 
         self.particleContainer.applyAssignmentListToParticleMeasurements(self.polymertypes)
         self.particleContainer.applyHQIListToParticleMeasurements(self.hqis)
-        self.parent.formatResults()
         
         if len(self.manualPolymers) > 0:
             self.reviewGroup.setDisabled(False)
+        
+        self.parent.applyHQIThresholdToResults()
+        self.loadBtn.setText('Data loaded')
+        QtWidgets.QMessageBox.about(self, 'Success', 'Results were imported successfully.\nYou can close this window or modify manual edits.')
 
     def closeEvent(self, event):
-#        self.datastats.resetResults(self.polymertypes, self.additives, 
-#                                    self.hqis, self.addhqis)
-        self.parent.updateBtn.clicked.connect(self.parent.formatResults)
-        self.parent.formatResults()
-        self.parent.show_hide_labels()
-#        minHQI = self.parent.hqiSpinBox.value()
-#        compHQI = self.parent.compHqiSpinBox.value()
-        self.parent.dataset.save()
-        
         #TODO: SANITY CHECK FOR DATA CONSISTENCY!!
         
 #        if not self.parent.datastats.saveAnalysisResults(minHQI, compHQI):
@@ -331,21 +306,4 @@ class ModifyManualEdits(QtWidgets.QWidget):
         self.parent.manualPolymers, self.parent.manualAdditives = self.polymerEdits, self.additiveEdits
         self.parent.runCalculations()
         self.close()
-
-
-if __name__ == "__main__":
-
-    wd=getcwd()
-    chdir(wd)
-
-    try:
-        del(app)
-    except:
-        pass
-    
-    app = QtWidgets.QApplication(sys.argv)
-    mainWin = LoadWITecResults(None)
-    mainWin.show()
-    app.exec_()
-        
     

analysis/particleInfo.py

@@ -72,22 +72,24 @@ class ParticleContainer(object):
             particle.applyHQITresholdToMeasurements(minHQI)
             
     def applyAssignmentListToParticleMeasurements(self, assignmentList):
-        indicesOfTransferredAssignments = []
+        '''AssignmentList is list of spectra assignments in order of spectra indices'''
+        indicesOfTransferredAssignments = [None]*len(assignmentList)
         for particle in self.particles:
             for meas in particle.getMeasurements():
                 scanIndex = meas.getScanIndex()
                 meas.setAssignment(assignmentList[scanIndex])
-                indicesOfTransferredAssignments.append(scanIndex)
-        assert np.unique(indicesOfTransferredAssignments) == np.unique((range(len(assignmentList))))
+                indicesOfTransferredAssignments[scanIndex] = scanIndex
+        assert not None in indicesOfTransferredAssignments
                 
     def applyHQIListToParticleMeasurements(self, hqiList):
-        indicesOfTransferredAssignments = []
+        '''HQI-List is list of spectra hqis in order of spectra indices'''
+        indicesOfTransferredHQIs = [None]*len(hqiList)
         for particle in self.particles:
             for meas in particle.getMeasurements():
                 scanIndex = meas.getScanIndex()
-                meas.setAssignment(hqiList[scanIndex])
-                indicesOfTransferredAssignments.append(scanIndex)
-        assert np.unique(indicesOfTransferredAssignments) == np.unique((range(len(hqiList))))
+                meas.setHQI(hqiList[scanIndex])
+                indicesOfTransferredHQIs[scanIndex] = scanIndex
+        assert not None in indicesOfTransferredHQIs
     
     def getParticleOfIndex(self, index):
         particle = self.particles[index]