.gitignore

+
+__pycache__/
+
+gepard\.cfg
+
+analysis/database_config\.txt
+
+*.so

analysis/analysisplots.py

@@ -115,11 +115,6 @@ class SpectraPlot(QtWidgets.QGroupBox):
         layout = QtWidgets.QHBoxLayout()
         self.canvas = FigureCanvas(Figure())
         self.spec_axis = self.canvas.figure.subplots()
-        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.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)
@@ -138,10 +133,13 @@ class SpectraPlot(QtWidgets.QGroupBox):
         #draw Sample Spectrum
         self.spec_axis.axis("on")
         self.spec_axis.clear()
-        self.spec_axis.set_title('{}, ScanPoint Number {}, Size = {} µm, HQI = {}'.format(assignment, specIndex+1, particleSize, hqi))
+        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)
         
         if self.spectra is not None:
             self.spec_axis.plot(self.spectra[:, 0], self.spectra[:, specIndex+1])
+            self.spec_axis.set_title('{}, ScanPoint Number {}, Size = {} µm, HQI = {}'.format(assignment, 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))

analysis/analysisview.py

@@ -548,13 +548,10 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
     def jumpToIndicatedSpectrum(self):
         self.currentSpectrumIndex = self.specNumberSelector.value()-1
         self.currentParticleIndex = self.particleContainer.getParticleIndexContainingSpecIndex(self.currentSpectrumIndex)
-        self.centerOnSpecIndex(self.currentSpectrumIndex)
+        self.viewparent.centerOnRamanIndex(self.currentSpectrumIndex)
         self.viewparent.highLightContour(self.currentParticleIndex)
         self.updateSpecPlot()
     
-    def centerOnSpecIndex(self, index):
-        self.viewparent.centerOnRamanIndex(index)
-    
     def darkenBackground(self):
         self.viewparent.darkenPixmap = self.darkenAct.isChecked()
         

analysis/particleContainer.py

@@ -39,9 +39,9 @@ class ParticleContainer(object):
         self.typeHistogram = None
     
     def addEmptyMeasurement(self):
-        self.measurements.append(Measurement())
-        indexOfNewMeas = len(self.measurements)-1
-        return indexOfNewMeas
+        newMeas = Measurement()
+        self.measurements.append(newMeas)
+        return self.measurements.index(newMeas)
     
     def clearParticles(self):
         self.particles = []
@@ -57,7 +57,7 @@ class ParticleContainer(object):
         self.measurements[indexOfMeasurment].pixelcoord_y = y
     
     def getMeasurementScanindex(self, indexOfMeasurement):
-        return self.measurements[indexOfMeasurement].ramanScanIndex
+        return self.measurements[indexOfMeasurement].getScanIndex()
     
     def getSpectraFromDisk(self):
         spectra = None
@@ -71,18 +71,19 @@ class ParticleContainer(object):
             if fname:
                 #TODO: implement a more elegant way of testing through the individual imports...
                 try:
-                    self.spectra, spectraNames = importSpectra.importWITecSpectra(fname)
+                    spectra, spectraNames = importSpectra.importWITecSpectra(fname)
                 except ImportError:
                     try:
-                        self.spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
+                        spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
                     except ImportError:
                         try:
-                            self.spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)
+                            spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)
                         except ImportError:
                             pass
                 
             if spectra is not None:
                 np.save(self.datasetParent.getSpectraFileName(), spectra)
+                
         return spectra
     
     def initializeParticles(self, numParticles):

dataset.py

@@ -242,6 +242,7 @@ class DataSet(object):
             self.version = 2
         
         if self.version == 2:
+            print("Converting legacy version 2 to 3")
             self.particleContainer = ParticleContainer(self)
  
             self.particleContainer.initializeParticles(len(self.particlestats))
@@ -249,20 +250,23 @@ class DataSet(object):
             self.particleContainer.setParticleStats(self.particlestats)
             self.particleContainer.applyPixelScaleToParticleStats(self.getPixelScale())
             
+            self.particleContainer.clearMeasurements()
+            
             if len(self.particlestats) > 0:   #i.e., particle detection was completed and particle data is there 
                 self.particleDetectionDone = True
                 for particleIndex, listOfScanIndices in enumerate(self.particles2spectra):
                     curParticle = self.particleContainer.getParticleOfIndex(particleIndex)
+                    curParticle.measurements = []
                     for scanIndex in listOfScanIndices:
                         indexOfNewMeas = self.particleContainer.addEmptyMeasurement()
-                        x, y = self.ramanpoints[indexOfNewMeas ][0], self.ramanpoints[indexOfNewMeas][1]
+                        x, y = self.ramanpoints[indexOfNewMeas][0], self.ramanpoints[indexOfNewMeas][1]
                         self.particleContainer.setMeasurementPixelCoords(indexOfNewMeas, x, y)
                         self.particleContainer.setMeasurementScanIndex(indexOfNewMeas, scanIndex)
                         curParticle.addMeasurement(self.particleContainer.measurements[indexOfNewMeas])
             
             for particle in self.particleContainer.particles:
                 for meas in particle.measurements:
-                    specIndex = meas.ramanScanIndex
+                    specIndex = meas.getScanIndex()
                     meas.setAssignment(self.results['polymers'][specIndex])
                     meas.setHQI(self.results['hqis'][specIndex])
             

detectionview.py

@@ -672,7 +672,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
                     particleContainer.setMeasurementPixelCoords(indexOfNewMeas, point.x, point.y)
                     curParticle.addMeasurement(particleContainer.measurements[indexOfNewMeas])
                     
-                    
+            self.dataset.ramanpoints = measurementPoints
             self.dataset.particleDetectionDone = True
             self.dataset.mode = "prepareraman"
             self.dataset.save()

gepard.cfg

-# rename this file to gepard.cfg and adapt these parameters
-
-[Defaults]
-# file path without "" !
-file_path = .
-
-[Interface]
-# possible values: SIMULATED_RAMAN_CONTROL, WITEC_CONTROL, RENISHAW_CONTROL
-raman_interface = SIMULATED_RAMAN_CONTROL
-
-
-[General Microscope Setup]
-magnification = 20
-
-[Renishaw]
-#information specific for renishaw control
-#image mikrometer sizes for bright and dark field camera, format: width*height
-#please insert, as it would represent an image at 1x magnification
-#if unavailable, export an image from the Renishaw Camera viewer. Export as jpeg (without axes) and, within Gepard, go to Tools->ConfigureRamanControl. 
-img_size_BF = 9016.0*5748.0
-img_size_DF = 4524.0*2874.0
-#Path to measuring templates (*.wxm)
-measTemplatePath = C:\RamanData
\ No newline at end of file

gepard.py

@@ -323,12 +323,12 @@ if __name__ == '__main__':
     logpath = QtCore.QStandardPaths.writableLocation(
               QtCore.QStandardPaths.AppLocalDataLocation)
     fp = None
-#    if logpath != "":
-#        if not os.path.exists(logpath):
-#            os.mkdir(logpath)
-#        logname = os.path.join(logpath, 'logfile.txt')
-#
-#        fp = open(logname, "a")
+    if logpath != "":
+        if not os.path.exists(logpath):
+            os.mkdir(logpath)
+        logname = os.path.join(logpath, 'logfile.txt')
+
+        fp = open(logname, "a")
 #        sys.stderr = fp
 #        sys.stdout = fp
     print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), flush=True)

ramanscanui.py

@@ -234,6 +234,7 @@ class RamanScanUI(QtWidgets.QWidget):
             for measIndex, ramanScanIndex in enumerate(cmin):
                 self.dataset.particleContainer.setMeasurementScanIndex(measIndex, ramanScanIndex)
             
+            self.dataset.ramanscansortindex = cmin
             self.view.saveDataSet()
             self.view.prepareAnalysis()
             self.view.scaleImage(2.0)

sampleview.py

@@ -555,14 +555,20 @@ class SampleView(QtWidgets.QGraphicsView):
     def prepareAnalysis(self):
         self.clearItems()
         if self.dataset.particleDetectionDone:
-            for measIndex, measPoint in enumerate(self.dataset.particleContainer.getMeasurementPixelCoords()):
-                scanIndex = self.dataset.particleContainer.getMeasurementScanindex(measIndex)
-                item = RamanScanIndicator(self, scanIndex+1, 20, (measPoint[0], measPoint[1]))
+            data = []
+            for i in self.dataset.ramanscansortindex:
+                data.append(list(self.dataset.ramanpoints[i]))
+            for i in range(len(data)):
+                item = RamanScanIndicator(self, i+1, 20, (data[i][0],data[i][1]))
                 self.scene().addItem(item)
                 self.ramanscanitems.append(item)
+#            for index, meas in enumerate(self.dataset.particleContainer.measurements):
+#                number = meas.ramanScanIndex+1
+#                item = RamanScanIndicator(self, number, 20, (meas.pixelcoord_x, meas.pixelcoord_y))
+#                self.scene().addItem(item)
+#                self.ramanscanitems.append(item)
     
     def resetParticleContours(self):
-#        self.resetBoundary()
         t0 = time.time()
         for cnt in self.contourItems:
             self.scene().removeItem(cnt)