Small Bugfixes / Optimizations

.gitignore

@@ -6,3 +6,7 @@ gepard\.cfg
 analysis/database_config\.txt
 
 *.so
+
+*.c
+
+external/build/

analysis/analysisview.py

@@ -111,8 +111,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.specNumberSelector = QtWidgets.QSpinBox()
         self.specNumberSelector.setMinimumWidth(100)
         self.specNumberSelector.setMinimum(1)
-        numParticles = self.particleContainer.getNumberOfParticles()
-        self.specNumberSelector.setMaximum(numParticles)
+        numSpectra = self.particleContainer.getNumberOfMeasurements()
+        self.specNumberSelector.setMaximum(numSpectra)
         
         self.jumpToSpecBtn = QtWidgets.QPushButton('Jump To Spectrum of Number:')
         self.jumpToSpecBtn.released.connect(self.jumpToIndicatedSpectrum)
@@ -387,8 +387,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.typeSelectorCombo.addItems(uniquePolymers)
         self.typeSelectorCombo.currentIndexChanged.connect(self.setTypeSelector)
         
-        numParticles = self.particleContainer.getNumberOfParticles()
-        self.specNumberSelector.setMaximum(numParticles)
+        numSpectra = self.particleContainer.getNumberOfMeasurements()
+        self.specNumberSelector.setMaximum(numSpectra)
         
     def initializeSpecPlot(self):
         self.specPlot.loadSpectraAndInitializeSpecPlot()
@@ -531,7 +531,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         
         self.particleSelector.setValue(partIndices.index(particleIndex)+1)
         
-        
         specIndices = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)
         self.spectrumSelector.setValue(1)
         self.spectrumSelector.setMaximum(len(specIndices))        

analysis/particleContainer.py

@@ -176,6 +176,9 @@ class ParticleContainer(object):
     def getNumberOfParticles(self):
         return len(self.particles)
     
+    def getNumberOfMeasurements(self):
+        return len(self.measurements)
+    
     def getParticleContours(self):
         contours = [part.contour for part in self.particles]
         return contours

analysis/particlePainter.py

@@ -166,7 +166,7 @@ class ParticlePainter(QtWidgets.QGraphicsItem):
             painter.drawEllipse(p[0]-p[2], p[1]-p[2], 2*p[2], 2*p[2])            
         
         if self.pixmap is not None:
-            painter.setOpacity(0.6)
+            painter.setOpacity(0.4)
             painter.drawPixmap(self.topLeft[1], self.topLeft[0], self.pixmap)
         
                 

dataset.py

@@ -252,6 +252,9 @@ class DataSet(object):
             
             self.particleContainer.clearMeasurements()
             
+            if self.particles2spectra is None:
+                self.particles2spectra = [[int(np.where(self.ramanscansortindex == i)[0])] for i in range(len(self.ramanscansortindex))]
+            
             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):
@@ -259,11 +262,12 @@ class DataSet(object):
                     curParticle.measurements = []
                     for scanIndex in listOfScanIndices:
                         indexOfNewMeas = self.particleContainer.addEmptyMeasurement()
-                        x, y = self.ramanpoints[indexOfNewMeas][0], self.ramanpoints[indexOfNewMeas][1]
+                        indexOfMeasInRamanPoints = self.ramanscansortindex[scanIndex]
+                        x, y = self.ramanpoints[indexOfMeasInRamanPoints][0], self.ramanpoints[indexOfMeasInRamanPoints][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.getScanIndex()

detectionview.py

@@ -672,7 +672,6 @@ 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.py

@@ -329,8 +329,8 @@ if __name__ == '__main__':
         logname = os.path.join(logpath, 'logfile.txt')
 
         fp = open(logname, "a")
-#        sys.stderr = fp
-#        sys.stdout = fp
+        sys.stderr = fp
+        sys.stdout = fp
     print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), flush=True)
     
     gepard = GEPARDMainWindow(logpath)

ramanscanui.py

@@ -234,7 +234,6 @@ 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

@@ -555,18 +555,11 @@ class SampleView(QtWidgets.QGraphicsView):
     def prepareAnalysis(self):
         self.clearItems()
         if self.dataset.particleDetectionDone:
-            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]))
+            for meas in 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)
-#            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):
         t0 = time.time()