Several Bugfixes

analysis/analysisplots.py

@@ -113,7 +113,7 @@ class SpectraPlot(QtWidgets.QGroupBox):
         layout = QtWidgets.QHBoxLayout()
         self.canvas = FigureCanvas(Figure())
         self.spec_axis = self.canvas.figure.subplots()
-        self.reference_ax = self.spec_axis.twinx()
+        self.reference_axis = 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)

analysis/particleCharacterization.py

@@ -60,12 +60,24 @@ def getParticleStatsWithPixelScale(cnt, fullimage, dataset):
     
     newStats.height = getParticleHeight(cnt, dataset)    
     newStats.shape = getParticleShape(cnt, newStats.height)
+    if newStats.shape == 'fibre':
+        newStats.longSize, newStats.shortSize = getFibreDimension(cnt)
+        newStats.longSize *= pixelscale
+        newStats.shortSize *= pixelscale
     
     partImg = getParticleImageFromFullimage(cnt, fullimage)
     newStats.color = getParticleColor(partImg)
-    
     return newStats
 
+def getFibreDimension(contour):
+    longSize = cv2.arcLength(contour, True)/2
+    img = contoursToImg([contour])[0]
+    dist = cv2.distanceTransform(img, cv2.DIST_L2, 3)
+    maxThickness = np.max(dist)*2
+    return longSize, maxThickness
+    
+    
+
 def getParticleColor(imgRGB, colorClassifier=None):
     img = cv2.cvtColor(imgRGB, cv2.COLOR_RGB2HSV_FULL)
     meanHSV = cv2.mean(img)

analysis/particleEditor.py

@@ -171,7 +171,7 @@ class ParticleEditor(QtCore.QObject):
                                        'Particle contours are not connected.\nThat is currently not supported!')
             return
 
-        self.mergeParticlesInParticleContainerAndSampleView(contourIndices,newContour, newAssignment)
+        self.mergeParticlesInParticleContainerAndSampleView(contourIndices, newContour, newAssignment)
     
     @QtCore.pyqtSlot(list, str)
     def reassignParticles(self, contourindices, newAssignment):
@@ -180,12 +180,14 @@ class ParticleEditor(QtCore.QObject):
         for partIndex in contourindices:
             self.particleContainer.reassignParticleToAssignment(partIndex, newAssignment)
         
+        self.viewparent.updateParticleInfoBox(partIndex)
         self.particleAssignmentChanged.emit()
      
     @QtCore.pyqtSlot(list, str)
     def paintParticles(self, contourIndices, newAssignment):
         print(f'painting indices {contourIndices} into {newAssignment}')
         self.createSafetyBackup()
+        self.viewparent.removeParticleInfoBox()
         self.storedIndices = contourIndices
         self.storedAssignmend = newAssignment
         
@@ -208,6 +210,7 @@ class ParticleEditor(QtCore.QObject):
         except NotConnectedContoursError:
             QtWidgets.QMessageBox.critical(self.viewparent, 'ERROR!', 
                                        'Particle contours are not connected.\nThat is currently not supported!')
+            self.viewparent.updateParticleInfoBox(self.storedIndices[-1])
             self.storedIndices = []
             self.storedAssignmend = None
             self.destroyParticlePainter()
@@ -238,6 +241,7 @@ class ParticleEditor(QtCore.QObject):
         
         self.viewparent.resetContourIndices()
         self.particleContainer.resetParticleIndices()
+        self.viewparent.updateParticleInfoBox(self.particleContainer.getNumberOfParticles()-1)
         self.particleAssignmentChanged.emit()
     
     @QtCore.pyqtSlot(list, str)
@@ -245,12 +249,14 @@ class ParticleEditor(QtCore.QObject):
         print(f'changing color of particles {contourIndices} into {newColor}')
         for partIndex in contourIndices:
             self.particleContainer.changeParticleColor(partIndex, newColor)
+        self.viewparent.updateParticleInfoBox(partIndex)
             
     @QtCore.pyqtSlot(list, str)
     def changeParticleShapes(self, contourIndices, newShape):
         print(f'changing shape of particles {contourIndices} into {newShape}')
         for partIndex in contourIndices:
             self.particleContainer.changeParticleShape(partIndex, newShape)
+        self.viewparent.updateParticleInfoBox(partIndex)
     
     @QtCore.pyqtSlot(list)
     def deleteParticles(self, contourIndices):

gepard.py

@@ -352,8 +352,8 @@ 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)

legacyConvert.py

@@ -191,6 +191,11 @@ def updateParticleStats(dset):
             except InvalidParticleError:
                 markForDeletion(particle)
             
+            if particle.shape == 'fibre':
+                particle.longSize, particle.shortSize = pc.getFibreDimension(particle.contour)
+                particle.longSize *= dset.getPixelScale()
+                particle.shortSize *= dset.getPixelScale()
+            
     print(f'deleting {len(deleteIndices)} particles')
     for index in sorted(deleteIndices, reverse=True):
         dset.particleContainer.removeParticle(index)

sampleview.py

@@ -129,7 +129,7 @@ class SampleView(QtWidgets.QGraphicsView):
                     
     def closeEvent(self, event):
         reply = QtWidgets.QMessageBox.question(self, 'Message',
-            "Are you sure to quit?", QtWidgets.QMessageBox.Yes | 
+            "Do you really want to quit?", QtWidgets.QMessageBox.Yes | 
             QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
 
         if reply == QtWidgets.QMessageBox.Yes:
@@ -394,12 +394,6 @@ class SampleView(QtWidgets.QGraphicsView):
             cnt.update()
             self.selectedParticleIndices.remove(cnt.particleIndex)
         
-        def updateParticleInfoBox(index):
-            if self.particleInfoBox is not None:
-                self.scene().removeItem(self.particleInfoBox)
-            self.particleInfoBox = ParticleInfo(self.dataset.particleContainer.getParticleOfIndex(index))
-            self.scene().addItem(self.particleInfoBox)
-            
         p = self.mapToScene(event.pos())
         p = QtCore.QPointF(p.x(), p.y())
         
@@ -422,10 +416,9 @@ class SampleView(QtWidgets.QGraphicsView):
                         self.selectedParticleIndices.remove(cnt.particleIndex)
 
         if len(self.selectedParticleIndices) > 0:
-            updateParticleInfoBox(self.selectedParticleIndices[-1])
+            self.updateParticleInfoBox(self.selectedParticleIndices[-1])
         else:
-            self.scene().removeItem(self.particleInfoBox)
-            self.particleInfoBox = None
+            self.removeParticleInfoBox()
             
         self.update()
 
@@ -614,12 +607,21 @@ class SampleView(QtWidgets.QGraphicsView):
         self.contourItems[index].isSelected = True
         self.selectedParticleIndices =[index]
         
+        self.updateParticleInfoBox(index)
+        self.update()
+    
+    def updateParticleInfoBox(self, particleIndex):
+        self.removeParticleInfoBox()
+        self.addParticleInfoBox(particleIndex)
+    
+    def removeParticleInfoBox(self):
         if self.particleInfoBox is not None:
             self.scene().removeItem(self.particleInfoBox)
+            self.particleInfoBox = None
     
-        self.particleInfoBox = ParticleInfo(self.dataset.particleContainer.getParticleOfIndex(index))
+    def addParticleInfoBox(self, particleIndex):
+        self.particleInfoBox = ParticleInfo(self.dataset.particleContainer.getParticleOfIndex(particleIndex))
         self.scene().addItem(self.particleInfoBox)
-        self.update()
     
     def centerOnRamanIndex(self, index, centerOn=True, highlightIndex=True):
         if centerOn: