Bugfix in selection

analysis/analysisview.py

@@ -149,7 +149,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         navigationLayout.addWidget(QtWidgets.QLabel('Select Spectrum'))
         navigationLayout.addWidget(self.spectrumSelector)
         navigationLayout.addWidget(self.spectrumNumberLabel)
-#        navigationLayout.addStretch()
         
         self.navigationGroup.setLayout(navigationLayout)
         
@@ -579,14 +578,12 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.currentSpectrumIndex = self.specNumberSelector.value()-1
         self.currentParticleIndex = self.particleContainer.getParticleIndexContainingSpecIndex(self.currentSpectrumIndex)
         self.centerOnSpecIndex(self.currentSpectrumIndex)
-        self.highLightContour(self.currentParticleIndex)
+        self.viewparent.highLightContour(self.currentParticleIndex)
+        self.updateSpecPlot()
     
     def centerOnSpecIndex(self, index):
         self.viewparent.centerOnRamanIndex(index)
     
-    def highLightContour(self, index):
-        self.viewparent.highLightContour(index)
-    
     def darkenBackground(self):
         self.viewparent.darkenPixmap = self.darkenAct.isChecked()
         

analysis/analysiswidgets.py

@@ -37,7 +37,6 @@ class ExpExcelDialog(QtWidgets.QDialog):
         
         self.dataset = dataset
         self.particleContainer = particleContainer
-#        self.particles = self.datastats.getParticleStats()
         self.polymers = self.particleContainer.getListOfParticleAssignments
 #        self.additives = self.datastats.currentAdditives
         self.hqis = self.particleContainer.getListOfHighestHQIs
@@ -62,10 +61,10 @@ class ExpExcelDialog(QtWidgets.QDialog):
             if option == 'Polymer Type (mandatory)':
                 self.checkBoxes[-1].setEnabled(False)           #is mandatory!!!
             
-            if option == 'Additives':
-                if self.additives is None:
-                    self.checkBoxes[-1].setEnabled(False)
-                    self.checkBoxes[-1].setChecked(False)
+#            if option == 'Additives':
+#                if self.additives is None:
+#                    self.checkBoxes[-1].setEnabled(False)
+#                    self.checkBoxes[-1].setChecked(False)
                     
             excelvbox.addWidget(self.checkBoxes[-1])
         

analysis/particleInfo.py

@@ -18,21 +18,13 @@ 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 os
 import numpy as np
 import operator
-#from PyQt5 import QtWidgets, QtCore
-
-#try:
-#    from dataset import loadData, recursiveDictCompare
-#    print('exported dataset methods from datastats')
-#except:
-#    print('failed exported dataset methods from datastats')
 
 class ParticleContainer(object):
-    def __init__(self, parent):
+    def __init__(self, datasetParent):
         super(ParticleContainer, self).__init__()
-        self.parent = parent
+        self.datasetParent = datasetParent
         self.particles = []
         self.spectra = None
         self.inconsistentParticles = []
@@ -223,7 +215,7 @@ class ParticleContainer(object):
         final_typehistogram = {i[0]: i[1] for i in sorted_typehistogram}
         return final_typehistogram
     
-    def mergeParticles(self, particleIndices, newContour, newStats, newAssignment=None):
+    def addMergedParticle(self, particleIndices, newContour, newStats, newAssignment=None):
         newParticle = Particle()
         #copy Measurements
         for index in particleIndices:
@@ -243,22 +235,16 @@ class ParticleContainer(object):
         newParticle.area = area
         newParticle.contour = newContour
         
-        self.removeParticles(particleIndices)
-        print('removed particles')
         self.particles.append(newParticle)
         print('added new particle')
-        self.resetParticleIndices()
-        print('resetted indices')
         
-    def removeParticles(self, indexList):
-        for index in sorted(indexList, reverse=True):
-            particle = self.getParticleOfIndex(index)   #just for asserting to have the correct particle!
-            del self.particles[index]
+    def removeParticle(self, index):
+        particle = self.getParticleOfIndex(index)   #just for asserting to have the correct particle!
+        del self.particles[index]
             
     def resetParticleIndices(self):
         for newIndex, particle in enumerate(self.particles):
             particle.index = newIndex
-        
 
 class Particle(object):
     def __init__(self):
@@ -271,6 +257,7 @@ class Particle(object):
         self.area = None
         self.contour = None
         self.measurements = []
+        self.viewItem = None
         
     def addExistingMeasurement(self, meas):
         self.measurements.append(meas)
@@ -362,6 +349,9 @@ class Particle(object):
         for measurement in self.measurements:
             measurement.applyHQIThreshold(minHQI)
     
+#    def recreateViewItem(self):
+#        pass
+            
     
 class Measurement(object):
     def __init__(self):

analysis/particleeditor.py

@@ -29,7 +29,27 @@ import numpy as np
 import cv2
 from PyQt5 import QtWidgets, QtCore
 
-from analysis.particlePainter import ParticlePainter
+from .particlePainter import ParticlePainter
+
+def getContourStatsWithPixelScale(contours, pixelscale):
+        ##characterize particle
+        longellipse, shortellipse = np.nan, np.nan
+        
+        cnt = contours
+        
+        if cnt.shape[0] >= 5:       ##at least 5 points required for ellipse fitting...
+            ellipse = cv2.fitEllipse(cnt)
+            shortellipse, longellipse = ellipse[1]
+
+        rect = cv2.minAreaRect(cnt)
+        long, short = rect[1]
+        if short>long:
+            long, short = short, long
+        
+        area = cv2.contourArea(cnt)
+    
+        return long*pixelscale, short*pixelscale, longellipse*pixelscale, shortellipse*pixelscale, area*pixelscale**2
+
 
 class ParticleContextMenu(QtWidgets.QMenu):
     combineParticlesSignal = QtCore.pyqtSignal(list, str)
@@ -110,7 +130,6 @@ class ParticleContextMenu(QtWidgets.QMenu):
 
 
 class ParticleEditor(QtCore.QObject):
-#    particleContoursChanged = QtCore.pyqtSignal()
     particleAssignmentChanged = QtCore.pyqtSignal()
     def __init__(self, viewparent, particleContainer):
         super(ParticleEditor, self).__init__()
@@ -142,19 +161,15 @@ class ParticleEditor(QtCore.QObject):
         self.createSafetyBackup()
         print(f'Combining particles {contourIndices} into {newAssignment}')
         contours = self.particleContainer.getParticleContoursByIndex(contourIndices)
-        newContour = self.mergeContours(contours.copy())        
+        try:
+            newContour = self.mergeContours(contours.copy()) 
+        except NotConnectedContoursError:
+            return
+        
         pixelscale = self.viewparent.dataset.getPixelScale()
-        stats = self.characterizeParticle(newContour, pixelscale)
+        stats = getContourStatsWithPixelScale(newContour, pixelscale)
 
-        self.particleContainer.mergeParticles(contourIndices, newContour, stats, newAssignment=newAssignment)
-        for ind in contourIndices:
-            self.viewparent.removeParticleContour(ind)
-        
-        self.viewparent.resetContourIndices()
-        self.viewparent.addParticleContour(newContour, len(self.viewparent.contourItems))
-        
-        self.particleAssignmentChanged.emit()
-        #TODO: INCLUDE SANITY CHECK!!!!!!!!!
+        self.mergeParticlesInParticleContainerAndSampleView(contourIndices,newContour, stats, newAssignment)
     
     @QtCore.pyqtSlot(list, str)
     def reassignParticles(self, contourindices, newAssignment):
@@ -167,7 +182,8 @@ class ParticleEditor(QtCore.QObject):
      
     @QtCore.pyqtSlot(list, str)
     def paintParticles(self, contourIndices, newAssignment):
-        self.createSafetyBackup
+        print(f'painting indices {contourIndices} into {newAssignment}')
+        self.createSafetyBackup()
         self.storedIndices = contourIndices
         self.storedAssignmend = newAssignment
         contours = self.particleContainer.getParticleContoursByIndex(contourIndices)
@@ -178,19 +194,19 @@ class ParticleEditor(QtCore.QObject):
         self.viewparent.update()
         
     def acceptPaintedResult(self):
-        newContour = self.mergeContours(self.particlePainter.contours.copy())
-        pixelscale = self.viewparent.dataset.getPixelScale()
-        stats = self.characterizeParticle(newContour, pixelscale)
+        try:
+            newContour = self.mergeContours(self.particlePainter.contours.copy())
+        except NotConnectedContoursError:
+            self.storedIndices = []
+            self.storedAssignmend = None
+            self.destroyParticlePainter()
+            return
         
-        self.particleContainer.mergeParticles(self.storedIndices, newContour, stats, newAssignment=self.storedAssignmend)
-        for ind in self.storedIndices:
-            self.viewparent.removeParticleContour(ind)
+        pixelscale = self.viewparent.dataset.getPixelScale()
+        stats = getContourStatsWithPixelScale(newContour, pixelscale)
         
-        self.particleAssignmentChanged.emit()
-        self.viewparent.resetContourIndices()
-        self.viewparent.addParticleContour(newContour, len(self.viewparent.contourItems))
+        self.mergeParticlesInParticleContainerAndSampleView(self.storedIndices, newContour, stats, self.storedAssignmend)
         
-        #TODO: INCLUDE SANITY CHECK!!!!!!!!!
         self.storedIndices = []
         self.storedAssignmend = None
         self.destroyParticlePainter()
@@ -230,7 +246,7 @@ class ParticleEditor(QtCore.QObject):
         if len(contours)>1:
             QtWidgets.QMessageBox.critical(self.viewparent, 'ERROR!', 
                                            'Particle contours are not connected and cannot be combined!')
-            return
+            raise NotConnectedContoursError
         
         newContour = contours[0]
         for i in range(len(newContour)):
@@ -238,26 +254,20 @@ class ParticleEditor(QtCore.QObject):
             newContour[i][0][1] += ymin-padding
             
         return newContour
+    
+    def mergeParticlesInParticleContainerAndSampleView(self, indices, newContour, stats, assignment):
+        self.viewparent.addParticleContourToIndex(newContour, len(self.viewparent.contourItems)-1)
+        self.particleContainer.addMergedParticle(indices, newContour, stats, newAssignment=assignment)
         
-    def characterizeParticle(self, contours, pixelscale):
-        ##characterize particle
-        longellipse, shortellipse = np.nan, np.nan
-        
-        cnt = contours
-        
-        if cnt.shape[0] >= 5:       ##at least 5 points required for ellipse fitting...
-            ellipse = cv2.fitEllipse(cnt)
-            shortellipse, longellipse = ellipse[1]
-
-        rect = cv2.minAreaRect(cnt)
-        long, short = rect[1]
-        if short>long:
-            long, short = short, long
+        for ind in sorted(indices, reverse=True):
+            self.viewparent.removeParticleContour(ind)
+            self.particleContainer.removeParticle(ind)
         
-        area = cv2.contourArea(cnt)
+        self.viewparent.resetContourIndices()
+        self.particleContainer.resetParticleIndices()
+        self.particleAssignmentChanged.emit()
+        #TODO: INCLUDE SANITY CHECK!!!!!!!!!
     
-        return long*pixelscale, short*pixelscale, longellipse*pixelscale, shortellipse*pixelscale, area*pixelscale**2
-
     @QtCore.pyqtSlot(list)
     def deleteParticles(self, contourIndices):
         reply = QtWidgets.QMessageBox.question(self, f'About to delete {len(contourIndices)} particles.',
@@ -272,6 +282,9 @@ class ParticleEditor(QtCore.QObject):
             self.viewparent.dataset.particleContainer.resetParticleIndices()
             self.viewparent.resetContourIndices()
             self.viewparent.analysiswidget.updateHistogramsAndContours()
-        
+
+
+class NotConnectedContoursError(Exception):
+    pass
         
     
\ No newline at end of file

sampleview.py

@@ -422,10 +422,12 @@ class SampleView(QtWidgets.QGraphicsView):
                         removeContourFromSelection(cnt)
             
             else:    #not clicked on particle
-                
-                if event.modifiers()!=QtCore.Qt.ShiftModifier and cnt.particleIndex in self.selectedParticleIndices:
-                    removeContourFromSelection(cnt)
-
+                if event.modifiers()!=QtCore.Qt.ShiftModifier:
+                    cnt.isSelected = False
+                    cnt.update()
+                    if cnt.particleIndex in self.selectedParticleIndices:
+                        self.selectedParticleIndices.remove(cnt.particleIndex)
+                    
         self.update()
 
     def scaleImage(self, factor):
@@ -584,11 +586,11 @@ class SampleView(QtWidgets.QGraphicsView):
         self.contourItems = []
         if self.dataset is not None:
             for particleIndex, contour in enumerate(self.dataset.particleContainer.getParticleContours()):
-                self.addParticleContour(contour, particleIndex)
+                self.addParticleContourToIndex(contour, particleIndex)
             self.update()
         print('resetted contours: {} ms'.format(round((time.time()-t0)*1000)))
         
-    def addParticleContour(self, contour, index):
+    def addParticleContourToIndex(self, contour, index):
         newCnt = SegmentationContour(self, contour)
         newCnt.setIndex(index)
         assignment = self.dataset.particleContainer.getParticleAssignmentByIndex(index)
@@ -616,10 +618,10 @@ class SampleView(QtWidgets.QGraphicsView):
             self.ramanscanitems[index].setHighLight(True)
     
     def highLightContour(self, index):
-        print('highlighting contour', index)
         for contour in self.contourItems:
             contour.isSelected = False
         self.contourItems[index].isSelected = True
+        self.selectedParticleIndices =[index]
     
     def centerOnRamanIndex(self, index, centerOn=True, highlightIndex=True):
         if centerOn:

viewitems.py

@@ -23,9 +23,9 @@ from PyQt5 import QtCore, QtWidgets, QtGui
 from analysis.particleeditor import ParticleContextMenu
 
 class SegmentationContour(QtWidgets.QGraphicsItem):
-    def __init__(self, parent, contourData, pos=(0,0)):
+    def __init__(self, viewparent, contourData, pos=(0,0)):
         super().__init__()
-        self.parent = parent
+        self.viewparent = viewparent
         self.setZValue(1)
         self.setPos(pos[0], pos[1])
         self.setFlag(QtWidgets.QGraphicsItem.ItemIsSelectable)
@@ -56,6 +56,9 @@ class SegmentationContour(QtWidgets.QGraphicsItem):
     def boundingRect(self):
         return self.brect
     
+#    def createRamanScanIndices(self):
+        
+    
     def setIndex(self, index):
         self.particleIndex = index
     
@@ -89,8 +92,8 @@ class SegmentationContour(QtWidgets.QGraphicsItem):
     
     def contextMenuEvent(self, event):
         if self.isSelected:
-            self.contextMenu = ParticleContextMenu(self.parent)
-            self.parent.particleEditor.connectToSignals(self.contextMenu)
+            self.contextMenu = ParticleContextMenu(self.viewparent)
+            self.viewparent.particleEditor.connectToSignals(self.contextMenu)
             self.contextMenu.executeAtScreenPos(event.screenPos())