Several Bugfixes

analysis/analysisview.py

@@ -336,9 +336,9 @@ class ParticleAnalysis(QtWidgets.QWidget):
         self.specCanvas.draw()
         
         ####fake data!!!
-        if self.spectraResults is None:
-            self.spectraResults = ['empty']*(self.spectra.shape[1]-1)
-            self.hqis = [100]*(self.spectra.shape[1]-1)
+#        if self.spectraResults is None:
+#            self.spectraResults = ['empty']*(self.spectra.shape[1]-1)
+#            self.hqis = [100]*(self.spectra.shape[1]-1)
         
         self.loadParticleData()
         
@@ -362,7 +362,16 @@ class ParticleAnalysis(QtWidgets.QWidget):
         
         #check, if dataset already contains results. Otherwise load them...
         if self.spectraResults is None or (len(self.spectraResults) != len(sortindices)):
-            QtWidgets.QMessageBox.about(self, 'Info', 'No (or inconsistent) spectra results found, please run import dialog.')
+            self.show()
+#            QtWidgets.QMessageBox.about(self, 'Info', 'No (or inconsistent) spectra results found, please run import dialog.')
+            answer = QtWidgets.QMessageBox.question(self, 'Warning', 'No (or inconsistent) spectra results found, please run import dialog.\nPress OK to import or cancel to set to empty.', QtWidgets.QMessageBox.Ok | QtWidgets.QMessageBox.Cancel)
+            if answer == QtWidgets.QMessageBox.Ok:
+                self.importResults()
+            elif answer == QtWidgets.QMessageBox.Cancel:
+                self.spectraResults = ['empty']*(self.spectra.shape[1]-1)
+                self.hqis = [100]*(self.spectra.shape[1]-1)
+                self.updateBtn.clicked.connect(self.formatResults)
+                self.formatResults()
         else:
             self.updateBtn.clicked.connect(self.formatResults)
             self.formatResults()
@@ -383,27 +392,28 @@ class ParticleAnalysis(QtWidgets.QWidget):
             self.additivePlot.show()
     
     def formatResults(self):
-        print('formatResults')
-        self.updateBtn.setDisabled(False)
-        self.optionsGroup.setDisabled(False)
-        del self.currentPolymers, self.currentAdditives
-        
-        #convert to arrays (makes indexing easier...)
-        self.currentPolymers, self.hqis = np.array(self.spectraResults), np.array(self.hqis)
-        
-        if self.additiveResults is not None:
-            self.currentAdditives, self.addhqis = np.array(self.additiveResults), np.array(self.addhqis)
-            self.compHqiSpinBox.setDisabled(False)
-        else:
-            self.currentAdditives = None
-        
-        #set poor HQI results to unknown
-        self.currentPolymers[self.hqis < self.hqiSpinBox.value()] = 'unknown'
-        
-        if self.currentAdditives is not None:
-            self.currentAdditives[self.addhqis < self.compHqiSpinBox.value()] = 'unknown'
-        
-        self.createHistogramData()
+        if self.spectraResults is not None:
+            print('formatResults')
+            self.updateBtn.setDisabled(False)
+            self.optionsGroup.setDisabled(False)
+            del self.currentPolymers, self.currentAdditives
+            
+            #convert to arrays (makes indexing easier...)
+            self.currentPolymers, self.hqis = np.array(self.spectraResults), np.array(self.hqis)
+            
+            if self.additiveResults is not None:
+                self.currentAdditives, self.addhqis = np.array(self.additiveResults), np.array(self.addhqis)
+                self.compHqiSpinBox.setDisabled(False)
+            else:
+                self.currentAdditives = None
+            
+            #set poor HQI results to unknown
+            self.currentPolymers[self.hqis < self.hqiSpinBox.value()] = 'unknown'
+            
+            if self.currentAdditives is not None:
+                self.currentAdditives[self.addhqis < self.compHqiSpinBox.value()] = 'unknown'
+            
+            self.createHistogramData()
             
     def createHistogramData(self):
         self.uniquePolymers = np.unique(self.currentPolymers)

analysis/editParticles.py

@@ -77,7 +77,7 @@ class ParticleEditor(object):
         cv2.drawContours(img, [cnt], 0, 1, 1)
         img = np.uint8(cv2.morphologyEx(img, cv2.MORPH_CLOSE, np.ones((3, 3))))
         
-        temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
+        temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
 
         newContour = contours[0]
         stats = self.characterizeParticle(newContour)

dataset.py

@@ -75,6 +75,7 @@ class DataSet(object):
         
         # parameters specifically for raman scan
         self.pshift = None    # shift of raman scan position relative to image center
+        self.coordOffset = [0, 0]   #offset of entire coordinate system
         self.seedpoints = np.array([])
         self.seeddeletepoints = np.array([])
         self.detectParams = {'points': np.array([[50,0],[100,200],[200,255]]),
@@ -230,6 +231,9 @@ class DataSet(object):
         if not force:
             assert not self.readin
         p0 = copy(self.lastpos)
+        p0[0] += self.coordOffset[0] 
+        p0[1] += self.coordOffset[1]
+        
         if mode == 'df':
             p0[0] -= self.imagedim_df[0]/2
             p0[1] += self.imagedim_df[1]/2

gepard.py

@@ -173,6 +173,14 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.snapshotAct.triggered.connect(self.view.takeScreenshot)
         self.snapshotAct.setDisabled(True)
         
+        self.checkCoordsAct = QtWidgets.QAction("Check Coordinate System", self)
+        self.checkCoordsAct.triggered.connect(self.view.checkCoords)
+        self.checkCoordsAct.setDisabled(True)
+        
+        self.configCoordsAct = QtWidgets.QAction("Reconfigure Coordinate System", self)
+        self.configCoordsAct.triggered.connect(self.view.configureCoords)
+        self.configCoordsAct.setDisabled(True)
+        
         self.configRamanCtrlAct = QtWidgets.QAction("Configure Raman Control", self)
         self.configRamanCtrlAct.triggered.connect(self.view.configureRamanControl)
         if self.view.simulatedRaman:
@@ -254,6 +262,9 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.toolsMenu = QtWidgets.QMenu("Tools")
         self.toolsMenu.addAction(self.snapshotAct)
         self.toolsMenu.addAction(self.configRamanCtrlAct)
+        self.toolsMenu.addSeparator()
+        self.toolsMenu.addAction(self.checkCoordsAct)
+        self.toolsMenu.addAction(self.configCoordsAct)
         
         self.helpMenu = QtWidgets.QMenu("&Help", self)
         self.helpMenu.addAction(self.aboutAct)

sampleview.py

@@ -86,6 +86,7 @@ class SampleView(QtWidgets.QGraphicsView):
         self.setMinimumSize(600,600)
         self.darkenPixmap = False
         self.microscopeMode = None
+        self.coordTestMode = False
         
     def takeScreenshot(self):
         #TODO:
@@ -210,8 +211,14 @@ class SampleView(QtWidgets.QGraphicsView):
         
     def open(self, fname):       
         self.saveDataSet()
-        if self.dataset is not None:  #####TODO: properly close and delete all widget instances for avoiding that data from a currently opened dataset is saved into the new...
+        if self.dataset is not None:
             self.dataset.save()
+            #close all widgets
+            for widget in [self.detectionwidget, self.ramanwidget, self.oscanwidget, self.analysiswidget]:
+                widget.close()
+                widget.destroy()
+            self.contouritem.resetContours()
+            
         self.dataset = loadData(fname)
         self.setMicroscopeMode()
         self.imparent.setWindowTitle(self.dataset.name + (" SIMULATION" if simulatedRaman else ""))
@@ -470,7 +477,11 @@ class SampleView(QtWidgets.QGraphicsView):
                 self.analysiswidget.currentSpectrumIndex = specIndex
                 
                 selectedPolymer = self.analysiswidget.currentPolymers[specIndex]
-                self.analysiswidget.polymerIndex = self.analysiswidget.uniquePolymers.index(selectedPolymer)
+                try:
+                    self.analysiswidget.polymerIndex = self.analysiswidget.uniquePolymers.index(selectedPolymer)
+                except:
+                    print(selectedPolymer)
+                    raise
                 
                 #subparticleIndex
                 partIndicesOfThatPolymer = self.analysiswidget.indices[self.analysiswidget.polymerIndex]
@@ -544,4 +555,19 @@ class SampleView(QtWidgets.QGraphicsView):
         for item in self.ramanscanitems:
             self.scene().removeItem(item)
         self.ramanscanitems = []
+    
+    def checkCoords(self):
+        if not os.path.exists(self.dataset.getImageName):
+            QtWidgets.QMessageBox.about(self, 'No Fullimage found', 'Optical scan was not complete.\nPlease acquire fullimage first with newly defined border points.')
+        else:
+            self.coordTestMode = True
+            QtWidgets.QMessageBox.about(self, 'Check Coordinate System', 'Microscope is moving to 5 positions.\nFirst, only x and y are moved, z only if x,y positions are confirmed')
+            points = (self.dataset.fitpoints if len(self.dataset.ramanpoints) == 0 else self.dataset.ramanpoints)
+            for i in range(5):
+                #get random scanindex:
+                point = points[np.random.randint(len(points))]
+            
+    
+    def configureCoords(self):
+        pass
         
\ No newline at end of file

viewitems.py

@@ -36,7 +36,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
     def boundingRect(self):
         return self.brect
     
-    def resetContours(self, contours):
+    def resetContours(self, contours=[]):
         cp = []
         x0 = None
         for c in contours: