bugfixes in particle analysis

analysis/analysisview.py

@@ -456,6 +456,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         #draw Sample Spectrum
         specIndex = self.currentSpectrumIndex
         spectra = self.datastats.spectra
+        particlestats = self.datastats.getParticleStats()
         self.spec_ax.axis("on")
         self.spec_ax.clear()
         self.spec_ax.plot(spectra[:, 0], spectra[:, specIndex+1])
@@ -463,7 +464,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.spec_ax.set_xlabel('Wavenumber (cm-1)', fontsize = 15)
         self.spec_ax.set_ylabel('Counts', fontsize = 15)
         self.spec_ax.set_title('ScanPoint Number {}, Size = {} µm'.format(specIndex+1, 
-                               np.round(self.datastats.particlestats[self.currentParticleIndex][2], 1)))
+                               np.round(particlestats[self.currentParticleIndex][2], 1)))
         self.spec_ax.set_xbound(100, (3400 if spectra[-1, 0] > 3400 else spectra[-1, 0]))
         wavenumber_diff = list(spectra[:, 0]-100)
         y_start = wavenumber_diff.index(min(wavenumber_diff))
@@ -498,8 +499,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         if uniquePolymers is not None:
             #the index is the contour index, find particle index:
             specIndex = self.datastats.particles2spectra[index][0]  #select first spectrum of partoicle
-            self.datastats.currentParticleIndex = index
-            self.datastats.currentSpectrumIndex = specIndex
+            self.currentParticleIndex = index
+            self.currentSpectrumIndex = specIndex
             
             selectedPolymer = self.datastats.currentPolymers[specIndex]
             try:
@@ -649,7 +650,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         
         #general size histogram
         self.bins = np.logspace(0.1, 3, 20)
-        self.sizes = [i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.particlestats]      #extract long size (if ellipse fit is nan -> box fit)
+        self.sizes = [i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.getParticleStats()]      #extract long size (if ellipse fit is nan -> box fit)
         sizehist = np.histogram(self.sizes, self.bins)
         self.totalhistx = []
         for i in range(19):

analysis/analysiswidgets.py

@@ -36,7 +36,7 @@ class ExpExcelDialog(QtWidgets.QDialog):
         self.setGeometry(200,200, 300, 300)
         
         self.datastats = datastats
-        self.particles = self.datastats.particlestats
+        self.particles = self.datastats.getParticleStats()
         self.polymers = self.datastats.particleResults
         self.additives = self.datastats.currentAdditives
         self.hqis = self.datastats.hqis

analysis/datastats.py

@@ -41,7 +41,6 @@ class DataStats(object):
         
         self.spectraResults = None                  #entire List of all spectra assignments
         self.additiveResults = None                 #entire List of all additives
-        self.particlestats = None
         self.particleResults = None                 #final assignment for each particle
         
         self.currentPolymers = None                 #list of polymers after setting entries with low hqi to unknown
@@ -113,15 +112,6 @@ class DataStats(object):
         return specs
     
     def loadParticleData(self):
-        self.particlestats = np.array(self.dataset.particlestats)
-        pixelscale = self.dataset.getPixelScale()
-        #convert to mikrometer scale
-        for index in range(len(self.particlestats)):
-            for subindex in range(5):
-                self.particlestats[index][subindex] = self.particlestats[index][subindex] * pixelscale    #multiply by pixelscale
-                if subindex == 4:
-                    self.particlestats[index][subindex] = self.particlestats[index][subindex] * pixelscale  #again for the area...
-        
         self.particles2spectra = self.dataset.particles2spectra
         
         sortindices = self.dataset.ramanscansortindex
@@ -161,12 +151,21 @@ class DataStats(object):
             return None
         return self.uniquePolymers
     
+    def getParticleStats(self):
+        particlestats = np.array(self.dataset.particlestats)
+        pixelscale = self.dataset.getPixelScale()
+        #convert to mikrometer scale
+        particlestats[:,:5] *= pixelscale
+        particlestats[:,4] *= pixelscale   #again for the area...
+        return particlestats
+    
     def createHistogramData(self):
+        particlestats = self.getParticleStats()
         self.uniquePolymers = np.unique(self.currentPolymers)
-        self.particleResults = [None]*len(self.particlestats)
+        self.particleResults = [None]*len(particlestats)
         self.typehistogram = {i: 0 for i in self.uniquePolymers}
         
-        if len(self.particles2spectra) != len(self.particlestats):
+        if len(self.particles2spectra) != len(particlestats):
             return False
         
         for particleID, specList in enumerate(self.particles2spectra):

analysis/particleeditor.py

@@ -57,8 +57,6 @@ class ParticleEditor(object):
             return
         
         contourIndices = sorted(contourIndices)   #we want to keep the contour with lowest index
-        print('merging contours:', contourIndices)
-        self.createSafetyBackup()
         #get contours:
         contours = [self.datastats.dataset.particlecontours[i] for i in contourIndices]
         cnt = np.vstack(tuple(contours))  #combine contous
@@ -73,7 +71,7 @@ class ParticleEditor(object):
 
         img = np.zeros((rangey, rangex))
         for i in contourIndices:
-            curCnt = self.datastats.dataset.particlecontours[i]
+            curCnt = self.datastats.dataset.particlecontours[i].copy()
             for i in range(len(curCnt)):
                 curCnt[i][0][0] -= xmin-padding
                 curCnt[i][0][1] -= ymin-padding
@@ -88,6 +86,11 @@ class ParticleEditor(object):
         else:
             temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
 
+        if len(contours)>1:
+            QtWidgets.QMessageBox.critical(self.parent, 'ERROR!', 
+                                           'Particle contours are not connected and cannot be combined!')
+            return
+        
         newContour = contours[0]
         stats = self.characterizeParticle(newContour)
 
@@ -95,6 +98,8 @@ class ParticleEditor(object):
             newContour[i][0][0] += xmin-padding
             newContour[i][0][1] += ymin-padding
         
+        print('merging contours:', contourIndices)
+        self.createSafetyBackup()
         
         #check, if dataset contains (already modified) particle2spectra, otherwise create new.
         if self.datastats.dataset.particles2spectra is None:  #create default assignment
@@ -134,6 +139,9 @@ class ParticleEditor(object):
             print('removing index from particles2spectra:', index)
             del self.datastats.dataset.particles2spectra[index]
 
+        #update contours in sampleview
+        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)
+        self.parent.loadParticleData()
         #save data
         minHQI = self.parent.hqiSpinBox.value()
         compHQI = self.parent.compHqiSpinBox.value()
@@ -142,9 +150,6 @@ class ParticleEditor(object):
                     'Data inconsistency after saving!', QtWidgets.QMessageBox.Ok, 
                     QtWidgets.QMessageBox.Ok)
         
-        #update contours in sampleview
-        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)
-        self.parent.loadParticleData()
        
     
     def reassignParticles(self, contourindices, new_assignment):
@@ -161,6 +166,9 @@ class ParticleEditor(object):
                 self.datastats.spectraResults[specIndex] = new_assignment
                 self.datastats.hqis[specIndex] = 100
 
+        #update contours in sampleview
+        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)
+        self.parent.loadParticleData()
         #save data
         minHQI = self.parent.hqiSpinBox.value()
         compHQI = self.parent.compHqiSpinBox.value()
@@ -169,8 +177,6 @@ class ParticleEditor(object):
                                 'Data inconsistency after saving!',
                                 QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
             
-        self.parent.loadParticleData()
-            
     
     def deleteParticles(self):
         self.createSafetyBackup()

analysis/sqlexport.py

@@ -21,16 +21,16 @@ class SQLExport(QtWidgets.QDialog):
         
         self.datastats = datastats
         self.polymerList = self.datastats.particleResults
-        self.longSizes = np.round(np.array([i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.particlestats]), 1)
-        self.shortSize = np.round(np.array([i[1] if np.isnan(i[3]) else i[3] for i in self.datastats.particlestats]), 1)
+        particlestats = self.datastats.getParticleStats()
+        self.longSizes = np.round(np.array([i[0] if np.isnan(i[2]) else i[2] for i in particlestats]), 1)
+        self.shortSize = np.round(np.array([i[1] if np.isnan(i[3]) else i[3] for i in particlestats]), 1)
         
         #spectra can be quite some data size, they are not copied here but referenced later on...
         
         self.particleImages = None
         self.log = []
         
-        configfilename = os.path.join(os.path.dirname(os.path.split(__file__)[0]), 
-                                      'database_config.txt')
+        configfilename = os.path.join(os.path.split(__file__)[0], 'database_config.txt')
         
         if not os.path.exists(configfilename):
             QtWidgets.QMessageBox.warning(self, 'Warning!',
@@ -338,6 +338,9 @@ class SQLExport(QtWidgets.QDialog):
             self.cnx = mysql.connector.connect(**self.config)  #port: 3306
         except mysql.connector.Error as err:
             print(err)
+            QtWidgets.QMessageBox.warning(self, 'Error!',
+                                str(err),
+                                QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
             self.cnx = None
     
     def getEntireTable(self, tablename):

dataset.py

@@ -54,11 +54,13 @@ def saveData(dataset, fname):
         dataset.zvalimg = zvalimg
 
 def arrayCompare(a1, a2):
+    if a1.shape!=a2.shape:
+        return False
+    if a1.dtype!=np.float32 and a1.dtype!=np.float64:
+        return np.all(a1==a2)
     ind = np.isnan(a1)
     if not np.any(ind):
         return np.all(a1==a2)
-    if a1.shape!=a2.shape:
-        return False
     return np.all(a1[~ind]==a2[~ind])
 
 def listCompare(l1, l2):
@@ -78,10 +80,11 @@ def listCompare(l1, l2):
 def recursiveDictCompare(d1, d2):
     for key in d1:
         if not key in d2:
+            print("key missing in d2:", key, flush=True)
             return False
         a = d1[key]
         b = d2[key]
-        print(key, type(a), type(b))
+        print(key, type(a), type(b), flush=True)
         if isinstance(a, np.ndarray):
             if not isinstance(b, np.ndarray) or not arrayCompare(a, b):
                 print("data is different!", a, b)
@@ -97,6 +100,7 @@ def recursiveDictCompare(d1, d2):
                 print("data is different!", a, b)
                 return False
         elif a != b:
+            if (a is not None) and (b is not None):
                 print("data is different!", a, b)
                 return False
     return True

viewitems.py

@@ -145,25 +145,16 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
         elif numParticles == 1:
             combineMenu.setDisabled(True)
 
-
         action = contextMenu.exec_(event.screenPos())
 
         if action == deleteAct:
             print('deleting')
         elif action in combineActs:
             newAssignment = action.text()
-#            if newAssignment == "other":
-#                QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
-#                return
-
             self.parent.analysiswidget.editor.combineParticles(self.selectedContours, newAssignment)
             
         elif action in reassignActs:
             newAssignment = action.text()                
-#            if newAssignment == "other":
-#                QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
-#                return
-                
             self.parent.analysiswidget.editor.reassignParticles(self.selectedContours, newAssignment)