Added database support,

several bugfixes

analysis/editParticles.py

@@ -125,8 +125,8 @@ class ParticleEditor(object):
             print('removing index from particles2spectra:', index)
             del self.parent.parent.dataset.particles2spectra[index]
 
-        #save dataset
-        self.parent.parent.dataset.save()        
+        #save data
+        self.parent.saveAnalysisResults()
         
         #update contours in sampleview
         self.parent.parent.contouritem.resetContours(self.parent.parent.dataset.particlecontours)
@@ -144,6 +144,9 @@ class ParticleEditor(object):
                 self.parent.spectraResults[specIndex] = new_assignment
                 self.parent.hqis[specIndex] = 100
 
+        #save data
+        self.parent.saveAnalysisResults()
+
         self.parent.loadParticleData()
             
     

gepard.py

@@ -92,9 +92,12 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
             fileName = QtWidgets.QFileDialog.getSaveFileName(self, "Create New Project",
                                         defaultPath, "*.pkl")[0]
         if fileName:
-            self.fname = str(fileName)
-            self.view.new(self.fname)  
-            self.scalingChanged(1.)
+            if fileName.find(' ') < 0:
+                self.fname = str(fileName)
+                self.view.new(self.fname)  
+                self.scalingChanged(1.)
+            else:
+                QtWidgets.QMessageBox.critical(self, "Error", "File path must not contain spaces.")
      
     @QtCore.pyqtSlot() 
     def about(self):

getOffset.py

+# -*- coding: utf-8 -*-
+"""
+Created on Mon Feb 11 14:33:22 2019
+
+@author: brandt
+"""
+from PyQt5 import QtWidgets, QtCore
+import numpy as np
+import sys
+
+class GetOffset(QtWidgets.QWidget):
+    def __init__(self, parent, ramanctrl):
+        super(GetOffset, self).__init__()
+        self.setWindowTitle('Get Coordinate Offset')
+        self.ramanctrl = ramanctrl
+        self.parent = parent
+        
+        layout = QtWidgets.QVBoxLayout()
+        self.setLayout(layout)
+        
+        layout.addWidget(QtWidgets.QLabel('Position of points'))
+        
+        numPoints = 5
+        self.pointBtns = []
+        self.coordLabels = []
+        self.old_coords = []
+        self.new_coords = []
+        
+        coordGroup = QtWidgets.QGroupBox()
+        coordLayout = QtWidgets.QGridLayout()
+        
+        for i in range(numPoints):
+            self.coordLabels.append(QtWidgets.QLabel())
+            self.coordLabels[-1].setFixedWidth(200)
+            coordLayout.addWidget(i, 0, QtCore.Qt.AlignLeft)
+            
+            self.pointBtns.append(QtWidgets.QPushButton('Point'+str(i+1)))
+            coordLayout.addWidget(i, )
+    
+    def connectButtonAndLabel(self, btn, lbl, index):
+        btn.released.connect(lambda: self.readPoint(lbl, index))
+        
+    def readPoint(self, lbl):
+        x, y, z = self.ramanctrl.getPosition()
+        z = self.ramanctrl.getUserZ()
+        lbl.setText(f'x = {np.round(x)} µm, y = {np.round(y)} µm, z = {np.round(z)} µm')
+        
+    
+if __name__ == '__main__':
+    app = QtWidgets.QApplication(sys.argv)
+    offset = GetOffset(None)
+    offset.show()
+    sys.exit(app.exec_())    
\ No newline at end of file

opticalscan.py

@@ -475,8 +475,9 @@ class OpticalScan(QtWidgets.QWidget):
             else:
                 return
         
-        self.view.imparent.ramanSwitch.df_btn.setChecked(self.df_btn.isChecked())    
+        self.view.imparent.ramanSwitch.df_btn.setChecked(self.df_btn.isChecked())
         self.view.imparent.ramanSwitch.setDisabled(True)
+        self.view.setMicroscopeMode()
 
         if self.df_btn.isChecked():
             self.view.dataset.imagescanMode = 'df'

ramanscanui.py

@@ -170,6 +170,7 @@ class RamanScanUI(QtWidgets.QWidget):
                                 QtWidgets.QMessageBox.Yes | 
                                 QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
             if reply == QtWidgets.QMessageBox.Yes:
+                self.ramanctrl.finishMeasurement()
                 self.timer.stop()
                 self.processstopevent.set()
                 self.process.join()
@@ -192,6 +193,8 @@ class RamanScanUI(QtWidgets.QWidget):
             else:
                 return
         self.view.imparent.ramanSwitch.hide()
+        self.view.setMicroscopeMode()
+        
         points = np.asarray(self.dataset.ramanpoints)
         ramanSettings = {'filename': self.dataset.name,
                          'numPoints': len(points),

sampleview.py

@@ -215,8 +215,9 @@ class SampleView(QtWidgets.QGraphicsView):
             self.dataset.save()
             #close all widgets
             for widget in [self.detectionwidget, self.ramanwidget, self.oscanwidget, self.analysiswidget]:
-                widget.close()
-                widget.destroy()
+                if widget is not None:
+                    widget.close()
+                    widget.destroy()
             self.contouritem.resetContours()
             
         self.dataset = loadData(fname)
@@ -508,7 +509,7 @@ class SampleView(QtWidgets.QGraphicsView):
                 self.analysiswidget.spectrumSelector.valueChanged.connect(self.analysiswidget.selectSpectrum)
                 self.analysiswidget.polymerComboBox.currentIndexChanged.connect(self.analysiswidget.displayNewPolymerType)
                 
-                self.analysiswidget.updatePolymerSpectrum(centerOn=centerOn)
+                self.analysiswidget.updateSpecPlot(centerOn=centerOn)
 
     
     def prepareAnalysis(self):

viewitems.py

@@ -64,6 +64,10 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
     def paint(self, painter, option, widget):           
         painter.setPen(QtCore.Qt.green)
         lenColorList = len(self.colorList)
+        if self.parent.analysiswidget is not None:
+            nonePaintMode = self.parent.analysiswidget.noOverlayAct.isChecked()
+        else:
+            nonePaintMode = False
         for index, c in enumerate(self.contours):
             if index not in self.selectedContours:
                 if lenColorList > 0:
@@ -72,14 +76,16 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
                 else:
                     color = QtCore.Qt.green
                     painter.setPen(color)
-                painter.setBrush(color)
+                if not nonePaintMode:
+                    painter.setBrush(color)
                 painter.drawPolygon(c)
             else:
                 if lenColorList > 0:
                     alpha = self.colorList[index].alpha()
                 else:
                     alpha = 255
-                painter.setBrush(QtGui.QColor(200, 200, 200, alpha))
+                if not nonePaintMode:
+                    painter.setBrush(QtGui.QColor(200, 200, 200, alpha))
                 painter.setPen(QtCore.Qt.white)
                 painter.drawPolygon(c)
 
@@ -92,7 +98,10 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
                 if cnt.containsPoint(p, QtCore.Qt.OddEvenFill):
                      
                     if event.modifiers()==QtCore.Qt.ShiftModifier:
-                        self.selectedContours.append(index)
+                        if index not in self.selectedContours:
+                            self.selectedContours.append(index)
+                        else:
+                            self.selectedContours.remove(index)
                     else:
                         self.selectedContours = [index]