new trial to include changes by Hannes Herrmann

libhreels/ViewHREELS.py

@@ -15,12 +15,12 @@ hhPath = os.path.dirname(__file__)
 from libhreels.HREELS import HREELS, myPath
 from datetime import datetime  
 import argparse
-# import libhreels.expLogbook as lgb
-import libhreels.NoExpLogbook as lgb
+import libhreels.expLogbook as lgb
+# import libhreels.NoExpLogbook as lgb
 
 # fix HighRes Displays
-# QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling, True)
-# QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_UseHighDpiPixmaps, True)
+QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling, True)
+QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_UseHighDpiPixmaps, True)
 
 class HREELS_Window(QtWidgets.QMainWindow):
     """ fill in some initial data """
@@ -33,12 +33,13 @@ class HREELS_Window(QtWidgets.QMainWindow):
         self.offset = 0.1
         self.useOffset = False
         self.normalized = False
+        self.Areanormalized = False
         self.comment = comment
         self.showComment = lgb.available
         if datapath and os.path.exists(datapath):
             self.datapath = datapath
         else:
-            self.datapath = "./"
+            self.datapath = './'
         self.directory = self.datapath
         if remoteDir and os.path.exists(remoteDir):
             self.remoteDir = remoteDir
@@ -78,6 +79,8 @@ class HREELS_Window(QtWidgets.QMainWindow):
         # Action on user events
         self.ui.checkBoxWideScans.toggled.connect(self.onWideScans)
         self.ui.checkBoxNormalized.toggled.connect(self.onNormalized)
+        self.ui.checkBoxAreaNormalization.toggled.connect(self.onAreaNormalized)
+        
         self.ui.checkBoxOffset.toggled.connect(self.onUseOffset)
         self.ui.checkBoxMarker.toggled.connect(self.onMarkerSet)
         self.ui.checkBoxComment.toggled.connect(self.onCommentSet)
@@ -143,9 +146,16 @@ class HREELS_Window(QtWidgets.QMainWindow):
     def onNormalized(self):
         '''Routine called by toggling "Normalized": If set, all spectra will be normalized to a maximum
         count rate of unity. It will trigger a data window update.'''
+        self.ui.checkBoxAreaNormalization.setChecked(False)
         self.normalized = self.ui.checkBoxNormalized.isChecked()
         self.onFileSelection()
 
+    def onAreaNormalized(self):
+        '''Routine called by toggling "Area Normalized": If set, all spectra will be normalized to a sum of counts between -100 to 1000cm^-1 (or less if the dataset is shorter). It will trigger a data window update.'''
+        self.ui.checkBoxNormalized.setChecked(False)
+        self.Areanormalized = self.ui.checkBoxAreaNormalization.isChecked()
+        self.onFileSelection()    
+
     def onActionDir(self):
         '''Routine calls Directory Selection Interface upon Menu selection. It will 
         create a data list from the chosen directory.'''
@@ -290,7 +300,7 @@ class HREELS_Window(QtWidgets.QMainWindow):
         self.d = HREELS(firstItem.text(),self.datapath)
         if self.d.valid:
             plotColor = plt.cm.gnuplot(0)     # Define the color map (coolwarm; plasma; inferno; gnuplot)         
-            self.updatePlot(xmin=self.xmin, factor=self.factor, normalized=self.normalized, color=plotColor)
+            self.updatePlot(xmin=self.xmin, factor=self.factor, normalized=self.normalized, Areanormalized=self.Areanormalized, color=plotColor)
             try:
                 self.dialog.ui.textArea.setPlainText(self.d.infoText())
             except:
@@ -305,7 +315,7 @@ class HREELS_Window(QtWidgets.QMainWindow):
             for item in myList:     # Add here sorting according to ...
                 plotColor = plt.cm.gnuplot(i/iMax)     # Define the color map (coolwarm; plasma; inferno; gnuplot)
                 self.d = HREELS(item.text(),self.datapath)
-                self.secondPlot(xmin=self.xmin, factor=self.factor, normalized=self.normalized, offset=i*self.offset*self.useOffset, color=plotColor)
+                self.secondPlot(xmin=self.xmin, factor=self.factor, normalized=self.normalized, Areanormalized=self.Areanormalized,offset=i*self.offset*self.useOffset, color=plotColor)
                 # print(i, item.text())
                 i += 1
         # Reversing the sequence of labels in the legend:
@@ -341,17 +351,17 @@ class HREELS_Window(QtWidgets.QMainWindow):
         return
     
 
-    def updatePlot(self,xmin=70, factor=10, normalized=False, color="red"):
+    def updatePlot(self,xmin=70, factor=10, normalized=False, Areanormalized=False, color="red"):
         '''Plotting the first of the selected spectra. '''
         self.drawing_pane.axes.cla()
-        self.plotWidget(normalized=normalized,showComment=False)
-        self.plotWidget(xmin=xmin, factor=factor, color=color, label='x %3i'%factor, normalized=normalized, showComment=self.showComment)
+        self.plotWidget(normalized=normalized, Areanormalized=Areanormalized, showComment=False)
+        self.plotWidget(xmin=xmin, factor=factor, color=color, label='x %3i'%factor, normalized=normalized, Areanormalized=Areanormalized, showComment=self.showComment)
 
-    def secondPlot(self,xmin=70, factor=10, normalized=False, offset = 0., color="b-"):
+    def secondPlot(self,xmin=70, factor=10, normalized=False, Areanormalized=False, offset = 0., color="b-"):
         '''Plotting the second and all further selected spectra. '''
-        self.plotWidget(xmin=xmin, factor=factor, color=color, label=self.d.fname, normalized=normalized, offset = offset)
+        self.plotWidget(xmin=xmin, factor=factor, color=color, label=self.d.fname, normalized=normalized, Areanormalized=Areanormalized, offset = offset)
 
-    def plotWidget(self, xmin=None, xmax=None, factor=1, label='x', normalized=False, color="black",
+    def plotWidget(self, xmin=None, xmax=None, factor=1, label='x', normalized=False, Areanormalized=False, color="black",
                         marker=True, offset = 0., showComment=False):
         ''' plot(self, xmin=None, xmax=None, factor=1, label='x', normalized=False, color="b-",marker=True)'''
         self.d.pFactor = factor
@@ -365,6 +375,19 @@ class HREELS_Window(QtWidgets.QMainWindow):
             nend = len(self.d.xdata)
         if normalized:
             factor /= self.d.maxIntensity
+            Areanormalized = False # just in case
+        elif Areanormalized:
+            try:                    
+                areanormalize_xstart = np.argmin(abs(self.d.xdata+100.)) #seems to be oddly complicated, but is way more stable than x.index(-100.)
+            except:
+                areanormalize_xstart = 0
+            try:
+                areanormalize_xend = np.argmin(abs(self.d.xdata-1000.))
+            except:
+                areanormalize_xend = len(self.d.xdata)
+
+            factor /= self.d.ydata[areanormalize_xstart:areanormalize_xend].sum()
+            #print("Area normalization in x[", self.d.xdata[areanormalize_xstart],":",self.d.xdata[areanormalize_xend],"] is used.")    
         if label == "x":
             label = self.d.fname        
         self.drawing_pane.axes.plot(self.d.xdata[nstart:nend], factor*self.d.ydata[nstart:nend] + offset, color=color, label=label)
@@ -373,8 +396,11 @@ class HREELS_Window(QtWidgets.QMainWindow):
         self.drawing_pane.axes.set_xlabel('Energy Loss (cm$^{-1}$)')
         if normalized:
             self.drawing_pane.axes.set_ylabel('Normalized Intensity')
-        else:
+        elif Areanormalized:
+            self.drawing_pane.axes.set_ylabel('Area Normalized Intensity')
+        else:    
             self.drawing_pane.axes.set_ylabel('Intensity (s$^{-1}$)')
+        
         if marker:
             for (x,y) in self.d.marker:
                 self.d.setMarker(x,y*factor)

libhreels/viewhreels.ui

@@ -179,6 +179,13 @@
             </property>
            </widget>
           </item>
+          <item>
+           <widget class="QCheckBox" name="checkBoxAreaNormalization">
+            <property name="text">
+             <string>Area Normalization</string>
+            </property>
+           </widget>
+          </item>
           <item>
            <widget class="QCheckBox" name="checkBoxOffset">
             <property name="text">

pyproject.toml

 [tool.poetry]
 name = "libhreels"
-version = "1.2.0"
+version = "1.4.0"
 description = "Handling, simulating, and plotting HREELS and Auger spectroscopy data"
 authors = ["Wolf Widdra <wolf.widdra@physik.uni-halle.de>"]
 include = ["*./libhreels/*"]