Support for off-resonance pulses was added, additionally file name changes have been put into place to better differentiate kernal and data files. Other bug fixes to .dmp files have been made, although .dmp file are still not robust for late stage processing.

akvo/gui/addFigure8Loop.ui

     <x>0</x>
     <y>0</y>
     <width>400</width>
-    <height>456</height>
+    <height>499</height>
    </rect>
   </property>
   <property name="windowTitle">
    <string>Dialog</string>
   </property>
   <layout class="QGridLayout" name="gridLayout">
-   <item row="12" column="2">
-    <widget class="QDoubleSpinBox" name="doubleSpinBox_3"/>
+   <item row="10" column="0">
+    <widget class="QLabel" name="label_4">
+     <property name="text">
+      <string>radius  (m)</string>
+     </property>
+    </widget>
+   </item>
+   <item row="0" column="2">
+    <widget class="QDoubleSpinBox" name="centreNorth1">
+     <property name="minimum">
+      <double>-999999999.000000000000000</double>
+     </property>
+     <property name="maximum">
+      <double>9999999999.000000000000000</double>
+     </property>
+    </widget>
    </item>
    <item row="7" column="0">
     <widget class="QLabel" name="label_8">
      </property>
     </widget>
    </item>
-   <item row="14" column="2">
-    <widget class="QSpinBox" name="segments">
-     <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Currently Akvo/Merlin calculates circular loops using segments of wire, forming a polygon. Analytic circular loops may be added in the future. &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
-     </property>
-     <property name="minimum">
-      <number>5</number>
-     </property>
-     <property name="maximum">
-      <number>200</number>
+   <item row="5" column="0">
+    <widget class="Line" name="line">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
      </property>
-     <property name="value">
-      <number>15</number>
+    </widget>
+   </item>
+   <item row="8" column="0">
+    <widget class="Line" name="line_5">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
      </property>
     </widget>
    </item>
    <item row="10" column="2">
-    <widget class="QDoubleSpinBox" name="loopHeight">
+    <widget class="QDoubleSpinBox" name="loopRadius">
      <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Akvo uses a positive down convention, a slight negative value to the loop height improves numerical stability using digital filtering hankel transforms. &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
-     </property>
-     <property name="decimals">
-      <number>3</number>
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Radius of the loop&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
      <property name="minimum">
-      <double>-99.000000000000000</double>
+      <double>0.100000000000000</double>
+     </property>
+     <property name="maximum">
+      <double>600.000000000000000</double>
      </property>
      <property name="value">
-      <double>-0.001000000000000</double>
+      <double>50.000000000000000</double>
      </property>
     </widget>
    </item>
-   <item row="13" column="0">
-    <widget class="QLabel" name="label_6">
-     <property name="text">
-      <string>turns</string>
+   <item row="17" column="2">
+    <widget class="QDialogButtonBox" name="buttonBox">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
      </property>
     </widget>
    </item>
-   <item row="6" column="2">
-    <widget class="QDoubleSpinBox" name="centreNorth2"/>
-   </item>
-   <item row="8" column="1">
-    <widget class="Line" name="line_4">
+   <item row="5" column="2">
+    <widget class="Line" name="line_2">
      <property name="orientation">
       <enum>Qt::Horizontal</enum>
      </property>
     </widget>
    </item>
-   <item row="5" column="0">
-    <widget class="Line" name="line">
+   <item row="8" column="1">
+    <widget class="Line" name="line_4">
      <property name="orientation">
       <enum>Qt::Horizontal</enum>
      </property>
     </widget>
    </item>
-   <item row="1" column="2">
-    <widget class="QDoubleSpinBox" name="centreEast1">
-     <property name="minimum">
-      <double>-99999999.000000000000000</double>
-     </property>
-     <property name="maximum">
-      <double>99999999.989999994635582</double>
+   <item row="11" column="0">
+    <widget class="QLabel" name="label_3">
+     <property name="text">
+      <string>height (m)</string>
      </property>
     </widget>
    </item>
-   <item row="12" column="0">
-    <widget class="QLabel" name="label_9">
+   <item row="9" column="0" colspan="2">
+    <widget class="QLabel" name="label_10">
      <property name="text">
-      <string>TextLabel</string>
+      <string>current flow in loop 1</string>
      </property>
     </widget>
    </item>
      </property>
     </widget>
    </item>
-   <item row="8" column="2">
-    <widget class="Line" name="line_3">
-     <property name="orientation">
-      <enum>Qt::Horizontal</enum>
+   <item row="13" column="2">
+    <widget class="QSpinBox" name="loopTurns">
+     <property name="minimum">
+      <number>1</number>
+     </property>
+     <property name="maximum">
+      <number>100000</number>
      </property>
     </widget>
    </item>
-   <item row="0" column="0">
-    <widget class="QLabel" name="label">
-     <property name="text">
-      <string>centre northing 1 (m)</string>
+   <item row="11" column="2">
+    <widget class="QDoubleSpinBox" name="loopHeight">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Akvo uses a positive down convention, a slight negative value to the loop height improves numerical stability using digital filtering hankel transforms. &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="decimals">
+      <number>3</number>
+     </property>
+     <property name="minimum">
+      <double>-99.000000000000000</double>
+     </property>
+     <property name="value">
+      <double>-0.001000000000000</double>
      </property>
     </widget>
    </item>
      </property>
     </widget>
    </item>
-   <item row="14" column="0">
-    <widget class="QLabel" name="label_5">
-     <property name="text">
-      <string>segments</string>
-     </property>
-    </widget>
-   </item>
-   <item row="17" column="2">
-    <widget class="QDialogButtonBox" name="buttonBox">
+   <item row="8" column="2">
+    <widget class="Line" name="line_3">
      <property name="orientation">
       <enum>Qt::Horizontal</enum>
      </property>
-     <property name="standardButtons">
-      <set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
-     </property>
     </widget>
    </item>
-   <item row="5" column="2">
-    <widget class="Line" name="line_2">
-     <property name="orientation">
-      <enum>Qt::Horizontal</enum>
+   <item row="7" column="2">
+    <widget class="QDoubleSpinBox" name="centreEast2">
+     <property name="minimum">
+      <double>-9999999999.000000000000000</double>
+     </property>
+     <property name="maximum">
+      <double>9999999999.000000000000000</double>
      </property>
     </widget>
    </item>
-   <item row="7" column="2">
-    <widget class="QDoubleSpinBox" name="centreEast2"/>
-   </item>
-   <item row="10" column="0">
-    <widget class="QLabel" name="label_3">
+   <item row="14" column="0">
+    <widget class="QLabel" name="label_5">
      <property name="text">
-      <string>height (m)</string>
+      <string>segments</string>
      </property>
     </widget>
    </item>
-   <item row="0" column="2">
-    <widget class="QDoubleSpinBox" name="centreNorth1">
-     <property name="minimum">
-      <double>-999999999.000000000000000</double>
-     </property>
-     <property name="maximum">
-      <double>9999999999.000000000000000</double>
+   <item row="0" column="0">
+    <widget class="QLabel" name="label">
+     <property name="text">
+      <string>centre northing 1 (m)</string>
      </property>
     </widget>
    </item>
-   <item row="13" column="2">
-    <widget class="QSpinBox" name="loopTurns">
+   <item row="14" column="2">
+    <widget class="QSpinBox" name="segments">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Currently Akvo/Merlin calculates circular loops using segments of wire, forming a polygon. Analytic circular loops may be added in the future. &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
      <property name="minimum">
-      <number>1</number>
+      <number>5</number>
      </property>
      <property name="maximum">
-      <number>100000</number>
+      <number>200</number>
+     </property>
+     <property name="value">
+      <number>15</number>
      </property>
     </widget>
    </item>
-   <item row="8" column="0">
-    <widget class="Line" name="line_5">
-     <property name="orientation">
-      <enum>Qt::Horizontal</enum>
-     </property>
+   <item row="9" column="2">
+    <widget class="QComboBox" name="cwiseBox">
+     <item>
+      <property name="text">
+       <string>clockwise</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string>anti-clockwise</string>
+      </property>
+     </item>
     </widget>
    </item>
-   <item row="9" column="0">
-    <widget class="QLabel" name="label_4">
-     <property name="text">
-      <string>radius  (m)</string>
+   <item row="6" column="2">
+    <widget class="QDoubleSpinBox" name="centreNorth2">
+     <property name="minimum">
+      <double>-9999999999.000000000000000</double>
+     </property>
+     <property name="maximum">
+      <double>99999999999.000000000000000</double>
      </property>
     </widget>
    </item>
-   <item row="9" column="2">
-    <widget class="QDoubleSpinBox" name="loopRadius">
-     <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Radius of the loop&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
-     </property>
+   <item row="1" column="2">
+    <widget class="QDoubleSpinBox" name="centreEast1">
      <property name="minimum">
-      <double>0.100000000000000</double>
+      <double>-99999999.000000000000000</double>
      </property>
      <property name="maximum">
-      <double>600.000000000000000</double>
+      <double>99999999.989999994635582</double>
      </property>
-     <property name="value">
-      <double>50.000000000000000</double>
+    </widget>
+   </item>
+   <item row="13" column="0">
+    <widget class="QLabel" name="label_6">
+     <property name="text">
+      <string>turns</string>
      </property>
     </widget>
    </item>

akvo/gui/akvoGUI.py

 import time
 import os
 from copy import deepcopy
-from matplotlib.backends.backend_qt4 import NavigationToolbar2QT #as NavigationToolbar
+from matplotlib.backends.backend_qt5 import NavigationToolbar2QT #as NavigationToolbar
 import datetime, time
 import pkg_resources  # part of setuptools
 from collections import OrderedDict
 from pyLemma import Merlin
 
 VERSION = pkg_resources.require("Akvo")[0].version
+GAMMAH = 42.577478518 * 1e-3  # Hz nT
 
 # Writes out numpy arrays into Eigen vectors as serialized by Lemma
 class MatrixXr(yaml.YAMLObject):
         self.ui.plotGI.setEnabled(False) 
         self.ui.plotGI.pressed.connect( self.plotGI )
 
+        # balance the Larmor frequency info and Tx off resonance info
+        self.ui.intensitySpinBox.valueChanged.connect( self.adjustLarmor )
+        self.ui.txv.valueChanged.connect( self.adjustB0 )
+        self.ui.larmorv.valueChanged.connect( self.adjustB02 )
+
         # Kernel         
         self.ui.calcK0.pressed.connect( self.calcK0 )       
 
             self.ui.lcdHNF2.setEnabled(False)
             self.ui.lcdf0NK2.setEnabled(False)
 
+    def adjustLarmor(self):
+        """ Triggers when the B0 intensity spin box is cycled
+        """
+        self.ui.larmorv.setValue( self.ui.intensitySpinBox.value() * GAMMAH )
+        self.ui.txv.setValue( self.RAWDataProc.transFreq - self.ui.larmorv.value() )
+
+    def adjustB0(self):
+        """ Triggers when tx frequency offset is cycled
+        """
+        self.ui.intensitySpinBox.setValue( (self.RAWDataProc.transFreq - self.ui.txv.value()) / GAMMAH )
+    
+    def adjustB02(self):
+        """ Triggers when Larmor frequency spin box is cycled o
+        """
+        self.ui.intensitySpinBox.setValue( (self.ui.larmorv.value()) / GAMMAH )
+
     def closeTabs(self):
         #self.ui.ProcTabs.removeTab(idx)    
         self.ui.ProcTabs.clear( )    
         except IOError as e:
             fpath = '.'
         
-        self.akvoDataFile = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Datafile File', fpath, r"Akvo datafiles (*.yaml)")[0]
+        self.akvoDataFile = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Datafile File', fpath, r"Akvo datafiles (*.akvoProcData *.yaml)")[0]
         self.ui.dataText.clear()   
         self.ui.dataText.append( self.akvoDataFile )   
     
         except IOError as e:
             fpath = '.'
         
-        self.K0akvoDataFile = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Datafile File', fpath, r"Akvo datafiles (*.yaml)")[0]
-        self.ui.K0DataText.clear()   
-        self.ui.K0DataText.append( self.K0akvoDataFile )  
+        self.K0akvoDataFile = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Datafile File', fpath, r"Akvo datafiles (*.akvoProcData *.yaml)")[0]
 
         # populate combo box with loops 
-
-        with open(self.K0akvoDataFile) as f:
-            parse = yaml.load( f, Loader=yaml.Loader )
-        
-        self.ui.txListWidget.clear()
-        self.ui.rxListWidget.clear()
-        for loop in parse.META["Loops"]:
-            print(loop)
-            self.ui.txListWidget.addItem( parse.META["Loops"][loop] )
-            self.ui.rxListWidget.addItem( parse.META["Loops"][loop] )
-            
-        self.ui.txListWidget.setCurrentRow(0)
-        self.ui.rxListWidget.setCurrentRow(0)
+        if os.path.isfile( self.K0akvoDataFile ): 
+        
+            self.ui.K0DataText.clear()   
+            self.ui.K0DataText.append( self.K0akvoDataFile )  
+
+            with open(self.K0akvoDataFile) as f:
+                parse = yaml.load( f, Loader=yaml.Loader )
+        
+            self.ui.txListWidget.clear()
+            self.ui.rxListWidget.clear()
+            for loop in parse.META["Loops"]:
+                print(loop)
+                self.ui.txListWidget.addItem( parse.META["Loops"][loop] )
+                self.ui.rxListWidget.addItem( parse.META["Loops"][loop] )
+           
+            # TODO, why are these necessary 
+            self.ui.txListWidget.setCurrentRow(0)
+            self.ui.rxListWidget.setCurrentRow(0)
+        # else do nothing
          
- 
     def invKernelSelect(self):
         try:
             with open('.akvo.last.path') as f: 
         except IOError as e:
             fpath = '.'
         
-        self.K0file = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Kernel File', fpath, r"Akvo kernels (*.yml)")[0]
+        self.K0file = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Kernel File', fpath, r"Akvo kernels (*.akvoK0)")[0]
         self.ui.kernelText.clear()   
         self.ui.kernelText.append(self.K0file)   
     
             rxCoils.append(rxCoil.text())
 
 
-        saveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save kernel as", fpath, r"Merlin KernelV0 (*.yml)")[0] 
+        saveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save kernel as", fpath, r"Merlin KernelV0 (*.akvoK0)")[0] 
 
         intDict = dict()
         intDict["origin_n"] = self.ui.originN.value()
                     points = np.linspace(0, 2*np.pi, dialog.ui.segments.value()+1)
                     for iseg, ipt in enumerate(points):
                         if cwise == 0:
-                            self.loops[self.ui.loopLabel.text()].SetPoint(iseg, (  cn+rad*np.sin(ipt), ce+rad*np.cos(ipt), ht) )
+                            self.loops[self.ui.loopLabel.text()].SetPoint(iseg, ( cn+rad*np.sin(ipt), ce+rad*np.cos(ipt), ht) )
                         else:
-                            self.loops[self.ui.loopLabel.text()].SetPoint(iseg, ( -cn+rad*np.sin(ipt), ce+rad*np.cos(ipt), ht) )
+                            self.loops[self.ui.loopLabel.text()].SetPoint(iseg, ( cn-rad*np.sin(ipt), ce+rad*np.cos(ipt), ht) )
                     self.loops[self.ui.loopLabel.text()].SetNumberOfFrequencies(1)
                     self.loops[self.ui.loopLabel.text()].SetCurrent(1.)
             
                     rad = dialog.ui.loopRadius.value()
                     turns = dialog.ui.loopTurns.value()
                     ns = dialog.ui.segments.value()
-                    #cwise = dialog.ui.cwiseBox.currentIndex()
-                    print(cn1, ce1, cn2, ce2, ht, rad, turns, ns)   
+                    cwise = dialog.ui.cwiseBox.currentIndex()
+
+                    self.loops[self.ui.loopLabel.text()] = FDEM1D.PolygonalWireAntenna()
+                    self.loops[self.ui.loopLabel.text()].SetNumberOfPoints( 2*dialog.ui.segments.value() + 1 )
+                    self.loops[self.ui.loopLabel.text()].SetNumberOfTurns( dialog.ui.loopTurns.value() )
+
+                    # first loop
+                    points = np.linspace(0, 2*np.pi, dialog.ui.segments.value())
+                    ptsL = []
+                    for iseg, ipt in enumerate(points):
+                        ptsL.append( np.array( [cn1+rad*np.sin(ipt), ce1+rad*np.cos(ipt)]  ))
+                    lenP = len(points)
+                    
+                    # search for closest point, ugly and not efficient, but it's not critical here 
+                    closest = 1e8
+                    iclosest = -1
+                    for iseg, ipt in enumerate(points):
+                        p2 = np.array([cn2-rad*np.sin(ipt), ce2-rad*np.cos(ipt)])
+                        for p1 in ptsL:
+                            dist = np.linalg.norm(p1-p2)
+                            if dist < closest:
+                                closest = dist
+                                iclosest = iseg
+
+                    points = np.concatenate([points[iclosest::],points[0:iclosest]])
+                    point1 = False
+                    for iseg, ipt in enumerate(points):
+                        if cwise == 0:
+                            self.loops[self.ui.loopLabel.text()].SetPoint(iseg, ( cn1+rad*np.sin(ipt), ce1+rad*np.cos(ipt), ht) )
+                            if not point1:
+                                point1 = ( cn1+rad*np.sin(ipt), ce1+rad*np.cos(ipt), ht) 
+                        else:
+                            self.loops[self.ui.loopLabel.text()].SetPoint(iseg, ( cn1-rad*np.sin(ipt), ce1+rad*np.cos(ipt), ht) )
+                            if not point1:
+                                point1 = ( cn1-rad*np.sin(ipt), ce1+rad*np.cos(ipt), ht) 
+
+                    lenP = len(points)
+
+                    # fill 
+                    for iseg, ipt in enumerate(points):
+                        if cwise == 0:
+                            self.loops[self.ui.loopLabel.text()].SetPoint(lenP+iseg, ( cn2-rad*np.cos(ipt), ce2-rad*np.sin(ipt), ht) )
+                        else:
+                            self.loops[self.ui.loopLabel.text()].SetPoint(lenP+iseg, ( cn2+rad*np.cos(ipt), ce2+rad*np.sin(ipt), ht) )
+
+                    # close loop        
+                    self.loops[self.ui.loopLabel.text()].SetPoint(lenP+iseg+1, point1) 
+
+
+                    self.loops[self.ui.loopLabel.text()].SetNumberOfFrequencies(1)
+                    self.loops[self.ui.loopLabel.text()].SetCurrent(1.)
+ 
             
             if self.ui.loopGeom.currentText() == "polygon":
                 
             # general across all types   
             if dialog.result():
 
-                yml = open( self.ui.loopLabel.text() + ".yml", 'w' )
+                yml = open( self.ui.loopLabel.text() + ".pwa", 'w' )
                 print( self.loops[self.ui.loopLabel.text()], file=yml)
 
                 # update the table 
         self.ui.lcdNumberNQ.display(self.RAWDataProc.nPulseMoments)
         self.ui.DeadTimeSpinBox.setValue(1e3*self.RAWDataProc.deadTime)
         self.ui.CentralVSpinBox.setValue( self.RAWDataProc.transFreq )
-            
+
+        # set the B0 field according to Tx as an initial guess
+        self.ui.intensitySpinBox.setValue( self.RAWDataProc.transFreq/GAMMAH )           
+ 
         if self.RAWDataProc.pulseType != "FID":
             self.ui.lcdNumberTauPulse2.setEnabled(1)
             self.ui.lcdNumberTauPulse2.display(1e3*self.RAWDataProc.pulseLength[1])
         
         fdir = os.path.dirname(fpath)
         # Pickle the preprocessed data dictionary 
-        SaveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save as", fdir, r"Processed data (*.yaml)")[0]
+        SaveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save as", fdir, r"Processed data (*.akvoProcData)")[0]
         
         spath,filen=os.path.split(str(SaveStr))
         f = open('.akvo.last.yaml.path', 'w')
             TXRX.append(txrx)
         INFO["TXRX"] = TXRX       
 
-        # 
+        if "Stacking" in self.YamlNode.Stacking.keys():
+            INFO["sigma"] = self.RawDataProc.sigma
+
+        if "Gate integrate" in self.YamlNode.Stacking.keys():
+            INFO["GATED"] = self.RAWDataProc.GATED
+
         print("META SAVE")
         print("INFO log", INFO["log"])
 
         #    self.YamlNode.Processing["Loaded"] = []
         #self.YamlNode.Processing["Loaded"].append(datetime.datetime.now().isoformat()) 
         #self.Log()
+
+        if "Stacking" in self.YamlNode.Stacking.keys():
+            self.RAWDataProc.sigma = self.RAWDataProc.DATADICT["sigma"]
+
+        # check to see if gate integration has been done, and it's ready to send to Merlin
+        if "Gate integrate" in self.YamlNode.Stacking.keys():
+            self.RAWDataProc.GATED = self.RAWDataProc.DATADICT["GATED"]
+            self.ui.actionExport_Preprocessed_Dataset.setEnabled(True)
+            #self.ui.plotGI.setEnabled(True)
  
         # If we got this far, enable all the widgets
         self.ui.lcdNumberTauPulse1.setEnabled(True)
         if u"Pulse 1" in self.RAWDataProc.DATADICT.keys():
             self.ui.lcdNumberFID1Length.display(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0])
             self.ui.lcdTotalDeadTime.display( round(1e3*(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0]-self.RAWDataProc.DATADICT["Pulse 1"]["PULSE_TIMES"][-1]), 3) )
-            print("CALC DEAD",    (1e3*(self.RAWDataProc.prePulseDelay))) # -  (self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0]-self.RAWDataProc.DATADICT["Pulse 1"]["PULSE_TIMES"][-1])), 3) )
+            #print("CALC DEAD",    (1e3*(self.RAWDataProc.prePulseDelay))) # -  (self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0]-self.RAWDataProc.DATADICT["Pulse 1"]["PULSE_TIMES"][-1])), 3) )
         if u"Pulse 2" in self.RAWDataProc.DATADICT.keys():
             self.ui.lcdNumberFID1Length.display(self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][0])
             self.ui.lcdTotalDeadTime.display( 1e3 * (self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][0]-self.RAWDataProc.DATADICT["Pulse 2"]["PULSE_TIMES"][-1]) )
         self.YamlNode.META["Loops"] = OrderedDict()
         for loop in self.loops:
             print(self.loops[loop])
-            self.YamlNode.META["Loops"][loop] = loop + ".yml" 
+            self.YamlNode.META["Loops"][loop] = loop + ".pwa" 
 
         self.Log()
 

akvo/gui/main.ui

                 <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
-&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Noto Sans'; font-size:9pt; font-weight:400; font-style:italic;&quot;&gt;
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Noto Sans'; font-size:12pt; font-weight:400; font-style:italic;&quot;&gt;
 &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'DejaVu Serif'; font-size:10pt;&quot;&gt;&lt;br /&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
                </property>
               </widget>
         <rect>
          <x>0</x>
          <y>0</y>
-         <width>543</width>
-         <height>889</height>
+         <width>537</width>
+         <height>982</height>
         </rect>
        </property>
        <property name="sizePolicy">
                <string>Survey site information</string>
               </property>
               <layout class="QGridLayout" name="gridLayout_10">
-               <item row="4" column="3">
-                <widget class="QDoubleSpinBox" name="tempSpinBox">
-                 <property name="value">
-                  <double>20.000000000000000</double>
+               <item row="2" column="3">
+                <widget class="QLabel" name="label_64">
+                 <property name="text">
+                  <string>Ellipsoid</string>
                  </property>
                 </widget>
                </item>
                  </item>
                 </widget>
                </item>
-               <item row="2" column="2">
-                <widget class="QLabel" name="label_63">
-                 <property name="text">
-                  <string>Lat. Band </string>
-                 </property>
-                </widget>
-               </item>
-               <item row="4" column="2">
-                <widget class="QTimeEdit" name="timeEdit">
-                 <property name="calendarPopup">
-                  <bool>true</bool>
-                 </property>
-                </widget>
-               </item>
-               <item row="5" column="1">
-                <widget class="QDoubleSpinBox" name="incSpinBox">
-                 <property name="decimals">
-                  <number>1</number>
-                 </property>
-                 <property name="minimum">
-                  <double>-90.000000000000000</double>
-                 </property>
-                 <property name="maximum">
-                  <double>90.000000000000000</double>
-                 </property>
-                 <property name="value">
-                  <double>45.000000000000000</double>
-                 </property>
-                </widget>
-               </item>
                <item row="5" column="0">
                 <widget class="QLabel" name="label_67">
                  <property name="text">
                  </property>
                 </widget>
                </item>
-               <item row="2" column="3">
-                <widget class="QLabel" name="label_64">
-                 <property name="text">
-                  <string>Ellipsoid</string>
+               <item row="6" column="1">
+                <widget class="QDoubleSpinBox" name="txv">
+                 <property name="minimum">
+                  <double>-500.000000000000000</double>
+                 </property>
+                 <property name="maximum">
+                  <double>500.000000000000000</double>
                  </property>
                 </widget>
                </item>
                  </property>
                 </widget>
                </item>
+               <item row="6" column="3">
+                <widget class="QDoubleSpinBox" name="larmorv">
+                 <property name="maximum">
+                  <double>3000.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
                <item row="3" column="2">
                 <widget class="QComboBox" name="latBand">
                  <property name="toolTip">
                  </item>
                 </widget>
                </item>
+               <item row="2" column="2">
+                <widget class="QLabel" name="label_63">
+                 <property name="text">
+                  <string>Lat. Band </string>
+                 </property>
+                </widget>
+               </item>
                <item row="4" column="1">
                 <widget class="QDateEdit" name="dateEdit">
                  <property name="calendarPopup">
                  </property>
                 </widget>
                </item>
-               <item row="2" column="1">
-                <widget class="QLabel" name="label_59">
-                 <property name="maximumSize">
-                  <size>
-                   <width>16777215</width>
-                   <height>20</height>
-                  </size>
+               <item row="5" column="2">
+                <widget class="QDoubleSpinBox" name="decSpinBox">
+                 <property name="decimals">
+                  <number>1</number>
+                 </property>
+                 <property name="minimum">
+                  <double>-90.000000000000000</double>
+                 </property>
+                 <property name="maximum">
+                  <double>90.000000000000000</double>
                  </property>
+                 <property name="value">
+                  <double>0.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
+               <item row="3" column="0">
+                <widget class="QLabel" name="label_61">
                  <property name="text">
-                  <string>UTM</string>
+                  <string>Coordinates</string>
                  </property>
                 </widget>
                </item>
-               <item row="5" column="2">
-                <widget class="QDoubleSpinBox" name="decSpinBox">
+               <item row="1" column="0" colspan="4">
+                <widget class="Line" name="line_13">
+                 <property name="orientation">
+                  <enum>Qt::Horizontal</enum>
+                 </property>
+                </widget>
+               </item>
+               <item row="5" column="1">
+                <widget class="QDoubleSpinBox" name="incSpinBox">
                  <property name="decimals">
                   <number>1</number>
                  </property>
                   <double>90.000000000000000</double>
                  </property>
                  <property name="value">
-                  <double>0.000000000000000</double>
+                  <double>45.000000000000000</double>
                  </property>
                 </widget>
                </item>
-               <item row="4" column="0">
-                <widget class="QLabel" name="label_57">
+               <item row="2" column="1">
+                <widget class="QLabel" name="label_59">
+                 <property name="maximumSize">
+                  <size>
+                   <width>16777215</width>
+                   <height>20</height>
+                  </size>
+                 </property>
                  <property name="text">
-                  <string>[Date, time,°C]</string>
+                  <string>UTM</string>
                  </property>
                 </widget>
                </item>
-               <item row="3" column="0">
-                <widget class="QLabel" name="label_61">
+               <item row="4" column="3">
+                <widget class="QDoubleSpinBox" name="tempSpinBox">
+                 <property name="value">
+                  <double>20.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
+               <item row="4" column="2">
+                <widget class="QTimeEdit" name="timeEdit">
+                 <property name="calendarPopup">
+                  <bool>true</bool>
+                 </property>
+                </widget>
+               </item>
+               <item row="4" column="0">
+                <widget class="QLabel" name="label_57">
                  <property name="text">
-                  <string>Coordinates</string>
+                  <string>[Date, time,°C]</string>
                  </property>
                 </widget>
                </item>
                  </item>
                 </widget>
                </item>
-               <item row="1" column="0" colspan="4">
-                <widget class="Line" name="line_13">
-                 <property name="orientation">
-                  <enum>Qt::Horizontal</enum>
+               <item row="6" column="2">
+                <widget class="QLabel" name="label_85">
+                 <property name="text">
+                  <string>Larmor 𝜈 [Hz]</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="6" column="0">
+                <widget class="QLabel" name="label_86">
+                 <property name="text">
+                  <string>Tx offset [Hz]</string>
                  </property>
                 </widget>
                </item>
               <rect>
                <x>0</x>
                <y>0</y>
-               <width>98</width>
-               <height>28</height>
+               <width>96</width>
+               <height>26</height>
               </rect>
              </property>
              <attribute name="label">
               <rect>
                <x>0</x>
                <y>0</y>
-               <width>411</width>
-               <height>79</height>
+               <width>96</width>
+               <height>26</height>
               </rect>
              </property>
              <attribute name="label">
              <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
-&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Noto Sans'; font-size:9pt; font-weight:400; font-style:normal;&quot;&gt;
-&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-family:'Sans Serif';&quot;&gt;All processing steps are recorded here for your records&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Noto Sans'; font-size:12pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-family:'Sans Serif'; font-size:9pt;&quot;&gt;All processing steps are recorded here for your records&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
             </property>
            </widget>
            <widget class="QLabel" name="label_74">
      <x>0</x>
      <y>0</y>
      <width>1230</width>
-     <height>22</height>
+     <height>30</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuOpen_GMR_RAW_Header">

akvo/terminal/plotKernelDiff.py

     q = np.array(K0.PulseI.data)* (float)(K0.Taup)
 
     #plt.pcolor(K0.Interfaces.data, K0.PulseI.data, np.abs(K))
-    plt.pcolor(q, K0.Interfaces.data, np.abs(K), cmap=cmocean.cm.gray_r)
+    #plt.pcolor(q, K0.Interfaces.data, np.abs(K), cmap=cmocean.cm.gray_r)
     #plt.contourf(q, K0.Interfaces.data[0:-1], np.abs(K), cmap=cmocean.cm.tempo)
     #plt.pcolor(q, K0.Interfaces.data, np.abs(K), cmap=cmocean.cm.tempo)
     
-    plt.pcolor(q, K0.Interfaces.data, np.abs(K - K2), cmap=cmocean.cm.gray_r)
+    plt.pcolor(q, K0.Interfaces.data, (np.abs(K) - np.abs(K2)), cmap=cmocean.cm.gray_r)
     plt.colorbar()
 
     ax1 = plt.gca()

akvo/tressel/mrsurvey.py

                 # convert to dB and add colorbars
                 #db = 20.*np.log10(np.abs(SFFT[:,istart:iend]))
                 db = (np.abs(SFFT[:,istart:iend]))
+                
                 #db = (np.real(SFFT[:,istart:iend]))
+                #db = (np.imag(SFFT[:,istart:iend]))
                 #dbr = (np.real(SFFT[:,istart:iend]))
                 #db = (np.imag(SFFT[:,istart:iend]))
                 
                 
                     # Bootstrap noise 
                     #self.GATED[chan]["isum"]
-                    print("bootstrappin") 
                     Means = rotate.bootstrapWindows( self.DATADICT["NR"][pulse][chan][ipm], 20000, isum[isum!=1], adapt=True)
                     # MAD, only for windows > 1 
                     c = stats.norm.ppf(3./4.)
                     sig_stack[isum!=1] = np.ma.median(np.ma.abs(Means), axis=1) / c 
                     self.GATED[chan]["BN"][ipm] = sig_stack[clip:] 
-                    print("end bootstrappin")
 
                     #self.GATED[chan]["DATA"][ipm] = GD.real
                     self.GATEDABSCISSA = GT[clip:]
 
                 #scolours = plt.cm.Spectral(np.linspace(0,1,len(self.DATADICT["stacks"])))
                 #scolours = plt.cm.Blues(np.linspace(0,1,1.5*len(self.DATADICT["stacks"])))
-                scolours = cmocean.cm.ice(np.linspace(0,1,1.5*len(self.DATADICT["stacks"])))
+                scolours = cmocean.cm.ice(np.linspace(0,1,int(1.5*len(self.DATADICT["stacks"]))))
                 iistack = 0
                 for istack in self.DATADICT["stacks"]:
                     #self.DATADICT[pulse]["PULSE_TIMES"]
             ilabel = True
             for ipm in range(self.DATADICT["nPulseMoments"]):
                 #scolours = np.array([0.,0.,1.])
-                scolours = cmocean.cm.ice(np.linspace(0,1,1.5*len(self.DATADICT["stacks"])))
+                scolours = cmocean.cm.ice(np.linspace(0,1,int(1.5*len(self.DATADICT["stacks"]))))
                 #scolours = plt.cm.Spectral(np.linspace(0,1,len(self.DATADICT["stacks"])))
                 #scolours = plt.cm.Spectral(np.linspace(0,1,len(self.DATADICT["stacks"])))
                 istack = 0

setup.py

     long_description = fh.read()
 
 setup(name='Akvo',
-      version='1.4.6',
+      version='1.5.0',
       python_requires='>3.7.0', # due to pyLemma
       description='Surface nuclear magnetic resonance workbench',
       long_description=long_description,
           'pandas',
           'pyqt-distutils',
           'cmocean',
-          'pyLemma >= 0.0.11'
+          'pyLemma >= 0.1.0'
       ],
       packages=['akvo', 'akvo.tressel', 'akvo.gui'],
       license=['GPL 4.0'],