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

@@ -7,15 +7,29 @@
     <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">
@@ -24,76 +38,71 @@
      </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>
@@ -104,17 +113,29 @@
      </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>
@@ -125,87 +146,91 @@
      </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

@@ -8,7 +8,7 @@ import numpy as np
 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
@@ -28,6 +28,7 @@ from pyLemma import FDEM1D
 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):
@@ -166,6 +167,11 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         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 )       
 
@@ -286,6 +292,22 @@ class ApplicationWindow(QtWidgets.QMainWindow):
             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( )    
@@ -338,7 +360,7 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         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 )   
     
@@ -350,26 +372,29 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         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: 
@@ -378,7 +403,7 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         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)   
     
@@ -455,7 +480,7 @@ class ApplicationWindow(QtWidgets.QMainWindow):
             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()
@@ -554,9 +579,9 @@ class ApplicationWindow(QtWidgets.QMainWindow):
                     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.)
             
@@ -576,8 +601,58 @@ class ApplicationWindow(QtWidgets.QMainWindow):
                     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":
                 
@@ -638,7 +713,7 @@ class ApplicationWindow(QtWidgets.QMainWindow):
             # 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 
@@ -845,7 +920,10 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         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])
@@ -874,7 +952,7 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         
         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')
@@ -991,7 +1069,12 @@ class ApplicationWindow(QtWidgets.QMainWindow):
             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"])
 
@@ -1099,6 +1182,15 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         #    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)
@@ -1136,7 +1228,7 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         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]) )
@@ -1612,7 +1704,7 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         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

@@ -638,7 +638,7 @@ background: dark grey;
                 <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>
@@ -710,8 +710,8 @@ background: dark grey;
         <rect>
          <x>0</x>
          <y>0</y>
-         <width>543</width>
-         <height>889</height>
+         <width>537</width>
+         <height>982</height>
         </rect>
        </property>
        <property name="sizePolicy">
@@ -2918,10 +2918,10 @@ background: dark grey;
                <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>
@@ -2947,36 +2947,6 @@ background: dark grey;
                  </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">
@@ -2984,10 +2954,13 @@ background: dark grey;
                  </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>
@@ -3011,6 +2984,13 @@ background: dark grey;
                  </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">
@@ -3133,6 +3113,13 @@ background: dark grey;
                  </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">
@@ -3160,21 +3147,38 @@ background: dark grey;
                  </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>
@@ -3185,21 +3189,41 @@ background: dark grey;
                   <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>
@@ -3515,10 +3539,17 @@ background: dark grey;
                  </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>
@@ -4112,8 +4143,8 @@ background: dark grey;
               <rect>
                <x>0</x>
                <y>0</y>
-               <width>98</width>
-               <height>28</height>
+               <width>96</width>
+               <height>26</height>
               </rect>
              </property>
              <attribute name="label">
@@ -4125,8 +4156,8 @@ background: dark grey;
               <rect>
                <x>0</x>
                <y>0</y>
-               <width>411</width>
-               <height>79</height>
+               <width>96</width>
+               <height>26</height>
               </rect>
              </property>
              <attribute name="label">
@@ -4422,8 +4453,8 @@ background: red;
              <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">
@@ -4454,7 +4485,7 @@ p, li { white-space: pre-wrap; }
      <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

@@ -36,11 +36,11 @@ if __name__ == "__main__":
     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

@@ -495,7 +495,9 @@ class GMRDataProcessor(SNMRDataProcessor):
                 # 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]))
                 
@@ -1269,13 +1271,11 @@ class GMRDataProcessor(SNMRDataProcessor):
                 
                     # 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:]
@@ -1650,7 +1650,7 @@ class GMRDataProcessor(SNMRDataProcessor):
 
                 #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"]
@@ -1706,7 +1706,7 @@ class GMRDataProcessor(SNMRDataProcessor):
             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

@@ -21,7 +21,7 @@ with open("README.md", "r") as fh:
     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,
@@ -53,7 +53,7 @@ setup(name='Akvo',
           'pandas',
           'pyqt-distutils',
           'cmocean',
-          'pyLemma >= 0.0.11'
+          'pyLemma >= 0.1.0'
       ],
       packages=['akvo', 'akvo.tressel', 'akvo.gui'],
       license=['GPL 4.0'],