All kernel params from GUI

akvo/gui/akvoGUI.py

         self.ui.layerTableWidget.setDragEnabled(True)
         self.ui.layerTableWidget.setDragDropMode(QtWidgets.QAbstractItemView.InternalMove)
         
-        pCell = QtWidgets.QTableWidgetItem()
-        pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable 
-        pCell.setBackground( QtGui.QColor("lightgrey").lighter(110) )
-        self.ui.layerTableWidget.setItem(0, 1, pCell)
+        pCell0 = QtWidgets.QTableWidgetItem()
+        pCell0.setFlags(QtCore.Qt.NoItemFlags) # not selectable 
+        pCell0.setBackground( QtGui.QColor("lightgrey").lighter(110) )
+        pCell0.setText(str("0"))
+        self.ui.layerTableWidget.setItem(0, 0, pCell0)
+        
+        pCell1 = QtWidgets.QTableWidgetItem()
+        #pCell1.setFlags(QtCore.Qt.NoItemFlags) # not selectable 
+        pCell1.setBackground( QtGui.QColor("lightgrey").lighter(110) )
+        pCell1.setForeground( QtGui.QColor("black").lighter(110) )
+        self.ui.layerTableWidget.setItem(0, 1, pCell1)
+
+
         for ir in range(1, self.ui.layerTableWidget.rowCount() ):
             for ic in range(0, self.ui.layerTableWidget.columnCount() ):
                 pCell = QtWidgets.QTableWidgetItem()
                 #pCell.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
                 pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable 
                 pCell.setBackground( QtGui.QColor("lightgrey").lighter(110) )
+                pCell.setForeground( QtGui.QColor("black"))
                 self.ui.layerTableWidget.setItem(ir, ic, pCell)
         self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged) 
 
         except IOError as e:
             fpath = '.'
 
-        akvoData = QtWidgets.QFileDialog.getOpenFileName(self, 'Open Datafile File', fpath, r"Akvo datafiles (*.yaml)")[0] # arg2 = File Type 'All Files (*)'
-        txCoil = QtWidgets.QFileDialog.getOpenFileName(self, 'Open Tx File', fpath, r"Akvo datafiles (*.yaml, *.yml)")[0] # arg2 = File Type 'All Files (*)'
-        saveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save kernel as", fpath, r"Merlin KernelV0 (*.yml)")[0] #[0]
+        akvoData = QtWidgets.QFileDialog.getOpenFileName(self, 'Open Datafile File', fpath, r"Akvo datafiles (*.yaml)")[0]
+        txCoil = QtWidgets.QFileDialog.getOpenFileName(self, 'Open Tx File', fpath, r"Akvo datafiles (*.yaml, *.yml)")[0] 
+        saveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save kernel as", fpath, r"Merlin KernelV0 (*.yml)")[0] 
+
+        intDict = dict()
+        intDict["origin_n"] = self.ui.originN.value()
+        intDict["origin_e"] = self.ui.originE.value()
+        intDict["origin_d"] = self.ui.originD.value()
+        intDict["size_n"] = self.ui.sizeN.value()
+        intDict["size_e"] = self.ui.sizeE.value()
+        intDict["size_d"] = self.ui.sizeD.value()
+        intDict["nLay"] = self.ui.NLayers.value()
+        intDict["thick1"] = self.ui.thick1.value()
+        intDict["thickN"] = self.ui.thickN.value()
+        intDict["Lspacing"] = self.ui.layerSpacing.currentText()
+        intDict["minLevel"] = self.ui.minLevel.value()
+        intDict["maxLevel"] = self.ui.maxLevel.value()
+        intDict["branchTol"] = self.ui.branchTol.value()
+
+        # conductivity model... 
+        #tops = self.ui.layerTableWidget.col(0)
+        #print("Tops", tops)
+        tops = []
+        itop = 0
+        while self.ui.layerTableWidget.item(itop, 0).text(): 
+            tops.append( float(self.ui.layerTableWidget.item(itop,0).text()) ) 
+            itop += 1
+
+        bots = []
+        ibot = 0
+        while self.ui.layerTableWidget.item(ibot, 1).text(): 
+            bots.append( float(self.ui.layerTableWidget.item(ibot, 1).text()) ) 
+            ibot += 1
+        
+        sigs = []
+        isig = 0
+        while self.ui.layerTableWidget.item(isig, 2).text(): 
+            sigs.append( 1./float(self.ui.layerTableWidget.item(isig, 2).text()) ) 
+            isig += 1
+
+        intDict["tops"] = tops
+        intDict["bots"] = bots
+        intDict["sigs"] = sigs
+
+        node = yaml.YAML()
+        kpo = open( "kparams.yml", 'w' )
+        node.dump(intDict, kpo)
+
 
         callBox = callScript(  ) #QtWidgets.QDialog() 
         
         callBox.ui = Ui_callScript()
         callBox.ui.setupUi( callBox )
-        callBox.setupCB( akvoData, txCoil, saveStr  )
+        callBox.setupCB( akvoData, txCoil, "kparams.yml", saveStr  )
         
         callBox.exec_()
         callBox.show()
         # do that. Would require instead dist of T2 I guess.
         jj = self.ui.layerTableWidget.currentColumn()
         ii = self.ui.layerTableWidget.currentRow()
-        val = "class 'NoneType'>" 
+        val = "class 'NoneType'>"
         try:
             val = eval (str( self.ui.layerTableWidget.item(ii, jj).text() ))
         except:
             # enable next layer
             pCell4 = self.ui.layerTableWidget.item(ii+1, jj)
             pCell4.setBackground( QtGui.QColor("lightblue") ) #.lighter(110))
+            pCell4.setForeground( QtGui.QColor("black"))
             pCell4.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled )
             
             pCell5 = self.ui.layerTableWidget.item(ii+1, jj+1)
             pCell5.setBackground( QtGui.QColor("white"))
+            pCell5.setForeground( QtGui.QColor("black"))
             pCell5.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled )
             
-        print("ii", ii, "jj", jj)
         if ii == 0 and jj == 0:
             pCell = self.ui.layerTableWidget.item(0, 1)
-            pCell.setBackground( QtGui.QColor("lightblue")) #.lighter(110) )
+            pCell.setBackground(QtGui.QColor("lightblue")) #.lighter(110) )
+            pCell.setForeground( QtGui.QColor("black"))
             pCell.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled )
 
         self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged) 

akvo/gui/callScript.py

     #def __init__(self):
     #    super().__init__()
     
-    def setupCB(self, akvoData, TxCoil, SaveStr):
+    def setupCB(self, akvoData, TxCoil, kernelParams, SaveStr):
 
         #QtGui.QWidget.__init__(self)
         #uic.loadUi('redirect.ui', self)
 
         #print ('Starting process')
         #self.process.start('python', ['calcAkvoKernel.py', akvoData, TxCoil, SaveStr])
-        self.process.start('akvoK0', [ akvoData, TxCoil, SaveStr])
+        self.process.start('akvoK0', [ akvoData, TxCoil, kernelParams, SaveStr])
 
     def append(self, text):
         cursor = self.ui.textEdit.textCursor()

akvo/gui/main.ui

        <property name="geometry">
         <rect>
          <x>0</x>
-         <y>0</y>
+         <y>-201</y>
          <width>537</width>
          <height>982</height>
         </rect>
            <enum>Qt::LeftToRight</enum>
           </property>
           <property name="currentIndex">
-           <number>0</number>
+           <number>4</number>
           </property>
           <property name="elideMode">
            <enum>Qt::ElideLeft</enum>
               <layout class="QGridLayout" name="gridLayout_2">
                <item row="2" column="2">
                 <widget class="QPushButton" name="removeLoopButton">
+                 <property name="styleSheet">
+                  <string notr="true">#removeLoopButton {
+    background: red;
+}
+
+#removeLoopButton:disabled {
+    background: black;
+}</string>
+                 </property>
                  <property name="text">
                   <string>Remove</string>
                  </property>
                </item>
                <item row="0" column="0">
                 <widget class="QPushButton" name="addLoopButton">
+                 <property name="styleSheet">
+                  <string notr="true">#addLoopButton {
+    background: green;
+}
+
+#addLoopButton:disabled {
+    background: black;
+}</string>
+                 </property>
                  <property name="text">
                   <string>Add </string>
                  </property>
                </item>
                <item row="2" column="3">
                 <widget class="QPushButton" name="plotLoops">
+                 <property name="styleSheet">
+                  <string notr="true">#plotLoops {
+    background: green;
+}
+
+#plotLoops:disabled {
+    background: black;
+}</string>
+                 </property>
                  <property name="text">
                   <string>Plot loops</string>
                  </property>
           </widget>
           <widget class="QWidget" name="KernTab">
            <attribute name="title">
-            <string>Kern</string>
+            <string>Kernel</string>
            </attribute>
-           <widget class="QGroupBox" name="groupBox_2">
-            <property name="geometry">
-             <rect>
-              <x>30</x>
-              <y>10</y>
-              <width>371</width>
-              <height>301</height>
-             </rect>
-            </property>
-            <property name="title">
-             <string>Integration Parameters</string>
-            </property>
-            <widget class="QSpinBox" name="spinBox">
-             <property name="geometry">
-              <rect>
-               <x>120</x>
-               <y>30</y>
-               <width>49</width>
-               <height>29</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QSpinBox" name="spinBox_2">
-             <property name="geometry">
-              <rect>
-               <x>120</x>
-               <y>70</y>
-               <width>49</width>
-               <height>29</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QDoubleSpinBox" name="doubleSpinBox_7">
-             <property name="geometry">
-              <rect>
-               <x>280</x>
-               <y>70</y>
-               <width>70</width>
-               <height>29</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QLabel" name="label_70">
-             <property name="geometry">
-              <rect>
-               <x>21</x>
-               <y>34</y>
-               <width>81</width>
-               <height>20</height>
-              </rect>
-             </property>
-             <property name="text">
-              <string>min. level</string>
-             </property>
-            </widget>
-            <widget class="QLabel" name="label_71">
-             <property name="geometry">
-              <rect>
-               <x>20</x>
-               <y>75</y>
-               <width>81</width>
-               <height>20</height>
-              </rect>
-             </property>
-             <property name="text">
-              <string>max. level</string>
-             </property>
-            </widget>
-            <widget class="QLabel" name="label_72">
-             <property name="geometry">
-              <rect>
-               <x>187</x>
-               <y>75</y>
-               <width>81</width>
-               <height>20</height>
-              </rect>
-             </property>
-             <property name="text">
-              <string>branch tol</string>
-             </property>
-            </widget>
-            <widget class="QDoubleSpinBox" name="doubleSpinBox_6">
-             <property name="geometry">
-              <rect>
-               <x>210</x>
-               <y>260</y>
-               <width>141</width>
-               <height>29</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QDoubleSpinBox" name="doubleSpinBox">
-             <property name="geometry">
-              <rect>
-               <x>10</x>
-               <y>160</y>
-               <width>171</width>
-               <height>29</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QDoubleSpinBox" name="doubleSpinBox_3">
-             <property name="geometry">
-              <rect>
-               <x>10</x>
-               <y>210</y>
-               <width>171</width>
-               <height>31</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QDoubleSpinBox" name="doubleSpinBox_5">
-             <property name="geometry">
-              <rect>
-               <x>210</x>
-               <y>210</y>
-               <width>141</width>
-               <height>29</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QDoubleSpinBox" name="doubleSpinBox_4">
-             <property name="geometry">
-              <rect>
-               <x>210</x>
-               <y>160</y>
-               <width>141</width>
-               <height>29</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QDoubleSpinBox" name="doubleSpinBox_2">
-             <property name="geometry">
-              <rect>
-               <x>10</x>
-               <y>260</y>
-               <width>171</width>
-               <height>29</height>
-              </rect>
-             </property>
-            </widget>
-            <widget class="QLabel" name="label_2">
-             <property name="geometry">
-              <rect>
-               <x>10</x>
-               <y>130</y>
-               <width>63</width>
-               <height>20</height>
-              </rect>
-             </property>
-             <property name="text">
-              <string>Origin</string>
-             </property>
-            </widget>
-            <widget class="QLabel" name="label_73">
-             <property name="geometry">
-              <rect>
-               <x>210</x>
-               <y>130</y>
-               <width>63</width>
-               <height>20</height>
-              </rect>
-             </property>
-             <property name="text">
-              <string>Size</string>
-             </property>
-            </widget>
-           </widget>
-           <widget class="QTableWidget" name="layerTableWidget">
-            <property name="geometry">
-             <rect>
-              <x>30</x>
-              <y>320</y>
-              <width>351</width>
-              <height>431</height>
-             </rect>
-            </property>
-            <property name="toolTip">
-             <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;This table is used to enter coil geometries the format is as follows: each row specifies a single point on a coil. The first column is the coil index (using the GMR channel is useful), the next three colums specify the point in Northing, Easting, and Elevation. These can either be local coordinates or global ones. The final column specifies the loop radius if it is a circle or figure 8, for non circular or figure 8 loops leave this column blank. For figure-8 loops the coils do not need to be touching (see Irons and Kass, 2017). If a given index has 1 row it will be a circular loop, two rows will be a figure 8, and more than that will be a polygonal representation of the points, linearlly interpolated between them. &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
-            </property>
-           </widget>
-           <widget class="QPushButton" name="calcK0">
-            <property name="geometry">
-             <rect>
-              <x>400</x>
-              <y>330</y>
-              <width>105</width>
-              <height>39</height>
-             </rect>
-            </property>
-            <property name="text">
-             <string>Calc Kernel</string>
-            </property>
-           </widget>
+           <layout class="QVBoxLayout" name="verticalLayout_11">
+            <item>
+             <widget class="QGroupBox" name="groupBox">
+              <property name="title">
+               <string>Conductivty model</string>
+              </property>
+              <layout class="QVBoxLayout" name="verticalLayout_10">
+               <item>
+                <widget class="QTableWidget" name="layerTableWidget">
+                 <property name="toolTip">
+                  <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;This table is used to enter coil geometries the format is as follows: each row specifies a single point on a coil. The first column is the coil index (using the GMR channel is useful), the next three colums specify the point in Northing, Easting, and Elevation. These can either be local coordinates or global ones. The final column specifies the loop radius if it is a circle or figure 8, for non circular or figure 8 loops leave this column blank. For figure-8 loops the coils do not need to be touching (see Irons and Kass, 2017). If a given index has 1 row it will be a circular loop, two rows will be a figure 8, and more than that will be a polygonal representation of the points, linearlly interpolated between them. &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+                 </property>
+                </widget>
+               </item>
+              </layout>
+             </widget>
+            </item>
+            <item>
+             <widget class="QGroupBox" name="integrationBox">
+              <property name="sizePolicy">
+               <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
+                <horstretch>0</horstretch>
+                <verstretch>0</verstretch>
+               </sizepolicy>
+              </property>
+              <property name="minimumSize">
+               <size>
+                <width>480</width>
+                <height>300</height>
+               </size>
+              </property>
+              <property name="title">
+               <string>Integration Parameters</string>
+              </property>
+              <layout class="QGridLayout" name="gridLayout_17">
+               <item row="5" column="1" colspan="2">
+                <widget class="QDoubleSpinBox" name="originD">
+                 <property name="minimum">
+                  <double>0.010000000000000</double>
+                 </property>
+                 <property name="value">
+                  <double>0.100000000000000</double>
+                 </property>
+                </widget>
+               </item>
+               <item row="5" column="3" colspan="2">
+                <widget class="QDoubleSpinBox" name="sizeD">
+                 <property name="minimum">
+                  <double>1.000000000000000</double>
+                 </property>
+                 <property name="maximum">
+                  <double>300.000000000000000</double>
+                 </property>
+                 <property name="value">
+                  <double>125.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
+               <item row="0" column="0">
+                <widget class="QLabel" name="label_70">
+                 <property name="text">
+                  <string>min. level</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="4" column="1" colspan="2">
+                <widget class="QDoubleSpinBox" name="originE"/>
+               </item>
+               <item row="1" column="3">
+                <widget class="QLabel" name="label_72">
+                 <property name="text">
+                  <string>branch tol [nT]</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="0" column="4">
+                <widget class="QSpinBox" name="maxLevel">
+                 <property name="minimum">
+                  <number>1</number>
+                 </property>
+                 <property name="maximum">
+                  <number>14</number>
+                 </property>
+                 <property name="value">
+                  <number>3</number>
+                 </property>
+                </widget>
+               </item>
+               <item row="7" column="0">
+                <widget class="QLabel" name="label_65">
+                 <property name="text">
+                  <string>Layers</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="2" column="1">
+                <widget class="QLabel" name="label_2">
+                 <property name="text">
+                  <string>Origin</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="1" column="4">
+                <widget class="QDoubleSpinBox" name="branchTol">
+                 <property name="decimals">
+                  <number>3</number>
+                 </property>
+                 <property name="minimum">
+                  <double>0.001000000000000</double>
+                 </property>
+                 <property name="value">
+                  <double>1.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
+               <item row="2" column="3">
+                <widget class="QLabel" name="label_73">
+                 <property name="text">
+                  <string>Size</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="4" column="0">
+                <widget class="QLabel" name="label_58">
+                 <property name="text">
+                  <string>easting</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="4" column="3" colspan="2">
+                <widget class="QDoubleSpinBox" name="sizeE">
+                 <property name="minimum">
+                  <double>1.000000000000000</double>
+                 </property>
+                 <property name="maximum">
+                  <double>500.000000000000000</double>
+                 </property>
+                 <property name="value">
+                  <double>200.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
+               <item row="0" column="3">
+                <widget class="QLabel" name="label_71">
+                 <property name="text">
+                  <string>max. level</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="3" column="0">
+                <widget class="QLabel" name="label_54">
+                 <property name="text">
+                  <string>northing</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="3" column="3" colspan="2">
+                <widget class="QDoubleSpinBox" name="sizeN">
+                 <property name="minimum">
+                  <double>1.000000000000000</double>
+                 </property>
+                 <property name="maximum">
+                  <double>500.000000000000000</double>
+                 </property>
+                 <property name="value">
+                  <double>200.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
+               <item row="3" column="1" colspan="2">
+                <widget class="QDoubleSpinBox" name="originN"/>
+               </item>
+               <item row="0" column="1">
+                <widget class="QSpinBox" name="minLevel">
+                 <property name="minimum">
+                  <number>1</number>
+                 </property>
+                 <property name="maximum">
+                  <number>10</number>
+                 </property>
+                </widget>
+               </item>
+               <item row="5" column="0">
+                <widget class="QLabel" name="label_60">
+                 <property name="text">
+                  <string>depth</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="7" column="2">
+                <widget class="QSpinBox" name="NLayers">
+                 <property name="minimum">
+                  <number>1</number>
+                 </property>
+                 <property name="maximum">
+                  <number>200</number>
+                 </property>
+                 <property name="value">
+                  <number>50</number>
+                 </property>
+                </widget>
+               </item>
+               <item row="7" column="1">
+                <widget class="QLabel" name="label_66">
+                 <property name="text">
+                  <string>N Layers</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="7" column="4">
+                <widget class="QComboBox" name="layerSpacing">
+                 <property name="minimumSize">
+                  <size>
+                   <width>100</width>
+                   <height>0</height>
+                  </size>
+                 </property>
+                 <item>
+                  <property name="text">
+                   <string>Geometric</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string>Log</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string>Linear</string>
+                  </property>
+                 </item>
+                </widget>
+               </item>
+               <item row="7" column="3">
+                <widget class="QLabel" name="label_68">
+                 <property name="text">
+                  <string>spacing</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="6" column="0" colspan="5">
+                <widget class="Line" name="line_14">
+                 <property name="orientation">
+                  <enum>Qt::Horizontal</enum>
+                 </property>
+                </widget>
+               </item>
+               <item row="8" column="1">
+                <widget class="QLabel" name="label_69">
+                 <property name="text">
+                  <string>Thick 1</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="8" column="3">
+                <widget class="QLabel" name="label_75">
+                 <property name="text">
+                  <string>Thick N</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="8" column="2">
+                <widget class="QDoubleSpinBox" name="thick1">
+                 <property name="minimum">
+                  <double>0.010000000000000</double>
+                 </property>
+                 <property name="value">
+                  <double>0.500000000000000</double>
+                 </property>
+                </widget>
+               </item>
+               <item row="8" column="4">
+                <widget class="QDoubleSpinBox" name="thickN">
+                 <property name="minimum">
+                  <double>0.010000000000000</double>
+                 </property>
+                 <property name="value">
+                  <double>10.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
+              </layout>
+             </widget>
+            </item>
+            <item>
+             <widget class="QPushButton" name="calcK0">
+              <property name="minimumSize">
+               <size>
+                <width>100</width>
+                <height>40</height>
+               </size>
+              </property>
+              <property name="styleSheet">
+               <string notr="true">#calcK0{
+    background: green;
+}
+
+#calcK0:disabled {
+    background: black;
+}</string>
+              </property>
+              <property name="text">
+               <string>Calc Kernel</string>
+              </property>
+             </widget>
+            </item>
+           </layout>
           </widget>
           <widget class="QWidget" name="ModelTab">
            <attribute name="title">
-            <string>Model</string>
+            <string>Modelling</string>
            </attribute>
            <widget class="QToolBox" name="toolBox">
             <property name="geometry">
               <rect>
                <x>0</x>
                <y>0</y>
-               <width>96</width>
-               <height>26</height>
+               <width>100</width>
+               <height>30</height>
               </rect>
              </property>
              <attribute name="label">

akvo/gui/redirect.ui

       <bool>false</bool>
      </property>
      <property name="placeholderText">
-      <string>This windows outputs STDOUT from a seperate process.</string>
+      <string>This windows outputs STDOUT from a separate process.</string>
      </property>
     </widget>
    </item>

akvo/tressel/calcAkvoKernel.py

 
 import numpy as np
 
-#import matplotlib.pyplot as plt 
-#import seaborn as sns
-#sns.set(style="ticks")
+import matplotlib.pyplot as plt 
+import seaborn as sns
+sns.set(style="ticks")
+
+from ruamel import yaml
+
 #import cmocean 
 #from SEGPlot import *
 #from matplotlib.ticker import FormatStrFormatter
 def main():
 
     if len(sys.argv) < 3:
-        print ("usage  python calcAkvoKernel.py   AkvoDataset.yaml  Coil1.yaml SaveString " )
+        print ("usage  python calcAkvoKernel.py   AkvoDataset.yaml  Coil1.yaml kparams.yaml  SaveString.yaml " )
         exit()
 
     AKVO = loadAkvoData(sys.argv[1])
     B_dec = AKVO.META["B_0"]["dec"]  
     B0    = AKVO.META["B_0"]["intensity"]  
 
-    gamma = 2.67518e8
     fT = AKVO.transFreq
+    #gamma = 2.67518e8
     #B0 = (fL*2.*np.pi) /gamma * 1e9
  
     Coil1 = em1d.PolygonalWireAntenna.DeSerialize( sys.argv[2] )
     Coil1.SetFrequency(0, fT) 
     Coil1.SetCurrent(1.)
 
+    # read in kernel params
+    kparams = loadAkvoData( sys.argv[3] )
+
+    ## TODO 
     # pass this in...
     lmod = em1d.LayeredEarthEM() 
-    lmod.SetNumberOfLayers(4)
-    lmod.SetLayerThickness([15.49, 28.18])
-    lmod.SetLayerConductivity([0.0, 1./16.91, 1./24.06, 1./33.23])
+
+    nlay = len(kparams["sigs"])
+    sigs = np.array(kparams["sigs"])
+    tops = np.array(kparams["tops"])
+    bots = np.array(kparams["bots"])
+    
+    if ( (len(tops)-1) != len(bots)):
+        print("Layer mismatch")
+        exit()
+
+    thicks = bots - tops[0:-1]
+    
+    lmod.SetNumberOfLayers(nlay + 1)
+    lmod.SetLayerThickness(thicks)
+    lmod.SetLayerConductivity( np.concatenate( ( [0.0], sigs ) ))
+
+    #lmod.SetNumberOfLayers(4)
+    #lmod.SetLayerThickness([15.49, 28.18])
+    #lmod.SetLayerConductivity([0.0, 1./16.91, 1./24.06, 1./33.23])
+
 
     lmod.SetMagneticFieldIncDecMag( B_inc, B_dec, B0, lc.NANOTESLA )
-   
 
     Kern = mrln.KernelV0()
     Kern.PushCoil( "Coil 1", Coil1 )
     Kern.SetLayeredEarthEM( lmod );
-    Kern.SetIntegrationSize( (200,200,200) )
-    Kern.SetIntegrationOrigin( (0,0,0) )
-    Kern.SetTolerance( 1e-9 )
-    Kern.SetMinLevel( 3 )
+    Kern.SetIntegrationSize( (kparams["size_n"], kparams["size_e"], kparams["size_d"]) )
+    Kern.SetIntegrationOrigin( (kparams["origin_n"], kparams["origin_e"], kparams["origin_d"]) )
+    Kern.SetTolerance( 1e-9*kparams["branchTol"] )
+    Kern.SetMinLevel( kparams["minLevel"] )
+    Kern.SetMaxLevel( kparams["maxLevel"] )
     Kern.SetHankelTransformType( lc.FHTKEY201 )
     Kern.AlignWithAkvoDataset( sys.argv[1] )
 
-    thick = np.geomspace(.5, 10,num=40)
+    if str(kparams["Lspacing"]).strip() == "Geometric":
+        thick = np.geomspace(kparams["thick1"], kparams["thickN"], num=kparams["nLay"])
+    elif str(kparams["Lspacing"]) == "Log":
+        thick = np.logspace(kparams["thick1"], kparams["thickN"], num=kparams["nLay"])
+    elif str(kparams["Lspacing"]) == "Linear":
+        thick = np.linspace(kparams["thick1"], kparams["thickN"], num=kparams["nLay"])
+    else:
+        print("DOOOM!, in calcAkvoKernel layer spacing was not <Geometric>, <Log>, or <Linear>")
+        print( str(kparams["Lspacing"]) )
+        exit()
+
     iface = np.cumsum(thick)
     Kern.SetDepthLayerInterfaces(iface)
     #Kern.SetDepthLayerInterfaces(np.geomspace(1, 110, num=40))
     Kern.CalculateK0( ["Coil 1"], ["Coil 1"], False )
 
     #yml = open( 'test' + str(Kern.GetTolerance()) + '.yaml', 'w')
-    yml = open( sys.argv[3], 'w' )
+    yml = open( sys.argv[4], 'w' )
     print(Kern, file=yml)
 
-    #K0 = Kern.GetKernel()
-    
-    #plt.matshow(np.abs(K0))
-    #plt.show()
+    K0 = Kern.GetKernel()
+    plt.matshow(np.abs(K0))
+    plt.show()
 
 if __name__ == "__main__":
     main()