Work towards kernel calc inside Akvo

akvo/gui/Loop.ui

@@ -0,0 +1,110 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>LoopAdd</class>
+ <widget class="QDialog" name="LoopAdd">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>400</width>
+    <height>300</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Dialog</string>
+  </property>
+  <layout class="QFormLayout" name="formLayout">
+   <item row="0" column="0">
+    <widget class="QLabel" name="label_2">
+     <property name="text">
+      <string>Label</string>
+     </property>
+    </widget>
+   </item>
+   <item row="1" column="0">
+    <widget class="QLabel" name="label">
+     <property name="text">
+      <string>Type</string>
+     </property>
+    </widget>
+   </item>
+   <item row="1" column="1">
+    <widget class="QComboBox" name="comboBox">
+     <item>
+      <property name="text">
+       <string>Circular</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string>figure-8</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string>square-8</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string>New Item</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string>polygon</string>
+      </property>
+     </item>
+    </widget>
+   </item>
+   <item row="2" column="0" colspan="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="0" column="1">
+    <widget class="QLineEdit" name="lineEdit"/>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>accepted()</signal>
+   <receiver>LoopAdd</receiver>
+   <slot>accept()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>248</x>
+     <y>254</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>157</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>rejected()</signal>
+   <receiver>LoopAdd</receiver>
+   <slot>reject()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>316</x>
+     <y>260</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>286</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+</ui>

akvo/gui/akvoGUI.py

@@ -18,6 +18,9 @@ from akvo.gui.main_ui import Ui_MainWindow
 from akvo.gui.addCircularLoop_ui import Ui_circularLoopAdd
 from akvo.gui.addFigure8Loop_ui import Ui_figure8LoopAdd
 from akvo.gui.addPolygonalLoop_ui import Ui_polygonalLoopAdd
+from akvo.gui.redirect_ui import Ui_callScript
+from akvo.gui.callScript import callScript
+
 from akvo.tressel import mrsurvey 
 
 from pyLemma import LemmaCore  
@@ -158,6 +161,10 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         self.ui.plotGI.setEnabled(False) 
         self.ui.plotGI.pressed.connect( self.plotGI )
 
+        # Kernel         
+        self.ui.calcK0.pressed.connect( self.calcK0 )       
+
+
         # META 
         self.ui.locEdit.editingFinished.connect( self.logSite )
         self.ui.UTMzone.currentIndexChanged.connect( self.logSite )
@@ -299,6 +306,28 @@ class ApplicationWindow(QtWidgets.QMainWindow):
             self.ui.ProcTabs.removeTab(0)    
             self.ui.ProcTabs.removeTab(0)    
     
+    def calcK0(self):
+        
+        try:
+            with open('.akvo.last.path') as f: 
+                fpath = f.readline()  
+                pass
+        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]
+
+        callBox = callScript(  ) #QtWidgets.QDialog() 
+        
+        callBox.ui = Ui_callScript()
+        callBox.ui.setupUi( callBox )
+        callBox.setupCB( akvoData, txCoil, saveStr  )
+        
+        callBox.exec_()
+        callBox.show()
+    
     def loopAdd(self):
 
         #print(self.ui.loopLabel.text())
@@ -329,7 +358,7 @@ class ApplicationWindow(QtWidgets.QMainWindow):
                     turns = dialog.ui.loopTurns.value()
                     ns = dialog.ui.segments.value()
                     cwise = dialog.ui.cwiseBox.currentIndex()
-                    print("cwise", cwise)
+                    #print("cwise", cwise)
                     #dip = dialog.ui.dip.value()
                     #azimuth = dialog.ui.az.value()
                     

akvo/gui/callScript.py

@@ -0,0 +1,55 @@
+from PyQt5 import uic
+from PyQt5 import QtGui, QtCore
+from PyQt5.QtWidgets import QMainWindow, QPushButton, QApplication, QTextEdit, QApplication, QDialog
+
+def p(x):
+    print (x)
+
+class callScript(QDialog):
+
+    #def __init__(self):
+    #    super().__init__()
+    
+    def setupCB(self, akvoData, TxCoil, SaveStr):
+
+        #QtGui.QWidget.__init__(self)
+        #uic.loadUi('redirect.ui', self)
+
+        print ('Connecting process')
+        self.process = QtCore.QProcess(self)
+        self.process.readyReadStandardOutput.connect(self.stdoutReady)
+        self.process.readyReadStandardError.connect(self.stderrReady)
+        self.process.started.connect(lambda: p('Started!'))
+        self.process.finished.connect(lambda: p('Finished!'))
+
+        print ('Starting process')
+        self.process.start('python', ['calcAkvoKernel.py', akvoData, TxCoil, SaveStr])
+
+    def append(self, text):
+        cursor = self.ui.textEdit.textCursor()
+        cursor.movePosition(cursor.End)
+        cursor.insertText(text)
+        self.ui.textEdit.ensureCursorVisible()
+        #MyTextEdit.verticalScrollBar()->setValue(MyTextEdit.verticalScrollBar()->maximum());
+
+
+    def stdoutReady(self):
+        text = str(self.process.readAllStandardOutput(), encoding='utf-8')
+        #print (text) 
+        self.append(text)
+
+    def stderrReady(self):
+        text = str(self.process.readAllStandardError())
+        #print (text) #.strip())
+        self.append(text)
+
+
+#def main():
+#    import sys
+#    app = QApplication(sys.argv)
+#    win = MainWindow()
+#    win.show()
+#    sys.exit(app.exec_())
+    
+#if __name__ == '__main__':
+   # main()

akvo/gui/main.ui

@@ -3825,13 +3825,26 @@ background: dark grey;
               <x>30</x>
               <y>320</y>
               <width>351</width>
-              <height>501</height>
+              <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>
           </widget>
           <widget class="QWidget" name="ModelTab">
            <attribute name="title">
@@ -3854,8 +3867,8 @@ background: dark grey;
               <rect>
                <x>0</x>
                <y>0</y>
-               <width>100</width>
-               <height>30</height>
+               <width>96</width>
+               <height>26</height>
               </rect>
              </property>
              <attribute name="label">

akvo/gui/redirect.ui

@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>callScript</class>
+ <widget class="QDialog" name="callScript">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>691</width>
+    <height>852</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Dialog</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout">
+   <item>
+    <widget class="QStatusBar" name="statusbar"/>
+   </item>
+   <item>
+    <widget class="QTextEdit" name="textEdit">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+     <property name="font">
+      <font>
+       <family>Monospace</family>
+      </font>
+     </property>
+     <property name="cursor" stdset="0">
+      <cursorShape>IBeamCursor</cursorShape>
+     </property>
+     <property name="mouseTracking">
+      <bool>false</bool>
+     </property>
+     <property name="readOnly">
+      <bool>true</bool>
+     </property>
+     <property name="overwriteMode">
+      <bool>true</bool>
+     </property>
+     <property name="acceptRichText">
+      <bool>false</bool>
+     </property>
+     <property name="placeholderText">
+      <string>This windows outputs STDOUT from a seperate process.</string>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>

akvo/terminal/plotyaml.py

@@ -52,7 +52,6 @@ def loadAkvoData(fnamein):
     return AKVO 
 
 def plotQt( akvo ):
- 
     plt.style.use('ggplot')
     #plt.style.use('seaborn-white')
     for pulse in akvo.Gated:
@@ -100,10 +99,9 @@ def plotQt( akvo ):
 
     #plt.matshow(RE)
     #plt.matshow(IM)
-
-
-
+    plt.savefig("data.pdf")
     plt.show()
+
 if __name__ == "__main__":
     akvo = loadAkvoData( sys.argv[1] ) #, "Chan. 1")
     plotQt(akvo)

akvo/tressel/calcAkvoKernel.py

@@ -0,0 +1,127 @@
+
+import os, sys
+import numpy as np
+from ruamel import yaml
+
+import pyLemma.LemmaCore as lc 
+import pyLemma.Merlin as mrln 
+import pyLemma.FDEM1D as em1d 
+
+import numpy as np
+
+import matplotlib.pyplot as plt 
+import seaborn as sns
+sns.set(style="ticks")
+import cmocean 
+from SEGPlot import *
+from matplotlib.ticker import FormatStrFormatter
+import matplotlib.ticker as plticker
+
+
+# Converts Lemma/Merlin/Akvo serialized Eigen arrays into numpy ones for use by Python 
+class VectorXr(yaml.YAMLObject):
+    """
+    Converts Lemma/Merlin/Akvo serialized Eigen arrays into numpy ones for use by Python 
+    """
+    yaml_tag = u'VectorXr'
+    def __init__(self, array):
+        self.size = np.shape(array)[0]
+        self.data = array.tolist()
+    def __repr__(self):
+        # Converts to numpy array on import 
+        return "np.array(%r)" % (self.data)
+
+class AkvoData(yaml.YAMLObject):
+    """
+    Reads an Akvo serialized dataset into a standard python dictionary 
+    """
+    yaml_tag = u'AkvoData'
+    def __init__(self, array):
+        pass
+        #self.size = np.shape(array)[0]
+        #self.Imp = array.tolist()
+    def __repr__(self):
+        # Converts to a dictionary with Eigen vectors represented as Numpy arrays 
+        return self
+
+def loadAkvoData(fnamein):
+    """ Loads data from an Akvo YAML file. The 0.02 is hard coded as the pulse length. This needs to be 
+        corrected in future kernel calculations. The current was reported but not the pulse length. 
+    """
+    fname = (os.path.splitext(fnamein)[0])
+    with open(fnamein, 'r') as stream:
+        try:
+            AKVO = (yaml.load(stream, Loader=yaml.Loader))
+        except yaml.YAMLError as exc:
+            print(exc)
+    return AKVO 
+
+if __name__ == "__main__":
+
+    if len(sys.argv) < 3:
+        print ("usage  python calcAkvoKernel.py   AkvoDataset.yaml  Coil1.yaml  " )
+        exit()
+    
+    gamma = 2.67518e8
+    fL = 2289.
+    B0 = (fL*2.*np.pi) /gamma * 1e9
+
+    AKVO = loadAkvoData(sys.argv[1])
+    Coil1 = em1d.PolygonalWireAntenna.DeSerialize( sys.argv[2] )
+    Coil1.SetNumberOfFrequencies(1)
+    Coil1.SetFrequency(0, fL) 
+    Coil1.SetCurrent(1.)
+
+
+    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])
+    lmod.SetMagneticFieldIncDecMag( 68.9, 0, 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.SetHankelTransformType( lc.FHTKEY201 )
+    Kern.AlignWithAkvoDataset( sys.argv[1] )
+
+    thick = np.geomspace(.5, 10,num=40)
+    iface = np.cumsum(thick)
+    Kern.SetDepthLayerInterfaces(iface)
+    #Kern.SetDepthLayerInterfaces(np.geomspace(1, 110, num=40))
+    #Kern.SetDepthLayerInterfaces(np.linspace(1, 110, num=50))
+    #Kern.SetDepthLayerInterfaces(np.geomspace(1, 110, num=40))
+ 
+    # autAkvoDataNode = YAML::LoadFile(argv[4]);
+    # Kern->AlignWithAkvoDataset( AkvoDataNode );
+
+    #Kern.SetPulseDuration(0.040)
+    #Kern.SetPulseCurrent(  [1.6108818092452406, 1.7549935078885168, 1.7666319459646016, 1.9270787752430283,
+    #    1.9455431806179229, 2.111931346726564, 2.1466747256211747, 2.3218217392379588,
+    #    2.358359967649008, 2.5495654202189058, 2.5957289164577992, 2.8168532605800802,
+    #    2.85505242699187, 3.1599429539069774, 3.2263673040205068, 3.6334182368296544,
+    #    3.827985200119751, 4.265671313014058, 4.582237014873297, 5.116839616183394,
+    #    5.515173073160611, 6.143620383280934, 6.647972282096122, 7.392577402979211,
+    #    8.020737177449933, 8.904435233295793, 9.701975105606063, 10.74508217792577,
+    #    11.743887525923592, 12.995985956061467, 14.23723766879807, 15.733870137824457,
+    #    17.290155933625808, 19.07016662950366, 21.013341340455703, 23.134181634845618,
+    #    25.570925414182238, 28.100862178905476, 31.13848909847073, 34.16791099558486,
+    #    37.95775984680512, 41.589619321873165, 46.327607251605286, 50.667786337299205,
+    #    56.60102493062895, 61.81174065797068, 69.23049946198458, 75.47409803238031,
+    #    84.71658869065816, 92.1855007134236, 103.77129947551164, 112.84577430578537,
+    #    127.55127257092909, 138.70199812969176, 157.7443764728878, 171.39653462998626]
+    #)
+
+    Kern.CalculateK0( ["Coil 1"], ["Coil 1"], False )
+
+    yml = open('akvoK3-' + str(Kern.GetTolerance()) + '.yaml', 'w')
+    print(Kern, file=yml)
+
+    K0 = Kern.GetKernel()
+    plt.matshow(np.abs(K0))
+    plt.show()

akvo/tressel/mrsurvey.py

@@ -1778,7 +1778,7 @@ class GMRDataProcessor(SNMRDataProcessor):
                                                      M, mu, PCA, flambda, H[pulse][ichan])
                             iloop = 0
                             #while False: 
-                            while (np.linalg.norm( H[pulse][ichan] - hm1) > .05):
+                            while (np.linalg.norm( H[pulse][ichan] - hm1) > .05): # threshold for recall 
                                 hm1 = np.copy(H[pulse][ichan]) 
                                 [e, H[pulse][ichan]] = Filt.adapt_filt_Ref( self.DATADICT[pulse][ichan][ipm][istack][::-1],\
                                                         RX,\

pyuic.json

@@ -15,6 +15,10 @@
         [
             "akvo/gui/addPolygonalLoop.ui",
             "akvo/gui"
+        ],
+        [
+            "akvo/gui/redirect.ui",
+            "akvo/gui"
         ]
     ],
     "pyrcc": "pyrcc5",

setup.py

@@ -21,7 +21,7 @@ with open("README.md", "r") as fh:
     long_description = fh.read()
 
 setup(name='Akvo',
-      version='1.3.3',
+      version='1.3.4',
       python_requires='>3.7.0', # due to pyLemma
       description='Surface nuclear magnetic resonance workbench',
       long_description=long_description,
@@ -59,6 +59,7 @@ setup(name='Akvo',
       entry_points = {
               'console_scripts': [
                   'akvo = akvo.gui.akvoGUI:main',                  
+                  'akvoK0 = akvo.tressel.calcAkvoKernel:main',                  
               ],              
           },
       #cmdclass = cmdclass,