Rework of yaml log of processing steps. The log is now a flow of steps, any of which can be repeated. Additionally, plotting of the harmonic modelling has been changed to frequency domain.

akvo/gui/akvoGUI.py

 """
 
 import matplotlib
-#matplotlib.use("QT4Agg")
+matplotlib.use("QT5Agg")
 from PyQt5 import QtCore, QtGui, QtWidgets
 
 import numpy as np
     def __init__(self):
         self.Akvo_VERSION = version
         self.Import = OrderedDict() # {}
-        self.Processing = OrderedDict() 
+        self.Processing = [] # OrderedDict() 
+        self.Stacking = OrderedDict() 
     #def __init__(self, node):
     #    self.Akvo_VERSION = node["version"]
     #    self.Import = OrderedDict( node["Import"] ) # {}
     #    self.Processing = OrderedDict( node["Processing"] ) 
     def __repr__(self):
         return "%s(name=%r, Akvo_VERSION=%r, Import=%r, Processing=%r)" % (
-            #self.__class__.__name__, self.Akvo_VERSION, self.Import, self.Processing )
-            self.__class__.__name__, self.Akvo_VERSION, self.Import, OrderedDict(self.Processing) ) 
-            #self.__class__.__name__, self.Akvo_VERSION, self.Import, OrderedDict(self.Processing)) 
+            self.__class__.__name__, self.Akvo_VERSION, self.Import, self.Processing, self.Stacking )
+            #self.__class__.__name__, self.Akvo_VERSION, self.Import, OrderedDict(self.Processing) ) 
     
 try:    
     import thread 
         self.ui.lcdNumberTauDelay.setEnabled(0)
         self.ui.lcdNumberNQ.setEnabled(0)
 
-        #MAK 20170126: add in a list to hold processing steps
         self.logText = []      
 
-        ####################
-        # Make connections #
-        ####################
+        #######################
+        ##################### #
+        ## Make connections # #
+        ##################### #
+        #######################
 
-        # Menu items 
+        ##############
+        # Menu items #
+        ##############
         self.ui.actionOpen_GMR.triggered.connect(self.openGMRRAWDataset)
         self.ui.actionSave_Preprocessed_Dataset.triggered.connect(self.SavePreprocess)
         self.ui.actionExport_Preprocessed_Dataset.triggered.connect(self.ExportPreprocess)
         self.ui.actionOpen_Preprocessed_Dataset.triggered.connect(self.OpenPreprocess)
         self.ui.actionAboutAkvo.triggered.connect(self.about)
 
-        # Buttons
+        ###########
+        # Buttons #
+        ###########
 #         #QtCore.QObject.connect(self.ui.fullWorkflowPushButton, QtCore.SIGNAL("clicked()"), self.preprocess )
         self.ui.loadDataPushButton.pressed.connect(self.loadRAW) 
         self.ui.sumDataGO.pressed.connect( self.sumDataChans )
 
         self.YamlNode.Import = OrderedDict((yaml.load( self.logText, Loader=yaml.Loader )).Import)
         self.YamlNode.Processing = OrderedDict((yaml.load( self.logText, Loader=yaml.Loader )).Processing)
-        self.Log() 
+        self.YamlNode.Stacking = OrderedDict((yaml.load( self.logText, Loader=yaml.Loader )).Stacking)
+        self.Log()
+ 
             #self.ui.logTextBrowser.append( yaml.dump(self.YamlNode)) #, default_flow_style=False)  )
         #except KeyError:
         #    pass
                 self.ui.mplwidget))
 
     def calcQ(self):
-        if "Calc Q" not in self.YamlNode.Processing.keys():
+        if "Calc Q" not in self.YamlNode.Stacking.keys():
             #print("In CalcQ", yaml.dump(self.YamlNode.Processing)  )
-            self.YamlNode.Processing["Calc Q"] = True
+            self.YamlNode.Stacking["Calc Q"] = True
             #print( yaml.dump(self.YamlNode.Processing)  )
             self.Log()
         else:
                 self.ui.mplwidget))
 
     def harmonicModel(self):
-
-        if "Harmonic modelling" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["Harmonic modelling"] = {}
-            self.YamlNode.Processing["Harmonic modelling"]["NF"] = str( self.ui.NHarmonicsFreqsSpin.value() ) 
-            self.YamlNode.Processing["Harmonic modelling"]["Segments"] = str( self.ui.NSegments.value() ) 
-            self.YamlNode.Processing["Harmonic modelling"]["f0K1"] = str( self.ui.f0K1Spin.value() )
-            self.YamlNode.Processing["Harmonic modelling"]["f0KN"] = str( self.ui.f0KNSpin.value() )
-            self.YamlNode.Processing["Harmonic modelling"]["f0Ks"] = str( self.ui.f0KsSpin.value() )
-            self.YamlNode.Processing["Harmonic modelling"]["f0"] = str( self.ui.f0Spin.value() )
-            if self.ui.NHarmonicsFreqsSpin.value() > 1:
-                self.YamlNode.Processing["Harmonic modelling"]["f1K1"] = str( self.ui.f1K1Spin.value() )
-                self.YamlNode.Processing["Harmonic modelling"]["f1KN"] = str( self.ui.f1KNSpin.value() )
-                self.YamlNode.Processing["Harmonic modelling"]["f1Ks"] = str( self.ui.f1KsSpin.value() )
-                self.YamlNode.Processing["Harmonic modelling"]["f1"] = str( self.ui.f1Spin.value() )
-            self.Log()
-        #else:
-        #    err_msg = "Harmonic modelling noise cancellation has already been applied!"
-        #    reply = QtWidgets.QMessageBox.critical(self, 'Error', 
-        #        err_msg) 
-        #    return 
-
+        
         self.lock("harmonic noise modelling")
+        
+        Harm = OrderedDict()
+        Harm["STEP"] = "Harmonic modelling"
+        Harm["NF"] = str( self.ui.NHarmonicsFreqsSpin.value() ) 
+        Harm["Segments"] = str( self.ui.NSegments.value() ) 
+        Harm["Proc. ref."] = self.ui.harmRef.isChecked() 
+        
+        
+        if self.ui.searchAll.currentText() == "All":
+            Harm["search"] = self.ui.searchAll.currentText()
+            Search = False  
+        else:
+            #Harm["search"] = self.ui.searchAll.currentText() 
+            Harm["search"] = str(self.ui.Nsearch.value()) 
+            Search = self.ui.Nsearch.value() 
+        if self.ui.boundsCheck.isChecked():
+            Harm["Bounds"] = str(self.ui.bounds.value()) 
+            Bounds = self.ui.bounds.value() 
+        else:
+            Harm["Bounds"] = self.ui.boundsCheck.isChecked() 
+            Bounds = 0
+
+        Harm["f0K1"] = str( self.ui.f0K1Spin.value() )
+        Harm["f0KN"] = str( self.ui.f0KNSpin.value() )
+        Harm["f0Ks"] = str( self.ui.f0KsSpin.value() )
+        Harm["f0"] = str( self.ui.f0Spin.value() )
+        if self.ui.NHarmonicsFreqsSpin.value() > 1:
+            Harm["f1K1"] = str( self.ui.f1K1Spin.value() )
+            Harm["f1KN"] = str( self.ui.f1KNSpin.value() )
+            Harm["f1Ks"] = str( self.ui.f1KsSpin.value() )
+            Harm["f1"] = str( self.ui.f1Spin.value() )
+        self.YamlNode.Processing.append(Harm)
+        self.Log()
 
         thread.start_new_thread(self.RAWDataProc.harmonicModel, \
                 ( \
                  self.ui.f1K1Spin.value(), \
                  self.ui.f1KNSpin.value(), \
                  self.ui.f1KsSpin.value(), \
+                 Search, \
+                 Bounds, \
+                 self.ui.harmRef.isChecked(), \
                  self.ui.plotHarmonic.isChecked(), \
                  self.ui.mplwidget \
                 ) \
 
     def FDSmartStack(self):
 
-        if "TD stack" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["TD stack"] = {}
-            self.YamlNode.Processing["TD stack"]["outlier"] = str( self.ui.outlierTestCB.currentText() ) 
-            self.YamlNode.Processing["TD stack"]["cutoff"] = str( self.ui.MADCutoff.value() )
+        if "TD stack" not in self.YamlNode.Stacking.keys():
+            self.YamlNode.Stacking["TD stack"] = {}
+            self.YamlNode.Stacking["TD stack"]["outlier"] = str( self.ui.outlierTestCB.currentText() ) 
+            self.YamlNode.Stacking["TD stack"]["cutoff"] = str( self.ui.MADCutoff.value() )
             self.Log()
         else:
             err_msg = "TD noise cancellation has already been applied!"
                 self.ui.mplwidget))
 
     def adaptFilter(self):
-
-        if "TD noise cancellation" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["TD noise cancellation"] = {}
-            self.YamlNode.Processing["TD noise cancellation"]["n_Taps"] = str(self.ui.MTapsSpinBox.value())
-            self.YamlNode.Processing["TD noise cancellation"]["lambda"] = str(self.ui.adaptLambdaSpinBox.value())
-            self.YamlNode.Processing["TD noise cancellation"]["truncate"] = str(self.ui.adaptTruncateSpinBox.value())
-            self.YamlNode.Processing["TD noise cancellation"]["mu"] = str(self.ui.adaptMuSpinBox.value()) 
-            self.YamlNode.Processing["TD noise cancellation"]["PCA"] = str(self.ui.PCAComboBox.currentText())
-            self.Log()
-        else:
-            err_msg = "TD noise cancellation has already been applied!"
-            reply =QtWidgets.QMessageBox.critical(self, 'Error', err_msg) 
-            #return 
         
         self.lock("TD noise cancellation filter")
+        
+        # Log processing 
+        Adapt = OrderedDict()
+        Adapt["STEP"] = "TD noise cancellation"
+        Adapt["n_Taps"] = str(self.ui.MTapsSpinBox.value())
+        Adapt["lambda"] = str(self.ui.adaptLambdaSpinBox.value())
+        Adapt["truncate"] = str(self.ui.adaptTruncateSpinBox.value())
+        Adapt["mu"] = str(self.ui.adaptMuSpinBox.value()) 
+        Adapt["PCA"] = str(self.ui.PCAComboBox.currentText())
+        self.YamlNode.Processing.append(Adapt)
+        self.Log( )
+
         thread.start_new_thread(self.RAWDataProc.adaptiveFilter, \
                 (self.ui.MTapsSpinBox.value(), \
                 self.ui.adaptLambdaSpinBox.value(), \
 
     def sumDataChans(self): 
 
-        if "Data sum" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["Data sum"] = True
-            self.Log()
-        else:
-            err_msg = "Data channels have already been summed!"
-            reply =QtWidgets.QMessageBox.critical(self, 'Error', 
-                err_msg) 
-            return 
-
         self.lock("Summing data channels")
+        
+        Sum = OrderedDict()
+        Sum["STEP"] = "Channel sum"
+        self.YamlNode.Processing.append(Sum)
+        self.Log( )
+
         self.dataChan = [self.dataChan[0]]
         self.ui.sumDataBox.setEnabled(False)    
         thread.start_new_thread( self.RAWDataProc.sumData, ( self.ui.mplwidget, 7 ) )
                 self.ui.mplwidget))
 
     def bandPassFilter(self):
-        if "Bandpass filter" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["Bandpass filter"] = {}
-            self.YamlNode.Processing["Bandpass filter"]["central_nu"] = str(self.ui.CentralVSpinBox.value())
-            self.YamlNode.Processing["Bandpass filter"]["passband"] = str(self.ui.passBandSpinBox.value())
-            self.YamlNode.Processing["Bandpass filter"]["stopband"] = str(self.ui.stopBandSpinBox.value()) 
-            self.YamlNode.Processing["Bandpass filter"]["gpass"] = str(self.ui.gpassSpinBox.value())
-            self.YamlNode.Processing["Bandpass filter"]["gstop"] = str(self.ui.gstopSpinBox.value())
-            self.YamlNode.Processing["Bandpass filter"]["type"] = str(self.ui.fTypeComboBox.currentText())
-            self.Log()
-        else:
-            err_msg = "Bandpass filter has already been applied!"
-            reply =QtWidgets.QMessageBox.critical(self, 'Error', 
-                err_msg) 
-            return 
+        
         self.lock("bandpass filter")        
+        
+        # Log processing 
+        Band = OrderedDict()
+        Band["STEP"] = "Bandpass filter"
+        Band["central_nu"] = str(self.ui.CentralVSpinBox.value())
+        Band["passband"] = str(self.ui.passBandSpinBox.value())
+        Band["stopband"] = str(self.ui.stopBandSpinBox.value()) 
+        Band["gpass"] = str(self.ui.gpassSpinBox.value())
+        Band["gstop"] = str(self.ui.gstopSpinBox.value())
+        Band["type"] = str(self.ui.fTypeComboBox.currentText())
+        self.YamlNode.Processing.append(Band)
+        self.Log( )
+
         nv = self.ui.lcdTotalDeadTime.value( ) + self.ui.lcdNumberFTauDead.value()
         self.ui.lcdTotalDeadTime.display( nv )
         thread.start_new_thread(self.RAWDataProc.bandpassFilter, \
                 (self.ui.mplwidget, 0, self.ui.plotBP.isChecked() ))
 
     def downsample(self):
+
         self.lock("resampling")
-        
-        if "Resample" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["Resample"] = {}
-            self.YamlNode.Processing["Resample"]["downsample factor"] = [] 
-            self.YamlNode.Processing["Resample"]["truncate length"] = []  
-        self.YamlNode.Processing["Resample"]["downsample factor"].append( str(self.ui.downSampleSpinBox.value() ) )
-        self.YamlNode.Processing["Resample"]["truncate length"].append(  str( self.ui.truncateSpinBox.value() ) )
+
+        # Log processing 
+        Resample = OrderedDict() 
+        Resample["STEP"] = "Resample"
+        Resample["downsample factor"] = str(self.ui.downSampleSpinBox.value())
+        Resample["truncate length"] = str(self.ui.truncateSpinBox.value()) 
+        self.YamlNode.Processing.append(Resample)
         self.Log( )
         
         thread.start_new_thread(self.RAWDataProc.downsample, \
         method = ['trf','dogbox','lm'][int(self.ui.QDMethod.currentIndex())]
         loss = ['linear','soft_l1','cauchy','huber'][int(self.ui.QDLoss.currentIndex())]         
 
-
         # allow overwrite of Quad Det.    
-        self.YamlNode.Processing["Quadrature detection"] = {}
-        self.YamlNode.Processing["Quadrature detection"]["trim"] = str( self.ui.trimSpin.value() )
-        self.YamlNode.Processing["Quadrature detection"]["method"] = method 
-        self.YamlNode.Processing["Quadrature detection"]["loss"] = loss
+        self.YamlNode.Stacking["Quadrature detection"] = {}
+        self.YamlNode.Stacking["Quadrature detection"]["trim"] = str( self.ui.trimSpin.value() )
+        self.YamlNode.Stacking["Quadrature detection"]["method"] = method 
+        self.YamlNode.Stacking["Quadrature detection"]["loss"] = loss
         self.Log()
 
         #if "Quadrature detection" not in self.YamlNode.Processing.keys():
 
     def gateIntegrate(self):
         
-        if "Gate integrate" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["Gate integrate"] = {}
-        self.YamlNode.Processing["Gate integrate"]["gpd"] = str(self.ui.GPDspinBox.value( ) )
+        if "Gate integrate" not in self.YamlNode.Stacking.keys():
+            self.YamlNode.Stacking["Gate integrate"] = {}
+        self.YamlNode.Stacking["Gate integrate"]["gpd"] = str(self.ui.GPDspinBox.value( ) )
         self.Log()
  
         self.lock("gate integration")
         self.ui.lcdNumberFilterOrder.display(bord)
         self.ui.lcdNumberFTauDead.display(1e3*fe)
         self.ui.bandPassGO.setEnabled(1)
+
+        ################################################################
         # Hack for MacOS to force refresh of group box and plot
+        # this has an undesirable effect that it causes the groupbox to 'jump' up
+        # TODO come up with a better solution  
         self.ui.mplwidget.hide()
         self.ui.mplwidget.show()
         self.ui.BandPassBox.hide()
  
     def windowFilter(self):
         
-        if "Window filter" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["Window filter"] = {}
-            self.YamlNode.Processing["Window filter"]["type"] = str(self.ui.windowTypeComboBox.currentText()) 
-            self.YamlNode.Processing["Window filter"]["width"] = str(self.ui.windowBandwidthSpinBox.value()) 
-            self.YamlNode.Processing["Window filter"]["centre"] = str(self.ui.CentralVSpinBox.value() )
-            self.Log()
-        else:
-            err_msg = "FD window has already been applied!"
-            reply =QtWidgets.QMessageBox.critical(self, 'Error', 
-                err_msg) 
-            return 
         self.lock("window filter")
         
+        # Log processing 
+        Window = OrderedDict()
+        Window["STEP"] = "Window filter"
+        Window["type"] = str(self.ui.windowTypeComboBox.currentText()) 
+        Window["width"] = str(self.ui.windowBandwidthSpinBox.value()) 
+        Window["centre"] = str(self.ui.CentralVSpinBox.value() )
+        Window["trim"] = str(self.ui.windowTrim.isChecked())
+        self.YamlNode.Processing.append(Window)
+        self.Log( )
+        
+        if self.ui.windowTrim.isChecked():
+            nv = self.ui.lcdTotalDeadTime.value( ) + self.ui.lcdWinDead.value()
+            self.ui.lcdTotalDeadTime.display( nv )
+        
         thread.start_new_thread(self.RAWDataProc.windowFilter, \
                 (str(self.ui.windowTypeComboBox.currentText()), \
                 self.ui.windowBandwidthSpinBox.value(), \
                 self.ui.CentralVSpinBox.value(), \
+                self.ui.windowTrim.isChecked(), \
                 self.ui.mplwidget))
 
     def designFDFilter(self):
-#         thread.start_new_thread(self.RAWDataProc.computeWindow, ( \
-#                 "Pulse 1",
-#                 self.ui.windowBandwidthSpinBox.value(), \
-#                 self.ui.CentralVSpinBox.value(), \
-#                 str(self.ui.windowTypeComboBox.currentText()), \
-#                 self.ui.mplwidget ))
 
         mPulse = "None"
         if u"Pulse 1" in self.RAWDataProc.DATADICT.keys():
             mPulse = u"Pulse 1"
         elif u"Pulse 2" in self.RAWDataProc.DATADICT.keys():
             mPulse = u"Pulse 2"
-        a,b,c,d,dead = self.RAWDataProc.computeWindow( \
+        a,b,c,d,dead,ndead = self.RAWDataProc.computeWindow( \
                 mPulse,
                 self.ui.windowBandwidthSpinBox.value(), \
                 self.ui.CentralVSpinBox.value(), \
                 self.ui.mplwidget )
 
         self.ui.lcdWinDead.display(dead)
+
+        ################################################################
         # Hack for MacOS to force refresh of group box and plot
+        # this has an undesirable effect that it causes the groupbox to 'jump' up
+        # TODO come up with a better solution  
         self.ui.mplwidget.hide()
         self.ui.mplwidget.show()
         self.ui.windowFilterGroupBox.hide()

akvo/gui/main.ui

                <bool>true</bool>
               </property>
               <layout class="QGridLayout" name="gridLayout_5">
-               <item row="0" column="0">
-                <widget class="QLabel" name="label_3">
-                 <property name="text">
-                  <string>Truncate [ms]</string>
-                 </property>
-                </widget>
-               </item>
                <item row="0" column="1">
                 <widget class="QSpinBox" name="truncateSpinBox">
                  <property name="maximumSize">
                  </property>
                 </widget>
                </item>
-               <item row="1" column="0">
-                <widget class="QLabel" name="label_12">
+               <item row="0" column="0">
+                <widget class="QLabel" name="label_3">
                  <property name="text">
-                  <string>Downsample factor</string>
+                  <string>Truncate [ms]</string>
                  </property>
                 </widget>
                </item>
                  </property>
                 </widget>
                </item>
+               <item row="1" column="0">
+                <widget class="QLabel" name="label_12">
+                 <property name="text">
+                  <string>Downsample factor</string>
+                 </property>
+                </widget>
+               </item>
                <item row="1" column="2">
                 <widget class="QPushButton" name="downSampleGO">
                  <property name="styleSheet">
                <bool>true</bool>
               </property>
               <layout class="QGridLayout" name="gridLayout_6">
-               <item row="4" column="1">
-                <widget class="QLCDNumber" name="lcdWinDead">
-                 <property name="sizePolicy">
-                  <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
-                   <horstretch>0</horstretch>
-                   <verstretch>0</verstretch>
-                  </sizepolicy>
+               <item row="4" column="0">
+                <widget class="QLabel" name="label_55">
+                 <property name="text">
+                  <string>dead time [ms]</string>
                  </property>
+                </widget>
+               </item>
+               <item row="1" column="3">
+                <widget class="QPushButton" name="fdDesignPushButton">
                  <property name="styleSheet">
-                  <string notr="true">#lcdWinDead {
-color: green;
-background: black;
-}
-
-#lcdWinDead:disabled {
-color: grey;
-background: dark grey;
-}</string>
+                  <string notr="true"/>
                  </property>
-                 <property name="segmentStyle">
-                  <enum>QLCDNumber::Flat</enum>
+                 <property name="text">
+                  <string>design</string>
                  </property>
                 </widget>
                </item>
                  </property>
                 </widget>
                </item>
-               <item row="0" column="0">
-                <widget class="QLabel" name="label_45">
-                 <property name="text">
-                  <string>Type</string>
+               <item row="4" column="1">
+                <widget class="QLCDNumber" name="lcdWinDead">
+                 <property name="sizePolicy">
+                  <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+                   <horstretch>0</horstretch>
+                   <verstretch>0</verstretch>
+                  </sizepolicy>
+                 </property>
+                 <property name="styleSheet">
+                  <string notr="true">#lcdWinDead {
+color: green;
+background: black;
+}
+
+#lcdWinDead:disabled {
+color: grey;
+background: dark grey;
+}</string>
+                 </property>
+                 <property name="segmentStyle">
+                  <enum>QLCDNumber::Flat</enum>
                  </property>
                 </widget>
                </item>
-               <item row="4" column="0">
-                <widget class="QLabel" name="label_55">
+               <item row="0" column="0">
+                <widget class="QLabel" name="label_45">
                  <property name="text">
-                  <string>dead time [ms]</string>
+                  <string>Type</string>
                  </property>
                 </widget>
                </item>
                  </item>
                 </widget>
                </item>
-               <item row="1" column="3">
-                <widget class="QPushButton" name="fdDesignPushButton">
-                 <property name="styleSheet">
-                  <string notr="true"/>
+               <item row="0" column="3">
+                <widget class="QCheckBox" name="windowTrim">
+                 <property name="toolTip">
+                  <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Sets whether or not the dead time will be trimmed from the beginning and end of the signal. When doing a cascade of filters, users may wish to hold off on edge effect removal. &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
                  </property>
                  <property name="text">
-                  <string>design</string>
+                  <string>Trim dead time </string>
+                 </property>
+                 <property name="checked">
+                  <bool>true</bool>
                  </property>
                 </widget>
                </item>
                <bool>true</bool>
               </property>
               <layout class="QGridLayout" name="gridLayout_9">
-               <item row="0" column="0">
-                <widget class="QLabel" name="label_26">
+               <item row="12" column="0">
+                <widget class="QLabel" name="label_34">
                  <property name="text">
-                  <string>N freqs</string>
+                  <string>First harmonic 2</string>
                  </property>
                 </widget>
                </item>
-               <item row="0" column="1">
-                <widget class="QSpinBox" name="NHarmonicsFreqsSpin">
-                 <property name="minimum">
-                  <number>1</number>
+               <item row="1" column="0">
+                <widget class="QLabel" name="label_49">
+                 <property name="text">
+                  <string>N segments</string>
                  </property>
-                 <property name="maximum">
-                  <number>2</number>
+                </widget>
+               </item>
+               <item row="17" column="2">
+                <widget class="QPushButton" name="harmonicGO">
+                 <property name="layoutDirection">
+                  <enum>Qt::LeftToRight</enum>
                  </property>
-                 <property name="value">
-                  <number>1</number>
+                 <property name="styleSheet">
+                  <string notr="true">#harmonicGO {background: green;}
+#harmonicGO:disabled{background: black;}</string>
+                 </property>
+                 <property name="text">
+                  <string>GO</string>
                  </property>
                 </widget>
                </item>
-               <item row="5" column="1">
-                <widget class="QSpinBox" name="f0KNSpin">
-                 <property name="minimum">
-                  <number>2</number>
-                 </property>
-                 <property name="value">
-                  <number>40</number>
+               <item row="13" column="0">
+                <widget class="QLabel" name="label_35">
+                 <property name="text">
+                  <string>Last harmonic 2</string>
                  </property>
                 </widget>
                </item>
-               <item row="4" column="1">
-                <widget class="QSpinBox" name="f0K1Spin">
+               <item row="14" column="1">
+                <widget class="QSpinBox" name="f1KsSpin">
                  <property name="minimum">
                   <number>1</number>
                  </property>
                  <property name="maximum">
-                  <number>50</number>
+                  <number>3</number>
+                 </property>
+                </widget>
+               </item>
+               <item row="11" column="1">
+                <widget class="QDoubleSpinBox" name="f1Spin">
+                 <property name="maximum">
+                  <double>25000.000000000000000</double>
                  </property>
                  <property name="value">
-                  <number>1</number>
+                  <double>60.000000000000000</double>
                  </property>
                 </widget>
                </item>
-               <item row="12" column="2">
-                <widget class="QLCDNumber" name="lcdf0NK2">
-                 <property name="styleSheet">
-                  <string notr="true">#lcdf0NK2 { 
-color: green;
-background: black;
-}
-
-#lcdf0NK2:disabled {
-color: grey;
-background: dark grey;
-}</string>
+               <item row="17" column="1">
+                <widget class="QCheckBox" name="plotHarmonic">
+                 <property name="text">
+                  <string>Plot</string>
                  </property>
-                 <property name="segmentStyle">
-                  <enum>QLCDNumber::Flat</enum>
+                 <property name="checked">
+                  <bool>true</bool>
                  </property>
                 </widget>
                </item>
-               <item row="6" column="2">
-                <widget class="QLCDNumber" name="lcdf0NK">
+               <item row="14" column="2">
+                <widget class="QLCDNumber" name="lcdf0NK2">
                  <property name="styleSheet">
-                  <string notr="true">#lcdf0NK { 
+                  <string notr="true">#lcdf0NK2 { 
 color: green;
 background: black;
 }
 
-#lcdf0NK:disabled {
+#lcdf0NK2:disabled {
 color: grey;
 background: dark grey;
 }</string>
                  <property name="segmentStyle">
                   <enum>QLCDNumber::Flat</enum>
                  </property>
-                 <property name="intValue" stdset="0">
-                  <number>0</number>
-                 </property>
-                </widget>
-               </item>
-               <item row="10" column="0">
-                <widget class="QLabel" name="label_34">
-                 <property name="text">
-                  <string>First harmonic 2</string>
-                 </property>
                 </widget>
                </item>
                <item row="12" column="1">
-                <widget class="QSpinBox" name="f1KsSpin">
+                <widget class="QSpinBox" name="f1K1Spin">
                  <property name="minimum">
                   <number>1</number>
                  </property>
-                 <property name="maximum">
-                  <number>3</number>
-                 </property>
                 </widget>
                </item>
-               <item row="13" column="2">
-                <widget class="Line" name="line_9">
-                 <property name="orientation">
-                  <enum>Qt::Horizontal</enum>
+               <item row="14" column="0">
+                <widget class="QLabel" name="label_41">
+                 <property name="text">
+                  <string>Sub-harmonics</string>
                  </property>
                 </widget>
                </item>
-               <item row="11" column="0">
-                <widget class="QLabel" name="label_35">
-                 <property name="text">
-                  <string>Last harmonic 2</string>
+               <item row="10" column="2">
+                <widget class="Line" name="line_6">
+                 <property name="orientation">
+                  <enum>Qt::Horizontal</enum>
                  </property>
                 </widget>
                </item>
-               <item row="5" column="2">
-                <widget class="QLCDNumber" name="lcdHNF">
-                 <property name="styleSheet">
-                  <string notr="true">#lcdHNF {
-color: green;
-background: black;
-}
-
-#lcdHNF:disabled {
-color: grey;
-background: dark grey;
-}</string>
+               <item row="7" column="1">
+                <widget class="QSpinBox" name="f0KNSpin">
+                 <property name="minimum">
+                  <number>2</number>
                  </property>
-                 <property name="segmentStyle">
-                  <enum>QLCDNumber::Flat</enum>
+                 <property name="value">
+                  <number>40</number>
                  </property>
                 </widget>
                </item>
-               <item row="4" column="2">
+               <item row="6" column="2">
                 <widget class="QLCDNumber" name="lcdH1F">
                  <property name="styleSheet">
                   <string notr="true">#lcdH1F {
                  </property>
                 </widget>
                </item>
-               <item row="10" column="2">
-                <widget class="QLCDNumber" name="lcdH1F2">
-                 <property name="styleSheet">
-                  <string notr="true">#lcdH1F2{ 
-color: green;
-background: black;
-}
-
-#lcdH1F2:disabled {
-color: grey;
-background: dark grey;
-}</string>
-                 </property>
-                 <property name="segmentStyle">
-                  <enum>QLCDNumber::Flat</enum>
+               <item row="7" column="0">
+                <widget class="QLabel" name="label_31">
+                 <property name="text">
+                  <string>Last harmonic 1</string>
                  </property>
                 </widget>
                </item>
-               <item row="12" column="0">
-                <widget class="QLabel" name="label_41">
-                 <property name="text">
-                  <string>Sub-harmonics</string>
+               <item row="10" column="1">
+                <widget class="Line" name="line_5">
+                 <property name="orientation">
+                  <enum>Qt::Horizontal</enum>
                  </property>
                 </widget>
                </item>
-               <item row="10" column="1">
-                <widget class="QSpinBox" name="f1K1Spin">
+               <item row="6" column="1">
+                <widget class="QSpinBox" name="f0K1Spin">
                  <property name="minimum">
                   <number>1</number>
                  </property>
-                </widget>
-               </item>
-               <item row="9" column="0">
-                <widget class="QLabel" name="label_27">
-                 <property name="text">
-                  <string>Base freq. 2 </string>
+                 <property name="maximum">
+                  <number>50</number>
+                 </property>
+                 <property name="value">
+                  <number>1</number>
                  </property>
                 </widget>
                </item>
-               <item row="8" column="1">
-                <widget class="Line" name="line_5">
+               <item row="15" column="1">
+                <widget class="Line" name="line_8">
                  <property name="orientation">
                   <enum>Qt::Horizontal</enum>
                  </property>
                 </widget>
                </item>
-               <item row="8" column="2">
-                <widget class="Line" name="line_6">
+               <item row="2" column="0">
+                <widget class="QLabel" name="label_50">
+                 <property name="text">
+                  <string>Base freq. search </string>
+                 </property>
+                </widget>
+               </item>
+               <item row="10" column="0">
+                <widget class="Line" name="line_4">
                  <property name="orientation">
                   <enum>Qt::Horizontal</enum>
                  </property>
                 </widget>
                </item>
-               <item row="3" column="1">
+               <item row="4" column="2">
+                <widget class="Line" name="line_2">
+                 <property name="orientation">
+                  <enum>Qt::Horizontal</enum>
+                 </property>
+                </widget>
+               </item>
+               <item row="8" column="0">
+                <widget class="QLabel" name="label_33">
+                 <property name="text">
+                  <string>Sub-harmonics </string>
+                 </property>
+                </widget>
+               </item>
+               <item row="6" column="0">
+                <widget class="QLabel" name="label_11">
+                 <property name="text">
+                  <string>First harmonic 1</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="0" column="1">
+                <widget class="QSpinBox" name="NHarmonicsFreqsSpin">
+                 <property name="minimum">
+                  <number>1</number>
+                 </property>
+                 <property name="maximum">
+                  <number>2</number>
+                 </property>
+                 <property name="value">
+                  <number>1</number>
+                 </property>
+                </widget>
+               </item>
+               <item row="5" column="1">
                 <widget class="QDoubleSpinBox" name="f0Spin">
                  <property name="maximum">
                   <double>25000.000000000000000</double>
                  </property>
                 </widget>
                </item>
-               <item row="9" column="1">
-                <widget class="QDoubleSpinBox" name="f1Spin">
-                 <property name="maximum">
-                  <double>25000.000000000000000</double>
+               <item row="12" column="2">
+                <widget class="QLCDNumber" name="lcdH1F2">
+                 <property name="styleSheet">
+                  <string notr="true">#lcdH1F2{ 
+color: green;
+background: black;
+}
+
+#lcdH1F2:disabled {
+color: grey;
+background: dark grey;
+}</string>
                  </property>
-                 <property name="value">
-                  <double>60.000000000000000</double>
+                 <property name="segmentStyle">
+                  <enum>QLCDNumber::Flat</enum>
                  </property>
                 </widget>
                </item>
-               <item row="2" column="2">
-                <widget class="Line" name="line_2">
+               <item row="4" column="0">
+                <widget class="Line" name="line_3">
                  <property name="orientation">
                   <enum>Qt::Horizontal</enum>
                  </property>
                 </widget>
                </item>
-               <item row="15" column="2">
-                <widget class="QPushButton" name="harmonicGO">
-                 <property name="layoutDirection">
-                  <enum>Qt::LeftToRight</enum>
-                 </property>
-                 <property name="styleSheet">
-                  <string notr="true">#harmonicGO {background: green;}
-#harmonicGO:disabled{background: black;}</string>
+               <item row="15" column="0">
+                <widget class="Line" name="line_7">
+                 <property name="orientation">
+                  <enum>Qt::Horizontal</enum>
                  </property>
+                </widget>
+               </item>
+               <item row="11" column="0">
+                <widget class="QLabel" name="label_27">
                  <property name="text">
-                  <string>GO</string>
+                  <string>Base freq. 2 </string>
                  </property>
                 </widget>
                </item>
-               <item row="6" column="1">
+               <item row="8" column="1">
                 <widget class="QSpinBox" name="f0KsSpin">
                  <property name="toolTip">
                   <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Would you like to calculate subharmonics? For instance, setting this to 1, will calculate only the exact harmonics, setting this to 2 will calculate 1/2 step subharmonics (i.e. if the baseline frequency is 60 Hz, this will result in calcualtion of 30 Hz subharmonics)&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
                  </property>
                 </widget>
                </item>
-               <item row="2" column="1">
-                <widget class="Line" name="line">
-                 <property name="orientation">
-                  <enum>Qt::Horizontal</enum>
-                 </property>
-                </widget>
-               </item>
-               <item row="5" column="0">
-                <widget class="QLabel" name="label_31">
+               <item row="0" column="0">
+                <widget class="QLabel" name="label_26">
                  <property name="text">
-                  <string>Last harmonic 1</string>
+                  <string>N freqs</string>
                  </property>
                 </widget>
                </item>
-               <item row="3" column="0">
-                <widget class="QLabel" name="label_25">
-                 <property name="text">
-                  <string>Base freq. 1</string>
+               <item row="13" column="1">
+                <widget class="QSpinBox" name="f1KNSpin">
+                 <property name="minimum">
+                  <number>2</number>
+                 </property>
+                 <property name="value">
+                  <number>40</number>
                  </property>
                 </widget>
                </item>
-               <item row="11" column="2">
-                <widget class="QLCDNumber" name="lcdHNF2">
+               <item row="8" column="2">
+                <widget class="QLCDNumber" name="lcdf0NK">
                  <property name="styleSheet">
-                  <string notr="true">#lcdHNF2 { 
- color: green;
- background: black;
+                  <string notr="true">#lcdf0NK { 
+color: green;
+background: black;
 }
 
-#lcdHNF2:disabled {
-  color: grey;
-  background: dark grey;
+#lcdf0NK:disabled {
+color: grey;
+background: dark grey;
 }</string>
                  </property>
                  <property name="segmentStyle">
                   <enum>QLCDNumber::Flat</enum>
                  </property>
-                </widget>
-               </item>
-               <item row="11" column="1">
-                <widget class="QSpinBox" name="f1KNSpin">
-                 <property name="minimum">
-                  <number>2</number>
-                 </property>
-                 <property name="value">
-                  <number>40</number>
+                 <property name="intValue" stdset="0">
+                  <number>0</number>
                  </property>
                 </widget>
                </item>
-               <item row="15" column="1">
-                <widget class="QCheckBox" name="plotHarmonic">
-                 <property name="text">
-                  <string>Plot</string>
+               <item row="7" column="2">
+                <widget class="QLCDNumber" name="lcdHNF">
+                 <property name="styleSheet">
+                  <string notr="true">#lcdHNF {
+color: green;
+background: black;
+}
+
+#lcdHNF:disabled {
+color: grey;
+background: dark grey;
+}</string>
                  </property>
-                 <property name="checked">
-                  <bool>true</bool>
+                 <property name="segmentStyle">
+                  <enum>QLCDNumber::Flat</enum>
                  </property>
                 </widget>
                </item>
-               <item row="13" column="1">
-                <widget class="Line" name="line_8">
+               <item row="4" column="1">
+                <widget class="Line" name="line">
                  <property name="orientation">
                   <enum>Qt::Horizontal</enum>
                  </property>
                 </widget>
                </item>
-               <item row="13" column="0">
-                <widget class="Line" name="line_7">
-                 <property name="orientation">
-                  <enum>Qt::Horizontal</enum>
+               <item row="1" column="1">
+                <widget class="QSpinBox" name="NSegments">
+                 <property name="minimum">
+                  <number>1</number>
+                 </property>
+                 <property name="maximum">
+                  <number>100</number>
+                 </property>
+                 <property name="value">
+                  <number>1</number>
                  </property>
                 </widget>
                </item>
-               <item row="6" column="0">
-                <widget class="QLabel" name="label_33">
-                 <property name="text">
-                  <string>Sub-harmonics </string>
+               <item row="13" column="2">
+                <widget class="QLCDNumber" name="lcdHNF2">
+                 <property name="styleSheet">
+                  <string notr="true">#lcdHNF2 { 
+ color: green;
+ background: black;
+}
+
+#lcdHNF2:disabled {
+  color: grey;
+  background: dark grey;
+}</string>
+                 </property>
+                 <property name="segmentStyle">
+                  <enum>QLCDNumber::Flat</enum>
                  </property>
                 </widget>
                </item>
-               <item row="4" column="0">
-                <widget class="QLabel" name="label_11">
+               <item row="5" column="0">
+                <widget class="QLabel" name="label_25">
                  <property name="text">
-                  <string>First harmonic 1</string>
+                  <string>Base freq. 1</string>
                  </property>
                 </widget>
                </item>
-               <item row="2" column="0">
-                <widget class="Line" name="line_3">
+               <item row="15" column="2">
+                <widget class="Line" name="line_9">
                  <property name="orientation">
                   <enum>Qt::Horizontal</enum>
                  </property>
                 </widget>
                </item>
-               <item row="8" column="0">
-                <widget class="Line" name="line_4">
-                 <property name="orientation">
-                  <enum>Qt::Horizontal</enum>
+               <item row="2" column="2">
+                <widget class="QSpinBox" name="Nsearch">
+                 <property name="prefix">
+                  <string/>
                  </property>
                 </widget>
                </item>
-               <item row="1" column="1">
-                <widget class="QSpinBox" name="NSegments">
+               <item row="2" column="1">
+                <widget class="QComboBox" name="searchAll">
+                 <property name="toolTip">
+                  <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;When searching for the fundamental frequency, should the entire ensemble of harmonics be included? Reducing this number can accelerate the algorithm significantly. If a selection other than &amp;quot;All&amp;quot; is chosen, once the fundamental frequency is found, the whole set of harmonics will be included in the modelling.  &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+                 </property>
+                 <item>
+                  <property name="text">
+                   <string>All</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string>First</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string/>
+                  </property>
+                 </item>
+                </widget>
+               </item>
+               <item row="3" column="2">
+                <widget class="QDoubleSpinBox" name="bounds">
+                 <property name="toolTip">
+                  <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;If bounds is selected, this is the variance in the fundamental frequency which will be searched from the &lt;span style=&quot; font-weight:600;&quot;&gt;prior &lt;/span&gt;result. As such, for each record, the fundamental frequency can shift by this much (in either direction) from the prior record. &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+                 </property>
+                 <property name="decimals">
+                  <number>3</number>
+                 </property>
                  <property name="minimum">
-                  <number>1</number>
+                  <double>0.005000000000000</double>
                  </property>
                  <property name="maximum">
-                  <number>100</number>
+                  <double>10.000000000000000</double>
+                 </property>
+                 <property name="singleStep">
+                  <double>0.001000000000000</double>
                  </property>
                  <property name="value">
-                  <number>1</number>
+                  <double>0.125000000000000</double>
                  </property>
                 </widget>
                </item>
-               <item row="1" column="0">
-                <widget class="QLabel" name="label_49">
+               <item row="3" column="1">
+                <widget class="QCheckBox" name="boundsCheck">
                  <property name="text">
-                  <string>N segments</string>
+                  <string>Bounded search</string>
+                 </property>
+                 <property name="checked">
+                  <bool>true</bool>
+                 </property>
+                </widget>
+               </item>
+               <item row="0" column="2">
+                <widget class="QCheckBox" name="harmRef">
+                 <property name="text">
+                  <string>proc ref. channels</string>
+                 </property>
+                 <property name="checked">
+                  <bool>true</bool>
                  </property>
                 </widget>
                </item>
               <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/tressel/harmonic.py

     ii =  sN < (3.* np.std(sN))
     return np.linalg.norm( harmonicEuler(sN, fs, t, f0, k1, kN, ks)[ii] ) 
 
-def minHarmonic(sN, fs, t, f0, k1, kN, ks):
+def minHarmonic(sN, fs, t, f0, k1, kN, ks, Bounds, Nsearch):
     
-    # CG, BFGS, Newton-CG, L-BFGS-B, TNC, SLSQP, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr
-    res = minimize(harmonicNorm, np.array((f0)), args=(sN, fs, t, k1, kN, ks), jac='2-point', method='BFGS') # hess=None, bounds=None )
+    kNs = kN
+    if Nsearch != False:
+        kNs = k1+Nsearch    
+    if Bounds == 0:
+        print("UNbounded search from ", k1, " to ", kNs) # for f0 with fN=10 in search", f0)
+        # CG, BFGS, Newton-CG, L-BFGS-B, TNC, SLSQP, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr
+        res = minimize(harmonicNorm, np.array((f0)), args=(sN, fs, t, k1, kNs, ks), jac='2-point', method='BFGS') # hess=None, bounds=None )
     
-    #############
-    # Reduced N #
-    #############
-    #print("min 10")
-    #res = minimize(harmonicNorm, np.array((f0)), args=(sN, fs, t, k1, 10, ks), jac='2-point', method='BFGS') # hess=None, bounds=None )
-    
-    ########## 
-    # Bounds #
-    ##########
-    #print("bounded search for f0 with 10", f0)
-    #bnds = ( (f0-0.125, f0+0.125), )
-    #print("len f0", len( [f0,] ))
-    #print("len bnds", len(bnds) )
-    #res = minimize(harmonicNorm, (f0,), args=(sN, fs, t, k1, kN, ks), jac='2-point', method='L-BFGS-B', bounds=bnds ) # hess=None, bounds=None )
-    #res = minimize(harmonicNorm, (f0,), args=(sN, fs, t, k1, 10, ks), jac='2-point', method='L-BFGS-B', bounds=bnds ) # hess=None, bounds=None )
-    
-    #print(res)
-    #print ( "guess", guessf0(  harmonicEuler(sN, fs, t, res.x[0], k1, kN, ks), fs  ) )
+    else:
+        bnds = ( (f0-Bounds, f0+Bounds), )
+        print("bounded ( +-", Bounds, ") search from ", k1, "to", kNs) # for f0 with fN=10 in search", f0)
+        res = minimize(harmonicNorm, (f0,), args=(sN, fs, t, k1, kNs, ks), jac='2-point', method='L-BFGS-B', bounds=bnds ) # hess=None, bounds=None )
+
     return harmonicEuler(sN, fs, t, res.x[0], k1, kN, ks), res.x[0]#[0]
 
 def harmonicEuler2 ( sN, fs, t, f0, f0k1, f0kN, f0ks, f1, f1k1, f1kN, f1ks ): 
         fs = sampling frequency
         t = time samples 
         f0 = first base frequency of the sinusoidal noise 
-        f0k1 = First harmonic to calulate for f0 
+        f0k1 = First harmonic to calula11te for f0 
         f0kN = Last base harmonic to calulate for f0
         f0ks = subharmonics to calculate 
         f1 = second base frequency of the sinusoidal noise 
     ii =  sN < (3.* np.std(sN))
     return np.linalg.norm( harmonicEuler2(sN, fs, t, f0[0], f0k1, f0kN, f0ks, f0[1], f1k1, f1kN, f1ks)[ii] ) 
 
-def minHarmonic2(sN, fs, t, f0, f0k1, f0kN, f0ks, f1, f1k1, f1kN, f1ks):
-    
-    # CG, BFGS, Newton-CG, L-BFGS-B, TNC, SLSQP, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr
-    #res = minimize(harmonic2Norm, np.array((f0, f1)), args=(sN, fs, t, f0k1, f0kN, f0ks, f1k1,f1kN, f1ks), jac='2-point', method='BFGS') # hess=None, bounds=None )
-    
-    print("search 10")
-    res = minimize(harmonic2Norm, np.array((f0, f1)), args=(sN, fs, t, f0k1, 10, f0ks, f1k1, 10, f1ks), jac='2-point', method='BFGS') # hess=None, bounds=None )
-    
-    #print(res)
-    #print ( "guess", guessf0(harmonicEuler2(sN, fs, t, res.x[0], f0k1, f0kN, f0ks, res.x[1], f1k1, f1kN, f1ks), fs)  )
+def minHarmonic2(sN, fs, t, f0, f0k1, f0kN, f0ks, f1, f1k1, f1kN, f1ks, Bounds, Nsearch):
+
+    kNs0 = f0kN
+    kNs1 = f1kN
+    if Nsearch != False:
+        kNs0 = f0k1+Nsearch    
+        kNs1 = f1k1+Nsearch    
+
+    if Bounds == 0:
+
+        # CG, BFGS, Newton-CG, L-BFGS-B, TNC, SLSQP, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr
+        print("2 UNbounded ( +-", Bounds,") search length ", kNs0, kNs1 ,"for f0", f0, f1)
+        res = minimize(harmonic2Norm, np.array((f0, f1)), args=(sN, fs, t, f0k1, f0k1+kNs0, f0ks, f1k1, f1k1+kNs1, f1ks), jac='2-point', method='BFGS') # hess=None, bounds=None )
+    else:
+        # Bounded
+        bnds = ( (f0-Bounds, f0+Bounds),(f1-Bounds, f1+Bounds) )
+        print("2 bounded ( +-", Bounds,") search length ", kNs0, kNs1 ,"for f0", f0, f1)
+        # L-BFGS-B hess=None, bounds=None )
+        res = minimize(harmonic2Norm, ((f0,f1)), args=(sN, fs, t, f0k1, f0k1+kNs0, f0ks, f1k1, f1k1+kNs1, f1ks), jac='2-point', method='L-BFGS-B', bounds=bnds ) 
+
     return harmonicEuler2(sN, fs, t, res.x[0], f0k1, f0kN, f0ks, res.x[1], f1k1, f1kN, f1ks), res.x[0], res.x[1]#[0]
 
 def guessf0( sN, fs ):
     S = np.fft.fft(sN)
     w = np.fft.fftfreq( len(sN), 1/fs )
     imax = np.argmax( np.abs(S) )
+
+    #np.save( "sN.npy", S )
+    #np.save( "w.npy", w )
+    #exit()
     #plt.plot( w, np.abs(S) )
     #plt.show()
     #print(w)
-    #print ( w[imax], w[imax+1] )
+    #print ( w[imax], w[imax+1] )esta bien in english
     return abs(w[imax])
 
 if __name__ == "__main__":

akvo/tressel/mrsurvey.py

         #canvas.fig.tight_layout() 
         canvas.draw()
         self.doneTrigger.emit() 
-
-    #def harmonicModel(self, nF, nK, f0, f1, plot, canvas):
     
     def harmonicModel(self, nF, \
         f0, f0K1, f0KN, f0Ks, f0ns, \
         f1, f1K1, f1KN, f1Ks,  \
+        Nsearch, Bounds, procRefs, \
         plot, canvas):
         """ nF = number of base frequencies, must be 1 or 2 
             f0 = first base frequency  
             f1K1 = first harmonic to model for second base frequency 
             f1KN = last harmonic to model for the second base frequency 
             f1Ks = subharmonic spacing for the second base frequency, set to 1 for no subharmonics.
+            Nsearch = the number of harmonics to use when determining base frequency 
+            bounds = 1/2 the width of the space where baseline frequency will be searched  
+            procRefs = should the reference loops be processed as well  
             plot = should Akvo plot the results 
             canvas = mpl plotting axis      
         """
         if plot:
-            canvas.reAx2()
+            canvas.reAx2(shy=False)
             canvas.ax1.set_ylabel(r"signal [nV]", fontsize=8)
-            canvas.ax2.set_xlabel(r"time [s]", fontsize=8)
+            #canvas.ax2.set_xlabel(r"time [s]", fontsize=8)
             canvas.ax2.set_ylabel(r"signal [nV]", fontsize=8)
-
+            canvas.ax2.set_xlabel(r"frequency [Hz]", fontsize=8)
+            canvas.ax1.set_yscale('log')
+            canvas.ax2.set_yscale('log')
         # Data
         iFID = 0
 
                 for ipm in range(self.DATADICT["nPulseMoments"]):
                     if plot:
                         canvas.softClear()
-                        mmax = 0
-                        for ichan in self.DATADICT[pulse]["rchan"]:
-                            canvas.ax1.plot( self.DATADICT[pulse]["TIMES"], 1e9*self.DATADICT[pulse][ichan][ipm][istack], alpha=.5) 
-                            mmax = max( mmax, np.max(1e9*self.DATADICT[pulse][ichan][ipm][istack])) 
+                        mmaxr = 0
+                        mmaxd = 0
+                        if procRefs: 
+                            for ichan in self.DATADICT[pulse]["rchan"]:
+                                #canvas.ax1.plot( self.DATADICT[pulse]["TIMES"], 1e9*self.DATADICT[pulse][ichan][ipm][istack], alpha=.5) 
+                                #mmaxr = max( mmaxr, np.max(1e9*self.DATADICT[pulse][ichan][ipm][istack])) 
+                                ww = np.fft.fftfreq(len(self.DATADICT[pulse][ichan][ipm][istack]), d=self.dt)
+                                X = np.fft.rfft(self.DATADICT[pulse][ichan][ipm][istack])
+                                canvas.ax1.plot(np.abs(ww[0:len(X)]), np.abs(X), alpha=.5)
+                            canvas.ax1.set_prop_cycle(None)
+                            #canvas.ax1.set_ylim(-mmaxr, mmaxr) 
                         for ichan in self.DATADICT[pulse]["chan"]:
-                            canvas.ax2.plot( self.DATADICT[pulse]["TIMES"], 1e9*self.DATADICT[pulse][ichan][ipm][istack], alpha=.5) 
-                            mmax = max( mmax, np.max(1e9*self.DATADICT[pulse][ichan][ipm][istack])) 
-                        canvas.ax1.set_prop_cycle(None)
+                            #canvas.ax2.plot( self.DATADICT[pulse]["TIMES"], 1e9*self.DATADICT[pulse][ichan][ipm][istack], alpha=.5) 
+                            #mmaxd = max( mmaxd, np.max(1e9*self.DATADICT[pulse][ichan][ipm][istack])) 
+                            ww = np.fft.fftfreq(len(self.DATADICT[pulse][ichan][ipm][istack]), d=self.dt)
+                            X = np.fft.rfft(self.DATADICT[pulse][ichan][ipm][istack])
+                            canvas.ax2.plot(np.abs(ww[0:len(X)]), np.abs(X), alpha=.5)
                         canvas.ax2.set_prop_cycle(None)
-                        canvas.ax1.set_ylim(-mmax, mmax) 
-                    for ichan in self.DATADICT[pulse]["rchan"]:
-                        if nF == 1:
-                            for iseg in range(f0ns):
-                                if iseg < f0ns-1:
-                                    self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg], f0p[ichan] = \
-                                        harmonic.minHarmonic( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg], \
+                        #canvas.ax2.set_ylim(-mmaxd, mmaxd)
+                    if procRefs: 
+                        for ichan in self.DATADICT[pulse]["rchan"]:
+                            if nF == 1:
+                                for iseg in range(f0ns):
+                                    if iseg < f0ns-1:
+                                        self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg], f0p[ichan] = \
+                                            harmonic.minHarmonic( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg], \
                                             self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg:(iseg+1)*Nseg], \
-                                            f0p[ichan], f0K1, f0KN, f0Ks ) 
-                                else:
-                                    self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], f0p[ichan] = \
-                                        harmonic.minHarmonic( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], \
+                                            f0p[ichan], f0K1, f0KN, f0Ks, Bounds, Nsearch ) 
+                                    else:
+                                        self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], f0p[ichan] = \
+                                            harmonic.minHarmonic( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], \
                                             self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg::], \
-                                            f0p[ichan], f0K1, f0KN, f0Ks ) 
-                        elif nF == 2:
-                            for iseg in range(f0ns):
-                                if iseg < f0ns-1:
-                                    self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg], f0p[ichan], f1p[ichan] = \
-                                        harmonic.minHarmonic2( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg],\
-                                     self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg:(iseg+1)*Nseg], \
-                                     f0p[ichan], f0K1, f0KN, f0Ks,  \
-                                     f1p[ichan], f1K1, f1KN, f1Ks ) 
-                                else:
-                                    self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], f0p[ichan], f1p[ichan] = \
-                                        harmonic.minHarmonic2( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::],\
-                                     self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg::], \
-                                     f0p[ichan], f0K1, f0KN, f0Ks,  \
-                                     f1p[ichan], f1K1, f1KN, f1Ks ) 
-                        # plot
-                        if plot:
-                            canvas.ax1.plot( self.DATADICT[pulse]["TIMES"], 1e9*self.DATADICT[pulse][ichan][ipm][istack], \
+                                            f0p[ichan], f0K1, f0KN, f0Ks, Bounds, Nsearch ) 
+                            elif nF == 2:
+                                for iseg in range(f0ns):
+                                    if iseg < f0ns-1:
+                                        self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg], f0p[ichan], f1p[ichan] = \
+                                            harmonic.minHarmonic2( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg],\
+                                        self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg:(iseg+1)*Nseg], \
+                                        f0p[ichan], f0K1, f0KN, f0Ks,  \
+                                        f1p[ichan], f1K1, f1KN, f1Ks, Bounds, Nsearch ) 
+                                    else:
+                                        self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], f0p[ichan], f1p[ichan] = \
+                                            harmonic.minHarmonic2( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::],\
+                                        self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg::], \
+                                        f0p[ichan], f0K1, f0KN, f0Ks,  \
+                                        f1p[ichan], f1K1, f1KN, f1Ks, Bounds, Nsearch ) 
+                            # plot
+                            if plot:
+                                #canvas.ax1.plot( self.DATADICT[pulse]["TIMES"], 1e9*self.DATADICT[pulse][ichan][ipm][istack], \
+                                #    label = pulse + " ipm=" + str(ipm) + " istack=" + str(istack) + " rchan="  + str(ichan))
+                                ww = np.fft.fftfreq(len(self.DATADICT[pulse][ichan][ipm][istack]), d=self.dt)
+                                X = np.fft.rfft(self.DATADICT[pulse][ichan][ipm][istack])
+                                canvas.ax1.plot(np.abs(ww[0:len(X)]), np.abs(X),\
                                 label = pulse + " ipm=" + str(ipm) + " istack=" + str(istack) + " rchan="  + str(ichan))
 
                     for ichan in self.DATADICT[pulse]["chan"]:
-                        
                         if nF == 1:
                             for iseg in range(f0ns):
                                 if iseg < f0ns-1:
                                     self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg], f0p[ichan] = \
                                         harmonic.minHarmonic( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg], 
                                             self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg:(iseg+1)*Nseg], \
-                                            f0p[ichan], f0K1, f0KN, f0Ks ) 
+                                            f0p[ichan], f0K1, f0KN, f0Ks, Bounds, Nsearch ) 
                                 else:
                                     self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], f0p[ichan] = \
                                         harmonic.minHarmonic( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], 
                                             self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg::], \
-                                            f0p[ichan], f0K1, f0KN, f0Ks )
+                                            f0p[ichan], f0K1, f0KN, f0Ks, Bounds, Nsearch )
 
                         elif nF == 2:
                             for iseg in range(f0ns):
                                         harmonic.minHarmonic2( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg:(iseg+1)*Nseg],\
                                      self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg:(iseg+1)*Nseg], \
                                      f0p[ichan], f0K1, f0KN, f0Ks,  \
-                                     f1p[ichan], f1K1, f1KN, f1Ks ) 
+                                     f1p[ichan], f1K1, f1KN, f1Ks, Bounds, Nsearch ) 
                                 else:
                                     self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::], f0p[ichan], f1p[ichan] = \
                                         harmonic.minHarmonic2( self.DATADICT[pulse][ichan][ipm][istack][iseg*Nseg::],\
                                      self.samp,  self.DATADICT[pulse]["TIMES"][iseg*Nseg::], \
                                      f0p[ichan], f0K1, f0KN, f0Ks,  \
-                                     f1p[ichan], f1K1, f1KN, f1Ks ) 
+                                     f1p[ichan], f1K1, f1KN, f1Ks, Bounds, Nsearch ) 
                
                         # plot
                         if plot:
-                            canvas.ax2.plot( self.DATADICT[pulse]["TIMES"], 1e9*self.DATADICT[pulse][ichan][ipm][istack], \
+                            #canvas.ax2.plot( self.DATADICT[pulse]["TIMES"], 1e9*self.DATADICT[pulse][ichan][ipm][istack], \
+                            #    label = pulse + " ipm=" + str(ipm) + " istack=" + str(istack) + " chan="  + str(ichan))
+                            ww = np.fft.fftfreq(len(self.DATADICT[pulse][ichan][ipm][istack]), d=self.dt)
+                            X = np.fft.rfft(self.DATADICT[pulse][ichan][ipm][istack])
+                            canvas.ax2.plot(np.abs(ww[0:len(X)]), np.abs(X), \
                                 label = pulse + " ipm=" + str(ipm) + " istack=" + str(istack) + " chan="  + str(ichan))
 
                     if plot:
-                        canvas.ax1.legend(prop={'size':6}, loc='upper right')
+                        if procRefs: 
+                            canvas.ax1.legend(prop={'size':6}, loc='upper right')
                         canvas.ax2.legend(prop={'size':6}, loc='upper right')
                         canvas.draw() 
                 
                 if phase == 1: # Amp phase
                     im1 = ax1.pcolormesh( time_sp, QQ, self.DATADICT["CA"][pulse][chan], cmap=dcmap, rasterized=True,
                          vmin=-self.DATADICT["CAmax"][pulse] , vmax=self.DATADICT["CAmax"][pulse]  )
-                    im2 = ax2.pcolormesh( time_sp, QQ, self.DATADICT["IP"][pulse][chan], cmap=cmocean.cm.balance, rasterized=True,\
+                    #im2 = ax2.pcolormesh( time_sp, QQ, self.DATADICT["IP"][pulse][chan], cmap=cmocean.cm.balance, rasterized=True,\
+                    im2 = ax2.pcolormesh( time_sp, QQ, self.DATADICT["IP"][pulse][chan], cmap=cmocean.cm.delta, rasterized=True,\
                          vmin=-np.pi, vmax=np.pi)
                 if phase == 2: # CA NR
                     im1 = ax1.pcolormesh( time_sp, QQ, self.DATADICT["CA"][pulse][chan], cmap=dcmap, rasterized=True,\
     def computeWindow(self, pulse, band, centre, ftype, canvas=None):
         
         # Compute window
-        nd = len(self.DATADICT[pulse][self.DATADICT[pulse]["chan"][0]][0][self.DATADICT["stacks"][0]])
+        nd = len(self.DATADICT[pulse][self.DATADICT[pulse]["chan"][0]][0][self.DATADICT["stacks"][0]]) # num. data 
         fft1 = np.fft.rfft(self.DATADICT[pulse][self.DATADICT[pulse]["chan"][0]][0][self.DATADICT["stacks"][0]])
         freqs   = np.fft.fftfreq(nd, self.dt)
         df      = freqs[1] - freqs[0]
             canvas.ax2.set_title("IFFT")
             canvas.draw()
 
-        return [WINDOW, nd, istart, iend, dead]
+        return [WINDOW, nd, istart, iend, dead, ift]
 
-    def windowFilter(self, ftype, band, centre, canvas):
+    def windowFilter(self, ftype, band, centre, trunc, canvas):
 
         ###############################
         # Window Filter (Ormsby filter http://www.xsgeo.com/course/filt.htm) 
         # apply window
         iFID = 0
         for pulse in self.DATADICT["PULSES"]:
-            [WINDOW, nd, istart, iend,dead] = self.computeWindow(pulse, band, centre, ftype)
+            [WINDOW, nd, istart, iend, dead, idead] = self.computeWindow(pulse, band, centre, ftype)
             for istack in self.DATADICT["stacks"]:
                 for ipm in range(self.DATADICT["nPulseMoments"]):
                     for ichan in np.append(self.DATADICT[pulse]["chan"], self.DATADICT[pulse]["rchan"]):
                         fft = np.fft.rfft( self.DATADICT[pulse][ichan][ipm][istack]  )
                         fft *= WINDOW
-                        self.DATADICT[pulse][ichan][ipm][istack] = np.fft.irfft(fft , nd)
+                        if trunc:
+                            self.DATADICT[pulse][ichan][ipm][istack] = np.fft.irfft(fft, nd)[idead:-idead]
+                        else:
+                            self.DATADICT[pulse][ichan][ipm][istack] = np.fft.irfft(fft, nd)
                 
                     percent = (int)(1e2*((float)(iFID*self.DATADICT["nPulseMoments"]+(ipm))/(len(self.DATADICT["PULSES"])*self.nPulseMoments)))
                     self.progressTrigger.emit(percent)  
                 iFID += 1
+            if trunc:
+                self.DATADICT[pulse]["TIMES"] = self.DATADICT[pulse]["TIMES"][idead:-idead]
 
         self.plotFT(canvas, istart, iend)
         self.doneTrigger.emit() 

setup.py

     long_description = fh.read()
 
 setup(name='Akvo',
-      version='1.2.6',
+      version='1.2.7',
       description='Surface nuclear magnetic resonance workbench',
       long_description=long_description,
       long_description_content_type='text/markdown',