Better legacy support, old FID data were not phase cycled.

akvo/gui/akvoGUI.py

         self.ui.lcdNumberNQ.display(self.RAWDataProc.nPulseMoments)
         self.ui.DeadTimeSpinBox.setValue(1e3*self.RAWDataProc.deadTime)
         self.ui.CentralVSpinBox.setValue( self.RAWDataProc.transFreq )
-       
+            
         if self.RAWDataProc.pulseType != "FID":
             self.ui.lcdNumberTauPulse2.setEnabled(1)
             self.ui.lcdNumberTauPulse2.display(1e3*self.RAWDataProc.pulseLength[1])
             self.ui.lcdNumberTauDelay.display(1e3*self.RAWDataProc.interpulseDelay)
 
         self.ui.FIDProcComboBox.clear() 
-        if self.RAWDataProc.pulseType == "4PhaseT1":
+        if self.RAWDataProc.pulseType == "4PhaseT1" or self.RAWDataProc.pulseType == "T1":
             self.ui.FIDProcComboBox.insertItem(0, "Pulse 1") 
             self.ui.FIDProcComboBox.insertItem(1, "Pulse 2") 
             self.ui.FIDProcComboBox.insertItem(2, "Both")    
         # Add some extra info 
         INFO = {}
         INFO["pulseType"] = self.RAWDataProc.pulseType
+        INFO["interpulseDelay"] = self.RAWDataProc.interpulseDelay
         INFO["transFreq"] = self.RAWDataProc.transFreq
         INFO["pulseLength"] = self.RAWDataProc.pulseLength
         INFO["TuneCapacitance"] = self.RAWDataProc.TuneCapacitance
         self.RAWDataProc.transFreq = self.RAWDataProc.DATADICT["INFO"]["transFreq"]
         self.RAWDataProc.dt = 1./self.RAWDataProc.samp 
 
+
+
         self.dataChan = self.RAWDataProc.DATADICT[ self.RAWDataProc.DATADICT["PULSES"][0] ]["chan"]
         # Keep backwards compatibility with prior saved pickles???
         #self.ui.logTextBrowser.clear() 
         self.YamlNode = AkvoYamlNode( )  #self.logText )
        
         self.YamlNode.Akvo_VERSION = (yaml.load( self.logText, Loader=yaml.Loader )).Akvo_VERSION
+        AKVO_VERSION = np.array(self.YamlNode.Akvo_VERSION.split("."), dtype=int)
+        if  AKVO_VERSION[0] >= 1 and AKVO_VERSION[1] >= 2 and AKVO_VERSION[2] >= 3:
+            self.RAWDataProc.interpulseDelay = self.RAWDataProc.DATADICT["INFO"]["interpulseDelay"]
+
         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.ui.lcdNumberTauDelay.display(1e3*self.RAWDataProc.interpulseDelay)
 
         self.ui.FIDProcComboBox.clear() 
-        if self.RAWDataProc.pulseType == "4PhaseT1":
+        if self.RAWDataProc.pulseType == "4PhaseT1" or self.RAWDataProc.pulseType == "T1":
             self.ui.FIDProcComboBox.insertItem(0, "Pulse 1") #, const QVariant & userData = QVariant() )
             self.ui.FIDProcComboBox.insertItem(1, "Pulse 2") #, const QVariant & userData = QVariant() )
             self.ui.FIDProcComboBox.insertItem(2, "Both")    #, const QVariant & userData = QVariant() )
                 (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \
                  str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \
                 1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self)) 
-            
         elif self.RAWDataProc.pulseType == "4PhaseT1":
             self.procThread = thread.start_new_thread(self.RAWDataProc.load4PhaseT1Data, \
                 (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \
                  str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \
                 1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self)) 
+        elif self.RAWDataProc.pulseType == "T1":
+            self.procThread = thread.start_new_thread(self.RAWDataProc.loadT1Data, \
+                (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \
+                 str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \
+                1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self)) 
+            #self.procThread = thread.start_new_thread(self.RAWDataProc.load4PhaseT1Data, \
+            #    (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \
+            #     str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \
+            #    1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self)) 
 
         self.YamlNode.Import["GMR Header"] = self.headerstr
         self.YamlNode.Import["opened"] = datetime.datetime.now().isoformat() 

akvo/gui/main.ui

               <property name="checkable">
                <bool>true</bool>
               </property>
-              <widget class="QLabel" name="label_8">
-               <property name="geometry">
-                <rect>
-                 <x>8</x>
-                 <y>84</y>
-                 <width>399</width>
-                 <height>10</height>
-                </rect>
-               </property>
-               <property name="sizePolicy">
-                <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
-                 <horstretch>0</horstretch>
-                 <verstretch>0</verstretch>
-                </sizepolicy>
-               </property>
-               <property name="minimumSize">
-                <size>
-                 <width>0</width>
-                 <height>10</height>
-                </size>
-               </property>
-               <property name="maximumSize">
-                <size>
-                 <width>16777215</width>
-                 <height>10</height>
-                </size>
-               </property>
-               <property name="text">
-                <string>Fourier-based calculation</string>
-               </property>
-              </widget>
-              <widget class="QPushButton" name="calcQGO">
-               <property name="geometry">
-                <rect>
-                 <x>400</x>
-                 <y>100</y>
-                 <width>84</width>
-                 <height>30</height>
-                </rect>
-               </property>
-               <property name="sizePolicy">
-                <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
-                 <horstretch>0</horstretch>
-                 <verstretch>0</verstretch>
-                </sizepolicy>
-               </property>
-               <property name="minimumSize">
-                <size>
-                 <width>80</width>
-                 <height>30</height>
-                </size>
-               </property>
-               <property name="styleSheet">
-                <string notr="true">#calcQGO {
+              <layout class="QGridLayout" name="gridLayout_13">
+               <item row="1" column="1">
+                <widget class="QPushButton" name="calcQGO">
+                 <property name="sizePolicy">
+                  <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+                   <horstretch>0</horstretch>
+                   <verstretch>0</verstretch>
+                  </sizepolicy>
+                 </property>
+                 <property name="minimumSize">
+                  <size>
+                   <width>80</width>
+                   <height>20</height>
+                  </size>
+                 </property>
+                 <property name="maximumSize">
+                  <size>
+                   <width>16777215</width>
+                   <height>16777215</height>
+                  </size>
+                 </property>
+                 <property name="styleSheet">
+                  <string notr="true">#calcQGO {
     background: green;
 }
 
 #calcQGO:disabled{
     background: black;
 }</string>
-               </property>
-               <property name="text">
-                <string>GO</string>
-               </property>
-              </widget>
+                 </property>
+                 <property name="text">
+                  <string>GO</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="1" column="0">
+                <widget class="QLabel" name="label_8">
+                 <property name="sizePolicy">
+                  <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+                   <horstretch>0</horstretch>
+                   <verstretch>0</verstretch>
+                  </sizepolicy>
+                 </property>
+                 <property name="minimumSize">
+                  <size>
+                   <width>0</width>
+                   <height>10</height>
+                  </size>
+                 </property>
+                 <property name="maximumSize">
+                  <size>
+                   <width>16777215</width>
+                   <height>10</height>
+                  </size>
+                 </property>
+                 <property name="text">
+                  <string>Fourier-based calculation</string>
+                 </property>
+                </widget>
+               </item>
+              </layout>
              </widget>
             </item>
             <item>
               <property name="checkable">
                <bool>true</bool>
               </property>
-              <widget class="QComboBox" name="outlierTestCB">
-               <property name="geometry">
-                <rect>
-                 <x>90</x>
-                 <y>65</y>
-                 <width>78</width>
-                 <height>25</height>
-                </rect>
-               </property>
-               <item>
-                <property name="text">
-                 <string>MAD</string>
-                </property>
+              <layout class="QGridLayout" name="gridLayout_14">
+               <item row="0" column="0">
+                <widget class="QLabel" name="label_37">
+                 <property name="text">
+                  <string>Outlier test</string>
+                 </property>
+                </widget>
                </item>
-               <item>
-                <property name="text">
-                 <string>none</string>
-                </property>
+               <item row="1" column="0">
+                <widget class="QComboBox" name="outlierTestCB">
+                 <item>
+                  <property name="text">
+                   <string>MAD</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string>none</string>
+                  </property>
+                 </item>
+                </widget>
                </item>
-              </widget>
-              <widget class="QLabel" name="label_37">
-               <property name="geometry">
-                <rect>
-                 <x>10</x>
-                 <y>70</y>
-                 <width>71</width>
-                 <height>16</height>
-                </rect>
-               </property>
-               <property name="text">
-                <string>Outlier test</string>
-               </property>
-              </widget>
-              <widget class="QPushButton" name="FDSmartStackGO">
-               <property name="geometry">
-                <rect>
-                 <x>350</x>
-                 <y>70</y>
-                 <width>99</width>
-                 <height>23</height>
-                </rect>
-               </property>
-               <property name="styleSheet">
-                <string notr="true">#FDSmartStackGO {
+               <item row="2" column="1">
+                <widget class="QPushButton" name="FDSmartStackGO">
+                 <property name="styleSheet">
+                  <string notr="true">#FDSmartStackGO {
     background: green;
 }
 
 #FDSmartStackGO:disabled{
     background: black;
 }</string>
-               </property>
-               <property name="text">
-                <string>GO</string>
-               </property>
-              </widget>
-              <widget class="QDoubleSpinBox" name="MADCutoff">
-               <property name="geometry">
-                <rect>
-                 <x>90</x>
-                 <y>90</y>
-                 <width>121</width>
-                 <height>22</height>
-                </rect>
-               </property>
-               <property name="toolTip">
-                <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The threshold value used in the median absolute deviation outlier test. The default value of 1.4826 follows from an assumption of Gaussian noise, lower cutoff values are stricter and will throw out more samples.  &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
-               </property>
-               <property name="decimals">
-                <number>4</number>
-               </property>
-               <property name="maximum">
-                <double>10.000000000000000</double>
-               </property>
-               <property name="value">
-                <double>1.480000000000000</double>
-               </property>
-              </widget>
+                 </property>
+                 <property name="text">
+                  <string>GO</string>
+                 </property>
+                </widget>
+               </item>
+               <item row="1" column="1">
+                <widget class="QDoubleSpinBox" name="MADCutoff">
+                 <property name="toolTip">
+                  <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The threshold value used in the median absolute deviation outlier test. The default value of 1.4826 follows from an assumption of Gaussian noise, lower cutoff values are stricter and will throw out more samples.  &lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+                 </property>
+                 <property name="decimals">
+                  <number>4</number>
+                 </property>
+                 <property name="maximum">
+                  <double>10.000000000000000</double>
+                 </property>
+                 <property name="value">
+                  <double>1.480000000000000</double>
+                 </property>
+                </widget>
+               </item>
+              </layout>
              </widget>
             </item>
             <item>
               <property name="checkable">
                <bool>true</bool>
               </property>
-              <widget class="QPushButton" name="qdGO">
-               <property name="geometry">
-                <rect>
-                 <x>350</x>
-                 <y>60</y>
-                 <width>99</width>
-                 <height>23</height>
-                </rect>
-               </property>
-               <property name="styleSheet">
-                <string notr="true">#qdGO {
+              <layout class="QGridLayout" name="gridLayout_15">
+               <item row="1" column="3">
+                <widget class="QPushButton" name="qdGO">
+                 <property name="styleSheet">
+                  <string notr="true">#qdGO {
     background: green;
 }
 
 #qdGO:disabled{
     background: black;
 }</string>
-               </property>
-               <property name="text">
-                <string>GO</string>
-               </property>
-              </widget>
-              <widget class="QSpinBox" name="trimSpin">
-               <property name="geometry">
-                <rect>
-                 <x>90</x>
-                 <y>30</y>
-                 <width>91</width>
-                 <height>28</height>
-                </rect>
-               </property>
-               <property name="minimum">
-                <number>0</number>
-               </property>
-               <property name="value">
-                <number>0</number>
-               </property>
-              </widget>
-              <widget class="QLabel" name="label_38">
-               <property name="geometry">
-                <rect>
-                 <x>20</x>
-                 <y>34</y>
-                 <width>61</width>
-                 <height>18</height>
-                </rect>
-               </property>
-               <property name="text">
-                <string>Trim</string>
-               </property>
-              </widget>
-              <widget class="QComboBox" name="QDType">
-               <property name="geometry">
-                <rect>
-                 <x>230</x>
-                 <y>90</y>
-                 <width>101</width>
-                 <height>22</height>
-                </rect>
-               </property>
-               <item>
-                <property name="text">
-                 <string>Real/Imag</string>
-                </property>
-               </item>
-               <item>
-                <property name="text">
-                 <string>Amp/Phase</string>
-                </property>
+                 </property>
+                 <property name="text">
+                  <string>GO</string>
+                 </property>
+                </widget>
                </item>
-               <item>
-                <property name="text">
-                 <string>Phased</string>
-                </property>
+               <item row="2" column="2">
+                <widget class="QComboBox" name="QDType">
+                 <item>
+                  <property name="text">
+                   <string>Real/Imag</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string>Amp/Phase</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string>Phased</string>
+                  </property>
+                 </item>
+                </widget>
                </item>
-              </widget>
-              <widget class="QPushButton" name="plotQD">
-               <property name="enabled">
-                <bool>false</bool>
-               </property>
-               <property name="geometry">
-                <rect>
-                 <x>350</x>
-                 <y>90</y>
-                 <width>99</width>
-                 <height>23</height>
-                </rect>
-               </property>
-               <property name="styleSheet">
-                <string notr="true">#plotQD {
+               <item row="2" column="3">
+                <widget class="QPushButton" name="plotQD">
+                 <property name="enabled">
+                  <bool>false</bool>
+                 </property>
+                 <property name="styleSheet">
+                  <string notr="true">#plotQD {
     background: green;
 }
 
 #plotQD:disabled{
     background: black;
 }</string>
-               </property>
-               <property name="text">
-                <string>PLOT</string>
-               </property>
-               <property name="checkable">
-                <bool>false</bool>
-               </property>
-              </widget>
+                 </property>
+                 <property name="text">
+                  <string>PLOT</string>
+                 </property>
+                 <property name="checkable">
+                  <bool>false</bool>
+                 </property>
+                </widget>
+               </item>
+               <item row="1" column="2">
+                <widget class="QSpinBox" name="trimSpin">
+                 <property name="minimum">
+                  <number>0</number>
+                 </property>
+                 <property name="value">
+                  <number>0</number>
+                 </property>
+                </widget>
+               </item>
+               <item row="1" column="0">
+                <widget class="QLabel" name="label_38">
+                 <property name="text">
+                  <string>Trim</string>
+                 </property>
+                </widget>
+               </item>
+              </layout>
              </widget>
             </item>
             <item>
               <property name="maximumSize">
                <size>
                 <width>505</width>
-                <height>16777215</height>
+                <height>200</height>
                </size>
               </property>
               <property name="title">
               <property name="checkable">
                <bool>true</bool>
               </property>
-              <widget class="QPushButton" name="gateIntegrateGO">
-               <property name="geometry">
-                <rect>
-                 <x>350</x>
-                 <y>30</y>
-                 <width>99</width>
-                 <height>23</height>
-                </rect>
-               </property>
-               <property name="styleSheet">
-                <string notr="true">#gateIntegrateGO {
+              <layout class="QGridLayout" name="gridLayout_16">
+               <item row="0" column="1">
+                <widget class="QSpinBox" name="GPDspinBox">
+                 <property name="minimum">
+                  <number>6</number>
+                 </property>
+                 <property name="maximum">
+                  <number>30</number>
+                 </property>
+                 <property name="value">
+                  <number>20</number>
+                 </property>
+                </widget>
+               </item>
+               <item row="0" column="3">
+                <widget class="QPushButton" name="gateIntegrateGO">
+                 <property name="styleSheet">
+                  <string notr="true">#gateIntegrateGO {
     background: green;
 }
 
 #gateIntegrateGO:disabled{
     background: black;
 }</string>
-               </property>
-               <property name="text">
-                <string>GO</string>
-               </property>
-              </widget>
-              <widget class="QSpinBox" name="GPDspinBox">
-               <property name="geometry">
-                <rect>
-                 <x>130</x>
-                 <y>28</y>
-                 <width>71</width>
-                 <height>23</height>
-                </rect>
-               </property>
-               <property name="minimum">
-                <number>6</number>
-               </property>
-               <property name="maximum">
-                <number>30</number>
-               </property>
-               <property name="value">
-                <number>20</number>
-               </property>
-              </widget>
-              <widget class="QLabel" name="label_53">
-               <property name="geometry">
-                <rect>
-                 <x>20</x>
-                 <y>30</y>
-                 <width>111</width>
-                 <height>16</height>
-                </rect>
-               </property>
-               <property name="text">
-                <string>Gates per decade </string>
-               </property>
-              </widget>
-              <widget class="QComboBox" name="QDType_2">
-               <property name="geometry">
-                <rect>
-                 <x>230</x>
-                 <y>60</y>
-                 <width>101</width>
-                 <height>22</height>
-                </rect>
-               </property>
-               <item>
-                <property name="text">
-                 <string>Real/Imag</string>
-                </property>
-               </item>
-               <item>
-                <property name="text">
-                 <string>Amp/Phase</string>
-                </property>
+                 </property>
+                 <property name="text">
+                  <string>GO</string>
+                 </property>
+                </widget>
                </item>
-               <item>
-                <property name="text">
-                 <string>Phased</string>
-                </property>
+               <item row="0" column="0">
+                <widget class="QLabel" name="label_53">
+                 <property name="text">
+                  <string>Gates per decade </string>
+                 </property>
+                </widget>
                </item>
-              </widget>
-              <widget class="QPushButton" name="plotGI">
-               <property name="enabled">
-                <bool>false</bool>
-               </property>
-               <property name="geometry">
-                <rect>
-                 <x>350</x>
-                 <y>60</y>
-                 <width>99</width>
-                 <height>23</height>
-                </rect>
-               </property>
-               <property name="styleSheet">
-                <string notr="true">#plotGI {
+               <item row="1" column="3">
+                <widget class="QPushButton" name="plotGI">
+                 <property name="enabled">
+                  <bool>false</bool>
+                 </property>
+                 <property name="styleSheet">
+                  <string notr="true">#plotGI {
     background: green;
 }
 
 #plotGI:disabled{
     background: black;
 }</string>
-               </property>
-               <property name="text">
-                <string>PLOT</string>
-               </property>
-               <property name="checkable">
-                <bool>false</bool>
-               </property>
-              </widget>
+                 </property>
+                 <property name="text">
+                  <string>PLOT</string>
+                 </property>
+                 <property name="checkable">
+                  <bool>false</bool>
+                 </property>
+                </widget>
+               </item>
+               <item row="1" column="2">
+                <widget class="QComboBox" name="QDType_2">
+                 <item>
+                  <property name="text">
+                   <string>Real/Imag</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string>Amp/Phase</string>
+                  </property>
+                 </item>
+                 <item>
+                  <property name="text">
+                   <string>Phased</string>
+                  </property>
+                 </item>
+                </widget>
+               </item>
+              </layout>
              </widget>
             </item>
            </layout>

akvo/tressel/adapt.py

             exit(1)
         
         if PCA == "Yes":
-            print("Performing PCA calculation in noise cancellation")
+            #print("Performing PCA calculation in noise cancellation")
             # PCA decomposition on ref channels so signals are less related
             R, K, means = pca.pca( R )
            
             #print ("resetting filter")
         else:
             H = H0
+            #H = np.zeros( (len(R)*M))
 
         Rn = np.ones(len(R)*M) / mu 
         

akvo/tressel/decay.py

             method=method 
             )
         x = res_lsq.x 
-        print ("df", x[0], x[1], x[2], x[3])
+        print ("A0={} zeta={} df={} T2={}".format(x[0],x[1],x[2],x[3]))
     else:
         res_lsq = least_squares(fun, x0, args=(tt, np.concatenate((X, Y))), loss=loss, f_scale=1.0,\
             bounds=( [1., -np.pi, -5, .005] , [1000., np.pi, 5, .800] ),

akvo/tressel/mrsurvey.py

         pass   
  
     def TDSmartStack(self, outlierTest, MADcutoff, canvas):
-
+        #print("Line 300 in mrsurvey")
         Stack = {}
         # align for stacking and modulate
         for pulse in self.DATADICT["PULSES"]:
                 istack = 0
                 for sstack in self.DATADICT["stacks"]:
                     if self.pulseType == "FID" or pulse == "Pulse 2":
-                        mod = (-1)**(ipm%2) * (-1)**(sstack%2)
+                        if floor(self.nDAQVersion) < 2:
+                            mod = 1
+                        else:
+                            mod = (-1.)**(ipm%2) * (-1.)**(sstack%2)
+                    elif self.pulseType == "T1":
+                        #mod = (-1.)**(sstack%2)
+                        #mod = (-1)**(ipm%2) * (-1)**(sstack%2)
+                        #mod = (-1)**(ipm%2) * (-1.**(((sstack-1)/2)%2))
+                        #print("mod", mod, ipm, sstack,  (-1.)**(ipm%2),  -1.0**(((sstack-1)/2)%2 ))
+                        #mod = (-1.)**((ipm+1)%2) * (-1.**(((sstack)/2)%2))
+                        #mod = (-1.)**((ipm-1)%2) * (-1.)**((sstack-1)%2)
+                        #mod = 1 # (-1.**(((sstack-1)/2)%2))
+
+                        # These two give great noise estimate
+                        #qcycler = np.array([1,-1,-1,1])
+                        #scycler = np.array([1,-1,1,-1])
+
+                        qcycler = np.array([ 1, 1])
+                        scycler = np.array([ 1, 1])
+                        mod = qcycler.take([ipm], mode='wrap')*scycler.take([sstack], mode='wrap')
+                        #mod = (-1.)**(ipm%2) * (-1.)**(sstack%2)
                     elif self.pulseType == "4PhaseT1":
-                        mod = (-1)**(ipm%2) * (-1)**(((sstack-1)/2)%2)
+                        mod = (-1.)**(ipm%2) * (-1.**(((sstack-1)/2)%2))
                     ichan = 0
                     for chan in self.DATADICT[pulse]["chan"]:
                         stack[ichan,ipm,istack,:] += mod*self.DATADICT[pulse][chan][ipm][sstack]
                 #dbr = (np.real(SFFT[:,istart:iend]))
                 #db = (np.imag(SFFT[:,istart:iend]))
                 
-                vvmin =  min(vvmin, np.min (db))
-                vvmax =  max(vvmax, np.max (db))
+                vvmin =  min(vvmin, np.min(db) + 1e-16 )
+                vvmax =  max(vvmax, np.max(db) + 1e-16 )
                 im2.append(ax2.matshow( db, aspect='auto', cmap=cmocean.cm.ice, vmin=vvmin, vmax=vvmax))
                 #im1.append(ax1.matshow( dbr, aspect='auto')) #, vmin=vvmin, vmax=vvmax))
                 #im2.append(ax2.matshow( db, aspect='auto', vmin=vvmin, vmax=vvmax))
             nds += ndr
             nps += ndr 
 
+    def loadGMRASCIIT1( self, rawfname, istack ):
+        """Based on the geoMRI instrument manufactured by VistaClara. Imports 
+        a suite of raw .lvm files with the following format (on one line)
+
+        time(s) DC_Bus/100(V) Current+/75(A)  Curr-/75(A)  Voltage+/200(V) \  
+        Ch1(V) Ch2(V) Ch3(V) Ch4(V)
+
+        Sampling rate is assumed at 50 kHz 
+        """
+        import pandas as pd 
+        #################################################################################
+        # figure out key data indices
+        # Pulse       
+        nps  = (int)((self.prePulseDelay)*self.samp)
+        npul = (int)(self.pulseLength[0]*self.samp) #+ 100 
+
+        # phase cycling 
+        # Older T1 GMR data had a curious phase cycling
+        npc = 2 #(int)( self.samp / self.transFreq / 6 )
+        #print("npc", npc)
+
+        # Data 
+        nds  = nps+npul+(int)((self.deadTime)*self.samp);           # indice pulse 1 data starts 
+        nd1 = (int)( (self.interpulseDelay) * self.samp) - nds      # samples in first pulse
+        ndr = (int)( (self.interpulseDelay) * self.samp)            # samples in record 
+
+        invGain = 1./self.RxGain        
+        invCGain = self.CurrentGain        
+
+        pulse = "Pulse 1"
+        chan = self.DATADICT[pulse]["chan"] 
+        rchan = self.DATADICT[pulse]["rchan"] 
+            
+        T = 1.5 #N_samp * self.dt 
+        TIMES = np.arange(0, T, self.dt) - .0002 # small offset in GMR DAQ?
+        
+        self.DATADICT["Pulse 1"]["TIMES"]       = TIMES[nds:nds+nd1]
+        self.DATADICT["Pulse 1"]["PULSE_TIMES"] = TIMES[nps:nps+npul]
+
+        # pandas is much faster than numpy for io
+        #DATA = np.loadtxt(rawfname)
+        DATA = pd.read_csv(rawfname, header=None, sep="\t").values
+        for ipm in range(self.nPulseMoments):
+            for ichan in np.append(chan,rchan):
+                if ipm%2:
+                    self.DATADICT["Pulse 1"][ichan][ipm][istack]     =  DATA[:, eval(ichan)+4][(nds+npc):(nds+nd1+npc)] * invGain
+                    #self.DATADICT["Pulse 1"][ichan][ipm][istack]     =  DATA[:, eval(ichan)+4][nds:(nds+nd1)] * invGain
+                    self.DATADICT["Pulse 1"]["CURRENT"][ipm][istack] =  DATA[:,2][nps+npc:nps+npul+npc] * invCGain
+                else:
+                    self.DATADICT["Pulse 1"][ichan][ipm][istack]     =  DATA[:, eval(ichan)+4][nds:(nds+nd1)] * invGain
+                    self.DATADICT["Pulse 1"]["CURRENT"][ipm][istack] =  DATA[:,2][nps:nps+npul] * invCGain
+            nds += ndr
+            nps += ndr 
 
     def loadFIDData(self, base, procStacks, chanin, rchanin, FIDProc, canvas, deadTime, plot):
         '''
         iistack = 0
         fnames = []
         for istack in procStacks:
-            if self.nDAQVersion < 2.3:
+            if self.nDAQVersion <= 1.0:
+                self.loadGMRASCIIFID( base + "_" + str(istack) + ".lvm", istack )
+            elif self.nDAQVersion < 2.3:
                 #rawfname = base + "_" + str(istack) 
                 self.loadGMRASCIIFID( base + "_" + str(istack), istack )
             else:
         #info["prePulseDelay"] = self.prePulseDelay
         #with multiprocessing.Pool() as pool: 
         #    results = pool.starmap( loadGMRBinaryFID, zip(itertools.repeat(self), fnames, info ) ) # zip(np.tile(vc, (ns, 1)), np.tile(vgc, (ns,1)), itertools.repeat(sys.argv[1]), itertools.repeat(sys.argv[2]), EPS_CMR))
-
         # Plotting
 
         if plot: 
 
         self.enableDSP()    
         self.doneTrigger.emit()
-    
+
+    def loadT1Data(self, base, procStacks, chanin, rchanin, FIDProc, canvas, deadTime, plot):
+        '''
+            Loads a GMR T1 dataset, reads binary and ASCII format files 
+        '''
+
+        canvas.reAx3(True,False)
+
+        chan = []
+        for ch in chanin:
+            chan.append(str(ch)) 
+        
+        rchan = []
+        for ch in rchanin:
+            rchan.append(str(ch)) 
+
+        # not in any headers but this has changed, NOT the place to do this. MOVE  
+        #self.prePulseDelay  = 0.01          # delay before pulse
+        self.deadTime       = deadTime       # instrument dead time before measurement
+        self.samp = 50000.                   # in case this is a reproc, these might have 
+        self.dt   = 1./self.samp             # changed
+
+
+        #################################################################################
+        # Data structures     
+        PULSES = [FIDProc]
+
+        self.DATADICT = {}
+        self.DATADICT["nPulseMoments"] = self.nPulseMoments
+        self.DATADICT["stacks"] = procStacks
+        self.DATADICT["PULSES"] = PULSES
+        for pulse in PULSES: 
+            self.DATADICT[pulse] = {}
+            self.DATADICT[pulse]["chan"] = chan        # TODO these should not be a subet of pulse! for GMR all 
+            self.DATADICT[pulse]["rchan"] = rchan      #      data are consistent 
+            self.DATADICT[pulse]["CURRENT"] = {} 
+            for ichan in np.append(chan,rchan):
+                self.DATADICT[pulse][ichan] = {}
+                for ipm in range(self.nPulseMoments):
+                    self.DATADICT[pulse][ichan][ipm] = {} 
+                    self.DATADICT[pulse]["CURRENT"][ipm] = {} 
+                    for istack in procStacks:
+                        self.DATADICT[pulse][ichan][ipm][istack] = np.zeros(3)
+                        self.DATADICT[pulse]["CURRENT"][ipm][istack] = np.zeros(3) 
+
+        ##############################################
+        # Read in binary (.lvm) data
+        iistack = 0
+        fnames = []
+        for istack in procStacks:
+            if self.nDAQVersion < 2.3:
+                #rawfname = base + "_" + str(istack) 
+                #self.loadGMRASCIIFID( base + "_" + str(istack), istack )
+                self.loadGMRASCIIT1( base + "_" + str(istack), istack )
+            else:
+                self.loadGMRBinaryFID( base + "_" + str(istack) + ".lvm", istack )
+                #fnames.append( base + "_" + str(istack) + ".lvm" )
+                
+            percent = (int) (1e2*((float)((iistack*self.nPulseMoments+ipm+1))  / (len(procStacks)*self.nPulseMoments)))
+            self.progressTrigger.emit(percent) 
+            iistack += 1
+
+        # multiprocessing load data
+        #info = {}
+        #info["prePulseDelay"] = self.prePulseDelay
+        #with multiprocessing.Pool() as pool: 
+        #    results = pool.starmap( loadGMRBinaryFID, zip(itertools.repeat(self), fnames, info ) ) # zip(np.tile(vc, (ns, 1)), np.tile(vgc, (ns,1)), itertools.repeat(sys.argv[1]), itertools.repeat(sys.argv[2]), EPS_CMR))
+        # Plotting
+
+        if plot: 
+            iistack = 0
+            for istack in procStacks:
+                #for ipm in range(0,7,1):
+                for ipm in range(self.nPulseMoments):
+                    canvas.ax1.clear()
+                    canvas.ax2.clear()
+                    canvas.ax3.clear()
+                    #canvas.fig.patch.set_facecolor('blue')
+                    for ichan in chan:
+                        canvas.ax1.plot(self.DATADICT["Pulse 1"]["PULSE_TIMES"], self.DATADICT["Pulse 1"]["CURRENT"][ipm][istack] , color='black')
+                        canvas.ax3.plot(self.DATADICT["Pulse 1"]["TIMES"],       self.DATADICT["Pulse 1"][ichan][ipm][istack], label="Pulse 1 FID data ch. "+str(ichan)) #, color='blue')
+
+                    for ichan in rchan:
+                        canvas.ax2.plot(self.DATADICT["Pulse 1"]["TIMES"], self.DATADICT["Pulse 1"][ichan][ipm][istack], label="Pulse 1 FID ref ch. "+str(ichan)) #, color='blue')
+
+                    canvas.ax3.legend(prop={'size':6})
+                    canvas.ax2.legend(prop={'size':6})
+                    
+                    canvas.ax1.set_title("stack "+str(istack)+" pulse index " + str(ipm), fontsize=8)
+                    canvas.ax1.set_xlabel("time [s]", fontsize=8)
+                    canvas.ax1.set_ylabel("Current [A]", fontsize=8) 
+                    canvas.ax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y') 
+                    
+                    canvas.ax2.set_ylabel("RAW signal [V]", fontsize=8)
+                    canvas.ax2.tick_params(axis='both', which='major', labelsize=8)
+                    canvas.ax2.tick_params(axis='both', which='minor', labelsize=6)
+                    canvas.ax2.set_xlabel("time [s]", fontsize=8)
+                    canvas.ax2.ticklabel_format(style='sci', scilimits=(0,0), axis='y') 
+                    canvas.ax3.ticklabel_format(style='sci', scilimits=(0,0), axis='y') 
+                    canvas.draw()
+                #canvas.draw()
+
+                percent = (int) (1e2*((float)((iistack*self.nPulseMoments+ipm+1))  / (len(procStacks)*self.nPulseMoments)))
+                self.progressTrigger.emit(percent) 
+                iistack += 1
+
+        self.enableDSP()    
+        self.doneTrigger.emit()   
+ 
     def load4PhaseT1Data(self, base, procStacks, chan, rchan, FIDProc, canvas, deadTime, plot): 
 
         """
                 # update GUI of where we are
                 percent = (int) (1e2*((float)((iistack*self.nPulseMoments+ipm+1))  / (len(procStacks)*self.nPulseMoments)))
                 self.progressTrigger.emit(percent)  
-
             iistack += 1
         
         self.enableDSP()    

setup.py

     long_description = fh.read()
 
 setup(name='Akvo',
-      version='1.2.2',
+      version='1.2.3',
       description='Surface nuclear magnetic resonance workbench',
       long_description=long_description,
       long_description_content_type='text/markdown',