From 72922b2b22a0b0c5f17cf833cede690353b7e865 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 3 Mar 2021 10:53:33 -0500
Subject: [PATCH 01/76] testing branch

---
 test.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 test.md

diff --git a/test.md b/test.md
new file mode 100644
index 0000000..f58162e
--- /dev/null
+++ b/test.md
@@ -0,0 +1 @@
+this should be in rtxi-plugin branch.

From 5d2a612d2098318ff04f12299dce5dccedf92f74 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 3 Mar 2021 11:21:54 -0500
Subject: [PATCH 02/76] RTXI user manual code added

---
 include/lfpRatiometer.h |  19 +++++++-
 src/lfpRatiometer.cpp   | 100 +++++++++++++++++++++++++++++++++++++++-
 2 files changed, 116 insertions(+), 3 deletions(-)

diff --git a/include/lfpRatiometer.h b/include/lfpRatiometer.h
index 414029f..4de2247 100644
--- a/include/lfpRatiometer.h
+++ b/include/lfpRatiometer.h
@@ -1,6 +1,8 @@
 #ifndef LFPRATIOMETER_H
 #define LFPRATIOMETER_H
 
+#include <default_gui_model.h>
+
 #include <stdio.h>
 #include <malloc.h>
 #include <math.h>
@@ -11,7 +13,10 @@
 
 #include <fftw3.h>
 
-class lfpRatiometer {
+class lfpRatiometer : public DefaultGUIModel {
+
+    Q_OBJECT
+
     public:
         // constructor
         lfpRatiometer(int N_input, double sampling_input);
@@ -21,9 +26,16 @@ class lfpRatiometer {
 
         // execute
         void execute();
+
+        // functions to make GUI
+        void createGUI(DefaultGUIModel::variable_t*, int);
+        void customizeGUI(void);
         
     protected:
 
+        // update function
+        virtual void update(DefaultGUIModel::update_flags_t)
+
     private:
     
         int N; // time window in samples
@@ -69,8 +81,13 @@ class lfpRatiometer {
             }
         }
 
+        void initParameters();
         void makePSD();
         void getRatio();
+    
+    private slots:
+        void aBttn_event(void);
+        void bBttn_event(void);
 
 
 };
diff --git a/src/lfpRatiometer.cpp b/src/lfpRatiometer.cpp
index 627b070..0b91839 100644
--- a/src/lfpRatiometer.cpp
+++ b/src/lfpRatiometer.cpp
@@ -1,11 +1,47 @@
 #include <lfpRatiometer.h>
+#include <main_window.h>
 
 using namespace std;
 
+extern "C" Plugin::Object *createRTXIPlugin(void){
+    int N = 10;
+    double sampling = 200;
+    return new lfpRatiometer(N, sampling);
+}
+
+static DefaultGUIModel::variable_t vars[] = {
+  {
+    "GUI label", "Tooltip description",
+    DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
+  },
+{
+    "input_LFP", "Input LFP",
+    DefaultGUIModel::INPUT | DefaultGUIModel::DOUBLE,
+  },
+{
+    "ratio", "Output LFP Power Ratio",
+    DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
+  },
+{
+    "A State", "Tooltip description", DefaultGUIModel::STATE,
+  },
+};
+
+static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 
 // defining what's in the object's constructor
 // user defines time window length (in samples) and sampling rate
-lfpRatiometer::lfpRatiometer(int N_input, double sampling_input) {
+lfpRatiometer::lfpRatiometer(int N_input, double sampling_input)
+    : DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars)
+{
+    setWhatsThis("<p><b>lfpRatiometer:</b><br>QWhatsThis description.</p>");
+    DefaultGUIModel::createGUI(vars, num_vars);
+    customizeGUI();
+    initParameters();
+    update(INIT);
+    refresh();
+    QTimer::singleShot(0, this, SLOT(resizeMe()));
+
     // setting user defined variables
     N=N_input;
     f_size=N/2 + 1;
@@ -127,4 +163,64 @@ void lfpRatiometer::getRatio() {
 
     // take ratio
     lf_hf_ratio = lf_total/hf_total;
-}
\ No newline at end of file
+}
+
+// RTXI function for initializing parameters
+void lfpRatiometer::initParameters(void)
+{
+  some_parameter = 0;
+  some_state = 0;
+}
+
+// update function (not running in real time)
+void lfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
+{
+  switch (flag) {
+    case INIT:
+      period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
+      setParameter("GUI label", some_parameter);
+      setState("A State", some_state);
+      break;
+
+    case MODIFY:
+      some_parameter = getParameter("GUI label").toDouble();
+      break;
+
+    case UNPAUSE:
+      break;
+
+    case PAUSE:
+      break;
+
+    case PERIOD:
+      period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
+      break;
+
+    default:
+      break;
+  }
+}
+
+// RTXI's customizeGUI function
+void lfpRatiometer::customizeGUI(void)
+{
+  QGridLayout* customlayout = DefaultGUIModel::getLayout();
+
+  QGroupBox* button_group = new QGroupBox;
+
+  QPushButton* abutton = new QPushButton("Button A");
+  QPushButton* bbutton = new QPushButton("Button B");
+  QHBoxLayout* button_layout = new QHBoxLayout;
+  button_group->setLayout(button_layout);
+  button_layout->addWidget(abutton);
+  button_layout->addWidget(bbutton);
+  QObject::connect(abutton, SIGNAL(clicked()), this, SLOT(aBttn_event()));
+  QObject::connect(bbutton, SIGNAL(clicked()), this, SLOT(bBttn_event()));
+
+  customlayout->addWidget(button_group, 0, 0);
+  setLayout(customlayout);
+}
+
+void lfpRatiometer::aBttn_event(void) { }
+
+void lfpRatiometer::bBttn_event(void) { }
\ No newline at end of file

From e0474c657b0b361783676d403828d80dca1b5d4e Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 3 Mar 2021 12:42:11 -0500
Subject: [PATCH 03/76] RTXI-specific makefile added

---
 Makefile              | 16 +++++++++-------
 src/lfpRatiometer.cpp | 42 ++++++++++++++++--------------------------
 2 files changed, 25 insertions(+), 33 deletions(-)

diff --git a/Makefile b/Makefile
index 7a8b267..0b7ca96 100644
--- a/Makefile
+++ b/Makefile
@@ -1,10 +1,12 @@
-CXX=g++
-CXX_FLAGS=-std=c++11 -Iinclude
+PLUGIN_NAME = lfpRatiometer
 
-LD_FLAGS=-lfftw3 -lm
+HEADERS = lfpRatiometer.h
 
-all: build/lfpRatiometer.o
-	$(CXX) $(CXX_FLAGS) -o build/test src/main.cpp build/lfpRatiometer.o $(LD_FLAGS)
+SOURCES = lfpRatiometer.cpp \
+			moc_lfpRatiometer.cpp
 
-build/lfpRatiometer.o:
-	$(CXX) $(CXX_FLAGS) -o build/lfpRatiometer.o -c src/lfpRatiometer.cpp
+LIBS = -lfftw3 -lm
+
+### Do note edit below this line ###
+
+include $(shell rtxi_plugin_config --pkgdata-dir)/Makefile.plugin_compile
\ No newline at end of file
diff --git a/src/lfpRatiometer.cpp b/src/lfpRatiometer.cpp
index 0b91839..184131e 100644
--- a/src/lfpRatiometer.cpp
+++ b/src/lfpRatiometer.cpp
@@ -70,18 +70,6 @@ lfpRatiometer::lfpRatiometer(int N_input, double sampling_input)
     // FFTW_MEASURE makes initialization long for faster...
     // calculations
     p = fftw_plan_dft_r2c_1d(N,in,out,FFTW_MEASURE);
-
-    // tmp
-    for (int j=0; j<N; j++){
-        in_raw.push_back(1);
-    }
-    in_raw.at(1) = 2;
-    in_raw.at(8) = 2;
-
-    // fill_n(in, N, 1); // making input a constant vector for now
-    // in[1] = 2;
-    // in[8] = 2;
-    cout << "constructed\n";
 }
 
 // defining what's in the object's destructor
@@ -93,27 +81,29 @@ lfpRatiometer::~lfpRatiometer(void) {
     // free input array
     fftw_free(in);
 
-    cout << "destroyed\n";
     return;
 }
 
-// function that operates on the input vector
+// real-time RTXI function
 void lfpRatiometer::execute() {
-    makePSD();
-    getRatio();
 
-    // my observation
-    cout << "window:\n";
-    for (int i=0; i<N;i++){
-        cout << window[i] << "\n";
-    }
+    // get new time series reading
+    in_raw.push_back(input(0));
 
-    cout << "freq, psd\n";
-    for (int i=0; i<f_size; i++) {
-        cout << allfreqs[i] << "," << psd[i] << "\n";
-    }
+    // if time series is full
+    if (in_raw.size() > N) {
+        // cut it to size
+        in_raw.erase(in_raw.begin());
+
+        // run our LF/HF analysis
+        makePSD();
+        getRatio();
 
-    cout << "LF/HF Ratio: " << lf_hf_ratio << "\n";
+        // output the calculated lf_hf_ratio
+        output(0) = lf_hf_ratio;
+        
+    }
+    
 }
 
 // function that calculates the power spectral density

From 37a3a0bc74b1421e28415ed02950f2ac0d4b6e72 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 3 Mar 2021 12:52:11 -0500
Subject: [PATCH 04/76] consolidate directories

---
 src/lfpRatiometer.cpp => lfpRatiometer.cpp |  0
 include/lfpRatiometer.h => lfpRatiometer.h |  0
 src/main.cpp                               | 11 -----------
 3 files changed, 11 deletions(-)
 rename src/lfpRatiometer.cpp => lfpRatiometer.cpp (100%)
 rename include/lfpRatiometer.h => lfpRatiometer.h (100%)
 delete mode 100644 src/main.cpp

diff --git a/src/lfpRatiometer.cpp b/lfpRatiometer.cpp
similarity index 100%
rename from src/lfpRatiometer.cpp
rename to lfpRatiometer.cpp
diff --git a/include/lfpRatiometer.h b/lfpRatiometer.h
similarity index 100%
rename from include/lfpRatiometer.h
rename to lfpRatiometer.h
diff --git a/src/main.cpp b/src/main.cpp
deleted file mode 100644
index 1f0a4f1..0000000
--- a/src/main.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
-#include <lfpRatiometer.h>
-
-int main () {
-    int N = 10;
-    double sampling = 200;
-    lfpRatiometer lfpratiometer(N, sampling);
-    lfpratiometer.execute();
-
-    return 0;
-
-}
\ No newline at end of file

From d2ee23ad0636956961785532c7eb3385a6e2845b Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 3 Mar 2021 13:07:04 -0500
Subject: [PATCH 05/76] edited makefile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 0b7ca96..f00385a 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ HEADERS = lfpRatiometer.h
 SOURCES = lfpRatiometer.cpp \
 			moc_lfpRatiometer.cpp
 
-LIBS = -lfftw3 -lm
+LIBS = -L/usr/lib/x86_64-linux-gnu -lfftw3 -lm
 
 ### Do note edit below this line ###
 

From ad7bce97abf25a363a93d70e155e3fd6e3d046e7 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 3 Mar 2021 13:47:32 -0500
Subject: [PATCH 06/76] edited makefile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index f00385a..0b7ca96 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ HEADERS = lfpRatiometer.h
 SOURCES = lfpRatiometer.cpp \
 			moc_lfpRatiometer.cpp
 
-LIBS = -L/usr/lib/x86_64-linux-gnu -lfftw3 -lm
+LIBS = -lfftw3 -lm
 
 ### Do note edit below this line ###
 

From afc09ad0b5a813acd465698b2dbcf2367041733b Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 3 Mar 2021 13:56:23 -0500
Subject: [PATCH 07/76] fixed missing declarations

---
 lfpRatiometer.h | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/lfpRatiometer.h b/lfpRatiometer.h
index 4de2247..fd7f44c 100644
--- a/lfpRatiometer.h
+++ b/lfpRatiometer.h
@@ -34,9 +34,14 @@ class lfpRatiometer : public DefaultGUIModel {
     protected:
 
         // update function
-        virtual void update(DefaultGUIModel::update_flags_t)
+        virtual void update(DefaultGUIModel::update_flags_t);
 
     private:
+        // RTXI complains without these
+        double some_parameter;
+        double some_state;
+        double period;
+        void initParameters();
     
         int N; // time window in samples
         int f_size; // nonredundant size of DFT
@@ -81,7 +86,6 @@ class lfpRatiometer : public DefaultGUIModel {
             }
         }
 
-        void initParameters();
         void makePSD();
         void getRatio();
     

From ffbdf275507e48755fc86e2d0ef7adc596b2ba2f Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 3 Mar 2021 14:35:19 -0500
Subject: [PATCH 08/76] changing parameters

---
 lfpRatiometer.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lfpRatiometer.cpp b/lfpRatiometer.cpp
index 184131e..8cd1c8c 100644
--- a/lfpRatiometer.cpp
+++ b/lfpRatiometer.cpp
@@ -4,8 +4,8 @@
 using namespace std;
 
 extern "C" Plugin::Object *createRTXIPlugin(void){
-    int N = 10;
-    double sampling = 200;
+    int N = 2000;
+    double sampling = 2000;
     return new lfpRatiometer(N, sampling);
 }
 

From 674c97169bd146054254e8972f1c279bc2924631 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Thu, 18 Mar 2021 19:34:44 -0400
Subject: [PATCH 09/76] updated to work with updated lfp-cpp-library

---
 Makefile               |   8 +-
 lfpRatiometer.cpp      | 216 -----------------------------------------
 lfpRatiometer.h        | 100 -------------------
 rtxi-lfpRatiometer.cpp | 119 +++++++++++++++++++++++
 rtxi-lfpRatiometer.h   |  51 ++++++++++
 5 files changed, 174 insertions(+), 320 deletions(-)
 delete mode 100644 lfpRatiometer.cpp
 delete mode 100644 lfpRatiometer.h
 create mode 100644 rtxi-lfpRatiometer.cpp
 create mode 100644 rtxi-lfpRatiometer.h

diff --git a/Makefile b/Makefile
index 0b7ca96..ec0b873 100644
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,9 @@
-PLUGIN_NAME = lfpRatiometer
+PLUGIN_NAME = rtxilfpRatiometer
 
-HEADERS = lfpRatiometer.h
+HEADERS = rtxilfpRatiometer.h
 
-SOURCES = lfpRatiometer.cpp \
-			moc_lfpRatiometer.cpp
+SOURCES = rtxolfpRatiometer.cpp \
+			moc_rtxilfpRatiometer.cpp
 
 LIBS = -lfftw3 -lm
 
diff --git a/lfpRatiometer.cpp b/lfpRatiometer.cpp
deleted file mode 100644
index 8cd1c8c..0000000
--- a/lfpRatiometer.cpp
+++ /dev/null
@@ -1,216 +0,0 @@
-#include <lfpRatiometer.h>
-#include <main_window.h>
-
-using namespace std;
-
-extern "C" Plugin::Object *createRTXIPlugin(void){
-    int N = 2000;
-    double sampling = 2000;
-    return new lfpRatiometer(N, sampling);
-}
-
-static DefaultGUIModel::variable_t vars[] = {
-  {
-    "GUI label", "Tooltip description",
-    DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
-  },
-{
-    "input_LFP", "Input LFP",
-    DefaultGUIModel::INPUT | DefaultGUIModel::DOUBLE,
-  },
-{
-    "ratio", "Output LFP Power Ratio",
-    DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
-  },
-{
-    "A State", "Tooltip description", DefaultGUIModel::STATE,
-  },
-};
-
-static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
-
-// defining what's in the object's constructor
-// user defines time window length (in samples) and sampling rate
-lfpRatiometer::lfpRatiometer(int N_input, double sampling_input)
-    : DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars)
-{
-    setWhatsThis("<p><b>lfpRatiometer:</b><br>QWhatsThis description.</p>");
-    DefaultGUIModel::createGUI(vars, num_vars);
-    customizeGUI();
-    initParameters();
-    update(INIT);
-    refresh();
-    QTimer::singleShot(0, this, SLOT(resizeMe()));
-
-    // setting user defined variables
-    N=N_input;
-    f_size=N/2 + 1;
-    sampling=sampling_input;
-
-    // setting default variables
-    lf_low = 1;
-    lf_high = 25;
-    hf_low = 30;
-    hf_high = 90;
-    
-    // setting default window
-    window_hamming();
-
-    // establishing frequencies that will be associated with DFT output
-    for (int n=0; n<f_size;n++){
-        allfreqs.push_back(sampling*n/N);
-    }
-
-    // allocating space for input time array
-    in = (double*) fftw_malloc(sizeof(double)*N);
-    // allocating space for N DFT terms
-    // note: this has to be N, not N/2 + 1, for fftw_free()
-    out = fftw_alloc_complex(N);
-    // creating the FFTW3 plan
-    // FFTW_MEASURE makes initialization long for faster...
-    // calculations
-    p = fftw_plan_dft_r2c_1d(N,in,out,FFTW_MEASURE);
-}
-
-// defining what's in the object's destructor
-lfpRatiometer::~lfpRatiometer(void) {
-    // destroy plan
-    fftw_destroy_plan(p);
-    // free output array
-    fftw_free(out);
-    // free input array
-    fftw_free(in);
-
-    return;
-}
-
-// real-time RTXI function
-void lfpRatiometer::execute() {
-
-    // get new time series reading
-    in_raw.push_back(input(0));
-
-    // if time series is full
-    if (in_raw.size() > N) {
-        // cut it to size
-        in_raw.erase(in_raw.begin());
-
-        // run our LF/HF analysis
-        makePSD();
-        getRatio();
-
-        // output the calculated lf_hf_ratio
-        output(0) = lf_hf_ratio;
-        
-    }
-    
-}
-
-// function that calculates the power spectral density
-void lfpRatiometer::makePSD() {
-    psd.clear(); // clear vector which stores PSD
-
-    // applying window
-    for (int n=0; n<N; n++){
-        in[n] = in_raw[n]*window[n];
-    }
-
-    fftw_execute(p); // FFTW3 calculate the DFT
-
-    // loop through DFT entries
-    for (int n=0; n<f_size; n++){
-        // calculate |y_n|^2
-        double fftsqr = out[n][0]*out[n][0] + out[n][1]*out[n][1];
-
-        // calculate PSD (described in Heinzel et al., 2002)
-        // DC & Nyquist freq is scaled to be consistent with MATLAB's spectrogram
-        // Usually, the edges should not matter because all frequencies of interest
-        // should be contained in the interior
-        // WILL CHANGE WITH WINDOWING
-        if (n==0 || n==f_size-1) {
-            psd.push_back((1/(sampling*s2)) * fftsqr);
-        }
-        else {
-            psd.push_back(2*(1/(sampling*s2)) * fftsqr);
-        }
-    }
-}
-
-// // function that calculates LF/HF ratio
-void lfpRatiometer::getRatio() {
-    double lf_total = 0;
-    double hf_total = 0;
-
-    // iterates over PSD, calculating running sums in each band
-    for (int n=0; n<f_size; n++){
-        if (allfreqs.at(n)>= lf_low && allfreqs.at(n) <= lf_high) {
-            lf_total = lf_total + psd.at(n);
-        }
-        if (allfreqs.at(n) >= hf_low && allfreqs.at(n) <= hf_high){
-            hf_total = hf_total + psd.at(n);
-        }
-    }
-
-    // take ratio
-    lf_hf_ratio = lf_total/hf_total;
-}
-
-// RTXI function for initializing parameters
-void lfpRatiometer::initParameters(void)
-{
-  some_parameter = 0;
-  some_state = 0;
-}
-
-// update function (not running in real time)
-void lfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
-{
-  switch (flag) {
-    case INIT:
-      period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
-      setParameter("GUI label", some_parameter);
-      setState("A State", some_state);
-      break;
-
-    case MODIFY:
-      some_parameter = getParameter("GUI label").toDouble();
-      break;
-
-    case UNPAUSE:
-      break;
-
-    case PAUSE:
-      break;
-
-    case PERIOD:
-      period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
-      break;
-
-    default:
-      break;
-  }
-}
-
-// RTXI's customizeGUI function
-void lfpRatiometer::customizeGUI(void)
-{
-  QGridLayout* customlayout = DefaultGUIModel::getLayout();
-
-  QGroupBox* button_group = new QGroupBox;
-
-  QPushButton* abutton = new QPushButton("Button A");
-  QPushButton* bbutton = new QPushButton("Button B");
-  QHBoxLayout* button_layout = new QHBoxLayout;
-  button_group->setLayout(button_layout);
-  button_layout->addWidget(abutton);
-  button_layout->addWidget(bbutton);
-  QObject::connect(abutton, SIGNAL(clicked()), this, SLOT(aBttn_event()));
-  QObject::connect(bbutton, SIGNAL(clicked()), this, SLOT(bBttn_event()));
-
-  customlayout->addWidget(button_group, 0, 0);
-  setLayout(customlayout);
-}
-
-void lfpRatiometer::aBttn_event(void) { }
-
-void lfpRatiometer::bBttn_event(void) { }
\ No newline at end of file
diff --git a/lfpRatiometer.h b/lfpRatiometer.h
deleted file mode 100644
index fd7f44c..0000000
--- a/lfpRatiometer.h
+++ /dev/null
@@ -1,100 +0,0 @@
-#ifndef LFPRATIOMETER_H
-#define LFPRATIOMETER_H
-
-#include <default_gui_model.h>
-
-#include <stdio.h>
-#include <malloc.h>
-#include <math.h>
-#include <complex.h>
-
-#include <vector>
-#include <iostream>
-
-#include <fftw3.h>
-
-class lfpRatiometer : public DefaultGUIModel {
-
-    Q_OBJECT
-
-    public:
-        // constructor
-        lfpRatiometer(int N_input, double sampling_input);
-
-        // destructor
-        ~lfpRatiometer(void);
-
-        // execute
-        void execute();
-
-        // functions to make GUI
-        void createGUI(DefaultGUIModel::variable_t*, int);
-        void customizeGUI(void);
-        
-    protected:
-
-        // update function
-        virtual void update(DefaultGUIModel::update_flags_t);
-
-    private:
-        // RTXI complains without these
-        double some_parameter;
-        double some_state;
-        double period;
-        void initParameters();
-    
-        int N; // time window in samples
-        int f_size; // nonredundant size of DFT
-        double sampling; // sampling rate (Hz)
-        double *in; // pointer to (windowed) time series
-        std::vector<double> in_raw; // vector to hold raw time series
-        fftw_complex *out; // pointer to DFT
-        fftw_plan p; // stores FFTW3 plan
-
-        std::vector<double> allfreqs;
-        std::vector<double> psd;
-        double lf_hf_ratio;
-        double lf_low;
-        double lf_high;
-        double hf_low;
-        double hf_high;
-
-        std::vector<double> window; // time domain of window
-        double s2; // window scaling factor
-
-        // method sets window as rectangle
-        void window_rect(){
-            window.clear();
-            s2 = 0;
-            for (int j=0; j<N; j++){
-                double val = 1;
-                window.push_back(val);
-                s2 = s2 + val*val;
-            }
-        }
-        // method sets window as Hamming
-        // supposed to be consistent with MATLAB hamming() function
-        void window_hamming(){
-            window.clear();
-            s2 = 0;
-            double pi = atan(1) * 4;
-            for (int j=0; j<N; j++){
-                double z = 2*pi*j/(N-1);
-                double val = 0.54 - 0.46*cos(z);
-                window.push_back(val);
-                s2 = s2 + val*val;
-            }
-        }
-
-        void makePSD();
-        void getRatio();
-    
-    private slots:
-        void aBttn_event(void);
-        void bBttn_event(void);
-
-
-};
-
-
-#endif
\ No newline at end of file
diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
new file mode 100644
index 0000000..8a3bc25
--- /dev/null
+++ b/rtxi-lfpRatiometer.cpp
@@ -0,0 +1,119 @@
+#include <rtxi-lfpRatiometer.h>
+
+using namespace std;
+
+extern "C" Plugin::Object *createRTXIPlugin(void){
+    return new rtxilfpRatiometer();
+}
+
+static DefaultGUIModel::variable_t vars[] = {
+  {
+    "GUI label", "Tooltip description",
+    DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
+  },
+{
+    "input_LFP", "Input LFP",
+    DefaultGUIModel::INPUT | DefaultGUIModel::DOUBLE,
+  },
+{
+    "ratio", "Output LFP Power Ratio",
+    DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
+  },
+{
+    "A State", "Tooltip description", DefaultGUIModel::STATE,
+  },
+};
+
+static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
+
+// defining what's in the object's constructor
+// user defines time window length (in samples) and sampling rate
+rtxilfpRatiometer::rtxilfpRatiometer() :
+DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars)
+lfpratiometer(N, sampling) // constructing lfpRatiometer object
+{
+    setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
+    DefaultGUIModel::createGUI(vars, num_vars);
+    customizeGUI();
+    initParameters();
+    update(INIT);
+    refresh();
+    QTimer::singleShot(0, this, SLOT(resizeMe()));
+}
+
+// defining what's in the object's destructor
+rtxilfpRatiometer::~rtxilfpRatiometer(void) {}
+
+// real-time RTXI function
+void rtxilfpRatiometer::execute() {
+
+  // push new time series reading to lfpRatiometer
+  lfpratiometer.pushTimeSample(input(0))
+
+  // calculate LF/HF ratio
+  lfpratiometer.calcRatio();
+
+  // put the LF/HF ratio into the output
+  output(0) = lfpratiometer.getRatio();
+    
+}
+
+// RTXI function for initializing parameters
+void lfpRatiometer::initParameters(void)
+{
+  some_parameter = 0;
+  some_state = 0;
+}
+
+// update function (not running in real time)
+void lfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
+{
+  switch (flag) {
+    case INIT:
+      period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
+      setParameter("GUI label", some_parameter);
+      setState("A State", some_state);
+      break;
+
+    case MODIFY:
+      some_parameter = getParameter("GUI label").toDouble();
+      break;
+
+    case UNPAUSE:
+      break;
+
+    case PAUSE:
+      break;
+
+    case PERIOD:
+      period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
+      break;
+
+    default:
+      break;
+  }
+}
+
+// RTXI's customizeGUI function
+void lfpRatiometer::customizeGUI(void)
+{
+  QGridLayout* customlayout = DefaultGUIModel::getLayout();
+
+  QGroupBox* button_group = new QGroupBox;
+
+  QPushButton* abutton = new QPushButton("Button A");
+  QPushButton* bbutton = new QPushButton("Button B");
+  QHBoxLayout* button_layout = new QHBoxLayout;
+  button_group->setLayout(button_layout);
+  button_layout->addWidget(abutton);
+  button_layout->addWidget(bbutton);
+  QObject::connect(abutton, SIGNAL(clicked()), this, SLOT(aBttn_event()));
+  QObject::connect(bbutton, SIGNAL(clicked()), this, SLOT(bBttn_event()));
+
+  customlayout->addWidget(button_group, 0, 0);
+  setLayout(customlayout);
+}
+
+void lfpRatiometer::aBttn_event(void) { }
+
+void lfpRatiometer::bBttn_event(void) { }
\ No newline at end of file
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
new file mode 100644
index 0000000..e50f358
--- /dev/null
+++ b/rtxi-lfpRatiometer.h
@@ -0,0 +1,51 @@
+#ifndef RTXILFPRATIOMETER_H
+#define RTXILFPRATIOMETER_H
+
+#include <default_gui_model.h>
+#include <main_window.h>
+
+class rtxilfpRatiometer : public DefaultGUIModel {
+
+    Q_OBJECT
+
+    public:
+        // constructor
+        rtxilfpRatiometer();
+
+        // destructor
+        ~rtxilfpRatiometer(void);
+
+        // execute
+        void execute();
+
+        // functions to make GUI
+        void createGUI(DefaultGUIModel::variable_t*, int);
+        void customizeGUI(void);
+        
+    protected:
+
+        // update function
+        virtual void update(DefaultGUIModel::update_flags_t);
+
+    private:
+        // I want to get rid of these
+        double some_parameter;
+        double some_state;
+        double period;
+        void initParameters();
+
+        // default parameters for lfpRatiometer object
+        int N = 2000;
+        int sampling = 2000;
+
+        // lfpRatiometer object
+        lfpRatiometer lfpratiometer;
+    
+    private slots:
+        void aBttn_event(void);
+        void bBttn_event(void);
+
+};
+
+
+#endif
\ No newline at end of file

From 1b5b8d59ac670235ed3983e8e0d6a513b6895390 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Thu, 18 Mar 2021 19:39:23 -0400
Subject: [PATCH 10/76] fixed typo in MakeFile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index ec0b873..9db68d7 100644
--- a/Makefile
+++ b/Makefile
@@ -2,7 +2,7 @@ PLUGIN_NAME = rtxilfpRatiometer
 
 HEADERS = rtxilfpRatiometer.h
 
-SOURCES = rtxolfpRatiometer.cpp \
+SOURCES = rtxilfpRatiometer.cpp \
 			moc_rtxilfpRatiometer.cpp
 
 LIBS = -lfftw3 -lm

From 60e7d8c9ebdf51da0433d2870ccb5dbeef1ed993 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Thu, 18 Mar 2021 19:41:21 -0400
Subject: [PATCH 11/76] fixed typo in Makefile

---
 Makefile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 9db68d7..54ba5e1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,9 @@
 PLUGIN_NAME = rtxilfpRatiometer
 
-HEADERS = rtxilfpRatiometer.h
+HEADERS = rtxi-lfpRatiometer.h
 
-SOURCES = rtxilfpRatiometer.cpp \
-			moc_rtxilfpRatiometer.cpp
+SOURCES = rtxi-lfpRatiometer.cpp \
+			moc_rtxi-lfpRatiometer.cpp
 
 LIBS = -lfftw3 -lm
 

From b2e16fd5683b4e3a738bb516d8ecbc3ef74783ca Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Thu, 18 Mar 2021 19:46:56 -0400
Subject: [PATCH 12/76] debugging

---
 rtxi-lfpRatiometer.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index e50f358..c3a0802 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -39,7 +39,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         int sampling = 2000;
 
         // lfpRatiometer object
-        lfpRatiometer lfpratiometer;
+        lfpRatiometer::lfpRatiometer lfpratiometer;
     
     private slots:
         void aBttn_event(void);

From 213a5229d2d3876f7cd13161afcee22f76b9cb09 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Thu, 18 Mar 2021 20:09:08 -0400
Subject: [PATCH 13/76] renaming to rtxi-lfpRatiometer object

---
 rtxi-lfpRatiometer.cpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 8a3bc25..97ca8ca 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -59,14 +59,14 @@ void rtxilfpRatiometer::execute() {
 }
 
 // RTXI function for initializing parameters
-void lfpRatiometer::initParameters(void)
+void rtxilfpRatiometer::initParameters(void)
 {
   some_parameter = 0;
   some_state = 0;
 }
 
 // update function (not running in real time)
-void lfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
+void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 {
   switch (flag) {
     case INIT:
@@ -95,7 +95,7 @@ void lfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 }
 
 // RTXI's customizeGUI function
-void lfpRatiometer::customizeGUI(void)
+void rtxilfpRatiometer::customizeGUI(void)
 {
   QGridLayout* customlayout = DefaultGUIModel::getLayout();
 
@@ -114,6 +114,6 @@ void lfpRatiometer::customizeGUI(void)
   setLayout(customlayout);
 }
 
-void lfpRatiometer::aBttn_event(void) { }
+void rtxilfpRatiometer::aBttn_event(void) { }
 
-void lfpRatiometer::bBttn_event(void) { }
\ No newline at end of file
+void rtxilfpRatiometer::bBttn_event(void) { }
\ No newline at end of file

From 50692c9e589029e9649643348c3c99b2a56f6544 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 14:22:30 -0400
Subject: [PATCH 14/76] small bug fixes

---
 rtxi-lfpRatiometer.cpp | 2 +-
 rtxi-lfpRatiometer.h   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 97ca8ca..b96e0ae 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -29,7 +29,7 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 // defining what's in the object's constructor
 // user defines time window length (in samples) and sampling rate
 rtxilfpRatiometer::rtxilfpRatiometer() :
-DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars)
+DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
 lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index c3a0802..e50f358 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -39,7 +39,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         int sampling = 2000;
 
         // lfpRatiometer object
-        lfpRatiometer::lfpRatiometer lfpratiometer;
+        lfpRatiometer lfpratiometer;
     
     private slots:
         void aBttn_event(void);

From d6ec49c73f595539bfa83836066bf20eff8cac89 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 14:44:06 -0400
Subject: [PATCH 15/76] added lfpRatiometer to LIBS Makefile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 54ba5e1..e2b3840 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ HEADERS = rtxi-lfpRatiometer.h
 SOURCES = rtxi-lfpRatiometer.cpp \
 			moc_rtxi-lfpRatiometer.cpp
 
-LIBS = -lfftw3 -lm
+LIBS = -lfftw3 -lm -llfpRatiometer
 
 ### Do note edit below this line ###
 

From 3587d93845932df4b436f5ac2409c8b99434be7d Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 15:04:28 -0400
Subject: [PATCH 16/76] modified Makefile to be aligned with
 rtxi-gldsController Makefile

---
 Makefile | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index e2b3840..2763846 100644
--- a/Makefile
+++ b/Makefile
@@ -5,8 +5,16 @@ HEADERS = rtxi-lfpRatiometer.h
 SOURCES = rtxi-lfpRatiometer.cpp \
 			moc_rtxi-lfpRatiometer.cpp
 
-LIBS = -lfftw3 -lm -llfpRatiometer
+LIBS =
 
-### Do note edit below this line ###
+OS := $(shell uname)
+CXX = g++
 
-include $(shell rtxi_plugin_config --pkgdata-dir)/Makefile.plugin_compile
\ No newline at end of file
+# lfpRatiometer
+CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
+LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
+
+# RTXI plug-in stuff
+include Makefile.plugin_compile
+
+print-% : ; @echo $* = $($*)
\ No newline at end of file

From ce021dd33a46e185d5eaf9061ebdedcb029ce75b Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 15:07:22 -0400
Subject: [PATCH 17/76] added Makefile.plugin_compile

---
 Makefile.plugin_compile | 43 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 Makefile.plugin_compile

diff --git a/Makefile.plugin_compile b/Makefile.plugin_compile
new file mode 100644
index 0000000..9519d2a
--- /dev/null
+++ b/Makefile.plugin_compile
@@ -0,0 +1,43 @@
+exec_modeldir =  /usr/local/lib/rtxi
+
+LIBTOOL    =  /usr/local/share/rtxi/libtool
+CXX        =  g++
+CXXLD      =  g++
+CXXCOMPILE = $(LIBTOOL) --mode=compile $(CXX)
+CXXLINK    = $(LIBTOOL) --mode=link $(CXXLD)
+MOC        =  /usr/bin/moc
+
+CXXFLAGS := $(CXXFLAGS) -I. -I/usr/local/include/rtxi -I/usr/local/include/rtxi/plugins -I/usr/local/include/rtxi/libs -pipe -I/usr/local/include -I/usr/include/x86_64-linux-gnu/qt5/QtOpenGL -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtPrintSupport -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtSvg -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtNetwork -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/X11R6/include -I/usr/include/hdf5/serial -I/usr/include/qwt -I/usr/local/include/qwt -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_WIDGETS_LIB -DQT_SVG_LIB -DQT_SHARED -w -O3 -std=c++11 -fPIC
+
+LDFLAGS  := $(LDFLAGS) -L/usr/local/lib/rtxi/libs -L/usr/local/lib -lQt5OpenGL -lQt5PrintSupport -lQt5Xml -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Network -lQt5Core -lgit2 -lqwt-qt5 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lhdf5_hl -lGL -lpthread -lgsl -lgslcblas -lm -ldl -Wl,--no-as-needed -Wl,@/usr/xenomai/lib/modechk.wrappers -lalchemy -lcopperplate /usr/xenomai/lib/xenomai/bootstrap-pic.o -L/usr/xenomai/lib -lcobalt -lmodechk -lpthread -lrt -module -avoid-version
+
+ifdef DEBUG
+CXXFLAGS += -DDEBUG
+endif
+
+# 2018-01-17 : MFB edited to prepend julia stuff to existing OBJECTS variable.
+OBJECTS += $(shell echo $(SOURCES) | sed "s/\.cpp[ \t\n]*/\.lo /g")
+MOOBJECTS = $(shell echo $(HEADERS) | sed "s/\.h[ \t\n]*/\.lo /g")
+
+all: $(PLUGIN_NAME).la
+
+%.lo: %.cpp
+	$(CXXCOMPILE) $(CXXFLAGS) -c $< -o $@
+
+$(PLUGIN_NAME).la: $(OBJECTS) $(SOURCES) $(HEADERS)
+	$(CXXLINK) $(CXXFLAGS) $(LIBS) $(LDFLAGS) -rpath `readlink -f $(exec_modeldir)` -o $(PLUGIN_NAME).la $(OBJECTS)
+
+install: $(PLUGIN_NAME).la
+	$(LIBTOOL) --mode=install cp $(PLUGIN_NAME).la `readlink -f $(exec_modeldir)`
+
+clean:
+	rm -f $(OBJECTS)
+	rm -f $(MOOBJECTS)
+	rm -f moc_*
+	rm -f *.o
+	rm -f $(PLUGIN_NAME).la
+	rm -f $(PLUGIN_NAME).o
+	rm -rf .libs
+
+moc_%.cpp: %.h
+	$(MOC) -o $@ $<
\ No newline at end of file

From 00463a6b7c106a046133bb856732438cb15c5939 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 15:17:10 -0400
Subject: [PATCH 18/76] including lfpRatiometer library now

---
 rtxi-lfpRatiometer.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index e50f358..7d09f52 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -3,6 +3,7 @@
 
 #include <default_gui_model.h>
 #include <main_window.h>
+#include <lfpRatiometer>
 
 class rtxilfpRatiometer : public DefaultGUIModel {
 

From a567f76857c7223f51d6b6e69edd1e0929ef3299 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 15:18:01 -0400
Subject: [PATCH 19/76] missing semicolon

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index b96e0ae..f1c0d65 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -48,7 +48,7 @@ rtxilfpRatiometer::~rtxilfpRatiometer(void) {}
 void rtxilfpRatiometer::execute() {
 
   // push new time series reading to lfpRatiometer
-  lfpratiometer.pushTimeSample(input(0))
+  lfpratiometer.pushTimeSample(input(0));
 
   // calculate LF/HF ratio
   lfpratiometer.calcRatio();

From 15682e263fd63b03801f05419e44e1012dc6c554 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 15:19:32 -0400
Subject: [PATCH 20/76] changed name of RTXI plugin

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 2763846..b653eb6 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-PLUGIN_NAME = rtxilfpRatiometer
+PLUGIN_NAME = lfpRatiometer
 
 HEADERS = rtxi-lfpRatiometer.h
 

From f7bc4972c16f85545cd98a77cbc1e7c74de54916 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 15:36:00 -0400
Subject: [PATCH 21/76] added cleanrtxi feature to Makefile

---
 Makefile | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index b653eb6..6e5e03b 100644
--- a/Makefile
+++ b/Makefile
@@ -17,4 +17,7 @@ LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
 # RTXI plug-in stuff
 include Makefile.plugin_compile
 
-print-% : ; @echo $* = $($*)
\ No newline at end of file
+print-% : ; @echo $* = $($*)
+
+cleanrtxi :
+		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*
\ No newline at end of file

From 90dd7a3060afb6dda8bc893e447d4069152b044f Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 19 Mar 2021 20:06:57 -0400
Subject: [PATCH 22/76] debugging

---
 rtxi-lfpRatiometer.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 7d09f52..d3be53b 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -14,7 +14,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         rtxilfpRatiometer();
 
         // destructor
-        ~rtxilfpRatiometer(void);
+        virtual ~rtxilfpRatiometer(void);
 
         // execute
         void execute();

From ac1bb35b197ef3fb254a6a5007609666d5aa88da Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Mon, 22 Mar 2021 13:56:41 -0400
Subject: [PATCH 23/76] added FFTW3 pkg-config to Makefile

---
 Makefile | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Makefile b/Makefile
index 6e5e03b..97f54d4 100644
--- a/Makefile
+++ b/Makefile
@@ -10,6 +10,10 @@ LIBS =
 OS := $(shell uname)
 CXX = g++
 
+# FFTW3
+CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
+LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
+
 # lfpRatiometer
 CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
 LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)

From 7da115dbc2e556981677e93715a0346af76b76ca Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Mon, 22 Mar 2021 15:07:26 -0400
Subject: [PATCH 24/76] Makefile changes

---
 Makefile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 97f54d4..a035d81 100644
--- a/Makefile
+++ b/Makefile
@@ -5,14 +5,14 @@ HEADERS = rtxi-lfpRatiometer.h
 SOURCES = rtxi-lfpRatiometer.cpp \
 			moc_rtxi-lfpRatiometer.cpp
 
-LIBS =
+LIBS = -lfftw3 -lm
 
 OS := $(shell uname)
 CXX = g++
 
 # FFTW3
-CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
-LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
+# CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
+# LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
 
 # lfpRatiometer
 CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)

From 11217d61baf296c532eb85047ba510794d41af0a Mon Sep 17 00:00:00 2001
From: Adriano <aborsa@gatech.edu>
Date: Mon, 22 Mar 2021 23:04:54 -0400
Subject: [PATCH 25/76] Makefile miscellaneous changes

---
 Makefile | 10 ++++++----
 test.md  |  1 -
 2 files changed, 6 insertions(+), 5 deletions(-)
 delete mode 100644 test.md

diff --git a/Makefile b/Makefile
index a035d81..c9c3f93 100644
--- a/Makefile
+++ b/Makefile
@@ -5,14 +5,16 @@ HEADERS = rtxi-lfpRatiometer.h
 SOURCES = rtxi-lfpRatiometer.cpp \
 			moc_rtxi-lfpRatiometer.cpp
 
-LIBS = -lfftw3 -lm
+LIBS =
 
 OS := $(shell uname)
 CXX = g++
 
+# 
+
 # FFTW3
-# CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
-# LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
+CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
+LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
 
 # lfpRatiometer
 CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
@@ -24,4 +26,4 @@ include Makefile.plugin_compile
 print-% : ; @echo $* = $($*)
 
 cleanrtxi :
-		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*
\ No newline at end of file
+		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*
diff --git a/test.md b/test.md
deleted file mode 100644
index f58162e..0000000
--- a/test.md
+++ /dev/null
@@ -1 +0,0 @@
-this should be in rtxi-plugin branch.

From dd76f2e270297b5f99a59e8eb50349c72fb34952 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Mon, 22 Mar 2021 23:18:53 -0400
Subject: [PATCH 26/76] minor changes to .cpp file

---
 rtxi-lfpRatiometer.cpp | 6 +++---
 rtxi-lfpRatiometer.h   | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index f1c0d65..958a317 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -28,7 +28,7 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 
 // defining what's in the object's constructor
 // user defines time window length (in samples) and sampling rate
-rtxilfpRatiometer::rtxilfpRatiometer() :
+rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
 lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
@@ -42,10 +42,10 @@ lfpratiometer(N, sampling) // constructing lfpRatiometer object
 }
 
 // defining what's in the object's destructor
-rtxilfpRatiometer::~rtxilfpRatiometer(void) {}
+rtxilfpRatiometer::~rtxilfpRatiometer(void) { }
 
 // real-time RTXI function
-void rtxilfpRatiometer::execute() {
+void rtxilfpRatiometer::execute(void) {
 
   // push new time series reading to lfpRatiometer
   lfpratiometer.pushTimeSample(input(0));
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index d3be53b..7d1773a 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -11,13 +11,13 @@ class rtxilfpRatiometer : public DefaultGUIModel {
 
     public:
         // constructor
-        rtxilfpRatiometer();
+        rtxilfpRatiometer(void);
 
         // destructor
         virtual ~rtxilfpRatiometer(void);
 
         // execute
-        void execute();
+        void execute(void);
 
         // functions to make GUI
         void createGUI(DefaultGUIModel::variable_t*, int);

From af58da82eae56b49b160347906b0a59ac437a731 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 23 Mar 2021 19:01:35 -0400
Subject: [PATCH 27/76] commenting out lfpRatiometer

---
 rtxi-lfpRatiometer.cpp | 14 +++++++-------
 rtxi-lfpRatiometer.h   |  4 ++--
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 958a317..e1f165f 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -30,7 +30,7 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 // user defines time window length (in samples) and sampling rate
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
-lfpratiometer(N, sampling) // constructing lfpRatiometer object
+// lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
     DefaultGUIModel::createGUI(vars, num_vars);
@@ -47,14 +47,14 @@ rtxilfpRatiometer::~rtxilfpRatiometer(void) { }
 // real-time RTXI function
 void rtxilfpRatiometer::execute(void) {
 
-  // push new time series reading to lfpRatiometer
-  lfpratiometer.pushTimeSample(input(0));
+  // // push new time series reading to lfpRatiometer
+  // lfpratiometer.pushTimeSample(input(0));
 
-  // calculate LF/HF ratio
-  lfpratiometer.calcRatio();
+  // // calculate LF/HF ratio
+  // lfpratiometer.calcRatio();
 
-  // put the LF/HF ratio into the output
-  output(0) = lfpratiometer.getRatio();
+  // // put the LF/HF ratio into the output
+  // output(0) = lfpratiometer.getRatio();
     
 }
 
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 7d1773a..11de508 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -39,8 +39,8 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         int N = 2000;
         int sampling = 2000;
 
-        // lfpRatiometer object
-        lfpRatiometer lfpratiometer;
+        // // lfpRatiometer object
+        // lfpRatiometer lfpratiometer;
     
     private slots:
         void aBttn_event(void);

From f8b50e32d7551d5d1493172611b3444f3b5d909b Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 23 Mar 2021 19:03:15 -0400
Subject: [PATCH 28/76] misc

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index e1f165f..c1d6a48 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -29,7 +29,7 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 // defining what's in the object's constructor
 // user defines time window length (in samples) and sampling rate
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
-DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
+DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars)
 // lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");

From 4e61e0bc8e25070d457998eeb3b64bee9c551287 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 23 Mar 2021 19:13:15 -0400
Subject: [PATCH 29/76] misc

---
 rtxi-lfpRatiometer.cpp | 16 ++++++++--------
 rtxi-lfpRatiometer.h   |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index c1d6a48..958a317 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -29,8 +29,8 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 // defining what's in the object's constructor
 // user defines time window length (in samples) and sampling rate
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
-DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars)
-// lfpratiometer(N, sampling) // constructing lfpRatiometer object
+DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
+lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
     DefaultGUIModel::createGUI(vars, num_vars);
@@ -47,14 +47,14 @@ rtxilfpRatiometer::~rtxilfpRatiometer(void) { }
 // real-time RTXI function
 void rtxilfpRatiometer::execute(void) {
 
-  // // push new time series reading to lfpRatiometer
-  // lfpratiometer.pushTimeSample(input(0));
+  // push new time series reading to lfpRatiometer
+  lfpratiometer.pushTimeSample(input(0));
 
-  // // calculate LF/HF ratio
-  // lfpratiometer.calcRatio();
+  // calculate LF/HF ratio
+  lfpratiometer.calcRatio();
 
-  // // put the LF/HF ratio into the output
-  // output(0) = lfpratiometer.getRatio();
+  // put the LF/HF ratio into the output
+  output(0) = lfpratiometer.getRatio();
     
 }
 
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 11de508..51527b9 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -40,7 +40,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         int sampling = 2000;
 
         // // lfpRatiometer object
-        // lfpRatiometer lfpratiometer;
+        lfpRatiometer lfpratiometer;
     
     private slots:
         void aBttn_event(void);

From 69876366f86fa996fc14fd80f55f433ac2813bc6 Mon Sep 17 00:00:00 2001
From: Adriano <aborsa@gatech.edu>
Date: Tue, 23 Mar 2021 19:20:57 -0400
Subject: [PATCH 30/76] Makefile edits

---
 Makefile         |  4 +++-
 lfpRatiometer.la | 41 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 lfpRatiometer.la

diff --git a/Makefile b/Makefile
index c9c3f93..4ef1167 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-PLUGIN_NAME = lfpRatiometer
+PLUGIN_NAME = rtxilfpRatiometer
 
 HEADERS = rtxi-lfpRatiometer.h
 
@@ -20,6 +20,8 @@ LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
 CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
 LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
 
+# CXXFLAGS := $(CXXFLAGS) -rpath  /home/amborsa10/.local/lib
+
 # RTXI plug-in stuff
 include Makefile.plugin_compile
 
diff --git a/lfpRatiometer.la b/lfpRatiometer.la
new file mode 100644
index 0000000..a8d7df1
--- /dev/null
+++ b/lfpRatiometer.la
@@ -0,0 +1,41 @@
+# lfpRatiometer.la - a libtool library file
+# Generated by libtool (GNU libtool) 2.4.6 Debian-2.4.6-0.1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname='lfpRatiometer.so'
+
+# Names of this library.
+library_names='lfpRatiometer.so lfpRatiometer.so lfpRatiometer.so'
+
+# The name of the static archive.
+old_library='lfpRatiometer.a'
+
+# Linker flags that cannot go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=' -lfftw3 -L/usr/local/lib/rtxi/libs -L/usr/local/lib -lQt5OpenGL -lQt5PrintSupport -lQt5Xml -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Network -lQt5Core -lgit2 -lqwt-qt5 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lhdf5_hl -lGL -lgsl -lgslcblas -ldl /usr/xenomai/lib/libalchemy.la /usr/xenomai/lib/libcopperplate.la -L/usr/xenomai/lib /usr/xenomai/lib/libcobalt.la /usr/xenomai/lib/libmodechk.la -lpthread -lrt'
+
+# Names of additional weak libraries provided by this library
+weak_library_names=''
+
+# Version information for lfpRatiometer.
+current=0
+age=0
+revision=0
+
+# Is this an already installed library?
+installed=no
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=yes
+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
+libdir='/usr/local/lib/rtxi'

From 8ad5445623247d2f0ee82c36bff65c13cd19e24f Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 23 Mar 2021 19:23:00 -0400
Subject: [PATCH 31/76] cleaning

---
 lfpRatiometer.la | 41 -----------------------------------------
 1 file changed, 41 deletions(-)
 delete mode 100644 lfpRatiometer.la

diff --git a/lfpRatiometer.la b/lfpRatiometer.la
deleted file mode 100644
index a8d7df1..0000000
--- a/lfpRatiometer.la
+++ /dev/null
@@ -1,41 +0,0 @@
-# lfpRatiometer.la - a libtool library file
-# Generated by libtool (GNU libtool) 2.4.6 Debian-2.4.6-0.1
-#
-# Please DO NOT delete this file!
-# It is necessary for linking the library.
-
-# The name that we can dlopen(3).
-dlname='lfpRatiometer.so'
-
-# Names of this library.
-library_names='lfpRatiometer.so lfpRatiometer.so lfpRatiometer.so'
-
-# The name of the static archive.
-old_library='lfpRatiometer.a'
-
-# Linker flags that cannot go in dependency_libs.
-inherited_linker_flags=''
-
-# Libraries that this one depends upon.
-dependency_libs=' -lfftw3 -L/usr/local/lib/rtxi/libs -L/usr/local/lib -lQt5OpenGL -lQt5PrintSupport -lQt5Xml -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Network -lQt5Core -lgit2 -lqwt-qt5 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lhdf5_hl -lGL -lgsl -lgslcblas -ldl /usr/xenomai/lib/libalchemy.la /usr/xenomai/lib/libcopperplate.la -L/usr/xenomai/lib /usr/xenomai/lib/libcobalt.la /usr/xenomai/lib/libmodechk.la -lpthread -lrt'
-
-# Names of additional weak libraries provided by this library
-weak_library_names=''
-
-# Version information for lfpRatiometer.
-current=0
-age=0
-revision=0
-
-# Is this an already installed library?
-installed=no
-
-# Should we warn about portability when linking against -modules?
-shouldnotlink=yes
-
-# Files to dlopen/dlpreopen
-dlopen=''
-dlpreopen=''
-
-# Directory that this library needs to be installed in:
-libdir='/usr/local/lib/rtxi'

From cfee09b479dcb8aae8103bfadf381b699b1da3cf Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 23 Mar 2021 19:25:38 -0400
Subject: [PATCH 32/76] added comments

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 4ef1167..8a70e6e 100644
--- a/Makefile
+++ b/Makefile
@@ -12,7 +12,7 @@ CXX = g++
 
 # 
 
-# FFTW3
+# FFTW3 (not sure if necessary)
 CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
 LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
 

From 027c3e0f76212654cd38f2a4632f4cecc8531e11 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 14:41:40 -0400
Subject: [PATCH 33/76] changed variable type

---
 rtxi-lfpRatiometer.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 51527b9..b16e80e 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -37,7 +37,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
 
         // default parameters for lfpRatiometer object
         int N = 2000;
-        int sampling = 2000;
+        double sampling = 2000;
 
         // // lfpRatiometer object
         lfpRatiometer lfpratiometer;

From acf67f73374dd391db379462ab6207931fbb060d Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 15:06:38 -0400
Subject: [PATCH 34/76] trying something

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 958a317..172cc17 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -30,7 +30,7 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 // user defines time window length (in samples) and sampling rate
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
-lfpratiometer(N, sampling) // constructing lfpRatiometer object
+lfpratiometer((int)2000, (double)2000) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
     DefaultGUIModel::createGUI(vars, num_vars);

From b352e3115944e232e1c23dcdcd97aa2421f2d897 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 15:22:33 -0400
Subject: [PATCH 35/76] changed output of destructor

---
 Makefile             | 2 --
 rtxi-lfpRatiometer.h | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 8a70e6e..65e76ed 100644
--- a/Makefile
+++ b/Makefile
@@ -10,8 +10,6 @@ LIBS =
 OS := $(shell uname)
 CXX = g++
 
-# 
-
 # FFTW3 (not sure if necessary)
 CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
 LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index b16e80e..7e577d0 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -14,7 +14,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         rtxilfpRatiometer(void);
 
         // destructor
-        virtual ~rtxilfpRatiometer(void);
+        virtual void ~rtxilfpRatiometer(void);
 
         // execute
         void execute(void);

From 9bb1aadd7bee655b813de4d92e3260eccea5779e Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 15:25:12 -0400
Subject: [PATCH 36/76] changed output of destructor

---
 rtxi-lfpRatiometer.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 7e577d0..38d421b 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -14,7 +14,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         rtxilfpRatiometer(void);
 
         // destructor
-        virtual void ~rtxilfpRatiometer(void);
+        ~rtxilfpRatiometer(void);
 
         // execute
         void execute(void);

From ae23f5cb5ab788c5036ee4a307d22e8dd0c8b948 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 15:26:38 -0400
Subject: [PATCH 37/76] changed output of destructor

---
 rtxi-lfpRatiometer.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 38d421b..b16e80e 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -14,7 +14,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         rtxilfpRatiometer(void);
 
         // destructor
-        ~rtxilfpRatiometer(void);
+        virtual ~rtxilfpRatiometer(void);
 
         // execute
         void execute(void);

From 59a624c3d26a0d36def3883ed184c61516d27acb Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 15:29:42 -0400
Subject: [PATCH 38/76] reverted Makefile to plugin-template

---
 Makefile | 37 ++++++++++++++++++++++---------------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/Makefile b/Makefile
index 65e76ed..2fdedec 100644
--- a/Makefile
+++ b/Makefile
@@ -5,25 +5,32 @@ HEADERS = rtxi-lfpRatiometer.h
 SOURCES = rtxi-lfpRatiometer.cpp \
 			moc_rtxi-lfpRatiometer.cpp
 
-LIBS =
+LIBS = -llfpRatiometer
 
-OS := $(shell uname)
-CXX = g++
+include Makefile.plugin_compile
 
-# FFTW3 (not sure if necessary)
-CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
-LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
+cleanrtxi :
+		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*
 
-# lfpRatiometer
-CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
-LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
+# LIBS =
 
-# CXXFLAGS := $(CXXFLAGS) -rpath  /home/amborsa10/.local/lib
+# OS := $(shell uname)
+# CXX = g++
 
-# RTXI plug-in stuff
-include Makefile.plugin_compile
+# # FFTW3 (not sure if necessary)
+# CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
+# LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
 
-print-% : ; @echo $* = $($*)
+# # lfpRatiometer
+# CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
+# LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
 
-cleanrtxi :
-		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*
+# # CXXFLAGS := $(CXXFLAGS) -rpath  /home/amborsa10/.local/lib
+
+# # RTXI plug-in stuff
+# include Makefile.plugin_compile
+
+# print-% : ; @echo $* = $($*)
+
+# cleanrtxi :
+# 		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*

From 5dcec5ddbcfbdcb213e188e51b620a0976342289 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 15:30:39 -0400
Subject: [PATCH 39/76] reverted Makefile to plugin-template

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 2fdedec..ec62d4f 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ HEADERS = rtxi-lfpRatiometer.h
 SOURCES = rtxi-lfpRatiometer.cpp \
 			moc_rtxi-lfpRatiometer.cpp
 
-LIBS = -llfpRatiometer
+LIBS = -L /home/amborsa10/.local -llfpRatiometer
 
 include Makefile.plugin_compile
 

From 96649f8e3c3e1ed530fa6a97f4d1c91eeadec473 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 15:45:36 -0400
Subject: [PATCH 40/76] reverting Makefile to Michael's version with pkgconfig

---
 Makefile | 37 +++++++++++++++----------------------
 1 file changed, 15 insertions(+), 22 deletions(-)

diff --git a/Makefile b/Makefile
index ec62d4f..65e76ed 100644
--- a/Makefile
+++ b/Makefile
@@ -5,32 +5,25 @@ HEADERS = rtxi-lfpRatiometer.h
 SOURCES = rtxi-lfpRatiometer.cpp \
 			moc_rtxi-lfpRatiometer.cpp
 
-LIBS = -L /home/amborsa10/.local -llfpRatiometer
+LIBS =
 
-include Makefile.plugin_compile
-
-cleanrtxi :
-		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*
-
-# LIBS =
+OS := $(shell uname)
+CXX = g++
 
-# OS := $(shell uname)
-# CXX = g++
+# FFTW3 (not sure if necessary)
+CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
+LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
 
-# # FFTW3 (not sure if necessary)
-# CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
-# LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
+# lfpRatiometer
+CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
+LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
 
-# # lfpRatiometer
-# CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
-# LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
+# CXXFLAGS := $(CXXFLAGS) -rpath  /home/amborsa10/.local/lib
 
-# # CXXFLAGS := $(CXXFLAGS) -rpath  /home/amborsa10/.local/lib
-
-# # RTXI plug-in stuff
-# include Makefile.plugin_compile
+# RTXI plug-in stuff
+include Makefile.plugin_compile
 
-# print-% : ; @echo $* = $($*)
+print-% : ; @echo $* = $($*)
 
-# cleanrtxi :
-# 		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*
+cleanrtxi :
+		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*

From ca835bc1210645b3ace0569db3ce551e925ac6d1 Mon Sep 17 00:00:00 2001
From: Adriano <aborsa@gatech.edu>
Date: Fri, 26 Mar 2021 17:06:18 -0400
Subject: [PATCH 41/76] alternatives commented in Makefile

---
 Makefile | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 65e76ed..6934a69 100644
--- a/Makefile
+++ b/Makefile
@@ -11,12 +11,14 @@ OS := $(shell uname)
 CXX = g++
 
 # FFTW3 (not sure if necessary)
-CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
-LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
+#CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags fftw3)
+#LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
 
 # lfpRatiometer
 CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
 LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
+#CXXFLAGS := $(CXXFLAGS) -I/home/amborsa10/.local/include
+#LDFLAGS := $(LDFLAGS)  -L/usr/lib/x86_64-linux-gnu -lfftw3 -L/home/amborsa10/.local/lib -llfpRatiometer
 
 # CXXFLAGS := $(CXXFLAGS) -rpath  /home/amborsa10/.local/lib
 

From db4086fc13415b1a56c5078ccee594a75d2fea85 Mon Sep 17 00:00:00 2001
From: Adriano <aborsa@gatech.edu>
Date: Sun, 28 Mar 2021 22:22:47 -0400
Subject: [PATCH 42/76] changes to Makefile that allow RTXI plugin to finally
 work

---
 Makefile | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 6934a69..b4c3757 100644
--- a/Makefile
+++ b/Makefile
@@ -15,11 +15,13 @@ CXX = g++
 #LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs fftw3)
 
 # lfpRatiometer
-CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
-LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
-#CXXFLAGS := $(CXXFLAGS) -I/home/amborsa10/.local/include
+#CXXFLAGS := $(CXXFLAGS) $(shell pkg-config --cflags lfpRatiometer)
+#LDFLAGS := $(LDFLAGS) $(shell pkg-config --libs lfpRatiometer)
+CXXFLAGS := $(CXXFLAGS) -I/home/amborsa10/.local/include
 #LDFLAGS := $(LDFLAGS)  -L/usr/lib/x86_64-linux-gnu -lfftw3 -L/home/amborsa10/.local/lib -llfpRatiometer
 
+LDFLAGS := $(LDFLAGS) -Wl,-rpath -Wl,/home/amborsa10/.local/lib -L/home/amborsa10/.local/lib -llfpRatiometer
+
 # CXXFLAGS := $(CXXFLAGS) -rpath  /home/amborsa10/.local/lib
 
 # RTXI plug-in stuff

From 6cc175ea69b6c0d41441919c7cf0a07d479b8bbb Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 16:37:11 -0400
Subject: [PATCH 43/76] changing constructor initialization

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 172cc17..958a317 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -30,7 +30,7 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 // user defines time window length (in samples) and sampling rate
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
-lfpratiometer((int)2000, (double)2000) // constructing lfpRatiometer object
+lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
     DefaultGUIModel::createGUI(vars, num_vars);

From c8028d3ea09ef1b1f89cce31a90e09f74b19f28b Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 19:50:00 -0400
Subject: [PATCH 44/76] changing GUI to have all relevant parameters

---
 rtxi-lfpRatiometer.cpp | 63 +++++++++++++++++++++++++-----------------
 1 file changed, 38 insertions(+), 25 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 958a317..2d38c81 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -7,10 +7,30 @@ extern "C" Plugin::Object *createRTXIPlugin(void){
 }
 
 static DefaultGUIModel::variable_t vars[] = {
-  {
-    "GUI label", "Tooltip description",
-    DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
+{ 
+  "Time Window", "Time Window (s)", 
+  DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE
   },
+{ 
+  "Sampling Rate", "Sampling Rate (Hz)", 
+  DefaultGUIModel::STATE | DefaultGUIModel::DOUBLE,
+  },
+{ 
+  "LF Lower Bound", "LF Lower Bound",
+  DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
+  },
+{ 
+  "LF Upper Bound", "LF Upper Bound",
+  DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
+  },
+{ 
+  "HF Lower Bound", "HF Lower Bound",
+  DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
+  },
+{ 
+  "HF Upper Bound", "HF Upper Bound",
+  DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
+  },  
 {
     "input_LFP", "Input LFP",
     DefaultGUIModel::INPUT | DefaultGUIModel::DOUBLE,
@@ -19,9 +39,6 @@ static DefaultGUIModel::variable_t vars[] = {
     "ratio", "Output LFP Power Ratio",
     DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
   },
-{
-    "A State", "Tooltip description", DefaultGUIModel::STATE,
-  },
 };
 
 static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
@@ -71,12 +88,15 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
   switch (flag) {
     case INIT:
       period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
-      setParameter("GUI label", some_parameter);
-      setState("A State", some_state);
+      setParameter("Time Window", sampling/N);
+      setParameter("Sampling Rate", RT::System::getInstance()->getFrequency());
+      setParameter("LF Lower Bound", (double)1); // need to amend where these come from
+      setParameter("LF Upper Bound", (double)10);
+      setParameter("HF Lower Bound", (double)30);
+      setParameter("HF Upper Bound", (double)90);
       break;
 
     case MODIFY:
-      some_parameter = getParameter("GUI label").toDouble();
       break;
 
     case UNPAUSE:
@@ -99,21 +119,14 @@ void rtxilfpRatiometer::customizeGUI(void)
 {
   QGridLayout* customlayout = DefaultGUIModel::getLayout();
 
-  QGroupBox* button_group = new QGroupBox;
-
-  QPushButton* abutton = new QPushButton("Button A");
-  QPushButton* bbutton = new QPushButton("Button B");
-  QHBoxLayout* button_layout = new QHBoxLayout;
-  button_group->setLayout(button_layout);
-  button_layout->addWidget(abutton);
-  button_layout->addWidget(bbutton);
-  QObject::connect(abutton, SIGNAL(clicked()), this, SLOT(aBttn_event()));
-  QObject::connect(bbutton, SIGNAL(clicked()), this, SLOT(bBttn_event()));
+  // adding dropdown menu for choosing FFT window shape
+  QLabel* windowLabel = new QLabel("Window:");
+  windowShape = new QComboBox;
+  windowShape->insertItem(1, "Rectangular")
+  windowShape->insertItem(2, "Hamming")
+  QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
 
-  customlayout->addWidget(button_group, 0, 0);
+  customlayout->addWidget(windowLabel, 0, 0);
+  customlayout->addWidget(windowShape, 0, 1);
   setLayout(customlayout);
-}
-
-void rtxilfpRatiometer::aBttn_event(void) { }
-
-void rtxilfpRatiometer::bBttn_event(void) { }
\ No newline at end of file
+}
\ No newline at end of file

From 780b4eeff709586b1ad843a32a98c16e59848520 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 19:57:09 -0400
Subject: [PATCH 45/76] addressing two errors for GUI modification

---
 rtxi-lfpRatiometer.cpp | 6 +++---
 rtxi-lfpRatiometer.h   | 6 +-----
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 2d38c81..faa8a29 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -87,9 +87,9 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 {
   switch (flag) {
     case INIT:
-      period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
+      period = RT::System::getInstance()->getPeriod() * 1e-9; // s
       setParameter("Time Window", sampling/N);
-      setParameter("Sampling Rate", RT::System::getInstance()->getFrequency());
+      setParameter("Sampling Rate", 1.0/period);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
       setParameter("LF Upper Bound", (double)10);
       setParameter("HF Lower Bound", (double)30);
@@ -121,7 +121,7 @@ void rtxilfpRatiometer::customizeGUI(void)
 
   // adding dropdown menu for choosing FFT window shape
   QLabel* windowLabel = new QLabel("Window:");
-  windowShape = new QComboBox;
+  QComboBox* windowShape = new QComboBox;
   windowShape->insertItem(1, "Rectangular")
   windowShape->insertItem(2, "Hamming")
   QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index b16e80e..5f794af 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -39,12 +39,8 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         int N = 2000;
         double sampling = 2000;
 
-        // // lfpRatiometer object
+        // lfpRatiometer object
         lfpRatiometer lfpratiometer;
-    
-    private slots:
-        void aBttn_event(void);
-        void bBttn_event(void);
 
 };
 

From c8f04343572734a0f752cf9343c714dbb8bbed8b Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 19:57:52 -0400
Subject: [PATCH 46/76] fixing typo bugs

---
 rtxi-lfpRatiometer.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index faa8a29..e31076e 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -122,8 +122,8 @@ void rtxilfpRatiometer::customizeGUI(void)
   // adding dropdown menu for choosing FFT window shape
   QLabel* windowLabel = new QLabel("Window:");
   QComboBox* windowShape = new QComboBox;
-  windowShape->insertItem(1, "Rectangular")
-  windowShape->insertItem(2, "Hamming")
+  windowShape->insertItem(1, "Rectangular");
+  windowShape->insertItem(2, "Hamming");
   QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
 
   customlayout->addWidget(windowLabel, 0, 0);

From 5d5a4aa0b77701cbc729225367ae8cabaf750a9b Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:01:43 -0400
Subject: [PATCH 47/76] minor tinkering

---
 rtxi-lfpRatiometer.cpp | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index e31076e..d68f6d5 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -8,11 +8,11 @@ extern "C" Plugin::Object *createRTXIPlugin(void){
 
 static DefaultGUIModel::variable_t vars[] = {
 { 
-  "Time Window", "Time Window (s)", 
+  "Time Window (s)", "Time Window (s)", 
   DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE
   },
 { 
-  "Sampling Rate", "Sampling Rate (Hz)", 
+  "Sampling Rate (Hz)", "Sampling Rate (Hz)", 
   DefaultGUIModel::STATE | DefaultGUIModel::DOUBLE,
   },
 { 
@@ -88,8 +88,8 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
   switch (flag) {
     case INIT:
       period = RT::System::getInstance()->getPeriod() * 1e-9; // s
-      setParameter("Time Window", sampling/N);
-      setParameter("Sampling Rate", 1.0/period);
+      setParameter("Time Window (s)", sampling/N);
+      setParameter("Sampling Rate (Hz)", period);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
       setParameter("LF Upper Bound", (double)10);
       setParameter("HF Lower Bound", (double)30);
@@ -106,7 +106,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       break;
 
     case PERIOD:
-      period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
+      period = RT::System::getInstance()->getPeriod() * 1e-9; // s
       break;
 
     default:
@@ -120,13 +120,13 @@ void rtxilfpRatiometer::customizeGUI(void)
   QGridLayout* customlayout = DefaultGUIModel::getLayout();
 
   // adding dropdown menu for choosing FFT window shape
-  QLabel* windowLabel = new QLabel("Window:");
+  QLabel* windowLabel = new QLabel("FFT Window:");
   QComboBox* windowShape = new QComboBox;
   windowShape->insertItem(1, "Rectangular");
   windowShape->insertItem(2, "Hamming");
   QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
 
-  customlayout->addWidget(windowLabel, 0, 0);
-  customlayout->addWidget(windowShape, 0, 1);
+  customlayout->addWidget(windowLabel);
+  customlayout->addWidget(windowShape);
   setLayout(customlayout);
 }
\ No newline at end of file

From 206d899a5c94ce92f622134317a80573e5640ba1 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:06:33 -0400
Subject: [PATCH 48/76] minor tinkering

---
 rtxi-lfpRatiometer.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index d68f6d5..aeab38e 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -87,7 +87,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 {
   switch (flag) {
     case INIT:
-      period = RT::System::getInstance()->getPeriod() * 1e-9; // s
+      period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
       setParameter("Time Window (s)", sampling/N);
       setParameter("Sampling Rate (Hz)", period);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
@@ -126,7 +126,7 @@ void rtxilfpRatiometer::customizeGUI(void)
   windowShape->insertItem(2, "Hamming");
   QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
 
-  customlayout->addWidget(windowLabel);
-  customlayout->addWidget(windowShape);
+  customlayout->addWidget(windowLabel, 1, 0);
+  customlayout->addWidget(windowShape, 1, 1);
   setLayout(customlayout);
 }
\ No newline at end of file

From c044b67d7ef3cd10ec2862fc82611d835544b640 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:10:45 -0400
Subject: [PATCH 49/76] more minor tinkering

---
 rtxi-lfpRatiometer.cpp | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index aeab38e..64011bb 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -89,7 +89,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
     case INIT:
       period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
       setParameter("Time Window (s)", sampling/N);
-      setParameter("Sampling Rate (Hz)", period);
+      setParameter("Sampling Rate (Hz)", 1.0/period);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
       setParameter("LF Upper Bound", (double)10);
       setParameter("HF Lower Bound", (double)30);
@@ -120,13 +120,11 @@ void rtxilfpRatiometer::customizeGUI(void)
   QGridLayout* customlayout = DefaultGUIModel::getLayout();
 
   // adding dropdown menu for choosing FFT window shape
-  QLabel* windowLabel = new QLabel("FFT Window:");
   QComboBox* windowShape = new QComboBox;
   windowShape->insertItem(1, "Rectangular");
   windowShape->insertItem(2, "Hamming");
   QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
 
-  customlayout->addWidget(windowLabel, 1, 0);
-  customlayout->addWidget(windowShape, 1, 1);
+  customlayout->addWidget(windowShape, 2, 0);
   setLayout(customlayout);
 }
\ No newline at end of file

From 27cf77ed0261d141c8acccf877bdd8fa111d4470 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:16:01 -0400
Subject: [PATCH 50/76] setState used for sampling rate

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 64011bb..d4b3365 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -89,7 +89,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
     case INIT:
       period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
       setParameter("Time Window (s)", sampling/N);
-      setParameter("Sampling Rate (Hz)", 1.0/period);
+      setState("Sampling Rate (Hz)", 1.0/period);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
       setParameter("LF Upper Bound", (double)10);
       setParameter("HF Lower Bound", (double)30);

From 092616d55c664e326f924f532476b372ddf5dd0a Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:17:31 -0400
Subject: [PATCH 51/76] minor change

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index d4b3365..8af3e81 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -89,7 +89,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
     case INIT:
       period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
       setParameter("Time Window (s)", sampling/N);
-      setState("Sampling Rate (Hz)", 1.0/period);
+      setState("Sampling Rate (Hz)", ((double)1.0)/period);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
       setParameter("LF Upper Bound", (double)10);
       setParameter("HF Lower Bound", (double)30);

From cd26eef67d240a1c017e864324eaad1c8d8a85d6 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:21:16 -0400
Subject: [PATCH 52/76] minor changes

---
 rtxi-lfpRatiometer.cpp | 5 +++--
 rtxi-lfpRatiometer.h   | 4 +---
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 8af3e81..9f592f7 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -88,8 +88,9 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
   switch (flag) {
     case INIT:
       period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
+      sampling_freq = 1.0/period;
       setParameter("Time Window (s)", sampling/N);
-      setState("Sampling Rate (Hz)", ((double)1.0)/period);
+      setState("Sampling Rate (Hz)", sampling_freq);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
       setParameter("LF Upper Bound", (double)10);
       setParameter("HF Lower Bound", (double)30);
@@ -106,7 +107,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       break;
 
     case PERIOD:
-      period = RT::System::getInstance()->getPeriod() * 1e-9; // s
+      period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
       break;
 
     default:
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 5f794af..7e4990e 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -29,10 +29,8 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         virtual void update(DefaultGUIModel::update_flags_t);
 
     private:
-        // I want to get rid of these
-        double some_parameter;
-        double some_state;
         double period;
+        double sampling_freq;
         void initParameters();
 
         // default parameters for lfpRatiometer object

From 5b26ca5a574753db7ea585d40b5de30529ddf321 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:22:25 -0400
Subject: [PATCH 53/76] more minor changes

---
 rtxi-lfpRatiometer.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 9f592f7..39b97eb 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -78,8 +78,7 @@ void rtxilfpRatiometer::execute(void) {
 // RTXI function for initializing parameters
 void rtxilfpRatiometer::initParameters(void)
 {
-  some_parameter = 0;
-  some_state = 0;
+  
 }
 
 // update function (not running in real time)

From 9022ce0828e53da285e8ff6c8b993601b41108c9 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:32:47 -0400
Subject: [PATCH 54/76] minor changes

---
 rtxi-lfpRatiometer.cpp | 10 ++++++----
 rtxi-lfpRatiometer.h   |  2 +-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 39b97eb..5302a88 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -47,6 +47,8 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 // user defines time window length (in samples) and sampling rate
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
+period(((double)RT::System::getInstance()->getPeriod())),
+sampling(1.0/period),
 lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
@@ -78,7 +80,7 @@ void rtxilfpRatiometer::execute(void) {
 // RTXI function for initializing parameters
 void rtxilfpRatiometer::initParameters(void)
 {
-  
+
 }
 
 // update function (not running in real time)
@@ -86,10 +88,10 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 {
   switch (flag) {
     case INIT:
-      period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
-      sampling_freq = 1.0/period;
+      //period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
+      //sampling_freq = 1.0/period;
       setParameter("Time Window (s)", sampling/N);
-      setState("Sampling Rate (Hz)", sampling_freq);
+      setState("Sampling Rate (Hz)", sampling);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
       setParameter("LF Upper Bound", (double)10);
       setParameter("HF Lower Bound", (double)30);
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 7e4990e..f5be6e7 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -35,7 +35,7 @@ class rtxilfpRatiometer : public DefaultGUIModel {
 
         // default parameters for lfpRatiometer object
         int N = 2000;
-        double sampling = 2000;
+        double sampling;
 
         // lfpRatiometer object
         lfpRatiometer lfpratiometer;

From 63a9fc7ad2f515cb0d1ef7d4ec329af380566569 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:41:22 -0400
Subject: [PATCH 55/76] more tweaking

---
 rtxi-lfpRatiometer.cpp | 7 +++----
 rtxi-lfpRatiometer.h   | 6 +++---
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 5302a88..8745bc6 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -44,11 +44,12 @@ static DefaultGUIModel::variable_t vars[] = {
 static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 
 // defining what's in the object's constructor
-// user defines time window length (in samples) and sampling rate
+// sampling set by RT period, N set so that window is ~1 second
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
-period(((double)RT::System::getInstance()->getPeriod())),
+period(((double)RT::System::getInstance()->getPeriod())*1e-9),
 sampling(1.0/period),
+N(int(sampling)),
 lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
@@ -88,8 +89,6 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 {
   switch (flag) {
     case INIT:
-      //period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
-      //sampling_freq = 1.0/period;
       setParameter("Time Window (s)", sampling/N);
       setState("Sampling Rate (Hz)", sampling);
       setParameter("LF Lower Bound", (double)1); // need to amend where these come from
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index f5be6e7..1bba0f1 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -30,11 +30,11 @@ class rtxilfpRatiometer : public DefaultGUIModel {
 
     private:
         double period;
-        double sampling_freq;
         void initParameters();
 
-        // default parameters for lfpRatiometer object
-        int N = 2000;
+        // needed to initialize lfpratiometer object
+        // set based on RT period
+        int N;
         double sampling;
 
         // lfpRatiometer object

From e9e537580d1eefd153ba13c2e392873e9d470b62 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 20:48:02 -0400
Subject: [PATCH 56/76] small change

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 8745bc6..733e5e0 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -49,7 +49,7 @@ rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
 period(((double)RT::System::getInstance()->getPeriod())*1e-9),
 sampling(1.0/period),
-N(int(sampling)),
+N((int) (sampling)),
 lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");

From bf1119450e112f4f267118056a8e0407e9affc92 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 21:00:50 -0400
Subject: [PATCH 57/76] minor

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 733e5e0..a3f1512 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -49,7 +49,7 @@ rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
 period(((double)RT::System::getInstance()->getPeriod())*1e-9),
 sampling(1.0/period),
-N((int) (sampling)),
+N((int) floor(sampling)),
 lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");

From 7aedf9ef4cc0dbd6a553337c716977afb4dbb16d Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 21:04:48 -0400
Subject: [PATCH 58/76] minor ptII

---
 rtxi-lfpRatiometer.cpp | 1 -
 rtxi-lfpRatiometer.h   | 5 ++---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index a3f1512..cbe6e98 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -49,7 +49,6 @@ rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
 period(((double)RT::System::getInstance()->getPeriod())*1e-9),
 sampling(1.0/period),
-N((int) floor(sampling)),
 lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 1bba0f1..e4757d8 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -33,9 +33,8 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         void initParameters();
 
         // needed to initialize lfpratiometer object
-        // set based on RT period
-        int N;
-        double sampling;
+        int N = 1000; // initialized to 1000 samples
+        double sampling; // set based on RT period
 
         // lfpRatiometer object
         lfpRatiometer lfpratiometer;

From 7803d947b41c01785355172acb28d43951483c43 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 21:18:24 -0400
Subject: [PATCH 59/76] frequency bounds now taken from lfpratiometer object

---
 rtxi-lfpRatiometer.cpp | 21 ++++++++-------------
 rtxi-lfpRatiometer.h   |  3 +--
 2 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index cbe6e98..04ace40 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -47,14 +47,13 @@ static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 // sampling set by RT period, N set so that window is ~1 second
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
-period(((double)RT::System::getInstance()->getPeriod())*1e-9),
-sampling(1.0/period),
+period(((double)RT::System::getInstance()->getPeriod())*1e-9), // grabbing RT period
+sampling(1.0/period), // calculating RT sampling rate
 lfpratiometer(N, sampling) // constructing lfpRatiometer object
 {
     setWhatsThis("<p><b>lfpRatiometer:</b><br>Given an input, this module calculates the LF/HF ratio over a specified causal time window.</p>");
     DefaultGUIModel::createGUI(vars, num_vars);
     customizeGUI();
-    initParameters();
     update(INIT);
     refresh();
     QTimer::singleShot(0, this, SLOT(resizeMe()));
@@ -77,12 +76,6 @@ void rtxilfpRatiometer::execute(void) {
     
 }
 
-// RTXI function for initializing parameters
-void rtxilfpRatiometer::initParameters(void)
-{
-
-}
-
 // update function (not running in real time)
 void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 {
@@ -90,10 +83,12 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
     case INIT:
       setParameter("Time Window (s)", sampling/N);
       setState("Sampling Rate (Hz)", sampling);
-      setParameter("LF Lower Bound", (double)1); // need to amend where these come from
-      setParameter("LF Upper Bound", (double)10);
-      setParameter("HF Lower Bound", (double)30);
-      setParameter("HF Upper Bound", (double)90);
+      // get bounds from lfpratiometer object
+      std::vector<double> freqbounds = lfpratiometer.getFreqBounds();
+      setParameter("LF Lower Bound", freqbounds[0]); // need to amend where these come from
+      setParameter("LF Upper Bound", freqbounds[1]);
+      setParameter("HF Lower Bound", freqbounds[2]);
+      setParameter("HF Upper Bound", freqbounds[3]);
       break;
 
     case MODIFY:
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index e4757d8..9ff8051 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -30,10 +30,9 @@ class rtxilfpRatiometer : public DefaultGUIModel {
 
     private:
         double period;
-        void initParameters();
 
         // needed to initialize lfpratiometer object
-        int N = 1000; // initialized to 1000 samples
+        int N = 1000; // initialized to 1000 samples (1s for 1kHz sampling)
         double sampling; // set based on RT period
 
         // lfpRatiometer object

From 10eda76d712f29f0cd8b16d0fbc7e45dec419a17 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 22:09:28 -0400
Subject: [PATCH 60/76] stuff

---
 rtxi-lfpRatiometer.cpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 04ace40..e75ba2e 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -84,11 +84,11 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       setParameter("Time Window (s)", sampling/N);
       setState("Sampling Rate (Hz)", sampling);
       // get bounds from lfpratiometer object
-      std::vector<double> freqbounds = lfpratiometer.getFreqBounds();
-      setParameter("LF Lower Bound", freqbounds[0]); // need to amend where these come from
-      setParameter("LF Upper Bound", freqbounds[1]);
-      setParameter("HF Lower Bound", freqbounds[2]);
-      setParameter("HF Upper Bound", freqbounds[3]);
+      //std::vector<double> freqbounds = lfpratiometer.getFreqBounds();
+      setParameter("LF Lower Bound", lfpratiometer.getFreqBounds()[0]); // need to amend where these come from
+      setParameter("LF Upper Bound", lfpratiometer.getFreqBounds()[1]);
+      setParameter("HF Lower Bound", lfpratiometer.getFreqBounds()[2]);
+      setParameter("HF Upper Bound", lfpratiometer.getFreqBounds()[3]);
       break;
 
     case MODIFY:

From 9987b3ffafe7b862eaac65dfff8f458bb02caa29 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 22:26:48 -0400
Subject: [PATCH 61/76] minor change

---
 rtxi-lfpRatiometer.cpp | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index e75ba2e..d81512d 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -39,12 +39,16 @@ static DefaultGUIModel::variable_t vars[] = {
     "ratio", "Output LFP Power Ratio",
     DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
   },
+{
+   "debug var", "debug var",
+   DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
+}
 };
 
 static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
 
 // defining what's in the object's constructor
-// sampling set by RT period, N set so that window is ~1 second
+// sampling set by RT period
 rtxilfpRatiometer::rtxilfpRatiometer(void) :
 DefaultGUIModel("lfpRatiometer with Custom GUI", ::vars, ::num_vars),
 period(((double)RT::System::getInstance()->getPeriod())*1e-9), // grabbing RT period
@@ -84,8 +88,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       setParameter("Time Window (s)", sampling/N);
       setState("Sampling Rate (Hz)", sampling);
       // get bounds from lfpratiometer object
-      //std::vector<double> freqbounds = lfpratiometer.getFreqBounds();
-      setParameter("LF Lower Bound", lfpratiometer.getFreqBounds()[0]); // need to amend where these come from
+      setParameter("LF Lower Bound", lfpratiometer.getFreqBounds()[0]);
       setParameter("LF Upper Bound", lfpratiometer.getFreqBounds()[1]);
       setParameter("HF Lower Bound", lfpratiometer.getFreqBounds()[2]);
       setParameter("HF Upper Bound", lfpratiometer.getFreqBounds()[3]);
@@ -118,7 +121,7 @@ void rtxilfpRatiometer::customizeGUI(void)
   QComboBox* windowShape = new QComboBox;
   windowShape->insertItem(1, "Rectangular");
   windowShape->insertItem(2, "Hamming");
-  QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
+  //QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
 
   customlayout->addWidget(windowShape, 2, 0);
   setLayout(customlayout);

From cd8211475f2b1088c5f006a2b9adb625ba15a01a Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 22:48:06 -0400
Subject: [PATCH 62/76] adding MODIFY instructions

---
 rtxi-lfpRatiometer.cpp | 27 ++++++++++++++++++++++++++-
 rtxi-lfpRatiometer.h   |  3 +++
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index d81512d..999b421 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -92,9 +92,35 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       setParameter("LF Upper Bound", lfpratiometer.getFreqBounds()[1]);
       setParameter("HF Lower Bound", lfpratiometer.getFreqBounds()[2]);
       setParameter("HF Upper Bound", lfpratiometer.getFreqBounds()[3]);
+
+      setParameter("debug var", window_tracker_dummy)
       break;
 
     case MODIFY:
+      // defining parameters needed for constructor
+      sampling = getParameter("Sampling Rate (Hz)").toDouble();
+      N = (int) (getParameter("Time Window (s)").toDouble() * sampling);
+
+      // reconstructing lfpratiometer object...LEGAL??
+      lfpratiometer(N, sampling);
+
+      // setting frequency bounds based on user input
+      lfpratiometer.setRatioParams(getParameter("LF Lower Bound").toDouble(),
+          getParameter("LF Upper Bound").toDouble(),
+          getParameter("HF Lower Bound").toDouble(),
+          getParameter("HF Upper Bound").toDouble());
+      
+      // setting DFT windowing function choice
+      if (windowShape->currentIndex() == 1) {
+        lfpratiometer.window_rect();
+      }
+      else if (windowShape->currentIndex() == 2) {
+        lfpratiometer.window_hamming();
+      }
+
+      // clearing time series
+      lfpratiometer.clrTimeSeries();
+
       break;
 
     case UNPAUSE:
@@ -121,7 +147,6 @@ void rtxilfpRatiometer::customizeGUI(void)
   QComboBox* windowShape = new QComboBox;
   windowShape->insertItem(1, "Rectangular");
   windowShape->insertItem(2, "Hamming");
-  //QObject::connect(windowShape, SIGNAL(activated(int)), this, SLOT(updateWindow(int)));
 
   customlayout->addWidget(windowShape, 2, 0);
   setLayout(customlayout);
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 9ff8051..06e1ce8 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -38,6 +38,9 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         // lfpRatiometer object
         lfpRatiometer lfpratiometer;
 
+        // window tracking var
+        int window_tracker_dummy = 0;
+
 };
 
 

From 9c30c340097ab9659276a2375e6978caba50cf39 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 22:49:48 -0400
Subject: [PATCH 63/76] minor changes

---
 rtxi-lfpRatiometer.cpp | 2 +-
 rtxi-lfpRatiometer.h   | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 999b421..677d602 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -93,7 +93,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       setParameter("HF Lower Bound", lfpratiometer.getFreqBounds()[2]);
       setParameter("HF Upper Bound", lfpratiometer.getFreqBounds()[3]);
 
-      setParameter("debug var", window_tracker_dummy)
+      setParameter("debug var", window_tracker_dummy);
       break;
 
     case MODIFY:
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 06e1ce8..d5b2d0f 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -38,6 +38,9 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         // lfpRatiometer object
         lfpRatiometer lfpratiometer;
 
+        // variables for GUI
+        QComboBox* windowShape;
+
         // window tracking var
         int window_tracker_dummy = 0;
 

From 891e6183e9e55e8866c1587d9090d3504c356d09 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:12:48 -0400
Subject: [PATCH 64/76] using lfpRatiometer's new changeFFTPlan method

---
 rtxi-lfpRatiometer.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 677d602..5a9a015 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -101,8 +101,8 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       sampling = getParameter("Sampling Rate (Hz)").toDouble();
       N = (int) (getParameter("Time Window (s)").toDouble() * sampling);
 
-      // reconstructing lfpratiometer object...LEGAL??
-      lfpratiometer(N, sampling);
+      // making new FFT plan
+      lfpratiometer.changeFFTPlan(N, sampling);
 
       // setting frequency bounds based on user input
       lfpratiometer.setRatioParams(getParameter("LF Lower Bound").toDouble(),
@@ -144,7 +144,7 @@ void rtxilfpRatiometer::customizeGUI(void)
   QGridLayout* customlayout = DefaultGUIModel::getLayout();
 
   // adding dropdown menu for choosing FFT window shape
-  QComboBox* windowShape = new QComboBox;
+  windowShape = new QComboBox;
   windowShape->insertItem(1, "Rectangular");
   windowShape->insertItem(2, "Hamming");
 

From dc4daede9cc2f4e41c221dc7c15158b0f209853c Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:14:18 -0400
Subject: [PATCH 65/76] debugging tracker

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 5a9a015..d04c8bb 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -41,7 +41,7 @@ static DefaultGUIModel::variable_t vars[] = {
   },
 {
    "debug var", "debug var",
-   DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
+   DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
 }
 };
 

From 41cad51a142082e39b044421c9862b5bc209f472 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:17:39 -0400
Subject: [PATCH 66/76] some debugging trackers

---
 rtxi-lfpRatiometer.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index d04c8bb..698d825 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -113,14 +113,19 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       // setting DFT windowing function choice
       if (windowShape->currentIndex() == 1) {
         lfpratiometer.window_rect();
+        window_tracker_dummy = 1;
       }
       else if (windowShape->currentIndex() == 2) {
         lfpratiometer.window_hamming();
+        window_tracker_dummy = 2;
       }
 
       // clearing time series
       lfpratiometer.clrTimeSeries();
 
+      // modifying states on GUI
+      setState("Sampling Rate (Hz)", sampling);
+
       break;
 
     case UNPAUSE:

From d98e8d39c480abe7aea89ba186dbcc489670ca16 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:20:41 -0400
Subject: [PATCH 67/76] debuggin

---
 rtxi-lfpRatiometer.cpp | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 698d825..c991128 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -98,7 +98,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 
     case MODIFY:
       // defining parameters needed for constructor
-      sampling = getParameter("Sampling Rate (Hz)").toDouble();
+      sampling = getState("Sampling Rate (Hz)").toDouble();
       N = (int) (getParameter("Time Window (s)").toDouble() * sampling);
 
       // making new FFT plan
@@ -123,9 +123,6 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       // clearing time series
       lfpratiometer.clrTimeSeries();
 
-      // modifying states on GUI
-      setState("Sampling Rate (Hz)", sampling);
-
       break;
 
     case UNPAUSE:

From 985cccb0b26b52ced534836249cbf977608434e3 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:23:13 -0400
Subject: [PATCH 68/76] more debuggin

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index c991128..6168454 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -98,7 +98,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 
     case MODIFY:
       // defining parameters needed for constructor
-      sampling = getState("Sampling Rate (Hz)").toDouble();
+      sampling = ((double)RT::System::getInstance()->getPeriod())*1e-9;
       N = (int) (getParameter("Time Window (s)").toDouble() * sampling);
 
       // making new FFT plan

From 2071bc79af76c06ea6abb5eeb606a94485837f72 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:28:12 -0400
Subject: [PATCH 69/76] more debugging

---
 rtxi-lfpRatiometer.cpp | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 6168454..180eac3 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -98,7 +98,9 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
 
     case MODIFY:
       // defining parameters needed for constructor
-      sampling = ((double)RT::System::getInstance()->getPeriod())*1e-9;
+      period = ((double)RT::System::getInstance()->getPeriod())*1e-9;
+      sampling = 1.0/period;
+      setState("Sampling Rate (Hz)", sampling); // updating GUI
       N = (int) (getParameter("Time Window (s)").toDouble() * sampling);
 
       // making new FFT plan
@@ -123,6 +125,9 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       // clearing time series
       lfpratiometer.clrTimeSeries();
 
+      // tracking dummy variable
+      setParameter("debug var", window_tracker_dummy);
+
       break;
 
     case UNPAUSE:

From aa7672da1439a6a08e5f2253cb658eafa8b190d6 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:33:21 -0400
Subject: [PATCH 70/76] debugging

---
 rtxi-lfpRatiometer.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 180eac3..123f203 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -113,11 +113,12 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
           getParameter("HF Upper Bound").toDouble());
       
       // setting DFT windowing function choice
-      if (windowShape->currentIndex() == 1) {
+      const int dropindex = windowShape->currentIndex();
+      if (dropindex == 1) {
         lfpratiometer.window_rect();
         window_tracker_dummy = 1;
       }
-      else if (windowShape->currentIndex() == 2) {
+      else if (dropindex == 2) {
         lfpratiometer.window_hamming();
         window_tracker_dummy = 2;
       }
@@ -126,7 +127,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       lfpratiometer.clrTimeSeries();
 
       // tracking dummy variable
-      setParameter("debug var", window_tracker_dummy);
+      setParameter("debug var", dropindex);
 
       break;
 

From efcc8c6a55cbaab1d282c1e5a8f11e82e0f010bc Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:34:43 -0400
Subject: [PATCH 71/76] debugging

---
 rtxi-lfpRatiometer.cpp | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 123f203..0306e04 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -113,12 +113,11 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
           getParameter("HF Upper Bound").toDouble());
       
       // setting DFT windowing function choice
-      const int dropindex = windowShape->currentIndex();
-      if (dropindex == 1) {
+      if (windowShape->currentIndex() == 1) {
         lfpratiometer.window_rect();
         window_tracker_dummy = 1;
       }
-      else if (dropindex == 2) {
+      else if (windowShape->currentIndex() == 2) {
         lfpratiometer.window_hamming();
         window_tracker_dummy = 2;
       }
@@ -127,7 +126,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       lfpratiometer.clrTimeSeries();
 
       // tracking dummy variable
-      setParameter("debug var", dropindex);
+      setParameter("debug var", windowShape->currentIndex());
 
       break;
 

From f6f6aeb78ac65287d2a34bd9e5a12305576f0acf Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:36:37 -0400
Subject: [PATCH 72/76] debugging

---
 rtxi-lfpRatiometer.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 0306e04..73006ec 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -113,11 +113,11 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
           getParameter("HF Upper Bound").toDouble());
       
       // setting DFT windowing function choice
-      if (windowShape->currentIndex() == 1) {
+      if (windowShape->currentIndex() == 0) {
         lfpratiometer.window_rect();
         window_tracker_dummy = 1;
       }
-      else if (windowShape->currentIndex() == 2) {
+      else if (windowShape->currentIndex() == 1) {
         lfpratiometer.window_hamming();
         window_tracker_dummy = 2;
       }
@@ -126,7 +126,7 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       lfpratiometer.clrTimeSeries();
 
       // tracking dummy variable
-      setParameter("debug var", windowShape->currentIndex());
+      setParameter("debug var", window_tracker_dummy);
 
       break;
 

From d420303a90cb825943a832ce68232e119d9e27d4 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:44:56 -0400
Subject: [PATCH 73/76] final changes 3.30.2021

---
 rtxi-lfpRatiometer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 73006ec..9b48831 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -134,10 +134,10 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       break;
 
     case PAUSE:
+      lfpratiometer.clrTimeSeries();
       break;
 
     case PERIOD:
-      period = ((double)RT::System::getInstance()->getPeriod()) * 1e-9; // s
       break;
 
     default:

From 0c66572b337f31745a380fbf0d56b9c60038278d Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Tue, 30 Mar 2021 23:46:16 -0400
Subject: [PATCH 74/76] final changes 3.30.2021

---
 rtxi-lfpRatiometer.cpp | 15 ++++-----------
 rtxi-lfpRatiometer.h   |  3 ---
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 9b48831..6737314 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -39,10 +39,10 @@ static DefaultGUIModel::variable_t vars[] = {
     "ratio", "Output LFP Power Ratio",
     DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
   },
-{
-   "debug var", "debug var",
-   DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
-}
+// {
+//    "debug var", "debug var",
+//    DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
+// }
 };
 
 static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
@@ -92,8 +92,6 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       setParameter("LF Upper Bound", lfpratiometer.getFreqBounds()[1]);
       setParameter("HF Lower Bound", lfpratiometer.getFreqBounds()[2]);
       setParameter("HF Upper Bound", lfpratiometer.getFreqBounds()[3]);
-
-      setParameter("debug var", window_tracker_dummy);
       break;
 
     case MODIFY:
@@ -115,19 +113,14 @@ void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
       // setting DFT windowing function choice
       if (windowShape->currentIndex() == 0) {
         lfpratiometer.window_rect();
-        window_tracker_dummy = 1;
       }
       else if (windowShape->currentIndex() == 1) {
         lfpratiometer.window_hamming();
-        window_tracker_dummy = 2;
       }
 
       // clearing time series
       lfpratiometer.clrTimeSeries();
 
-      // tracking dummy variable
-      setParameter("debug var", window_tracker_dummy);
-
       break;
 
     case UNPAUSE:
diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index d5b2d0f..8d3c5bc 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -41,9 +41,6 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         // variables for GUI
         QComboBox* windowShape;
 
-        // window tracking var
-        int window_tracker_dummy = 0;
-
 };
 
 

From 6402b541224375eda2eb90c0db18b25fc38c9dd3 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Wed, 31 Mar 2021 00:02:46 -0400
Subject: [PATCH 75/76] final changes 3.30.2021

---
 rtxi-lfpRatiometer.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtxi-lfpRatiometer.h b/rtxi-lfpRatiometer.h
index 8d3c5bc..e0f684b 100644
--- a/rtxi-lfpRatiometer.h
+++ b/rtxi-lfpRatiometer.h
@@ -29,10 +29,10 @@ class rtxilfpRatiometer : public DefaultGUIModel {
         virtual void update(DefaultGUIModel::update_flags_t);
 
     private:
-        double period;
 
         // needed to initialize lfpratiometer object
         int N = 1000; // initialized to 1000 samples (1s for 1kHz sampling)
+        double period; // set from RT period
         double sampling; // set based on RT period
 
         // lfpRatiometer object

From 10a3c6adc7b654252a0c85a4254045c58bd3e987 Mon Sep 17 00:00:00 2001
From: Adriano Borsa <aborsa@gatech.edu>
Date: Mon, 3 May 2021 20:30:22 -0400
Subject: [PATCH 76/76] added outputs to track LF & HF power, separately

---
 rtxi-lfpRatiometer.cpp | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/rtxi-lfpRatiometer.cpp b/rtxi-lfpRatiometer.cpp
index 6737314..8e0c68d 100644
--- a/rtxi-lfpRatiometer.cpp
+++ b/rtxi-lfpRatiometer.cpp
@@ -39,10 +39,14 @@ static DefaultGUIModel::variable_t vars[] = {
     "ratio", "Output LFP Power Ratio",
     DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
   },
-// {
-//    "debug var", "debug var",
-//    DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE,
-// }
+{
+    "LF Power", "Power in LF Band",
+    DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
+  },
+{
+    "HF Power", "Power in HF Band",
+    DefaultGUIModel::OUTPUT | DefaultGUIModel::DOUBLE,
+  }
 };
 
 static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);
@@ -77,6 +81,8 @@ void rtxilfpRatiometer::execute(void) {
 
   // put the LF/HF ratio into the output
   output(0) = lfpratiometer.getRatio();
+  output(1) = lfpratiometer.getLFpower();
+  output(2) = lfpratiometer.getHFpower();
     
 }