Rtxi plugin

Makefile

@@ -1,10 +1,33 @@
-CXX=g++
-CXX_FLAGS=-std=c++11 -Iinclude
+PLUGIN_NAME = rtxilfpRatiometer
 
-LD_FLAGS=-lfftw3 -lm
+HEADERS = rtxi-lfpRatiometer.h
 
-all: build/lfpRatiometer.o
-	$(CXX) $(CXX_FLAGS) -o build/test src/main.cpp build/lfpRatiometer.o $(LD_FLAGS)
+SOURCES = rtxi-lfpRatiometer.cpp \
+			moc_rtxi-lfpRatiometer.cpp
 
-build/lfpRatiometer.o:
-	$(CXX) $(CXX_FLAGS) -o build/lfpRatiometer.o -c src/lfpRatiometer.cpp
+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)
+
+# 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
+
+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
+include Makefile.plugin_compile
+
+print-% : ; @echo $* = $($*)
+
+cleanrtxi :
+		sudo rm -rf /usr/local/lib/rtxi/$(PLUGIN_NAME).*

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 $@ $<

rtxi-lfpRatiometer.cpp

@@ -0,0 +1,159 @@
+#include <rtxi-lfpRatiometer.h>
+
+using namespace std;
+
+extern "C" Plugin::Object *createRTXIPlugin(void){
+    return new rtxilfpRatiometer();
+}
+
+static DefaultGUIModel::variable_t vars[] = {
+{ 
+  "Time Window (s)", "Time Window (s)", 
+  DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE
+  },
+{ 
+  "Sampling Rate (Hz)", "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,
+  },
+{
+    "ratio", "Output LFP Power Ratio",
+    DefaultGUIModel::OUTPUT | 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);
+
+// defining what's in the object's constructor
+// 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
+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();
+    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(void) {
+
+  // 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();
+  output(1) = lfpratiometer.getLFpower();
+  output(2) = lfpratiometer.getHFpower();
+
+}
+
+// update function (not running in real time)
+void rtxilfpRatiometer::update(DefaultGUIModel::update_flags_t flag)
+{
+  switch (flag) {
+    case INIT:
+      setParameter("Time Window (s)", sampling/N);
+      setState("Sampling Rate (Hz)", sampling);
+      // get bounds from lfpratiometer object
+      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]);
+      break;
+
+    case MODIFY:
+      // defining parameters needed for constructor
+      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
+      lfpratiometer.changeFFTPlan(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() == 0) {
+        lfpratiometer.window_rect();
+      }
+      else if (windowShape->currentIndex() == 1) {
+        lfpratiometer.window_hamming();
+      }
+
+      // clearing time series
+      lfpratiometer.clrTimeSeries();
+
+      break;
+
+    case UNPAUSE:
+      break;
+
+    case PAUSE:
+      lfpratiometer.clrTimeSeries();
+      break;
+
+    case PERIOD:
+      break;
+
+    default:
+      break;
+  }
+}
+
+// RTXI's customizeGUI function
+void rtxilfpRatiometer::customizeGUI(void)
+{
+  QGridLayout* customlayout = DefaultGUIModel::getLayout();
+
+  // adding dropdown menu for choosing FFT window shape
+  windowShape = new QComboBox;
+  windowShape->insertItem(1, "Rectangular");
+  windowShape->insertItem(2, "Hamming");
+
+  customlayout->addWidget(windowShape, 2, 0);
+  setLayout(customlayout);
+}

rtxi-lfpRatiometer.h

@@ -0,0 +1,47 @@
+#ifndef RTXILFPRATIOMETER_H
+#define RTXILFPRATIOMETER_H
+
+#include <default_gui_model.h>
+#include <main_window.h>
+#include <lfpRatiometer>
+
+class rtxilfpRatiometer : public DefaultGUIModel {
+
+    Q_OBJECT
+
+    public:
+        // constructor
+        rtxilfpRatiometer(void);
+
+        // destructor
+        virtual ~rtxilfpRatiometer(void);
+
+        // execute
+        void execute(void);
+
+        // functions to make GUI
+        void createGUI(DefaultGUIModel::variable_t*, int);
+        void customizeGUI(void);
+
+    protected:
+
+        // update function
+        virtual void update(DefaultGUIModel::update_flags_t);
+
+    private:
+
+        // 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
+        lfpRatiometer lfpratiometer;
+
+        // variables for GUI
+        QComboBox* windowShape;
+
+};
+
+
+#endif