Merge Champalimaud updates

Builds/Linux/Makefile

@@ -20,7 +20,7 @@ ifeq ($(CONFIG),Debug)
   CPPFLAGS := $(DEPFLAGS) -D "LINUX=1" -D "DEBUG=1" -D "_DEBUG=1" -D "JUCER_LINUX_MAKE_7346DA2A=1" -I "/usr/include" -I "/usr/include/freetype2"
   CFLAGS += $(CPPFLAGS) $(TARGET_ARCH) -g -ggdb -O0
   CXXFLAGS += $(CFLAGS) -export-dynamic -g -pg
-  LDFLAGS += -L$(BINDIR) -L$(LIBDIR) -L"/usr/X11R6/lib/" -L"../../JuceLibraryCode/bin" -lfreetype -lpthread -lrt -lX11 -lGL -lGLU -lXinerama -lasound -lftdi -lftgl -pg  -ldl -lXext
+  LDFLAGS += -L$(BINDIR) -L$(LIBDIR) -L"/usr/X11R6/lib/" -L"../../JuceLibraryCode/bin" -lfreetype -lpthread -lrt -lX11 -lGL -lGLU -lXinerama -lasound -lftdi -lftgl -pg -ldl -lXext
   LDDEPS :=
   RESFLAGS :=  -D "LINUX=1" -D "DEBUG=1" -D "_DEBUG=1" -D "JUCER_LINUX_MAKE_7346DA2A=1" -I "/usr/include" -I "/usr/include/freetype2"
   TARGET := open-ephys
@@ -35,7 +35,7 @@ ifeq ($(CONFIG),Release)
   CPPFLAGS := $(DEPFLAGS) -D "LINUX=1" -D "NDEBUG=1" -D "JUCER_LINUX_MAKE_7346DA2A=1" -I "/usr/include" -I "/usr/include/freetype2"
   CFLAGS += $(CPPFLAGS) $(TARGET_ARCH) -O3
   CXXFLAGS += $(CFLAGS) -export-dynamic -g -pg
-  LDFLAGS += -L$(BINDIR) -L$(LIBDIR) -L"/usr/X11R6/lib/" -L"../../JuceLibraryCode/bin" -lfreetype -lpthread -lrt -lX11 -lGL -lGLU -lXinerama -lasound -lftdi -lftgl -pg
+  LDFLAGS += -L$(BINDIR) -L$(LIBDIR) -L"/usr/X11R6/lib/" -L"../../JuceLibraryCode/bin" -lfreetype -lpthread -lrt -lX11 -lGL -lGLU -lXinerama -lasound -lftdi -lftgl -pg -ldl -lXext
   LDDEPS :=
   RESFLAGS :=  -D "LINUX=1" -D "NDEBUG=1" -D "JUCER_LINUX_MAKE_7346DA2A=1" -I "/usr/include" -I "/usr/include/freetype2"
   TARGET := open-ephys
@@ -63,6 +63,10 @@ OBJECTS := \
   $(OBJDIR)/RootFinder_239a995f.o \
   $(OBJDIR)/State_22979684.o \
   $(OBJDIR)/AudioComponent_521bd9c9.o \
+  $(OBJDIR)/FPGAOutput_73b5ffd4.o \
+  $(OBJDIR)/EventDetector_4807aa7b.o \
+  $(OBJDIR)/ofArduino_12f202a5.o \
+  $(OBJDIR)/ofSerial_c3b0a9e1.o \
   $(OBJDIR)/ArduinoOutput_391e90c4.o \
   $(OBJDIR)/Parameter_ae008024.o \
   $(OBJDIR)/SpikeDisplayNode_9c52e4ad.o \
@@ -70,13 +74,11 @@ OBJECTS := \
   $(OBJDIR)/LfpDisplayNode_30ef22fd.o \
   $(OBJDIR)/Merger_2f90542e.o \
   $(OBJDIR)/Splitter_6e27a57b.o \
-  $(OBJDIR)/StereotrodePlot_4710b8f1.o \
-  $(OBJDIR)/ElectrodePlot_7a206ec4.o \
+  $(OBJDIR)/SpikePlot_c1cf98bd.o \
   $(OBJDIR)/BaseUIElement_ec903c4d.o \
   $(OBJDIR)/GenericAxes_d802ed92.o \
   $(OBJDIR)/PlotUtils_9ef52686.o \
   $(OBJDIR)/ProjectionAxes_7c67c3e8.o \
-  $(OBJDIR)/TetrodePlot_b42fd798.o \
   $(OBJDIR)/WaveAxes_8adc45d2.o \
   $(OBJDIR)/SpikeObject_24e8c655.o \
   $(OBJDIR)/SpikeDisplayCanvas_b208ff6e.o \
@@ -249,6 +251,26 @@ $(OBJDIR)/AudioComponent_521bd9c9.o: ../../Source/Audio/AudioComponent.cpp
 	@echo "Compiling AudioComponent.cpp"
 	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
 
+$(OBJDIR)/FPGAOutput_73b5ffd4.o: ../../Source/Processors/FPGAOutput.cpp
+	-@mkdir -p $(OBJDIR)
+	@echo "Compiling FPGAOutput.cpp"
+	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
+
+$(OBJDIR)/EventDetector_4807aa7b.o: ../../Source/Processors/EventDetector.cpp
+	-@mkdir -p $(OBJDIR)
+	@echo "Compiling EventDetector.cpp"
+	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
+
+$(OBJDIR)/ofArduino_12f202a5.o: ../../Source/Processors/Serial/ofArduino.cpp
+	-@mkdir -p $(OBJDIR)
+	@echo "Compiling ofArduino.cpp"
+	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
+
+$(OBJDIR)/ofSerial_c3b0a9e1.o: ../../Source/Processors/Serial/ofSerial.cpp
+	-@mkdir -p $(OBJDIR)
+	@echo "Compiling ofSerial.cpp"
+	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
+
 $(OBJDIR)/ArduinoOutput_391e90c4.o: ../../Source/Processors/ArduinoOutput.cpp
 	-@mkdir -p $(OBJDIR)
 	@echo "Compiling ArduinoOutput.cpp"
@@ -284,14 +306,9 @@ $(OBJDIR)/Splitter_6e27a57b.o: ../../Source/Processors/Utilities/Splitter.cpp
 	@echo "Compiling Splitter.cpp"
 	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
 
-$(OBJDIR)/StereotrodePlot_4710b8f1.o: ../../Source/Processors/Visualization/SpikePlotting/StereotrodePlot.cpp
+$(OBJDIR)/SpikePlot_c1cf98bd.o: ../../Source/Processors/Visualization/SpikePlotting/SpikePlot.cpp
 	-@mkdir -p $(OBJDIR)
-	@echo "Compiling StereotrodePlot.cpp"
-	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
-
-$(OBJDIR)/ElectrodePlot_7a206ec4.o: ../../Source/Processors/Visualization/SpikePlotting/ElectrodePlot.cpp
-	-@mkdir -p $(OBJDIR)
-	@echo "Compiling ElectrodePlot.cpp"
+	@echo "Compiling SpikePlot.cpp"
 	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
 
 $(OBJDIR)/BaseUIElement_ec903c4d.o: ../../Source/Processors/Visualization/SpikePlotting/BaseUIElement.cpp
@@ -314,11 +331,6 @@ $(OBJDIR)/ProjectionAxes_7c67c3e8.o: ../../Source/Processors/Visualization/Spike
 	@echo "Compiling ProjectionAxes.cpp"
 	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
 
-$(OBJDIR)/TetrodePlot_b42fd798.o: ../../Source/Processors/Visualization/SpikePlotting/TetrodePlot.cpp
-	-@mkdir -p $(OBJDIR)
-	@echo "Compiling TetrodePlot.cpp"
-	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
-
 $(OBJDIR)/WaveAxes_8adc45d2.o: ../../Source/Processors/Visualization/SpikePlotting/WaveAxes.cpp
 	-@mkdir -p $(OBJDIR)
 	@echo "Compiling WaveAxes.cpp"

Builds/VisualStudio2010/open-ephys.vcxproj

@@ -142,6 +142,10 @@
     <ClCompile Include="..\..\Source\Dsp\RootFinder.cpp"/>
     <ClCompile Include="..\..\Source\Dsp\State.cpp"/>
     <ClCompile Include="..\..\Source\Audio\AudioComponent.cpp"/>
+    <ClCompile Include="..\..\Source\Processors\FPGAOutput.cpp"/>
+    <ClCompile Include="..\..\Source\Processors\EventDetector.cpp"/>
+    <ClCompile Include="..\..\Source\Processors\Serial\ofArduino.cpp"/>
+    <ClCompile Include="..\..\Source\Processors\Serial\ofSerial.cpp"/>
     <ClCompile Include="..\..\Source\Processors\ArduinoOutput.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Parameter.cpp"/>
     <ClCompile Include="..\..\Source\Processors\SpikeDisplayNode.cpp"/>
@@ -149,13 +153,11 @@
     <ClCompile Include="..\..\Source\Processors\LfpDisplayNode.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Utilities\Merger.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Utilities\Splitter.cpp"/>
-    <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\StereotrodePlot.cpp"/>
-    <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\ElectrodePlot.cpp"/>
+    <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\SpikePlot.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\BaseUIElement.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\GenericAxes.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\PlotUtils.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\ProjectionAxes.cpp"/>
-    <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\TetrodePlot.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\WaveAxes.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikeObject.cpp"/>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikeDisplayCanvas.cpp"/>
@@ -240,6 +242,11 @@
     <ClInclude Include="..\..\Source\Dsp\Types.h"/>
     <ClInclude Include="..\..\Source\Dsp\Utilities.h"/>
     <ClInclude Include="..\..\Source\Audio\AudioComponent.h"/>
+    <ClInclude Include="..\..\Source\Processors\FPGAOutput.h"/>
+    <ClInclude Include="..\..\Source\Processors\EventDetector.h"/>
+    <ClInclude Include="..\..\Source\Processors\Serial\ofArduino.h"/>
+    <ClInclude Include="..\..\Source\Processors\Serial\ofConstants.h"/>
+    <ClInclude Include="..\..\Source\Processors\Serial\ofSerial.h"/>
     <ClInclude Include="..\..\Source\Processors\ArduinoOutput.h"/>
     <ClInclude Include="..\..\Source\Processors\Parameter.h"/>
     <ClInclude Include="..\..\Source\Processors\SpikeDisplayNode.h"/>
@@ -247,14 +254,12 @@
     <ClInclude Include="..\..\Source\Processors\LfpDisplayNode.h"/>
     <ClInclude Include="..\..\Source\Processors\Utilities\Merger.h"/>
     <ClInclude Include="..\..\Source\Processors\Utilities\Splitter.h"/>
-    <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\StereotrodePlot.h"/>
-    <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\ElectrodePlot.h"/>
+    <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\SpikePlot.h"/>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\BaseUIElement.h"/>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\GenericAxes.h"/>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\PlotUtils.h"/>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\ProjectionAxes.h"/>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\SimpleKeyEvent.h"/>
-    <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\TetrodePlot.h"/>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\WaveAxes.h"/>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikeObject.h"/>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikeDisplayCanvas.h"/>

Builds/VisualStudio2010/open-ephys.vcxproj.filters

@@ -38,6 +38,9 @@
     <Filter Include="open-ephys\Source\Processors">
       <UniqueIdentifier>{3B2598F1-7B02-E3D4-A09B-367B20D97672}</UniqueIdentifier>
     </Filter>
+    <Filter Include="open-ephys\Source\Processors\Serial">
+      <UniqueIdentifier>{BE825C10-A046-0824-C18C-358D08C18D78}</UniqueIdentifier>
+    </Filter>
     <Filter Include="open-ephys\Source\Processors\Utilities">
       <UniqueIdentifier>{A81F416A-5186-4D5E-E159-A4E41A74C9AB}</UniqueIdentifier>
     </Filter>
@@ -283,6 +286,18 @@
     <ClCompile Include="..\..\Source\Audio\AudioComponent.cpp">
       <Filter>open-ephys\Source\Audio</Filter>
     </ClCompile>
+    <ClCompile Include="..\..\Source\Processors\FPGAOutput.cpp">
+      <Filter>open-ephys\Source\Processors</Filter>
+    </ClCompile>
+    <ClCompile Include="..\..\Source\Processors\EventDetector.cpp">
+      <Filter>open-ephys\Source\Processors</Filter>
+    </ClCompile>
+    <ClCompile Include="..\..\Source\Processors\Serial\ofArduino.cpp">
+      <Filter>open-ephys\Source\Processors\Serial</Filter>
+    </ClCompile>
+    <ClCompile Include="..\..\Source\Processors\Serial\ofSerial.cpp">
+      <Filter>open-ephys\Source\Processors\Serial</Filter>
+    </ClCompile>
     <ClCompile Include="..\..\Source\Processors\ArduinoOutput.cpp">
       <Filter>open-ephys\Source\Processors</Filter>
     </ClCompile>
@@ -304,10 +319,7 @@
     <ClCompile Include="..\..\Source\Processors\Utilities\Splitter.cpp">
       <Filter>open-ephys\Source\Processors\Utilities</Filter>
     </ClCompile>
-    <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\StereotrodePlot.cpp">
-      <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
-    </ClCompile>
-    <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\ElectrodePlot.cpp">
+    <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\SpikePlot.cpp">
       <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
     </ClCompile>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\BaseUIElement.cpp">
@@ -322,9 +334,6 @@
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\ProjectionAxes.cpp">
       <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
     </ClCompile>
-    <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\TetrodePlot.cpp">
-      <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
-    </ClCompile>
     <ClCompile Include="..\..\Source\Processors\Visualization\SpikePlotting\WaveAxes.cpp">
       <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
     </ClCompile>
@@ -573,6 +582,21 @@
     <ClInclude Include="..\..\Source\Audio\AudioComponent.h">
       <Filter>open-ephys\Source\Audio</Filter>
     </ClInclude>
+    <ClInclude Include="..\..\Source\Processors\FPGAOutput.h">
+      <Filter>open-ephys\Source\Processors</Filter>
+    </ClInclude>
+    <ClInclude Include="..\..\Source\Processors\EventDetector.h">
+      <Filter>open-ephys\Source\Processors</Filter>
+    </ClInclude>
+    <ClInclude Include="..\..\Source\Processors\Serial\ofArduino.h">
+      <Filter>open-ephys\Source\Processors\Serial</Filter>
+    </ClInclude>
+    <ClInclude Include="..\..\Source\Processors\Serial\ofConstants.h">
+      <Filter>open-ephys\Source\Processors\Serial</Filter>
+    </ClInclude>
+    <ClInclude Include="..\..\Source\Processors\Serial\ofSerial.h">
+      <Filter>open-ephys\Source\Processors\Serial</Filter>
+    </ClInclude>
     <ClInclude Include="..\..\Source\Processors\ArduinoOutput.h">
       <Filter>open-ephys\Source\Processors</Filter>
     </ClInclude>
@@ -594,10 +618,7 @@
     <ClInclude Include="..\..\Source\Processors\Utilities\Splitter.h">
       <Filter>open-ephys\Source\Processors\Utilities</Filter>
     </ClInclude>
-    <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\StereotrodePlot.h">
-      <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
-    </ClInclude>
-    <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\ElectrodePlot.h">
+    <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\SpikePlot.h">
       <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
     </ClInclude>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\BaseUIElement.h">
@@ -615,9 +636,6 @@
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\SimpleKeyEvent.h">
       <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
     </ClInclude>
-    <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\TetrodePlot.h">
-      <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
-    </ClInclude>
     <ClInclude Include="..\..\Source\Processors\Visualization\SpikePlotting\WaveAxes.h">
       <Filter>open-ephys\Source\Processors\Visualization\SpikePlotting</Filter>
     </ClInclude>

Source/Processors/ArduinoOutput.cpp

@@ -24,13 +24,9 @@
 #include "ArduinoOutput.h"
 
 #include <stdio.h>
-#include <unistd.h>  /*UNIX standard function definitions */
-#include <termios.h> /*POSIX terminal control definitions */
-#include <fcntl.h>   /*File control definitions */
-
 
 ArduinoOutput::ArduinoOutput()
-	: GenericProcessor("Arduino Output"), serialport("/dev/ttyACM0")
+	: GenericProcessor("Arduino Output")
 {
 
 }
@@ -76,49 +72,25 @@ void ArduinoOutput::setParameter (int parameterIndex, float newValue)
 
 bool ArduinoOutput::enable()
 {
-	struct termios toptions;
-	int fd;
-
-	handle = open(serialport, O_RDWR | O_NOCTTY | O_NDELAY);
-
-	if (handle == -1)
-	{
-		std::cout << "Arduino Output unable to open port." << std::endl;
-		return false;
-	}
-
-	if (tcgetattr(handle, &toptions) < 0)
-	{
-		std::cout << "Arduino Output couldn't get term attributes" << std::endl;
-		return false;
-	}
-
-	speed_t brate = B9600;
-
-	cfsetispeed(&toptions, brate);
-	cfsetospeed(&toptions, brate);
+	if (arduino.connect("ttyACM0"))
+    {
+       
+    } 
 
-	  // 8N1
-    toptions.c_cflag &= ~PARENB;
-    toptions.c_cflag &= ~CSTOPB;
-    toptions.c_cflag &= ~CSIZE;
-    toptions.c_cflag |= CS8;
-    // no flow control
-    toptions.c_cflag &= ~CRTSCTS;
+    if (arduino.isArduinoReady()) 
+    {  
 
-    toptions.c_cflag |= CREAD | CLOCAL;  // turn on READ & ignore ctrl lines
-    toptions.c_iflag &= ~(IXON | IXOFF | IXANY); // turn off s/w flow ctrl
+        arduino.sendProtocolVersionRequest();
+        //sleep(2);
+        arduino.update();
+        arduino.sendFirmwareVersionRequest();
 
-    toptions.c_lflag &= ~(ICANON | ECHO | ECHOE | ISIG); // make raw
-    toptions.c_oflag &= ~OPOST; // make raw
+        //sleep(2);
+        arduino.update();
+ 
+        std::cout << "firmata v" << arduino.getMajorFirmwareVersion() 
+             << "." << arduino.getMinorFirmwareVersion() << std::endl;
 
-    // see: http://unixwiz.net/techtips/termios-vmin-vtime.html
-    toptions.c_cc[VMIN]  = 0;
-    toptions.c_cc[VTIME] = 20;
-    
-    if( tcsetattr(handle, TCSANOW, &toptions) < 0) {
-        std::cout << "Arduino Output couldn't set term attributes" << std::endl;
-        return false;
     }
 }
 
@@ -126,7 +98,6 @@ bool ArduinoOutput::disable()
 {
 
 
-
 }
 
 void ArduinoOutput::process(AudioSampleBuffer &buffer, 

Source/Processors/ArduinoOutput.h

@@ -26,13 +26,16 @@
 
 #include "../../JuceLibraryCode/JuceHeader.h"
 
+#include "Serial/ofArduino.h"
 #include "GenericProcessor.h"
 
 /** 
 
+	*UNDER CONSTRUCTION*
+
 	Provides a serial interface to an Arduino board.
 
-	Based on arduino-serial.c (http://todbot.com/blog/2006/12/06/arduino-serial-c-code-to-talk-to-arduino/)
+	Based on Open Frameworks ofArduino class
 
 	@see GenericProcessor
 
@@ -60,10 +63,7 @@ public:
 	
 private:
 
-	//void timerCallback();
-	int handle;
-
-	const char* serialport;
+	ofArduino arduino;
 
 	JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR (ArduinoOutput);