diff --git a/README b/README
index 7393e37..ae915eb 100644
--- a/README
+++ b/README
@@ -9,3 +9,7 @@ RTS (my personal codebase) https://github.com/dmayerich/RTS
 CUDA http://www.nvidia.com/object/cuda_home_new.html
 
 If CMake is unable to find these, make sure to specify their locations.
+
+Known Bugs in Source Version
+---------------------------------
+*)  Simulation of the spectrum at the shortest wavelength is returning NaN in Linux.
diff --git a/SimulateSpectrum.cpp b/SimulateSpectrum.cpp
index 90d6861..52a33af 100644
--- a/SimulateSpectrum.cpp
+++ b/SimulateSpectrum.cpp
@@ -2,7 +2,8 @@
 #include <complex>
 #include <iostream>
 #include <fstream>
-#include "globals.h"
+#include "globals.h"
+#include <QProgressDialog>
 #include <stdlib.h>
 //#include "cufft.h"
 using namespace std;
@@ -137,7 +138,7 @@ void Legendre(double* P, double x, int Nl)
 	for(int l = 2; l < Nl; l++)
 	{
 		P[l] = ((2*l - 1)*x*P[l-1] - (l - 1)*P[l-2])/l;
-	}	
+	}
 
 }
 
@@ -190,7 +191,7 @@ void computeCondenserAlpha(double* alpha, int Nl, double cAngleI, double cAngleO
 
 }
 
-complex<double> integrateUs(double r, double lambda, complex<double> eta, 
+complex<double> integrateUs(double r, double lambda, complex<double> eta,
 						   double cAngleI, double cAngleO, double oAngleI, double oAngleO, double M = 2*pi)
 {
 	/*This function integrates the incident field of magnitude M in the far zone
@@ -223,7 +224,7 @@ complex<double> integrateUs(double r, double lambda, complex<double> eta,
 
 	//store the index of refraction;
 	complex<double> IR(eta.real(), eta.imag());
-	
+
 	//compute the scattering coefficients
 	computeB(B, r, IR, lambda, Nl);
 
@@ -248,8 +249,8 @@ complex<double> integrateUs(double r, double lambda, complex<double> eta,
 		}
 		c = (2*pi)/(2.0 * l + 1.0);
 		Us += c * alpha * beta * B[l] * M;
-		
-			
+
+
 	}
 	free(PcNAo);
 	free(PcNAi);
@@ -269,7 +270,7 @@ void pointSpectrum()
 
 	double dNu = 2.0f;
 	double lambda;
-	
+
 	//compute the angles based on NA
 	double cAngleI = asin(cNAi);
 	double cAngleO = asin(cNAo);
@@ -278,7 +279,7 @@ void pointSpectrum()
 
 	//implement a reflection-mode system if necessary
 	if(opticsMode == ReflectionOpticsType){
-		
+
 		//set the condenser to match the objective
 		cAngleI = oAngleI;
 		cAngleO = oAngleO;
@@ -293,7 +294,7 @@ void pointSpectrum()
 	double I0 = Ui.real() * Ui.real() + Ui.imag() * Ui.imag();
 	I0 *= scaleI0;
 
-	
+
 
 	//double I;
 	SpecPair temp;
@@ -316,7 +317,7 @@ void pointSpectrum()
 		Us = integrateUs(radius, lambda, eta, cAngleI, cAngleO, oAngleI, oAngleO, 2*pi);
 		U = Us + Ui;
 		double I = U.real() * U.real() + U.imag() * U.imag();
-		
+
 		temp.nu = nu;
 
 		//set the spectrum value based on the current display type
@@ -327,8 +328,8 @@ void pointSpectrum()
 
 		if(dispNormalize)
 			vecLen += temp.A * temp.A;
-		
-		SimSpectrum.push_back(temp);		
+
+		SimSpectrum.push_back(temp);
 	}
 	vecLen = sqrt(vecLen);
 
@@ -352,8 +353,10 @@ void updateSpectrum(double* I, double I0, int n)
 		//set the spectrum value based on the current display type
 		if(dispSimType == AbsorbanceSpecType)
 			temp.A = -log10(I[i]/I0);
-		else
-			temp.A = I[i];
+		else
+		{
+			temp.A = I[i];
+        }
 
 		SimSpectrum.push_back(temp);
 	}
@@ -369,7 +372,7 @@ void computeCassegrainAngles(double& cAngleI, double& cAngleO, double& oAngleI, 
 
 	//implement a reflection-mode system if necessary
 	if(opticsMode == ReflectionOpticsType){
-		
+
 		//set the condenser to match the objective
 		cAngleI = oAngleI;
 		cAngleO = oAngleO;
@@ -410,7 +413,7 @@ void computeBArray(complex<double>* B, int Nl, int nLambda)
 			eta = complex<double>(baseIR, 0.0);
 
 		//allocate memory for the scattering coefficients
-		//complex<float>* B = (complex<float>*)malloc(sizeof(complex<float>)*Nl);		
+		//complex<float>* B = (complex<float>*)malloc(sizeof(complex<float>)*Nl);
 
 		complex<double> IR(eta.real(), eta.imag());
 		computeB(&B[i * Nl], radius, IR, Lambda[i], Nl);
@@ -419,7 +422,7 @@ void computeBArray(complex<double>* B, int Nl, int nLambda)
 
 void computeOpticalParameters(double& cAngleI, double& cAngleO, double& oAngleI, double& oAngleO, double& I0, double* alpha, int Nl)
 {
-	computeCassegrainAngles(cAngleI, cAngleO, oAngleI, oAngleO);	
+	computeCassegrainAngles(cAngleI, cAngleO, oAngleI, oAngleO);
 
 	//evaluate the incident field intensity
 	I0 = 0.0;
@@ -437,7 +440,7 @@ void gpuDetectorSpectrum(int numSamples)
 	//integrate across the objective aperature and calculate the resulting intensity on a detector
 	PD.StartTimer(SIMULATE_SPECTRUM);
 	//clear the previous spectrum
-	SimSpectrum.clear();	
+	SimSpectrum.clear();
 
 	//compute Nl (maximum order of the spectrum)
 	int Nl = computeNl();
@@ -448,11 +451,11 @@ void gpuDetectorSpectrum(int numSamples)
 
 	//allocate space for a list of wavelengths
 	int nLambda = EtaK.size();
-	
+
 	//allocate space for the 2D array (Nl x nu) of scattering coefficients
 	complex<double>* B = (complex<double>*)malloc(sizeof(complex<double>) * Nl * nLambda);
 	computeBArray(B, Nl, nLambda);
-	
+
 
 	//allocate temporary space for the spectrum
 	double* I = (double*)malloc(sizeof(double) * EtaK.size());
@@ -500,33 +503,37 @@ double absorbanceDistortion(){
 
 double intensityDistortion(){
 
-	//compute the magnitude of the spectrum
+	//compute the mean intensity of the spectrum
 	double sumSim = 0.0;
 	for(unsigned int i=0; i<SimSpectrum.size(); i++)
 	{
-		sumSim += SimSpectrum[i].A * SimSpectrum[i].A;
+		sumSim += pow(SimSpectrum[i].A, 2);
 	}
 	double magSim = sqrt(sumSim);
 
 	//compute the distortion (MSE from the mean)
-	double sumSE = 0.0;
+	double proj = 0.0;
 	for(unsigned int i=0; i<SimSpectrum.size(); i++)
 	{
-		sumSE += (SimSpectrum[i].A/magSim) * (1.0/SimSpectrum.size());
+		proj += (SimSpectrum[i].A/magSim) * (1.0/SimSpectrum.size());
 	}
-	double MSE = sumSE;
+	double error = proj;
 
-	return MSE;
+	return error;
 }
 
-void MinimizeDistortion(){
+void DistortionMap(float* distortionMap, int nSteps){
 	ofstream outFile("distortion.txt");
 
-	//set the parameters for the distortion simulation
-	double step = 0.001;
+	//set the parameters for the distortion simulation
+	double range = 0.4;
+	double step = (range)/(nSteps-1);
 
 	oNAi = 0.2;
-	oNAo = 0.5;
+	oNAo = 0.5;
+
+	double startNAi = 0.0;
+	double startNAo = 0.3;
 
 	//compute the optical parameters
 	//compute Nl (maximum order of the spectrum)
@@ -534,7 +541,7 @@ void MinimizeDistortion(){
 
 	double* alpha = (double*)malloc(sizeof(double)*(Nl + 1));
 	double cAngleI, cAngleO, oAngleI, oAngleO, I0;
-	
+
 	//allocate space for a list of wavelengths
 	int nLambda = EtaK.size();
 
@@ -546,20 +553,29 @@ void MinimizeDistortion(){
 	complex<double>* B = (complex<double>*)malloc(sizeof(complex<double>) * Nl * nLambda);
 	computeBArray(B, Nl, nLambda);
 
-
+    QProgressDialog progress("Computing distortion map...", "Stop", 0, nSteps * nSteps);
+    progress.setWindowModality(Qt::WindowModal);
 
 	double D;
-	double e = 0.001;
-	for(double i=0.0; i<=oNAo-step; i+=step)
-	{
-		
-		for(double o=oNAi+step; o<=1.0; o+=step)
-		{
-			
-			
+	double e = 0.001;
+	int i, o;
+	for(i=0; i<nSteps; i++)
+	{
+        for(o=0; o<nSteps; o++)
+		{
+            //update the progress bar and check for an exit
+            progress.setValue(i * nSteps + o);
+            if (progress.wasCanceled())
+                break;
+
+            //set the current optical parameters
+			cNAi = startNAi + i * step;
+			cNAo = startNAo + o * step;
+			//cout<<cNAi<<"   "<<cNAo<<endl;
+
 			//set the current optical parameters
-			cNAi = i;
-			cNAo = o;
+			//cNAi = i;
+			//cNAo = o;
 
 			//compute the optical parameters
 			computeOpticalParameters(cAngleI, cAngleO, oAngleI, oAngleO, I0, alpha, Nl);
@@ -570,22 +586,26 @@ void MinimizeDistortion(){
 
 			if(dispSimType == AbsorbanceSpecType)
 			{
-				if(i + e >= o || i + e >= oNAo || oNAi + e >= o || oNAi + e >= oNAo)
-					D = 0.0;
+				if(cNAi >= cNAo || cNAi >= oNAo || oNAi >= cNAo || oNAi >= oNAo)
+					D = -1.0;
 				else
 					D = absorbanceDistortion();
 			}
 			else
 			{
-				if(i >= o || oNAi >= oNAo)
-					D=0;
+				if(cNAi >= cNAo || oNAi >= oNAo)
+					D = -1.0;
 				else
 					D = intensityDistortion();
-			}
+			}
+			distortionMap[o * nSteps + i] = D;
 			outFile<<D<<"       ";
 		}
 		outFile<<endl;
-		cout<<i<<endl;
-	}
+		//cout<<i<<endl;
+    }
+
+	progress.setValue(nSteps * nSteps);
+
 	outFile.close();
-}
\ No newline at end of file
+}
diff --git a/cudaKK.h b/cudaKK.h
index 185d800..203cf1f 100644
--- a/cudaKK.h
+++ b/cudaKK.h
@@ -54,16 +54,18 @@ void cudaKramersKronig(double* cpuN, double* cpuK, int nVals, double nuStart, do
 	HANDLE_ERROR(cudaFree(gpuN));
 }
 
-__global__ void devComputeSpectrum(double* I, double2* B, double* alpha, int Nl, 
-								   int nSamples, double oThetaI, double oThetaO, double cThetaI, double cThetaO)
+__global__ void devComputeSpectrum(double* I, double2* B, double* alpha, int Nl,
+								   int nSamples, int nLambda, double oThetaI, double oThetaO, double cThetaI, double cThetaO)
 {
-	int i = blockIdx.x * blockDim.x + threadIdx.x;
+	int i = blockIdx.x * blockDim.x + threadIdx.x;
+	if(i >= nLambda-1)
+        return;
 
 	//compute the delta-theta value
 	double dTheta = (oThetaO - oThetaI)/nSamples;
 
 	//allocate space for the Legendre polynomials
-	double Ptheta[2];	
+	double Ptheta[2];
 
 	double cosTheta, theta;
 	cuDoubleComplex Us;
@@ -122,7 +124,7 @@ __global__ void devComputeSpectrum(double* I, double2* B, double* alpha, int Nl,
 
 			complexFac = cMult(B[Nl * i + l], exp_numer);
 			complexFac = cMult(complexFac, iL);
-			
+
 
 			//combine the real and complex components
 			UsSample = cMult(complexFac, realFac);
@@ -131,7 +133,7 @@ __global__ void devComputeSpectrum(double* I, double2* B, double* alpha, int Nl,
 			//increment the imaginary exponent i^l
 			iL = cMult(iL, imag);
 
-		
+
 		}
 
 		//sum the scattered and incident fields
@@ -158,8 +160,9 @@ void cudaComputeSpectrum(double* cpuI, double* cpuB, double* cpuAlpha,
 	HANDLE_ERROR(cudaMemcpy(gpuAlpha, cpuAlpha, sizeof(double) * Nl, cudaMemcpyHostToDevice));
 
 	double* gpuI;
-	HANDLE_ERROR(cudaMalloc(&gpuI, sizeof(double) * nLambda));
-	
+	HANDLE_ERROR(cudaMalloc(&gpuI, sizeof(double) * nLambda));
+	HANDLE_ERROR(cudaMemset(gpuI, 0, sizeof(double) * nLambda));
+
 
 	//call the kernel to compute the spectrum
 	dim3 block(BLOCK_SIZE*BLOCK_SIZE);
@@ -167,15 +170,17 @@ void cudaComputeSpectrum(double* cpuI, double* cpuB, double* cpuAlpha,
 
 	//devComputeSpectrum
 	devComputeSpectrum<<<grid, block>>>(gpuI, (double2*)gpuB, gpuAlpha, Nl,
-										nSamples, oThetaI, oThetaO, cThetaI, cThetaO);
+										nSamples, nLambda, oThetaI, oThetaO, cThetaI, cThetaO);
 
 	HANDLE_ERROR(cudaMemcpy(cpuI, gpuI, sizeof(double) * nLambda, cudaMemcpyDeviceToHost));
 
+	//printf("Final array value: %f\n", cpuI[nLambda-1]);
+
 	HANDLE_ERROR(cudaFree(gpuB));
 	HANDLE_ERROR(cudaFree(gpuAlpha));
 	HANDLE_ERROR(cudaFree(gpuI));
 
-	
 
 
-}
\ No newline at end of file
+
+}
diff --git a/globals.h b/globals.h
index ad8934e..6a7474d 100644
--- a/globals.h
+++ b/globals.h
@@ -4,7 +4,7 @@
 #include <vector>
 #include <string>
 #include <iostream>
-#include "PerformanceData.h"
+#include "PerformanceData.h"
 #include <complex>
 using namespace std;
 
@@ -102,9 +102,13 @@ extern int maxFitIter;
 void EstimateMaterial();
 extern double scaleI0;
 extern double refSlope;
-
+
+
+//distortion maps
 double ComputeDistortion();
-void MinimizeDistortion();
+void DistortionMap(float* distortionMap, int nSteps);
+
+
 
 
-#endif
\ No newline at end of file
+#endif
diff --git a/interactivemie.cpp b/interactivemie.cpp
index 8504eda..a76543f 100644
--- a/interactivemie.cpp
+++ b/interactivemie.cpp
@@ -1,4 +1,7 @@
 #include "interactivemie.h"
+#include <stdlib.h>
+
+qtDistortionDialog* distortionDialog;
 
 InteractiveMie::InteractiveMie(QWidget *parent, Qt::WFlags flags)
 	: QMainWindow(parent, flags)
@@ -9,4 +12,11 @@ InteractiveMie::InteractiveMie(QWidget *parent, Qt::WFlags flags)
 InteractiveMie::~InteractiveMie()
 {
 	updating = false;
+}
+
+void InteractiveMie::closeEvent(QCloseEvent *event)
+{
+	cout<<"Exiting"<<endl;
+    exit(0);
+
 }
diff --git a/interactivemie.h b/interactivemie.h
index ade8118..0755ec7 100644
--- a/interactivemie.h
+++ b/interactivemie.h
@@ -5,16 +5,20 @@
 #include <QDragEnterEvent>
 #include <qfiledialog.h>
 #include <qinputdialog.h>
-#include "ui_interactivemie.h"
-#include "globals.h"
-
+#include "ui_interactivemie.h"
+#include "qtDistortionDialog.h"
+#include "globals.h"
+
+extern qtDistortionDialog* distortionDialog;
+
 class InteractiveMie : public QMainWindow
 {
 	Q_OBJECT
 
 public:
 	InteractiveMie(QWidget *parent = 0, Qt::WFlags flags = 0);
-	~InteractiveMie();
+	~InteractiveMie();
+	void closeEvent(QCloseEvent *event);
 	bool updating;
 
 	void refreshUI()
@@ -53,7 +57,6 @@ public:
 		ui.cmbMaterial->setCurrentIndex(currentMaterial);
 
 		updating = false;
-
 	}
 
 	void dragEnterEvent(QDragEnterEvent *event)
@@ -64,7 +67,7 @@ public:
 			event->mimeData()->hasFormat("text/plain"))
 		{
 			event->acceptProposedAction();
-			
+
 		}
 	}
 
@@ -104,7 +107,7 @@ public slots:
 	void on_chkDisplayRefSpec_clicked(bool b){
 		dispRefSpec = b;
 		UpdateDisplay();
-	}	
+	}
 	void on_chkDisplaySimK_clicked(bool b){
 		dispSimK = b;
 		UpdateDisplay();
@@ -287,7 +290,9 @@ public slots:
 	}
 	void on_btnDistortion_clicked(){
 		//ComputeDistortion();
-		MinimizeDistortion();
+		//DistortionMap();
+		cout<<"Distortion"<<endl;
+		distortionDialog->show();
 	}
 	void on_btnTimings_clicked(){
 		PD.PrintResults(cout);
@@ -308,7 +313,7 @@ public slots:
 
 		//first load the imaginary part
 		QString kFileName = QFileDialog::getOpenFileName(this, tr("Open Imaginary (k) Spectrum"));
-		
+
 		//exit if no file was selected
 		if(kFileName == QString::null)
 			return;
diff --git a/interactivemie.ui b/interactivemie.ui
index 4c440bf..d85c580 100644
--- a/interactivemie.ui
+++ b/interactivemie.ui
@@ -6,7 +6,7 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>464</width>
+    <width>511</width>
     <height>525</height>
    </rect>
   </property>
@@ -32,7 +32,7 @@
     <widget class="QDoubleSpinBox" name="spinScaleK">
      <property name="geometry">
       <rect>
-       <x>70</x>
+       <x>80</x>
        <y>80</y>
        <width>62</width>
        <height>22</height>
@@ -48,7 +48,7 @@
     <widget class="QDoubleSpinBox" name="spinBaseIR">
      <property name="geometry">
       <rect>
-       <x>70</x>
+       <x>80</x>
        <y>50</y>
        <width>62</width>
        <height>22</height>
@@ -80,7 +80,7 @@
     <widget class="QDoubleSpinBox" name="spinRadius">
      <property name="geometry">
       <rect>
-       <x>70</x>
+       <x>80</x>
        <y>20</y>
        <width>62</width>
        <height>22</height>
@@ -127,7 +127,7 @@
       <rect>
        <x>20</x>
        <y>110</y>
-       <width>101</width>
+       <width>121</width>
        <height>17</height>
       </rect>
      </property>
@@ -166,7 +166,7 @@
       <rect>
        <x>5</x>
        <y>50</y>
-       <width>71</width>
+       <width>81</width>
        <height>20</height>
       </rect>
      </property>
@@ -177,7 +177,7 @@
     <widget class="QDoubleSpinBox" name="spinCondNAi">
      <property name="geometry">
       <rect>
-       <x>80</x>
+       <x>90</x>
        <y>20</y>
        <width>62</width>
        <height>22</height>
@@ -195,7 +195,7 @@
       <rect>
        <x>5</x>
        <y>20</y>
-       <width>71</width>
+       <width>91</width>
        <height>20</height>
       </rect>
      </property>
@@ -244,7 +244,7 @@
     <widget class="QDoubleSpinBox" name="spinObjNAi">
      <property name="geometry">
       <rect>
-       <x>80</x>
+       <x>90</x>
        <y>50</y>
        <width>62</width>
        <height>22</height>
@@ -262,7 +262,7 @@
       <rect>
        <x>20</x>
        <y>80</y>
-       <width>82</width>
+       <width>111</width>
        <height>17</height>
       </rect>
      </property>
@@ -278,7 +278,7 @@
       <rect>
        <x>150</x>
        <y>80</y>
-       <width>82</width>
+       <width>91</width>
        <height>17</height>
       </rect>
      </property>
@@ -296,15 +296,15 @@
       </rect>
      </property>
      <property name="text">
-      <string>Point Detector</string>
+      <string>Point Det.</string>
      </property>
     </widget>
     <widget class="QSpinBox" name="spinObjectiveSamples">
      <property name="geometry">
       <rect>
-       <x>10</x>
+       <x>1</x>
        <y>100</y>
-       <width>42</width>
+       <width>51</width>
        <height>22</height>
       </rect>
      </property>
@@ -320,7 +320,7 @@
       <rect>
        <x>60</x>
        <y>100</y>
-       <width>71</width>
+       <width>81</width>
        <height>16</height>
       </rect>
      </property>
@@ -334,7 +334,7 @@
      <rect>
       <x>280</x>
       <y>20</y>
-      <width>161</width>
+      <width>181</width>
       <height>411</height>
      </rect>
     </property>
@@ -454,9 +454,9 @@
     <widget class="QLabel" name="label">
      <property name="geometry">
       <rect>
-       <x>20</x>
+       <x>10</x>
        <y>20</y>
-       <width>61</width>
+       <width>71</width>
        <height>16</height>
       </rect>
      </property>
@@ -469,7 +469,7 @@
       <rect>
        <x>10</x>
        <y>230</y>
-       <width>131</width>
+       <width>151</width>
        <height>17</height>
       </rect>
      </property>
@@ -485,7 +485,7 @@
       <rect>
        <x>10</x>
        <y>170</y>
-       <width>131</width>
+       <width>151</width>
        <height>17</height>
       </rect>
      </property>
@@ -624,7 +624,7 @@
     <widget class="QDoubleSpinBox" name="spinDispScaleK">
      <property name="geometry">
       <rect>
-       <x>90</x>
+       <x>120</x>
        <y>290</y>
        <width>51</width>
        <height>22</height>
@@ -637,7 +637,7 @@
     <widget class="QDoubleSpinBox" name="spinDispScaleN">
      <property name="geometry">
       <rect>
-       <x>90</x>
+       <x>120</x>
        <y>340</y>
        <width>51</width>
        <height>22</height>
@@ -665,7 +665,7 @@
       <rect>
        <x>50</x>
        <y>190</y>
-       <width>82</width>
+       <width>101</width>
        <height>17</height>
       </rect>
      </property>
@@ -692,7 +692,7 @@
     <widget class="QDoubleSpinBox" name="spinNormFactor">
      <property name="geometry">
       <rect>
-       <x>90</x>
+       <x>120</x>
        <y>380</y>
        <width>62</width>
        <height>22</height>
@@ -868,8 +868,8 @@
       <rect>
        <x>120</x>
        <y>50</y>
-       <width>46</width>
-       <height>13</height>
+       <width>51</width>
+       <height>16</height>
       </rect>
      </property>
      <property name="text">
@@ -883,8 +883,8 @@
     <rect>
      <x>0</x>
      <y>0</y>
-     <width>464</width>
-     <height>21</height>
+     <width>511</width>
+     <height>25</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuFile">
diff --git a/main.cpp b/main.cpp
index 53fe4d9..ac06f65 100644
--- a/main.cpp
+++ b/main.cpp
@@ -1,7 +1,10 @@
 #include <fstream>
 using namespace std;
 #include "interactivemie.h"
-#include <QtGui/QApplication>
+#include <QtGui/QApplication>
+#include <QGraphicsScene>
+#include <QGraphicsView>
+#include <QGraphicsPixmapItem>
 #include "qtSpectrumDisplay.h"
 #include "globals.h"
 #include "rtsGUIConsole.h"
@@ -11,7 +14,11 @@ using namespace std;
 
 PerformanceData PD;
 
-qtSpectrumDisplay* gpSpectrumDisplay;
+qtSpectrumDisplay* gpSpectrumDisplay;
+
+QGraphicsScene* distortionScene = NULL;
+QGraphicsView* distortionWindow = NULL;
+QGraphicsPixmapItem* pixmapItem = NULL;
 
 vector<vector<SpecPair> > RefSpectrum;
 vector<SpecPair> SimSpectrum;
@@ -209,7 +216,7 @@ void FitDisplay(){
 void ChangeAbsorbance(){
 
 	//compute the real part of the index of refraction
-	
+
 	//copy the absorbance values into a linear array
 	int nSamples = MaterialList[currentMaterial].eta.size();
 	double startNu = MaterialList[currentMaterial].nu.front();
@@ -280,11 +287,11 @@ void SetMaterial()
 
 int main(int argc, char *argv[])
 {
-	
+
 
 	//load the default project file (any previous optical settings)
 	LoadState();
-	
+
 	//load the default materials
 	LoadMaterial("eta_TolueneK.txt", "eta_TolueneN.txt", "Toluene");
 	LoadMaterial("kPMMA.txt", "PMMA");
@@ -294,25 +301,36 @@ int main(int argc, char *argv[])
 	//compute the analytical solution for the Mie scattered spectrum
 	SimulateSpectrum();
 
-	QApplication a(argc, argv);
+	QApplication a(argc, argv);
+
+	//create and position the UI window
 	InteractiveMie w;
-	
-
 	w.show();
-	
-	
 	w.move(0, 0);
-	QRect frame = w.frameGeometry();
-	QRect inside = w.geometry();
+	QRect uiFrame = w.frameGeometry();
+	QRect uiNoFrame = w.geometry();
+	int frameHeight = uiFrame.height() - uiNoFrame.height();
 
 	//activate a console for output
-	RedirectIOToConsole(0, frame.height(), frame.width());
-
+	RedirectIOToConsole(0, uiFrame.height(), uiFrame.width(), 400);
+	printf("Frame height: %d\n", frameHeight);
+
+	//set the size and position of the spectrum window
+	int visWinSize = uiFrame.height()/2 - frameHeight;
+	//create the far field window
 	gpSpectrumDisplay = new qtSpectrumDisplay();
-	gpSpectrumDisplay->move(frame.width(), 0);
-	gpSpectrumDisplay->resize(2*inside.height(), inside.height());
-
-	gpSpectrumDisplay->show();
+	gpSpectrumDisplay->resize(visWinSize*2, visWinSize);
+	gpSpectrumDisplay->move(uiFrame.width(), 0);
+	gpSpectrumDisplay->show();
+
+	//distortion dialog box
+	distortionDialog = new qtDistortionDialog();
+	distortionDialog->move(0, 0);
+
+	//display the distortion map
+	distortionScene = new QGraphicsScene();
+	distortionWindow = new QGraphicsView(distortionScene);
+	distortionWindow->move(uiFrame.width(), visWinSize);
 
 	//refresh the UI
 	w.refreshUI();
diff --git a/qtSpectrumDisplay.cpp b/qtSpectrumDisplay.cpp
index 4945415..0f41a27 100644
--- a/qtSpectrumDisplay.cpp
+++ b/qtSpectrumDisplay.cpp
@@ -1,298 +1,224 @@
- #include <QtGui>
- #include <QtOpenGL/QtOpenGL>
+#include <QtGui>
+#include <QtOpenGL/QtOpenGL>
 #include <GL/glu.h>
 
- #include <math.h>
-
- #include "qtSpectrumDisplay.h"
-
- qtSpectrumDisplay::qtSpectrumDisplay(QWidget *parent)
-     : QGLWidget(parent)
- {
-     object = 0;
-     xRot = 0;
-     yRot = 0;
-     zRot = 0;
-
-     qtGreen = QColor::fromCmykF(0.40, 0.0, 1.0, 0.0);
-     qtPurple = QColor::fromCmykF(0.39, 0.39, 0.0, 0.0);
- }
-
- qtSpectrumDisplay::~qtSpectrumDisplay()
- {
-     makeCurrent();
-     glDeleteLists(object, 1);
- }
-
- QSize qtSpectrumDisplay::minimumSizeHint() const
- {
-     return QSize(50, 50);
- }
-
- QSize qtSpectrumDisplay::sizeHint() const
- {
-     return QSize(400, 400);
- }
-
- /*void qtSpectrumDisplay::setXRotation(int angle)
- {
-     normalizeAngle(&angle);
-     if (angle != xRot) {
-         xRot = angle;
-         emit xRotationChanged(angle);
-         updateGL();
+#include <math.h>
+
+#include "qtSpectrumDisplay.h"
+
+qtSpectrumDisplay::qtSpectrumDisplay(QWidget *parent)
+ : QGLWidget(parent)
+{
+ object = 0;
+ xRot = 0;
+ yRot = 0;
+ zRot = 0;
+
+ qtGreen = QColor::fromCmykF(0.40, 0.0, 1.0, 0.0);
+ qtPurple = QColor::fromCmykF(0.39, 0.39, 0.0, 0.0);
+}
+
+qtSpectrumDisplay::~qtSpectrumDisplay()
+{
+ makeCurrent();
+ glDeleteLists(object, 1);
+}
+
+QSize qtSpectrumDisplay::minimumSizeHint() const
+{
+ return QSize(50, 50);
+}
+
+QSize qtSpectrumDisplay::sizeHint() const
+{
+ return QSize(400, 400);
+}
+
+void qtSpectrumDisplay::initializeGL()
+{
+ qglClearColor(qtPurple.dark());
+ //object = makeObject();
+ glShadeModel(GL_FLAT);
+ glEnable(GL_DEPTH_TEST);
+ glEnable(GL_CULL_FACE);
+}
+
+void qtSpectrumDisplay::printWavenumber(int xPos)
+{
+ int viewParams[4];
+ glGetIntegerv(GL_VIEWPORT, viewParams);
+
+ float a = (float)xPos/(float)viewParams[2];
+
+ int wn = a * (nuMax - nuMin) + nuMin;
+ cout<<wn<<endl;
+
+
+
+}
+
+void qtSpectrumDisplay::paintGL()
+{
+    //prepare the projection (orthographic, bounded by spectral values)
+    glMatrixMode(GL_PROJECTION);
+    glLoadIdentity();
+    gluOrtho2D(nuMin, nuMax, aMin, aMax);
+    glMatrixMode(GL_MODELVIEW);
+    glLoadIdentity();
+
+    //clear the screen
+    glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
+
+    //set the line width
+    glLineWidth(2);
+
+    //draw the simulated spectrum (in white)
+    if(dispSimSpec)
+    {
+     glColor3f(1.0, 1.0, 1.0);
+     glBegin(GL_LINE_STRIP);
+     for(unsigned int i=0; i<SimSpectrum.size(); i++)
+         glVertex2f(SimSpectrum[i].nu, SimSpectrum[i].A);
+     glEnd();
+    }
+    //draw the reference spectrum in gray
+    if(dispRefSpec && RefSpectrum.size() > 0)
+    {
+     glColor3f(0.5, 0.5, 0.5);
+     glBegin(GL_LINE_STRIP);
+     float nu;
+     for(unsigned int i=0; i<RefSpectrum[currentSpec].size(); i++)
+     {
+         nu = RefSpectrum[currentSpec][i].nu;
+         glVertex2f(nu, RefSpectrum[currentSpec][i].A + nu * refSlope);
      }
- }
-
- void qtSpectrumDisplay::setYRotation(int angle)
- {
-     normalizeAngle(&angle);
-     if (angle != yRot) {
-         yRot = angle;
-         emit yRotationChanged(angle);
-         updateGL();
+     glEnd();
+    }
+
+    //draw the material properties
+
+    //change the viewport properties (materials are plotted on a different scale)
+
+    //compute the maximum k and n
+    int nSamples = MaterialList[currentMaterial].eta.size();
+    float maxK = 0.0;
+    float maxN = 0.0;
+    float thisN, thisK;
+    for(int i=0; i<nSamples; i++)
+    {
+        thisN = fabs(MaterialList[currentMaterial].eta[i].real() - 1.49);
+        if(thisN > maxN)
+            maxN = thisN;
+        thisK = fabs(MaterialList[currentMaterial].eta[i].imag());
+        if(thisK > maxK)
+            thisK = maxK;
+    }
+    cout<<maxN<<"---------"<<maxK<<endl;
+
+
+    glMatrixMode(GL_PROJECTION);
+    glLoadIdentity();
+    gluOrtho2D(nuMin, nuMax, aMin, aMax);
+
+
+    float nu;
+    //display absorbance
+    if(dispMatK)
+    {
+
+     glColor3f(1.0, 0.0, 0.0);
+     glBegin(GL_LINE_STRIP);
+     for(int i=0; i<nSamples; i++){
+         nu = MaterialList[currentMaterial].nu[i];
+         glVertex2f(nu, MaterialList[currentMaterial].eta[i].imag() * dispScaleK);
      }
- }
-
- void qtSpectrumDisplay::setZRotation(int angle)
- {
-     normalizeAngle(&angle);
-     if (angle != zRot) {
-         zRot = angle;
-         emit zRotationChanged(angle);
-         updateGL();
+     glEnd();
+    }
+    if(dispSimK)
+    {
+     glColor3f(1.0, 1.0, 0.0);
+     glBegin(GL_LINE_STRIP);
+     for(unsigned int i=0; i<EtaK.size(); i++){
+         glVertex2f(EtaK[i].nu, EtaK[i].A * dispScaleK);
      }
- }*/
-
- void qtSpectrumDisplay::initializeGL()
- {
-     qglClearColor(qtPurple.dark());
-     //object = makeObject();
-     glShadeModel(GL_FLAT);
-     glEnable(GL_DEPTH_TEST);
-     glEnable(GL_CULL_FACE);
- }
-
- void qtSpectrumDisplay::printWavenumber(int xPos)
- {
-	 int viewParams[4];
-	 glGetIntegerv(GL_VIEWPORT, viewParams);
-
-	 float a = (float)xPos/(float)viewParams[2];
-
-	 int wn = a * (nuMax - nuMin) + nuMin;
-	 cout<<wn<<endl;
-
- }
-
- void qtSpectrumDisplay::paintGL()
- {
-	 glMatrixMode(GL_PROJECTION);
-     glLoadIdentity();
-     //glOrtho(-0.5, +0.5, +0.5, -0.5, 4.0, 15.0);
-	 gluOrtho2D(nuMin, nuMax, aMin, aMax);
-     glMatrixMode(GL_MODELVIEW);
-
-     glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
-     glLoadIdentity();
-     /*glTranslated(0.0, 0.0, -10.0);
-     glRotated(xRot / 16.0, 1.0, 0.0, 0.0);
-     glRotated(yRot / 16.0, 0.0, 1.0, 0.0);
-     glRotated(zRot / 16.0, 0.0, 0.0, 1.0);*/
-	 glLineWidth(2);
-	 if(dispSimSpec)
-	 {
-		 glColor3f(1.0, 1.0, 1.0);
-		 glBegin(GL_LINE_STRIP);
-		 for(unsigned int i=0; i<SimSpectrum.size(); i++)
-			 glVertex2f(SimSpectrum[i].nu, SimSpectrum[i].A);
-		 glEnd();
-	 }
-	 if(dispRefSpec && RefSpectrum.size() > 0)
-	 {
-		 glColor3f(0.5, 0.5, 0.5);
-		 glBegin(GL_LINE_STRIP);
-		 float nu;
-		 for(unsigned int i=0; i<RefSpectrum[currentSpec].size(); i++)
-		 {
-			 nu = RefSpectrum[currentSpec][i].nu;
-			 glVertex2f(nu, RefSpectrum[currentSpec][i].A + nu * refSlope);
-		 }
-		 glEnd();
-	 }
-
-	 int nSamples = MaterialList[currentMaterial].eta.size();
-	 float nu;
-	 //display absorbance
-	 if(dispMatK)
-	 {
-		 
-		 glColor3f(1.0, 0.0, 0.0);
-		 glBegin(GL_LINE_STRIP);
-		 for(int i=0; i<nSamples; i++){
-			 nu = MaterialList[currentMaterial].nu[i];
-			 glVertex2f(nu, MaterialList[currentMaterial].eta[i].imag() * dispScaleK);
-		 }
-		 glEnd();
-	 }
-	 if(dispSimK)
-	 {
-		 glColor3f(1.0, 1.0, 0.0);
-		 glBegin(GL_LINE_STRIP);
-		 for(unsigned int i=0; i<EtaK.size(); i++){
-			 glVertex2f(EtaK[i].nu, EtaK[i].A * dispScaleK);
-		 }
-		 glEnd();
-	 }
-
-	 //display refractive index (real)
-	 if(dispMatN)
-	 {
-		 glColor3f(0.0, 1.0, 0.0);
-		 glBegin(GL_LINE_STRIP);
-		 for(int i=0; i<nSamples; i++){
-			 nu = MaterialList[currentMaterial].nu[i];
-			 glVertex2f(nu, (MaterialList[currentMaterial].eta[i].real() - baseIR) * dispScaleN);
-		 }
-		 glEnd();
-	 }
-	 if(dispSimN)
-	 {
-		 glColor3f(0.0, 1.0, 1.0);
-		 glBegin(GL_LINE_STRIP);
-		 for(unsigned int i=0; i<EtaN.size(); i++)
-			 glVertex2f(EtaN[i].nu, (EtaN[i].A - baseIR) * dispScaleN);
-		 glEnd();
-	 }
-	 
-
-     glCallList(object);
- }
-
- void qtSpectrumDisplay::resizeGL(int width, int height)
- {
-     int side = qMin(width, height);
-     //glViewport((width - side) / 2, (height - side) / 2, side, side);
-	 glViewport(0, 0, width, height);
-
-     /*glMatrixMode(GL_PROJECTION);
-     glLoadIdentity();
-     //glOrtho(-0.5, +0.5, +0.5, -0.5, 4.0, 15.0);
-	 gluOrtho2D(nuMin, nuMax, aMin, aMax);
-     glMatrixMode(GL_MODELVIEW);*/
- }
-
- void qtSpectrumDisplay::mousePressEvent(QMouseEvent *event)
- {
-     lastPos = event->pos();
-
-	 if(event->buttons() & Qt::LeftButton)
-	 {
-		 int wn = 0;
-		 printWavenumber(event->x());
-	 }
- }
-
- void qtSpectrumDisplay::mouseMoveEvent(QMouseEvent *event)
- {
-     int dx = event->x() - lastPos.x();
-     int dy = event->y() - lastPos.y();
-	 /*
-     if (event->buttons() & Qt::LeftButton) {
-         setXRotation(xRot + 8 * dy);
-         setYRotation(yRot + 8 * dx);
-     } else if (event->buttons() & Qt::RightButton) {
-         setXRotation(xRot + 8 * dy);
-         setZRotation(zRot + 8 * dx);
-     }*/
-     lastPos = event->pos();
+     glEnd();
+}
+
+//display refractive index (real)
+if(dispMatN)
+{
+ glColor3f(0.0, 1.0, 0.0);
+ glBegin(GL_LINE_STRIP);
+ for(int i=0; i<nSamples; i++){
+     nu = MaterialList[currentMaterial].nu[i];
+     glVertex2f(nu, (MaterialList[currentMaterial].eta[i].real() - baseIR) * dispScaleN);
  }
+ glEnd();
+}
+if(dispSimN)
+{
+ glColor3f(0.0, 1.0, 1.0);
+ glBegin(GL_LINE_STRIP);
+ for(unsigned int i=0; i<EtaN.size(); i++)
+     glVertex2f(EtaN[i].nu, (EtaN[i].A - baseIR) * dispScaleN);
+ glEnd();
+}
 
- /*GLuint qtSpectrumDisplay::makeObject()
- {
-     GLuint list = glGenLists(1);
-     glNewList(list, GL_COMPILE);
-
-     glBegin(GL_QUADS);
-
-     GLdouble x1 = +0.06;
-     GLdouble y1 = -0.14;
-     GLdouble x2 = +0.14;
-     GLdouble y2 = -0.06;
-     GLdouble x3 = +0.08;
-     GLdouble y3 = +0.00;
-     GLdouble x4 = +0.30;
-     GLdouble y4 = +0.22;
-
-     quad(x1, y1, x2, y2, y2, x2, y1, x1);
-     quad(x3, y3, x4, y4, y4, x4, y3, x3);
 
-     extrude(x1, y1, x2, y2);
-     extrude(x2, y2, y2, x2);
-     extrude(y2, x2, y1, x1);
-     extrude(y1, x1, x1, y1);
-     extrude(x3, y3, x4, y4);
-     extrude(x4, y4, y4, x4);
-     extrude(y4, x4, y3, x3);
+glCallList(object);
+
+glFlush();
 
-     const double Pi = 3.14159265358979323846;
-     const int NumSectors = 200;
+//display the values at the mouse location
+renderText(50, 50, "test");
+}
 
-     for (int i = 0; i < NumSectors; ++i) {
-         double angle1 = (i * 2 * Pi) / NumSectors;
-         GLdouble x5 = 0.30 * sin(angle1);
-         GLdouble y5 = 0.30 * cos(angle1);
-         GLdouble x6 = 0.20 * sin(angle1);
-         GLdouble y6 = 0.20 * cos(angle1);
+void qtSpectrumDisplay::resizeGL(int width, int height)
+{
+ int side = qMin(width, height);
+ glViewport(0, 0, width, height);
 
-         double angle2 = ((i + 1) * 2 * Pi) / NumSectors;
-         GLdouble x7 = 0.20 * sin(angle2);
-         GLdouble y7 = 0.20 * cos(angle2);
-         GLdouble x8 = 0.30 * sin(angle2);
-         GLdouble y8 = 0.30 * cos(angle2);
+}
 
-         quad(x5, y5, x6, y6, x7, y7, x8, y8);
-
-         extrude(x6, y6, x7, y7);
-         extrude(x8, y8, x5, y5);
-     }
-
-     glEnd();
+void qtSpectrumDisplay::mousePressEvent(QMouseEvent *event)
+{
+ lastPos = event->pos();
 
-     glEndList();
-     return list;
- }*/
-
- void qtSpectrumDisplay::quad(GLdouble x1, GLdouble y1, GLdouble x2, GLdouble y2,
-                     GLdouble x3, GLdouble y3, GLdouble x4, GLdouble y4)
+ if(event->buttons() & Qt::LeftButton)
  {
-     qglColor(qtGreen);
-
-     glVertex3d(x1, y1, -0.05);
-     glVertex3d(x2, y2, -0.05);
-     glVertex3d(x3, y3, -0.05);
-     glVertex3d(x4, y4, -0.05);
-
-     glVertex3d(x4, y4, +0.05);
-     glVertex3d(x3, y3, +0.05);
-     glVertex3d(x2, y2, +0.05);
-     glVertex3d(x1, y1, +0.05);
+     int wn = 0;
+     printWavenumber(event->x());
  }
-
- /*void qtSpectrumDisplay::extrude(GLdouble x1, GLdouble y1, GLdouble x2, GLdouble y2)
- {
-     qglColor(qtGreen.dark(250 + int(100 * x1)));
-
-     glVertex3d(x1, y1, +0.05);
-     glVertex3d(x2, y2, +0.05);
-     glVertex3d(x2, y2, -0.05);
-     glVertex3d(x1, y1, -0.05);
- }*/
-
- void qtSpectrumDisplay::normalizeAngle(int *angle)
- {
-     while (*angle < 0)
-         *angle += 360 * 16;
-     while (*angle > 360 * 16)
-         *angle -= 360 * 16;
- }
\ No newline at end of file
+}
+
+void qtSpectrumDisplay::mouseMoveEvent(QMouseEvent *event)
+{
+ int dx = event->x() - lastPos.x();
+ int dy = event->y() - lastPos.y();
+
+ lastPos = event->pos();
+}
+
+void qtSpectrumDisplay::quad(GLdouble x1, GLdouble y1, GLdouble x2, GLdouble y2,
+                 GLdouble x3, GLdouble y3, GLdouble x4, GLdouble y4)
+{
+ qglColor(qtGreen);
+
+ glVertex3d(x1, y1, -0.05);
+ glVertex3d(x2, y2, -0.05);
+ glVertex3d(x3, y3, -0.05);
+ glVertex3d(x4, y4, -0.05);
+
+ glVertex3d(x4, y4, +0.05);
+ glVertex3d(x3, y3, +0.05);
+ glVertex3d(x2, y2, +0.05);
+ glVertex3d(x1, y1, +0.05);
+}
+
+void qtSpectrumDisplay::normalizeAngle(int *angle)
+{
+ while (*angle < 0)
+     *angle += 360 * 16;
+ while (*angle > 360 * 16)
+     *angle -= 360 * 16;
+}
diff --git a/rtsGUIConsole.cpp b/rtsGUIConsole.cpp
deleted file mode 100644
index 07559fc..0000000
--- a/rtsGUIConsole.cpp
+++ /dev/null
@@ -1,65 +0,0 @@
-#ifdef WIN32
-#include <windows.h>
-#include <stdio.h>
-#include <fcntl.h>
-#include <io.h>
-#include <iostream>
-#include <fstream>
-
-#ifndef _USE_OLD_IOSTREAMS
-
-using namespace std;
-#endif
-
-// maximum mumber of lines the output console should have
-
-static const WORD MAX_CONSOLE_LINES = 500;
-//#ifdef _DEBUG
-
-void RedirectIOToConsole(int Xpos, int Ypos, int Width, int Height)
-{
-	int hConHandle;
-	long lStdHandle;
-	CONSOLE_SCREEN_BUFFER_INFO coninfo;
-	FILE *fp;
-	// allocate a console for this app
-	AllocConsole();
-	// set the screen buffer to be big enough to let us scroll text
-	GetConsoleScreenBufferInfo(GetStdHandle(STD_OUTPUT_HANDLE), &coninfo);
-	coninfo.dwSize.Y = MAX_CONSOLE_LINES;
-	SetConsoleScreenBufferSize(GetStdHandle(STD_OUTPUT_HANDLE),
-	coninfo.dwSize);
-	// redirect unbuffered STDOUT to the console
-	lStdHandle = (long)GetStdHandle(STD_OUTPUT_HANDLE);
-	hConHandle = _open_osfhandle(lStdHandle, _O_TEXT);
-	fp = _fdopen( hConHandle, "w" );
-	*stdout = *fp;
-	setvbuf( stdout, NULL, _IONBF, 0 );
-	// redirect unbuffered STDIN to the console
-	lStdHandle = (long)GetStdHandle(STD_INPUT_HANDLE);
-	hConHandle = _open_osfhandle(lStdHandle, _O_TEXT);
-	fp = _fdopen( hConHandle, "r" );
-	*stdin = *fp;
-	setvbuf( stdin, NULL, _IONBF, 0 );
-
-	// redirect unbuffered STDERR to the console
-	lStdHandle = (long)GetStdHandle(STD_ERROR_HANDLE);
-	hConHandle = _open_osfhandle(lStdHandle, _O_TEXT);
-	fp = _fdopen( hConHandle, "w" );
-	*stderr = *fp;
-	setvbuf( stderr, NULL, _IONBF, 0 );
-
-	// make cout, wcout, cin, wcin, wcerr, cerr, wclog and clog
-	// point to console as well
-	ios::sync_with_stdio();
-	//position
-	MoveWindow(GetConsoleWindow(), Xpos, Ypos, Width, Height, true);
-}
-
-#else
-void RedirectIOToConsole(int Xpos, int Ypos, int Width, int Height)
-{
-}
-#endif
-
-//End of File
\ No newline at end of file
diff --git a/rtsGUIConsole.h b/rtsGUIConsole.h
deleted file mode 100644
index d74d721..0000000
--- a/rtsGUIConsole.h
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef __GUICON_H__
-
-#define __GUICON_H__
-
-//#ifdef _DEBUG
-
-void RedirectIOToConsole(int Xpos = 0, int Ypos = 0, int Width = 700, int Height = 400);
-
-//#endif
-
-#endif
-
-/* End of File */
\ No newline at end of file
--
libgit2 0.21.4