diff --git a/apps/specular_estimation/CMakeFiles/specular_estimation.dir/src/specular_estimation.cc.o b/apps/specular_estimation/CMakeFiles/specular_estimation.dir/src/specular_estimation.cc.o
index 29f286b396353394d9c6de2eded299c2d79ce50a..8fdb5fd66b50683eaab1cb5b09a01b2498042308 100644
Binary files a/apps/specular_estimation/CMakeFiles/specular_estimation.dir/src/specular_estimation.cc.o and b/apps/specular_estimation/CMakeFiles/specular_estimation.dir/src/specular_estimation.cc.o differ
diff --git a/apps/specular_estimation/src/Charuco.h b/apps/specular_estimation/src/Charuco.h
index 6ae96fdc7b598250eee9df4f1612144642ba1288..75d48e75bc2e9f3035c9510d698a7aeb76a29161 100644
--- a/apps/specular_estimation/src/Charuco.h
+++ b/apps/specular_estimation/src/Charuco.h
@@ -32,8 +32,8 @@ void charucoCalibration(int width, int height, cv::Ptr<cv::aruco::CharucoBoard>
 	cv::Ptr<cv::aruco::Dictionary> dictionary = cv::aruco::getPredefinedDictionary(cv::aruco::PREDEFINED_DICTIONARY_NAME(dictionaryId));
 
 	// Create a ChArUco board
-	int xSquares = 9;
-	int ySquares = 11;
+	int xSquares = 11;
+	int ySquares = 9;
 	float squareSideLength = 0.04f;
 	float markerSideLength = 0.02f;
 	charucoBoard = cv::aruco::CharucoBoard::create(xSquares, ySquares, squareSideLength, markerSideLength, dictionary);
@@ -41,8 +41,8 @@ void charucoCalibration(int width, int height, cv::Ptr<cv::aruco::CharucoBoard>
 	//charucoBoardImage = drawCharuco(charucoBoard, height, ((height * xSquares) / ySquares), false, false);
 
 	// Rotate ChArUco board
-	cv::Mat tempImage = drawCharuco(charucoBoard, ((width * ySquares) / xSquares), width, false, false);
-	cv::rotate(tempImage, charucoBoardImage, cv::ROTATE_90_COUNTERCLOCKWISE);
+	//cv::Mat tempImage = drawCharuco(charucoBoard, ((width * ySquares) / xSquares), width, false, false);
+	//cv::rotate(tempImage, charucoBoardImage, cv::ROTATE_90_COUNTERCLOCKWISE);
 
 	// Calibrate the camera using the ChArUco board images to obtain the camera matrix and distortion coefficients
 	calibrateCamera(xSquares, ySquares, squareSideLength, markerSideLength, dictionaryId, charucoImages, cameraMatrix, distortionCoefficients);
diff --git a/apps/specular_estimation/src/OpenGL.h b/apps/specular_estimation/src/OpenGL.h
index 484f93187543058daf87c24adfa35fad84d7c92a..48bd920ab4e8253cb1d0d1a4e2c3a9836de3026f 100644
--- a/apps/specular_estimation/src/OpenGL.h
+++ b/apps/specular_estimation/src/OpenGL.h
@@ -112,7 +112,7 @@ void initialiseOpenGL(cv::Mat cv_depth, cv::Mat cv_normals, cv::Mat cv_texture,
 	glBindVertexArray(VertexArrayID);
 
 	// Create and compile the GLSL program from the shaders
-	depthProgramID = LoadShaders("DepthRTT.vertexshader", "DepthRTT.fragmentshader");
+	depthProgramID = LoadShaders("/home/thomas/Documents/Minimisation/apps/specular_estimation/src/DepthRTT.vertexshader", "/home/thomas/Documents/Minimisation/apps/specular_estimation/src/DepthRTT.fragmentshader");
 
 	// Get a handle for the "MVP" uniform
 	GLuint depthMatrixID = glGetUniformLocation(depthProgramID, "depthMVP");
@@ -200,13 +200,13 @@ void initialiseOpenGL(cv::Mat cv_depth, cv::Mat cv_normals, cv::Mat cv_texture,
 	glBufferData(GL_ARRAY_BUFFER, sizeof(g_quad_vertex_buffer_data), g_quad_vertex_buffer_data, GL_STATIC_DRAW);
 
 	// Create and compile the GLSL program from the shaders
-	quad_programID = LoadShaders("Passthrough.vertexshader", "SimpleTexture.fragmentshader");
+	quad_programID = LoadShaders("/home/thomas/Documents/Minimisation/apps/specular_estimation/src/Passthrough.vertexshader", "/home/thomas/Documents/Minimisation/apps/specular_estimation/src/SimpleTexture.fragmentshader");
 	std::cout << "Shaders loaded.\n";
 	GLuint texID = glGetUniformLocation(quad_programID, "texture");
 	std::cout << "Uniform Location of texture found.\n";
 
 	// Create and compile the GLSL program from the shaders
-	programID = LoadShaders("ShadowMapping.vertexshader", "ShadowMapping.fragmentshader");
+	programID = LoadShaders("/home/thomas/Documents/Minimisation/apps/specular_estimation/src/ShadowMapping.vertexshader", "/home/thomas/Documents/Minimisation/apps/specular_estimation/src/ShadowMapping.fragmentshader");
 
 	// Get a handle for the "myTextureSampler" uniform
 	TextureID = glGetUniformLocation(programID, "myTextureSampler");
diff --git a/apps/specular_estimation/src/specular_estimation.cc b/apps/specular_estimation/src/specular_estimation.cc
index c955a26ba939630766a1cd2a4381af04eec1077f..be1f60ca97999a89c0e77cdbb1aa13ebbb81b6f5 100644
--- a/apps/specular_estimation/src/specular_estimation.cc
+++ b/apps/specular_estimation/src/specular_estimation.cc
@@ -108,7 +108,16 @@ int main(int argc, char** argv) {
 	
 	charucoCalibration(width, height, charucoBoard, charucoBoardImage, cameraMatrix, distortionCoefficients);
 
-	charucoAlignment(charucoImages, textureImages, numberOfLights, width, height, rotationMatrix, rotationVector, perspectiveTransform, lightDirections, lightDirectionsPerspective, rvecs, tvecs, charucoBoard, charucoBoardImage, cameraMatrix, distortionCoefficients);
+	//charucoAlignment(charucoImages, textureImages, numberOfLights, width, height, rotationMatrix, rotationVector, perspectiveTransform, lightDirections, lightDirectionsPerspective, rvecs, tvecs, charucoBoard, charucoBoardImage, cameraMatrix, distortionCoefficients);
+
+/*
+	rotationMatrix = 
+	rotationVector = 
+	perspectiveTransform = 
+	lightDirectionsPerspective = 
+	std::vector< cv::Vec3d > & rvecs
+	std::vector< cv::Vec3d > & tvecs
+*/
 
 	photometricStereo(imageName, calibration, modelPath, imageScale, cropping, showTexture, heightMap, normalMap, texture, lightDirections, lightDirectionsPerspective, textureImages, modelImages, calibrationImages, calibrationBoundingBox, width, height, rvecs, tvecs);
 	//photometricStereo(imageName, calibration, modelPath, imageScale, cropping, showTexture, heightMap, normalMap, texture, lightDirections, lightDirectionsPerspective, charucoImages, modelImages, calibrationImages, calibrationBoundingBox, width, height, rvecs, tvecs);
diff --git a/bin/specular_estimation b/bin/specular_estimation
index 83432c42febbb68c2d0b017531d9c95b7f3c6914..655deac80b3188a31c444e3a1e56a6db0efa6f1b 100755
Binary files a/bin/specular_estimation and b/bin/specular_estimation differ