--- a
+++ b/combinedDeepLearningActiveContour/functions/sparseAutoencoderCost.m
@@ -0,0 +1,111 @@
+function [cost,grad] = sparseAutoencoderCost(theta, visibleSize, hiddenSize, ...
+                                             lambda, sparsityParam, beta, data)
+% visibleSize: the number of input units (probably 64) 
+% hiddenSize: the number of hidden units (probably 25) 
+% lambda: weight decay parameter
+% sparsityParam: The desired average activation for the hidden units (denoted in the lecture
+%                           notes by the greek alphabet rho, which looks like a lower-case "p").
+% beta: weight of sparsity penalty term
+% data: Our 64x10000 matrix containing the training data.  So, data(:,i) is the i-th training example. 
+  
+% The input theta is a vector (because minFunc expects the parameters to be a vector). 
+% We first convert theta to the (W1, W2, b1, b2) matrix/vector format, so that this 
+% follows the notation convention of the lecture notes. 
+
+W1 = reshape(theta(1:hiddenSize*visibleSize), hiddenSize, visibleSize);
+W2 = reshape(theta(hiddenSize*visibleSize+1:2*hiddenSize*visibleSize), visibleSize, hiddenSize);
+b1 = theta(2*hiddenSize*visibleSize+1:2*hiddenSize*visibleSize+hiddenSize);
+b2 = theta(2*hiddenSize*visibleSize+hiddenSize+1:end);
+
+% Cost and gradient variables (your code needs to compute these values). 
+% Here, we initialize them to zeros. 
+cost = 0;
+W1grad = zeros(size(W1)); 
+W2grad = zeros(size(W2));
+b1grad = zeros(size(b1)); 
+b2grad = zeros(size(b2));
+
+%% ---------- YOUR CODE HERE --------------------------------------
+%  Instructions: Compute the cost/optimization objective J_sparse(W,b) for the Sparse Autoencoder,
+%                and the corresponding gradients W1grad, W2grad, b1grad, b2grad.
+%
+% W1grad, W2grad, b1grad and b2grad should be computed using backpropagation.
+% Note that W1grad has the same dimensions as W1, b1grad has the same dimensions
+% as b1, etc.  Your code should set W1grad to be the partial derivative of J_sparse(W,b) with
+% respect to W1.  I.e., W1grad(i,j) should be the partial derivative of J_sparse(W,b) 
+% with respect to the input parameter W1(i,j).  Thus, W1grad should be equal to the term 
+% [(1/m) \Delta W^{(1)} + \lambda W^{(1)}] in the last block of pseudo-code in Section 2.2 
+% of the lecture notes (and similarly for W2grad, b1grad, b2grad).
+% 
+% Stated differently, if we were using batch gradient descent to optimize the parameters,
+% the gradient descent update to W1 would be W1 := W1 - alpha * W1grad, and similarly for W2, b1, b2. 
+% 
+
+% input data
+x=data;
+% for autoencoder output y is equal to x
+y=x; 
+
+% length of training data
+m=size(x,2);
+
+% Vectorized implementation of forward propagation
+z2 = W1 * x + repmat(b1,1,m);
+a2 = sigmoid(z2);
+z3 = W2 * a2 + repmat(b2,1,m);
+h = sigmoid(z3);
+
+% squared error term
+hmy=h-y;
+J_sq=sum(sum(hmy.*hmy))/(2*m);
+
+% weight decay term
+J_wd=lambda/(2)*(trace(W1'*W1)+trace(W2'*W2));
+
+% sparsity penalty
+rho=sparsityParam;
+rho_hat=mean(a2,2);
+KL=rho.*log(rho./rho_hat)+(1-rho).*log((1-rho)./(1-rho_hat));
+J_sp=beta*sum(KL);
+
+% cost= J_[squared_error]+J_[weight_decay]+J_[sparsity_penalty]
+cost=J_sq+J_wd+J_sp;
+
+% gradient
+a1=x;
+delta3 = -(y - h) .* fprime(z3); 
+sparsity_delta = - rho ./ rho_hat + (1 - rho) ./ (1 - rho_hat);
+sd_mat=repmat(sparsity_delta,1,m);
+delta2 = (W2'*delta3+beta*sd_mat) .* fprime(z2);
+ 
+W2grad =  delta3*a2'/m+lambda*W2;
+W1grad =  delta2*a1'/m+lambda*W1; 
+  
+b2grad = delta3 * ones(m,1)/m;
+b1grad = delta2* ones(m,1)/m;
+  
+%-------------------------------------------------------------------
+% After computing the cost and gradient, we will convert the gradients back
+% to a vector format (suitable for minFunc).  Specifically, we will unroll
+% your gradient matrices into a vector.
+grad = [W1grad(:) ; W2grad(:) ; b1grad(:) ; b2grad(:)];
+
+end
+
+%-------------------------------------------------------------------
+% Here's an implementation of the sigmoid function, which you may find useful
+% in your computation of the costs and the gradients.  This inputs a (row or
+% column) vector (say (z1, z2, z3)) and returns (f(z1), f(z2), f(z3)). 
+
+function sigm = sigmoid(x) 
+    sigm = 1 ./ (1 + exp(-x));
+end
+
+% derivative of sigmoid function
+% also we can implement it using: f'(x)= f(x)(1-f(x)) if f(x)=sigmoid
+function fp = fprime(x)
+  
+    fp = exp(-x) ./ (1 + exp(-x)).^2;
+end
+
+