diff --git a/envi/bsq.h b/envi/bsq.h
index 205c3be..98978f6 100644
--- a/envi/bsq.h
+++ b/envi/bsq.h
@@ -575,7 +575,17 @@ public:
 		return true;	
 	}		
 	
-	//peak area to peak area ratio
+	/// This function computes the ratio between two peak areas.
+
+	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
+	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
+	/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
+	/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
+	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
+	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
+	/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
+	/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)	
+	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
 	bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
 					double lb2, double rb2, double lab2, double rab2, T* result){
 		
@@ -598,7 +608,13 @@ public:
 		return true;	
 	}		
 
-	//x * f(x)
+	/// This function computes the definite integral of a baseline corrected peak.
+
+	/// @param lb is the label value for the left baseline point
+	/// @param rb is the label value for the right baseline point
+	/// @param lab is the label for the start of the definite integral
+	/// @param rab is the label for the end of the definite integral
+	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
 	bool x_area(double lb, double rb, double lab, double rab, T* result){
 		T* lp;	//left band pointer
 		T* rp;	//right band pointer
@@ -673,7 +689,13 @@ public:
 		return true;
 	}
 
-	//centroid point
+	/// This function computes the centroid of a baseline corrected peak.
+
+	/// @param lb is the label value for the left baseline point
+	/// @param rb is the label value for the right baseline point
+	/// @param lab is the label for the start of the peak
+	/// @param rab is the label for the end of the peak
+	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
 	bool cpoint(double lb, double rb, double lab, double rab, T* result){
 		T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));	
 		T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));	
@@ -694,7 +716,13 @@ public:
 		return true;	
 	}
 
-	//create mask file
+	/// This function creates a mask based on a given band and threshold value.
+
+	/// All pixels in the
+	/// specified band greater than the threshold are true and all pixels less than the threshold are false.
+	/// @param mask_band is the band used to specify the mask
+	/// @param threshold is the threshold used to determine if the mask value is true or false
+	/// @param p is a pointer to a pre-allocated array at least X * Y in size
 	bool build_mask(double mask_band, double threshold, unsigned char* p = NULL){
 
 		T* temp = (T*)malloc(R[0] * R[1] * sizeof(T));		//allocate memory for the certain band
@@ -712,7 +740,10 @@ public:
 
 	}
 
-	//apply mask
+	/// This function applies a mask file to the BSQ image, setting all values outside the mask to zero.
+
+	/// @param outfile is the name of the masked output file
+	/// @param p is a pointer to memory of size X * Y, where p(i) = 0 for pixels that will be set to zero.
 	bool apply_mask(std::string outfile, unsigned char* p){
 
 		std::ofstream target(outfile.c_str(), std::ios::binary);
@@ -741,7 +772,9 @@ public:
 		return true;
 	}
 
-	//calculate the average band
+	/// This function calculates the mean band value (average along B) at each pixel location.
+
+	/// @param p is a pointer to memory of size X * Y * sizeof(T) that will store the band averages.
 	bool band_avg(T* p){
 		unsigned long long XY = R[0] * R[1];
 		T* temp = (T*)malloc(sizeof(T) * XY);
--
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