From 1a55a328300dc8bae2d0576f3a8b8bb16e16c84c Mon Sep 17 00:00:00 2001
From: David Mayerich <mayerich@uh.edu>
Date: Wed, 3 Jun 2015 18:09:19 -0500
Subject: [PATCH] Added comments for apply_mask for Brad

---
 stim/envi/bil.h | 13 +++++++------
 stim/envi/bip.h | 28 ++++++++++++++--------------
 2 files changed, 21 insertions(+), 20 deletions(-)

diff --git a/stim/envi/bil.h b/stim/envi/bil.h
index a770292..8142a8b 100644
--- a/stim/envi/bil.h
+++ b/stim/envi/bil.h
@@ -814,15 +814,16 @@ public:
 
 		std::ofstream target(outfile.c_str(), std::ios::binary);
 
-		unsigned XZ = R[0] * R[2];		//calculate number of a band
-		unsigned L = XZ * sizeof(T);
+		//I THINK THIS IS WRONG
+		unsigned XZ = R[0] * R[2];		//calculate the number of values in a page on disk
+		unsigned L = XZ * sizeof(T);	//calculate the size of the page (in bytes)
 
-		T * temp = (T*)malloc(L);
+		T * temp = (T*)malloc(L);		//allocate memory for a temporary page
 
-		for (unsigned i = 0; i < R[1]; i++)
+		for (unsigned i = 0; i < R[1]; i++)			//for each value in R[1] (BIP should be X)
 		{
-			getY(temp, i);
-			for ( unsigned j = 0; j < R[2]; j++)
+			getY(temp, i);							//retrieve an ZX slice, stored in temp
+			for ( unsigned j = 0; j < R[2]; j++)	//for each R[2] (BIP should be Y)
 			{
 				for (unsigned k = 0; k < R[0]; k++)
 				{
diff --git a/stim/envi/bip.h b/stim/envi/bip.h
index 565f086..c2788ff 100644
--- a/stim/envi/bip.h
+++ b/stim/envi/bip.h
@@ -905,29 +905,29 @@ public:
 
 		std::ofstream target(outfile.c_str(), std::ios::binary);
 
-		unsigned ZX = R[2] * R[0];		//calculate number of a band
-		unsigned L = ZX * sizeof(T);
+		unsigned ZX = R[2] * R[0];		//calculate the number of values in a page (XZ in BIP)
+		unsigned L = ZX * sizeof(T);	//calculate the number of bytes in a page
 
-		T * temp = (T*)malloc(L);
+		T * temp = (T*)malloc(L);		//allocate space for that page
 
-		for (unsigned i = 0; i < R[1]; i++)
+		for (unsigned i = 0; i < R[1]; i++)			//for each page (Y in BIP)
 		{
-			getY(temp, i);
-			for ( unsigned j = 0; j < R[0]; j++)
+			getY(temp, i);							//load that page (it's pointed to by temp)
+			for ( unsigned j = 0; j < R[0]; j++)	//for each X value
 			{
-				for (unsigned k = 0; k < R[2]; k++)
+				for (unsigned k = 0; k < R[2]; k++)	//for each B value (band)
 				{
-				if(p[i * R[0] + k] == 0)
-					temp[j * R[2] + k] = 0;
-				else
+				if(p[i * R[0] + k] == 0)			//if the mask value is zero
+					temp[j * R[2] + k] = 0;			//set the pixel value to zero
+				else								//otherwise just continue
 					continue;
 				}
 			}
-			target.write(reinterpret_cast<const char*>(temp), L);   //write a band data into target file	
+			target.write(reinterpret_cast<const char*>(temp), L);   //write the edited band data into target file
 		}
-		target.close();
-		free(temp);
-		return true;
+		target.close();						//close the target file
+		free(temp);							//free allocated memory
+		return true;						//return true
 	}
 
 	/// Calculate the mean band value (average along B) at each pixel location.
--
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