diff --git a/Scripts_20210119/hit_analyse_v2 b/Scripts_20210119/hit_analyse_v2
index 3da64f0..aad5564 100755
Binary files a/Scripts_20210119/hit_analyse_v2 and b/Scripts_20210119/hit_analyse_v2 differ
diff --git a/Scripts_20210119/hit_analyse_v2.c b/Scripts_20210119/hit_analyse_v2.c
index 5af3e17..376dd84 100644
--- a/Scripts_20210119/hit_analyse_v2.c
+++ b/Scripts_20210119/hit_analyse_v2.c
@@ -132,13 +132,21 @@ int analyse(int argc, char **argv)
 	  else  if (boardnumber==3) {BPMbeamrecon_3=BPMbeamrecon_Zeroed;}
 	  
 	}
-	for (int j = 0;j<320;j++){
+	//	cout << "fill hist " << int(board_b[0].nrChannels) << endl;
+
+	for (int j = 0;j< board_b[0].nrChannels;j++){
 	  if (board_b[0].maxchannel_amp>100.) TH2D_b0_signal_vs_channel->Fill(j, board_b[0].channel_amp[j]);
+	}
+	for (int j = 0;j< board_b[1].nrChannels;j++){
 	  if (board_b[1].maxchannel_amp>100.) TH2D_b1_signal_vs_channel->Fill(j, board_b[1].channel_amp[j]);
+	}
+	for (int j = 0;j< board_b[2].nrChannels;j++){
 	  if (board_b[2].maxchannel_amp>100.) TH2D_b2_signal_vs_channel->Fill(j, board_b[2].channel_amp[j]);
+	}
+	for (int j = 0;j< board_b[3].nrChannels;j++){
 	  if (board_b[3].maxchannel_amp>100.) TH2D_b3_signal_vs_channel->Fill(j, board_b[3].channel_amp[j]);
-
 	}
+	//	cout << "fill tree" << endl;
 	rootTree->Fill(); 
 
       }
@@ -215,6 +223,14 @@ int set_background_v2(int start_frame, int max_frames){
    
   //Read first record to find board configuration
   Fullframe sampleframe;
+  file.seekg(start_frame * sampleframe.sizeInFile() , std::ios::beg);
+  if (sampleframe.read(&file) == 0) //read the next frame and catch if returns error
+    {
+      std::cerr << " ### Hitdata: First frame could not be read!" << std::endl;
+      file.close();		//read error, finish!
+      return 0;
+    }
+ 
  
   //Read
   // file.seekg(sampleframe.sizeInFile(), std::ios::beg);
@@ -228,6 +244,7 @@ int set_background_v2(int start_frame, int max_frames){
 	  return 0;
 	}
       for (int boardnumber = 0; boardnumber<4; boardnumber++){
+
 	for (int j = 0; j<sampleframe.boards[boardnumber].nrChannels;j++){
 	  board_b_bkg[boardnumber].channel_amp[j] += sampleframe.boards[boardnumber].data[j] / double(max_frames);
 	  //  std::cout <<  j << " " << board.channel_amp[j] << "    "  << dataptr->sensor_data[j] << std::endl;
@@ -245,26 +262,21 @@ bpm_frame_v2 readboard(Fullframe frame, int boardnumber){
   
   board.integratedsignalamp = 0.;
   board.maxchannel_amp = 0.;
+  board.nrChannels = frame.boards[boardnumber].nrChannels;
+  board.board_number = boardnumber;
+  
   //  file.seekg(boardnumber*sizeof(BufferData)+4*frame*sizeof(BufferData));
   //file.read ((char*)dataptr ,sizeof(BufferData));
 
   if (frame.boards[boardnumber].syncframe.device_nr==boardnumber){
+    
+    // cout << "nrChannels" <<  frame.boards[boardnumber].nrChannels << endl;
     for (int j = 0; j<frame.boards[boardnumber].nrChannels;j++){
       //subtract the background from the data
-      if (boardnumber==0){
-      // board_0 has the even and odd channels swapped in the hardware.
-	if(j%2==0){
-	  board.channel_amp[j] = frame.boards[boardnumber].data[j+1] -  board_b_bkg[boardnumber].channel_amp[j+1];
-	}
-	else{
-	  board.channel_amp[j] = frame.boards[boardnumber].data[j-1] -  board_b_bkg[boardnumber].channel_amp[j-1];
-	}
-      }
-      else{
-	board.channel_amp[j] = frame.boards[boardnumber].data[j] -  board_b_bkg[boardnumber].channel_amp[j];
+      board.channel_amp[j] = frame.boards[boardnumber].data[j] -  board_b_bkg[boardnumber].channel_amp[j];
 	//   std::cout <<  j << " " << board.channel_amp[j] << "    "  << frame.boards[boardnumber].data[j] << std::endl;
-      }
-
+	
+     
 
 
       //sum the signal across channels
@@ -323,14 +335,30 @@ beamRecon beamreconstruction(bpm_frame_v2 frametoanalyse, double threshold = 30.
 
   
   //  const int array_length = sizeof(frametoanalyse.channel_amp)/sizeof(double);
-  const int array_length = 320;
+  const int array_length = frametoanalyse.nrChannels ;
   vector<Channel> channel_reducedlist; //for anomaly detection
   vector<Channel> channel_reducedlistcopy; //for anomaly detection
 
+  //hardcoded pixels to mask for this data set.
+  const int arr_0[] = {139 };
+  //const  int arr_1[] = {};
+  const int arr_2[] = { 11,12 };
+  const int arr_3[] = { 1, 2, };
+
+  vector<int> masked_channels[4];
+  masked_channels[0].assign( arr_0, arr_0 + sizeof(arr_0) / sizeof(*arr_0) );
+  //  masked_channels[0].assign( arr_0, arr_0 + sizeof(arr_0) / sizeof(*arr_0) );
+  masked_channels[2].assign( arr_2, arr_2 + sizeof(arr_2) / sizeof(*arr_2) );
+  masked_channels[3].assign( arr_3, arr_3 + sizeof(arr_3) / sizeof(*arr_3) );
+
+ 
+  
+  
   Channel tmp;
   
   int temp_lastneighbour= -128;
   for (int i = 0; i< array_length; i++){
+    if (std::count( masked_channels[frametoanalyse.board_number].begin(), masked_channels[frametoanalyse.board_number].end(), i)) continue; //check masked pixel list, and do not add it to the list of channels for analysis. 
     if (frametoanalyse.channel_amp[i]>=threshold) {
       //  cout << "ch: " << i << endl;
       //    signal_list.push_back(frametoanalyse.channel_amp[i]);
diff --git a/Scripts_20210119/hit_analyse_v2.h b/Scripts_20210119/hit_analyse_v2.h
index c30bd93..7c24423 100644
--- a/Scripts_20210119/hit_analyse_v2.h
+++ b/Scripts_20210119/hit_analyse_v2.h
@@ -4,6 +4,7 @@
 #include <iostream>
 #include <numeric>
 #include <vector>
+#include <algorithm>    // std::count
 #include <utility>
 #include <TH2.h>
 #include <TF1.h>
@@ -57,6 +58,8 @@ struct bpm_frame_v2 {
   double avg_width;
   double integratedsignalamp;
   int maxchannel;
+  int nrChannels;
+  int board_number;
   double maxchannel_amp;
 };
 
@@ -64,7 +67,6 @@ struct bpm_frame_v2 {
 bpm_frame_v2 board_b[4];
 bpm_frame_v2 board_b_bkg[4];
 
-
 bpm_frame_v2 readboard(Fullframe frame, int boardnumber);
 int framestart = 0;
 
diff --git a/Scripts_20210119/hitreader.h b/Scripts_20210119/hitreader.h
index 4af0858..8bb465d 100644
--- a/Scripts_20210119/hitreader.h
+++ b/Scripts_20210119/hitreader.h
@@ -1,6 +1,7 @@
 //This is an object interface for reading HIT data files
 //See HIT documentation for details and examples.
 /*
+  THIS DOESN'T WORK!
   .L hitreader.c
 
   Hitdata data;
@@ -146,7 +147,7 @@ class Boardframe
       return 0;
     //  std::cout<< "data[" << nrChannels << "]: ";
     // for (int i = 0;i<nrChannels;i++) std::cout << data[i] << " ";
-    // std::cout << std::endl;
+    //  std::cout << std::endl;
     
     return 1;
   };