From fd9ab176aa360f16def68ecbffbbade7215ce2e3 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Tue, 25 Jun 2019 07:13:43 -0500
Subject: [PATCH 01/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 53 +++++++++++++++------
 1 file changed, 39 insertions(+), 14 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 9114820..4c24d6c 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -15,7 +15,8 @@ class VFATdata
     uint16_t fcrc_calc;                ///<Check Sum value recalculated, 16 bits
     int      fSlotNumber;              ///<Calculated chip position
     bool     fisBlockGood;             ///<Shows if block is good (control bits, chip ID and CRC checks)
-  
+    uint16_t controlData;	       ///<For ZeroSuppression. Shows which packets (out of sixteen) are nonempty	
+    uint8_t packets[16];
   public:
     //!Empty constructor. Functions used to assign data members.
     VFATdata(){}
@@ -46,28 +47,52 @@ class VFATdata
     ~VFATdata(){}
 
     //!Read first word from the block.
-    void read_fw(uint64_t word)
+    void read_fw(uint64_t word, int c)
     {
-      fPos = 0x3f & (word >> 56);
-      fCRCcheck = 0xff & (word >> 48);
-      fHeader = 0xff & (word >> 40);
-      fEC = 0xff & (word >> 32);
-      fBC = 0xffff & (word >> 16);
-      fmsData = 0xffff000000000000 & (word << 48);
+	switch(c){
+		case 1:fPos = 0x3f & (word >> 56);
+			fCRCcheck = 0xff & (word >> 48);
+			fHeader = 0xff & (word >> 40);
+			fEC = 0xff & (word >> 32);
+			fBC = 0xffff & (word >> 16);
+			fmsData = 0xffff000000000000 & (word << 48);
+			break;
+		case 2:fPos = 0x3f & (word >> 56);
+			fCRCcheck = 0xff & (word >> 48);
+			fHeader = 0xff & (word >> 40);
+			fEC = 0xff & (word >> 32);
+			fBC = 0xffff & (word >> 16);
+			//fmsData = 0xffff000000000000 & (word << 48);
+			controlData = word << 16
+			break;
+	}
     }
     
     //!Read second word from the block.
-    void read_sw(uint64_t word)
+    void read_sw(uint64_t word, int c)
     {
-      fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
-      flsData = 0xffff000000000000 & (word << 48);
+	    switch(c){
+		    case 1:fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
+			   flsData = 0xffff000000000000 & (word << 48);
+			   break;
+		    case 2:
+			    if(){fcrc = 0xffff & word;}
+			    break;
+	    }
+      
+      
     }
     
     //!Read third word from the block.
-    void read_tw(uint64_t word)
+    void read_tw(uint64_t word,int c)
     {
-      flsData = flsData | (0x0000ffffffffffff & word >> 16);
-      fcrc = 0xffff & word;
+	    switch(c){
+		    case 1:flsData = flsData | (0x0000ffffffffffff & word >> 16);
+			    fcrc = 0xffff & word;
+			    break;
+		    case 2: break;
+	    
+	    }
     }
     
     uint8_t   Pos        (){ return fPos;        }

From 584957e2f3deaa0ffbf618a99e47b89064a0d213 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Wed, 26 Jun 2019 06:02:36 -0500
Subject: [PATCH 02/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 23 +++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 4c24d6c..59f9808 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -16,7 +16,8 @@ class VFATdata
     int      fSlotNumber;              ///<Calculated chip position
     bool     fisBlockGood;             ///<Shows if block is good (control bits, chip ID and CRC checks)
     uint16_t controlData;	       ///<For ZeroSuppression. Shows which packets (out of sixteen) are nonempty	
-    uint8_t packets[16];
+    int count;			       ///<For ZeroSuppression. Shows how many packets are nonempty
+    uint8_t packets[16];	       ///<For Containing the Packets
   public:
     //!Empty constructor. Functions used to assign data members.
     VFATdata(){}
@@ -58,6 +59,8 @@ class VFATdata
 			fmsData = 0xffff000000000000 & (word << 48);
 			break;
 		case 2:fPos = 0x3f & (word >> 56);
+			//The method is exactly the same as before, except the laft 16 bits of line 1 are not vfat data, but
+			//a 16 bit number with bits indicating which packet is populated with anything (8 channels for a packet)
 			fCRCcheck = 0xff & (word >> 48);
 			fHeader = 0xff & (word >> 40);
 			fEC = 0xff & (word >> 32);
@@ -75,9 +78,21 @@ class VFATdata
 		    case 1:fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
 			   flsData = 0xffff000000000000 & (word << 48);
 			   break;
-		    case 2:
-			    if(){fcrc = 0xffff & word;}
-			    break;
+		    case 2:count=0;
+			   //This populates an array of 8 bit numbers whose length corresponds to the number of packets.
+			   uint16_t helper=controlData;
+			   int i=0;
+			   while (helper > 0) {
+            			count += helper & 1;
+            			helper >>= 1;
+        		   }
+			   while(count>0){
+				packets[i] = (word >> 64-(i+1)*8);
+			   	i+=1;
+				count-=1;
+				if(i*8==56){break;}
+			   }
+			   
 	    }
       
       

From b3d5e885db7174693e5dada59fd35906be802672 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Wed, 26 Jun 2019 06:18:41 -0500
Subject: [PATCH 03/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 59f9808..c77ac74 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -66,7 +66,7 @@ class VFATdata
 			fEC = 0xff & (word >> 32);
 			fBC = 0xffff & (word >> 16);
 			//fmsData = 0xffff000000000000 & (word << 48);
-			controlData = word << 16
+			controlData = word
 			break;
 	}
     }

From 7e8725234b93ed6d34cb0461033fc6ae4b379e6a Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Thu, 27 Jun 2019 03:15:42 -0500
Subject: [PATCH 04/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index c77ac74..9b65feb 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -18,7 +18,8 @@ class VFATdata
     uint16_t controlData;	       ///<For ZeroSuppression. Shows which packets (out of sixteen) are nonempty	
     int count;			       ///<For ZeroSuppression. Shows how many packets are nonempty
     uint8_t packets[16];	       ///<For Containing the Packets
-  public:
+    int counter2;		       ///<Purely counting variable. Must be in so that packets aren't overwritten
+   public:
     //!Empty constructor. Functions used to assign data members.
     VFATdata(){}
     //!Constructor requiring arguments.
@@ -66,7 +67,7 @@ class VFATdata
 			fEC = 0xff & (word >> 32);
 			fBC = 0xffff & (word >> 16);
 			//fmsData = 0xffff000000000000 & (word << 48);
-			controlData = word
+			controlData = 0xffff & word
 			break;
 	}
     }
@@ -81,17 +82,18 @@ class VFATdata
 		    case 2:count=0;
 			   //This populates an array of 8 bit numbers whose length corresponds to the number of packets.
 			   uint16_t helper=controlData;
-			   int i=0;
 			   while (helper > 0) {
             			count += helper & 1;
             			helper >>= 1;
         		   }
+			   int i=0
 			   while(count>0){
-				packets[i] = (word >> 64-(i+1)*8);
-			   	i+=1;
+				packets[i] =0xffff & (word >> 64-(counter2+1)*8);
+			   	counter2+=1;
 				count-=1;
-				if(i*8==56){break;}
+				if(counter2*8==56){break;}
 			   }
+			   break;
 			   
 	    }
       
@@ -105,8 +107,7 @@ class VFATdata
 		    case 1:flsData = flsData | (0x0000ffffffffffff & word >> 16);
 			    fcrc = 0xffff & word;
 			    break;
-		    case 2: break;
-	    
+		    case 2: 	    
 	    }
     }
     

From b6fef93d3ff6bd0bed062cdd0ddd78bd40d199a1 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Thu, 27 Jun 2019 04:25:04 -0500
Subject: [PATCH 05/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 55 ++++++++++++++++-----
 1 file changed, 43 insertions(+), 12 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 9b65feb..0aa8def 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -18,7 +18,9 @@ class VFATdata
     uint16_t controlData;	       ///<For ZeroSuppression. Shows which packets (out of sixteen) are nonempty	
     int count;			       ///<For ZeroSuppression. Shows how many packets are nonempty
     uint8_t packets[16];	       ///<For Containing the Packets
-    int counter2;		       ///<Purely counting variable. Must be in so that packets aren't overwritten
+    int need3=0;		       ///<Determines if we need to read the crc off in the third line
+    int need4=0;		       ///<Determines if we need to read a fourth instance to read off CRC codes.
+
    public:
     //!Empty constructor. Functions used to assign data members.
     VFATdata(){}
@@ -88,18 +90,19 @@ class VFATdata
         		   }
 			   int i=0
 			   while(count>0){
-				packets[i] =0xffff & (word >> 64-(counter2+1)*8);
-			   	counter2+=1;
+				packets[i] = 0xffff & (word >> 64-(i+1)*8);
+			   	i+=1;
 				count-=1;
-				if(counter2*8==56){break;}
+				if((i*8==56&&count==0)){need3=1;}
+				if((i*8==64&&count==0)){need3=2;}
+				//need3 will take 0 if third line not needed, 1 if needed just to read of half of crc,2 if all, 3 if needed for data and crc
+				if(i*8==64){break;}
 			   }
-			   break;
-			   
-	    }
-      
-      
+			   if(i<7){fcrc = 0xffff & word;need3=0;break;}//In case we don't even need a third line
+			   fcrc= 0xffff & (word << 8);//In case it cuts it off
+			   break;		   
+	    }   
     }
-    
     //!Read third word from the block.
     void read_tw(uint64_t word,int c)
     {
@@ -107,10 +110,38 @@ class VFATdata
 		    case 1:flsData = flsData | (0x0000ffffffffffff & word >> 16);
 			    fcrc = 0xffff & word;
 			    break;
-		    case 2: 	    
+		    case 2:
+			    if(need3==1){fcrc=fcrc|(0xff & word >> 56);break;}//If it was cut off before
+			    if(need3==2){fcrc=0xffff & (word >> 48);break;}//If we just barely needed the full line
+			    if(need3==3){
+				    int i=0;
+				    while(count>0){
+					    packets[i+8] = 0xff & (word >> 64-(i+1)*8);
+					    i+=1;
+					    count-=1;
+					    if(i*8==56){need4=1;}//Takes 0 if 4rth line not needed, Takes 1 if 1/2 crc needed, Takes 2 otherwise
+					    if(i*8==64){need4=2;break;}
+				    }
+				    if(0<i&&i<7){fcrc= 0xffff & (word >> 64-(i+2)*8);}//In case the whole word stays in
+				    if(i*8==56){fcrc= 0xffff & (word << 8)};//In case it cuts it off
+				    break;
+			    } 
+			    break;	    
 	    }
     }
-    
+    void read_4w(uint64_t word)
+    {
+	    if(need4==1){fcrc=fcrc|(0xff & word >> 56);break;}//if it had previously cut it off before
+	    fcrc=0xffff & (word >> 48);
+	    break;	    
+    }
+    int getNeed3(){
+	    return need3;	
+    }
+    int getNeed4(){
+	    return need4;	
+    }
+
     uint8_t   Pos        (){ return fPos;        }
     uint16_t  BC         (){ return fBC;         }
     uint8_t   Header     (){ return fHeader;     }

From 1eeb1fb44a75362121eb4cfaea7f54561c48a27a Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Thu, 27 Jun 2019 04:36:11 -0500
Subject: [PATCH 06/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index c281ec5..a4d046f 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -110,15 +110,21 @@ class GEMUnpacker
               std::fread(&m_word, sizeof(uint64_t), 1, m_file);
         //printf("VFAT WORD 1\n");
         //printf("%016llX\n", m_word);
-              m_vfatdata->read_fw(m_word);
+              int helper=2
+              m_vfatdata->read_fw(m_word,helper);
               std::fread(&m_word, sizeof(uint64_t), 1, m_file);
         //printf("VFAT WORD 2\n");
         //printf("%016llX\n", m_word);
-              m_vfatdata->read_sw(m_word);
-              std::fread(&m_word, sizeof(uint64_t), 1, m_file);
+              m_vfatdata->read_sw(m_word,helper);
+              if(getNeed3()>0||helper==1){
+               std::fread(&m_word, sizeof(uint64_t), 1, m_file); 
         //printf("VFAT WORD 3\n");
         //printf("%016llX\n", m_word);
-              m_vfatdata->read_tw(m_word);
+              m_vfatdata->read_tw(m_word);}
+              if(getNeed4()>0){
+                std::fread(&m_word, sizeof(uint64_t), 1, m_file); 
+                m_vfatdata->read_4w(m_word);
+              }
               //
         //printf("VFAT MS Data 3\n");
         //printf("%016llX\n", m_vfatdata->msData());

From 30e3c4d5557b33fb7029247857bb492d8adbd2f1 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 28 Jun 2019 06:08:48 -0500
Subject: [PATCH 07/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 119 +++++++++-----------
 1 file changed, 55 insertions(+), 64 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 0aa8def..69dcaf6 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -20,6 +20,7 @@ class VFATdata
     uint8_t packets[16];	       ///<For Containing the Packets
     int need3=0;		       ///<Determines if we need to read the crc off in the third line
     int need4=0;		       ///<Determines if we need to read a fourth instance to read off CRC codes.
+    uint4_t Suppression;	       ///<Determines what type, if any, of suppression is used
 
    public:
     //!Empty constructor. Functions used to assign data members.
@@ -53,80 +54,70 @@ class VFATdata
     //!Read first word from the block.
     void read_fw(uint64_t word, int c)
     {
-	switch(c){
-		case 1:fPos = 0x3f & (word >> 56);
-			fCRCcheck = 0xff & (word >> 48);
-			fHeader = 0xff & (word >> 40);
-			fEC = 0xff & (word >> 32);
-			fBC = 0xffff & (word >> 16);
-			fmsData = 0xffff000000000000 & (word << 48);
-			break;
-		case 2:fPos = 0x3f & (word >> 56);
-			//The method is exactly the same as before, except the laft 16 bits of line 1 are not vfat data, but
-			//a 16 bit number with bits indicating which packet is populated with anything (8 channels for a packet)
-			fCRCcheck = 0xff & (word >> 48);
-			fHeader = 0xff & (word >> 40);
-			fEC = 0xff & (word >> 32);
-			fBC = 0xffff & (word >> 16);
-			//fmsData = 0xffff000000000000 & (word << 48);
-			controlData = 0xffff & word
-			break;
+	suppression = 0x4 & (word >> 61);
+	fPos = 0x3f & (word >> 56);
+	fCRCcheck = 0xff & (word >> 48);
+	fHeader = 0xff & (word >> 40);
+	fEC = 0xff & (word >> 32);
+	fBC = 0xffff & (word >> 16);
+	if(suppression< 0x4){
+		fmsData = 0xffff000000000000 & (word << 48);
+		return;
 	}
+	//fmsData = 0xffff000000000000 & (word << 48);
+	controlData = 0xffff & word//a 16 bit number with bits indicating which packet is populated with anything (8 channels for a packet)
     }
     
     //!Read second word from the block.
     void read_sw(uint64_t word, int c)
     {
-	    switch(c){
-		    case 1:fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
-			   flsData = 0xffff000000000000 & (word << 48);
-			   break;
-		    case 2:count=0;
-			   //This populates an array of 8 bit numbers whose length corresponds to the number of packets.
-			   uint16_t helper=controlData;
-			   while (helper > 0) {
-            			count += helper & 1;
-            			helper >>= 1;
-        		   }
-			   int i=0
-			   while(count>0){
-				packets[i] = 0xffff & (word >> 64-(i+1)*8);
-			   	i+=1;
-				count-=1;
-				if((i*8==56&&count==0)){need3=1;}
-				if((i*8==64&&count==0)){need3=2;}
-				//need3 will take 0 if third line not needed, 1 if needed just to read of half of crc,2 if all, 3 if needed for data and crc
-				if(i*8==64){break;}
-			   }
-			   if(i<7){fcrc = 0xffff & word;need3=0;break;}//In case we don't even need a third line
-			   fcrc= 0xffff & (word << 8);//In case it cuts it off
-			   break;		   
-	    }   
+	    if(suppression< 0x4){
+	    	fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
+		flsData = 0xffff000000000000 & (word << 48);
+		return;
+	    }
+	    count=0;
+	    //This populates an array of 8 bit numbers whose length corresponds to the number of packets.
+ 	    uint16_t helper=controlData;
+	    while (helper > 0) {
+            	count += helper & 1;
+            	helper >>= 1;
+	    }
+	    int i=0;
+	    while(count>0){
+		    packets[i] = 0xffff & (word >> 64-(i+1)*8);
+		    i+=1;
+		    count-=1;
+		    if((i*8==56&&count==0)){need3=1;}
+		    if((i*8==64&&count==0)){need3=2;}
+		    //need3 will take 0 if third line not needed, 1 if needed just to read of half of crc,2 if all, 3 if needed for data and crc
+		    if(i*8==64){break;}
+	    }
+	    if(i<7){fcrc = 0xffff & word;need3=0;break;}//In case we don't even need a third line
+	    fcrc= 0xffff & (word << 8);//In case it cuts it off		     
     }
     //!Read third word from the block.
     void read_tw(uint64_t word,int c)
     {
-	    switch(c){
-		    case 1:flsData = flsData | (0x0000ffffffffffff & word >> 16);
-			    fcrc = 0xffff & word;
-			    break;
-		    case 2:
-			    if(need3==1){fcrc=fcrc|(0xff & word >> 56);break;}//If it was cut off before
-			    if(need3==2){fcrc=0xffff & (word >> 48);break;}//If we just barely needed the full line
-			    if(need3==3){
-				    int i=0;
-				    while(count>0){
-					    packets[i+8] = 0xff & (word >> 64-(i+1)*8);
-					    i+=1;
-					    count-=1;
-					    if(i*8==56){need4=1;}//Takes 0 if 4rth line not needed, Takes 1 if 1/2 crc needed, Takes 2 otherwise
-					    if(i*8==64){need4=2;break;}
-				    }
-				    if(0<i&&i<7){fcrc= 0xffff & (word >> 64-(i+2)*8);}//In case the whole word stays in
-				    if(i*8==56){fcrc= 0xffff & (word << 8)};//In case it cuts it off
-				    break;
-			    } 
-			    break;	    
+	    if(suppression< 0x4){
+		    flsData = flsData | (0x0000ffffffffffff & word >> 16);
+		    fcrc = 0xffff & word;
+	 	    break;
+		    return;
+	    }
+	    if(need3==1){fcrc=fcrc|(0xff & word >> 56);return;}//If it was cut off before
+	    if(need3==2){fcrc=0xffff & (word >> 48);return;}//If we just barely needed the full line
+	    if(need3==3){
+		    int i=0;
+		    while(count>0){
+			    packets[i+8] = 0xff & (word >> 64-(i+1)*8);
+			    i+=1;
+			    count-=1;
+			    if(i*8==56){need4=1;}//Takes 0 if 4rth line not needed, Takes 1 if 1/2 crc needed, Takes 2 otherwise
+			    if(i*8==64){need4=2;break;}
+		    }
+		    if(0<i&&i<7){fcrc= 0xffff & (word >> 64-(i+2)*8);}//In case the whole word stays in
+		    if(i*8==56){fcrc= 0xffff & (word << 8)};//In case it cuts it off
 	    }
     }
     void read_4w(uint64_t word)

From 8e20ae5a893f017dd099df99a5ae8ef1ce2c789d Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 28 Jun 2019 06:23:00 -0500
Subject: [PATCH 08/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 69dcaf6..b8e84a9 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -71,7 +71,13 @@ class VFATdata
     //!Read second word from the block.
     void read_sw(uint64_t word, int c)
     {
-	    if(suppression< 0x4){
+	    if(suppression<4){
+		if(suppression>=1){//Package suppression
+			
+			if(suppression==1){//Data Suppression
+			
+			}
+		}
 	    	fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
 		flsData = 0xffff000000000000 & (word << 48);
 		return;

From 354d5bf6261091b28771718991becaf9848ac5c1 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 28 Jun 2019 08:41:14 -0500
Subject: [PATCH 09/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index b8e84a9..d4870e9 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -18,6 +18,7 @@ class VFATdata
     uint16_t controlData;	       ///<For ZeroSuppression. Shows which packets (out of sixteen) are nonempty	
     int count;			       ///<For ZeroSuppression. Shows how many packets are nonempty
     uint8_t packets[16];	       ///<For Containing the Packets
+    int need2=0;		       ///<Determines if we need a second line
     int need3=0;		       ///<Determines if we need to read the crc off in the third line
     int need4=0;		       ///<Determines if we need to read a fourth instance to read off CRC codes.
     uint4_t Suppression;	       ///<Determines what type, if any, of suppression is used
@@ -58,6 +59,8 @@ class VFATdata
 	fPos = 0x3f & (word >> 56);
 	fCRCcheck = 0xff & (word >> 48);
 	fHeader = 0xff & (word >> 40);
+	if((suppression==2||suppression==3||suppression==6||suppression==7)&&Empty){need2=1;return;}//Package suppression
+	if((suppression==1||suppression==5)&&Empty){fEC = 0xff & (word >> 32);fBC = 0xffff & (word >> 16);fcrc = 0xffff & word;need2=1;return;}//Data Suppression
 	fEC = 0xff & (word >> 32);
 	fBC = 0xffff & (word >> 16);
 	if(suppression< 0x4){
@@ -72,12 +75,6 @@ class VFATdata
     void read_sw(uint64_t word, int c)
     {
 	    if(suppression<4){
-		if(suppression>=1){//Package suppression
-			
-			if(suppression==1){//Data Suppression
-			
-			}
-		}
 	    	fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
 		flsData = 0xffff000000000000 & (word << 48);
 		return;
@@ -132,6 +129,9 @@ class VFATdata
 	    fcrc=0xffff & (word >> 48);
 	    break;	    
     }
+    int getNeed2(){
+	    return need2;	
+    }
     int getNeed3(){
 	    return need3;	
     }

From 05919bc75c96d4b6c64b8be41ac607f3271dd879 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 28 Jun 2019 08:45:19 -0500
Subject: [PATCH 10/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index a4d046f..f7290f3 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -110,13 +110,13 @@ class GEMUnpacker
               std::fread(&m_word, sizeof(uint64_t), 1, m_file);
         //printf("VFAT WORD 1\n");
         //printf("%016llX\n", m_word);
-              int helper=2
-              m_vfatdata->read_fw(m_word,helper);
+              m_vfatdata->read_fw(m_word);
+              if(getNeed2()>0){
               std::fread(&m_word, sizeof(uint64_t), 1, m_file);
         //printf("VFAT WORD 2\n");
         //printf("%016llX\n", m_word);
-              m_vfatdata->read_sw(m_word,helper);
-              if(getNeed3()>0||helper==1){
+              m_vfatdata->read_sw(m_word);}
+              if(getNeed3()>0){
                std::fread(&m_word, sizeof(uint64_t), 1, m_file); 
         //printf("VFAT WORD 3\n");
         //printf("%016llX\n", m_word);

From a3f812378cbe438b06923c6a85cd91cf6f108e37 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 28 Jun 2019 08:48:05 -0500
Subject: [PATCH 11/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index d4870e9..db3b2b6 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -59,8 +59,9 @@ class VFATdata
 	fPos = 0x3f & (word >> 56);
 	fCRCcheck = 0xff & (word >> 48);
 	fHeader = 0xff & (word >> 40);
-	if((suppression==2||suppression==3||suppression==6||suppression==7)&&Empty){need2=1;return;}//Package suppression
-	if((suppression==1||suppression==5)&&Empty){fEC = 0xff & (word >> 32);fBC = 0xffff & (word >> 16);fcrc = 0xffff & word;need2=1;return;}//Data Suppression
+	if((suppression==2||suppression==3||suppression==6||suppression==7)&&Empty){return;}//Package suppression
+	if((suppression==1||suppression==5)&&Empty){fEC = 0xff & (word >> 32);fBC = 0xffff & (word >> 16);fcrc = 0xffff & word;return;}//Data Suppression
+	need2=1;
 	fEC = 0xff & (word >> 32);
 	fBC = 0xffff & (word >> 16);
 	if(suppression< 0x4){
@@ -77,6 +78,7 @@ class VFATdata
 	    if(suppression<4){
 	    	fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
 		flsData = 0xffff000000000000 & (word << 48);
+		need3=1;
 		return;
 	    }
 	    count=0;

From 57280743aeaadc8c14eff9b9edde8dede9c8e152 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 28 Jun 2019 09:00:27 -0500
Subject: [PATCH 12/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index db3b2b6..1c90512 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -53,14 +53,14 @@ class VFATdata
     ~VFATdata(){}
 
     //!Read first word from the block.
-    void read_fw(uint64_t word, int c)
+    void read_fw(uint64_t word)
     {
 	suppression = 0x4 & (word >> 61);
 	fPos = 0x3f & (word >> 56);
 	fCRCcheck = 0xff & (word >> 48);
 	fHeader = 0xff & (word >> 40);
-	if((suppression==2||suppression==3||suppression==6||suppression==7)&&Empty){return;}//Package suppression
-	if((suppression==1||suppression==5)&&Empty){fEC = 0xff & (word >> 32);fBC = 0xffff & (word >> 16);fcrc = 0xffff & word;return;}//Data Suppression
+	if((suppression==2||suppression==3||suppression==6||suppression==7)&&(fHeader==26||fHeader==86)){return;}//Package suppression
+	if((suppression==1||suppression==5)&&(fHeader==26||fHeader==86)){fEC = 0xff & (word >> 32);fBC = 0xffff & (word >> 16);fcrc = 0xffff & word;return;}//Data Suppression
 	need2=1;
 	fEC = 0xff & (word >> 32);
 	fBC = 0xffff & (word >> 16);
@@ -73,7 +73,7 @@ class VFATdata
     }
     
     //!Read second word from the block.
-    void read_sw(uint64_t word, int c)
+    void read_sw(uint64_t word)
     {
 	    if(suppression<4){
 	    	fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
@@ -102,7 +102,7 @@ class VFATdata
 	    fcrc= 0xffff & (word << 8);//In case it cuts it off		     
     }
     //!Read third word from the block.
-    void read_tw(uint64_t word,int c)
+    void read_tw(uint64_t word)
     {
 	    if(suppression< 0x4){
 		    flsData = flsData | (0x0000ffffffffffff & word >> 16);

From f24700772ae3a617b0143fe6d70402722094ef8d Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Wed, 3 Jul 2019 03:48:52 -0500
Subject: [PATCH 13/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 1c90512..1281843 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -231,7 +231,7 @@ class GEBdata
     {
       m_ZeroSup = 0x00ffffff & (word >> 40);        /*!Zero Suppression*/
       m_InputID = 0b00011111 & (word >> 35);        /*!GLIB Input ID*/
-      m_Vwh = 0x0fff & (word >> 23);                /*!VFAT word count*/
+      m_Vwh = 0x0fff & (word >> 23);                /*!VFAT word count*///LOOK
       m_ErrorC = 0b0001111111111111 & (word >> 10);    /*!Thirteen Flags*/
       for(int i=0; i<13; ++i)
       {

From daf843bf32b251079393d6843950029cf6268cfb Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Thu, 4 Jul 2019 04:13:41 -0500
Subject: [PATCH 14/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 130 +++++---------------
 1 file changed, 33 insertions(+), 97 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 1281843..b25cf45 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -15,14 +15,9 @@ class VFATdata
     uint16_t fcrc_calc;                ///<Check Sum value recalculated, 16 bits
     int      fSlotNumber;              ///<Calculated chip position
     bool     fisBlockGood;             ///<Shows if block is good (control bits, chip ID and CRC checks)
-    uint16_t controlData;	       ///<For ZeroSuppression. Shows which packets (out of sixteen) are nonempty	
-    int count;			       ///<For ZeroSuppression. Shows how many packets are nonempty
-    uint8_t packets[16];	       ///<For Containing the Packets
-    int need2=0;		       ///<Determines if we need a second line
-    int need3=0;		       ///<Determines if we need to read the crc off in the third line
-    int need4=0;		       ///<Determines if we need to read a fourth instance to read off CRC codes.
-    uint4_t Suppression;	       ///<Determines what type, if any, of suppression is used
-
+    uint16_t fcontrolData;	       ///<For ZeroSuppression. Shows which packets (out of sixteen) are nonempty	
+    uint8_t fpackets[16];	       ///<For Containing the Packets
+    int fCH;
    public:
     //!Empty constructor. Functions used to assign data members.
     VFATdata(){}
@@ -53,93 +48,6 @@ class VFATdata
     ~VFATdata(){}
 
     //!Read first word from the block.
-    void read_fw(uint64_t word)
-    {
-	suppression = 0x4 & (word >> 61);
-	fPos = 0x3f & (word >> 56);
-	fCRCcheck = 0xff & (word >> 48);
-	fHeader = 0xff & (word >> 40);
-	if((suppression==2||suppression==3||suppression==6||suppression==7)&&(fHeader==26||fHeader==86)){return;}//Package suppression
-	if((suppression==1||suppression==5)&&(fHeader==26||fHeader==86)){fEC = 0xff & (word >> 32);fBC = 0xffff & (word >> 16);fcrc = 0xffff & word;return;}//Data Suppression
-	need2=1;
-	fEC = 0xff & (word >> 32);
-	fBC = 0xffff & (word >> 16);
-	if(suppression< 0x4){
-		fmsData = 0xffff000000000000 & (word << 48);
-		return;
-	}
-	//fmsData = 0xffff000000000000 & (word << 48);
-	controlData = 0xffff & word//a 16 bit number with bits indicating which packet is populated with anything (8 channels for a packet)
-    }
-    
-    //!Read second word from the block.
-    void read_sw(uint64_t word)
-    {
-	    if(suppression<4){
-	    	fmsData = fmsData | (0x0000ffffffffffff & word >> 16);
-		flsData = 0xffff000000000000 & (word << 48);
-		need3=1;
-		return;
-	    }
-	    count=0;
-	    //This populates an array of 8 bit numbers whose length corresponds to the number of packets.
- 	    uint16_t helper=controlData;
-	    while (helper > 0) {
-            	count += helper & 1;
-            	helper >>= 1;
-	    }
-	    int i=0;
-	    while(count>0){
-		    packets[i] = 0xffff & (word >> 64-(i+1)*8);
-		    i+=1;
-		    count-=1;
-		    if((i*8==56&&count==0)){need3=1;}
-		    if((i*8==64&&count==0)){need3=2;}
-		    //need3 will take 0 if third line not needed, 1 if needed just to read of half of crc,2 if all, 3 if needed for data and crc
-		    if(i*8==64){break;}
-	    }
-	    if(i<7){fcrc = 0xffff & word;need3=0;break;}//In case we don't even need a third line
-	    fcrc= 0xffff & (word << 8);//In case it cuts it off		     
-    }
-    //!Read third word from the block.
-    void read_tw(uint64_t word)
-    {
-	    if(suppression< 0x4){
-		    flsData = flsData | (0x0000ffffffffffff & word >> 16);
-		    fcrc = 0xffff & word;
-	 	    break;
-		    return;
-	    }
-	    if(need3==1){fcrc=fcrc|(0xff & word >> 56);return;}//If it was cut off before
-	    if(need3==2){fcrc=0xffff & (word >> 48);return;}//If we just barely needed the full line
-	    if(need3==3){
-		    int i=0;
-		    while(count>0){
-			    packets[i+8] = 0xff & (word >> 64-(i+1)*8);
-			    i+=1;
-			    count-=1;
-			    if(i*8==56){need4=1;}//Takes 0 if 4rth line not needed, Takes 1 if 1/2 crc needed, Takes 2 otherwise
-			    if(i*8==64){need4=2;break;}
-		    }
-		    if(0<i&&i<7){fcrc= 0xffff & (word >> 64-(i+2)*8);}//In case the whole word stays in
-		    if(i*8==56){fcrc= 0xffff & (word << 8)};//In case it cuts it off
-	    }
-    }
-    void read_4w(uint64_t word)
-    {
-	    if(need4==1){fcrc=fcrc|(0xff & word >> 56);break;}//if it had previously cut it off before
-	    fcrc=0xffff & (word >> 48);
-	    break;	    
-    }
-    int getNeed2(){
-	    return need2;	
-    }
-    int getNeed3(){
-	    return need3;	
-    }
-    int getNeed4(){
-	    return need4;	
-    }
 
     uint8_t   Pos        (){ return fPos;        }
     uint16_t  BC         (){ return fBC;         }
@@ -152,7 +60,21 @@ class VFATdata
     uint16_t  crc_calc   (){ return fcrc_calc;   }
     int       SlotNumber (){ return fSlotNumber; }
     bool      isBlockGood(){ return fisBlockGood;}
-
+    uint16_t  controlData(){ return fcontrolData;}
+    int       CH         (){ return fCH;}
+	
+	
+    void rPos(uint8_t _rPos){this.fPos=_rPos;}
+    void rCRCcheck(uint8_t _rCRCcheck){this.fCRCcheck=_rCRCcheck;}
+    void rHeader(uint8t_t _rHeader){this.fHeader=_rHeader;}
+    void rEC(uint8_t _rEC){this.fEC=_rEC;}
+    void rBC(uint16_t _rBC){this.fBC=_rBC;}
+    void rcrc(uint16_t _rcrc){this.fcrc=_rcrc;}
+    void rlsData(uint64_t _rlsData){this.flsData=_rlsData;}
+    void rmsData(uint64_t _rmsData){this.fmsData=_rmsData;}
+    void rcontrolData(uint16_t _rcontrolData){this.fcontrolData=_rcontrolData;}
+    void rpacket(uint8_t _rpacket,int i){this.fpackets[i]=_rpacket;}
+    void rCH(int _rCH){this.fCH=_rCH}
 };
 
 //!A class for GEB data
@@ -198,6 +120,8 @@ class GEBdata
       //!(7 0's):7    Stuck data:1    
       /*!Input status (warning): Data in InFIFO or EvtFIFO when L1A FIFO was empty. Only resets with resync or reset*/
 		  uint8_t m_Stuckd; 
+      unint8_t m_Calib;
+	//Bits for calibration mode to determine the channel
 
   public:
     //!Empty constructor. Functions used to assign data members.
@@ -229,6 +153,7 @@ class GEBdata
      */
     void setChamberHeader(uint64_t word)
     {
+      m_Calib=0b0111111 & (word >> 57);
       m_ZeroSup = 0x00ffffff & (word >> 40);        /*!Zero Suppression*/
       m_InputID = 0b00011111 & (word >> 35);        /*!GLIB Input ID*/
       m_Vwh = 0x0fff & (word >> 23);                /*!VFAT word count*///LOOK
@@ -269,7 +194,8 @@ class GEBdata
     uint8_t  InputID()  {return m_InputID;}   ///<Returns GLIB input ID
     uint16_t Vwh()      {return m_Vwh;}       ///<Returns VFAT word count (size of VFAT payload)
     uint16_t ErrorC()   {return m_ErrorC;}    ///<Returns thirteen flags in GEM Chamber Header
-
+    uint16_t Calib()    {return m_Calib;}
+	
     uint16_t OHCRC()    {return m_OHCRC;}     ///<Returns OH CRC 
     uint16_t Vwt()      {return m_Vwt;}       ///<Returns VFAT word count
     uint8_t  InFu()     {return m_InFu;}      ///<Returns InFIFO underflow flag
@@ -333,6 +259,9 @@ class AMCdata
       //!0000:4    TTS state:4    
       /*!Debug: GLIB TTS state at the moment when this event was built*/
       uint8_t  m_Tstate;
+	
+      unit4_t m_suppression;
+      //Variable for suppression data
 
     //GEM event trailer
 
@@ -427,6 +356,12 @@ class AMCdata
       m_Bstatus = 0x00ffffff & (word >> 16);  /*!Buffer Status*/
       m_GDcount = 0b00011111 & (word >> 11);  /*!GEM DAV count*/
       m_Tstate = 0b00000111 & word;           /*!TTS state*/
+      m_suppression = (word >> 4);	      /*!suppresion word*/
+    }
+	
+    uint4_t getSupp()
+    {
+      return this.suppression
     }
 
     //!Reads the word for the GEM Event Trailer
@@ -471,6 +406,7 @@ class AMCdata
     uint32_t CRC()    {return m_CRC;}
     uint8_t L1AT()    {return m_L1AT;}
     uint32_t DlengthT()    {return m_DlengthT;}
+    uint4_t suppression()   {return m_suppression;}
 
     //!Adds GEB data to vector
     void g_add(GEBdata g){gebd.push_back(g);}

From a1f3efce5e5886aeb5a40aa906a98d4e32a05a35 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Thu, 4 Jul 2019 04:13:54 -0500
Subject: [PATCH 15/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 81 +++++++++++++++++--------
 1 file changed, 55 insertions(+), 26 deletions(-)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index f7290f3..ed8668e 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -102,38 +102,67 @@ class GEMUnpacker
         //printf("%016llX\n", m_word);
             // fill the vfat data here
             //std::cout << "Number of VFAT words " << m_gebdata->Vwh() << std::endl;
-            int m_nvb = m_gebdata->Vwh() / 3; // number of VFAT2 blocks. Eventually add here sanity check
+            //int m_nvb = m_gebdata->Vwh() / 3; // number of VFAT2 blocks. Eventually add here sanity check
             //printf("N vfat blocks %d\n",m_nvb);
-            for (unsigned short k = 0; k < m_nvb; k++){
+              
+            //START OF VFAT READER  
+            
+            uint4_t helper=m_amcdata->suppression();
+            int bitcount=0;
+            while((bitcount/64)<m_gebdata- > Vwh()){
               VFATdata * m_vfatdata = new VFATdata();
-              // read 3 vfat block words, totaly 192 bits
-              std::fread(&m_word, sizeof(uint64_t), 1, m_file);
-        //printf("VFAT WORD 1\n");
-        //printf("%016llX\n", m_word);
-              m_vfatdata->read_fw(m_word);
-              if(getNeed2()>0){
-              std::fread(&m_word, sizeof(uint64_t), 1, m_file);
-        //printf("VFAT WORD 2\n");
-        //printf("%016llX\n", m_word);
-              m_vfatdata->read_sw(m_word);}
-              if(getNeed3()>0){
-               std::fread(&m_word, sizeof(uint64_t), 1, m_file); 
-        //printf("VFAT WORD 3\n");
-        //printf("%016llX\n", m_word);
-              m_vfatdata->read_tw(m_word);}
-              if(getNeed4()>0){
-                std::fread(&m_word, sizeof(uint64_t), 1, m_file); 
-                m_vfatdata->read_4w(m_word);
+              if(helper > 8){//PORTION THAT DEALS WITH CALIBRATION MODE
+                  std::fread(&m_word, sizeof(uint8_t), 1, m_file); bitcount+=8;
+                  m_vfatdata->rCH((int) m_word>>7);
+                  m_vfatdata->rEC(0b00000011& m_word);                  
+                  m_vfatdata->rPos(0b00011111& m_word);
+                  //ADD METHOD SPECIFICALLY FOR CHANNEL COUNT              
+                  m_gebdata->v_add(*m_vfatdata);
+                  delete m_vfatdata;
+                  continue;
+              }
+              std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rPos(0b00011111& m_word); bitcount+=8;
+              std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rCRCcheck(m_word); bitcount+=8;
+              std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rHeader(m_word); bitcount+=8;
+              if((helper==2||helper==3||helper==6||helper==7)&&(m_word==26||m_word==86)){
+                  m_gebdata->v_add(*m_vfatdata);
+                  delete m_vfatdata;
+                  continue;
+              }//Package suppression
+	          if((helper==1||helper==5)&&(mword==26||mword==86)){
+                  std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rEC(m_word); bitcount+=8;
+                  std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rBC(m_word); bitcount+=16;
+                  std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word); bitcount+=16;                
+                  m_gebdata->v_add(*m_vfatdata);
+                  delete m_vfatdata;
+                  continue;
+              }//Data Suppression
+              std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rEC(m_word); bitcount+=8;
+              std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rBC(m_word); bitcount+=16;
+              if(helper<4){
+                  std::fread(&m_word, sizeof(uint64_t), 1, m_file); m_vfatdata->rlsData(m_word); bitcount+=64;
+                  std::fread(&m_word, sizeof(uint64_t), 1, m_file); m_vfatdata->rmsData(m_word); bitcount+=64;
+                  std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word); bitcount+=16;
+                  m_gebdata->v_add(*m_vfatdata);
+                  delete m_vfatdata;
+                  continue;
+              }
+              std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rcontrolData(m_word); bitcount+=16;
+              uint16_t count=0xffff;
+              while (m_word > 0) {
+                  count += m_word & 0bx0000000000000001;
+                  m_word >>= 1;
+              }
+              for(int i=0; i< (int) count;i++){
+                  std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rpacket(m_word,i); bitcount+=8;
               }
-              //
-        //printf("VFAT MS Data 3\n");
-        //printf("%016llX\n", m_vfatdata->msData());
-        //printf("VFAT LS Data 3\n");
-        //printf("%016llX\n", m_vfatdata->lsData());
-              //
+              std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word); bitcount+=16;                
               m_gebdata->v_add(*m_vfatdata);
               delete m_vfatdata;
             }
+            //END OF VFAT READER
+              
+              
             std::fread(&m_word, sizeof(uint64_t), 1, m_file);
             m_gebdata->setChamberTrailer(m_word);
             m_amcdata->g_add(*m_gebdata);

From ee77398b421863bfa93c7dc0db32f7aeeaa690bd Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 5 Jul 2019 04:52:59 -0500
Subject: [PATCH 16/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index ed8668e..df7b569 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -122,7 +122,8 @@ class GEMUnpacker
                   continue;
               }
               std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rPos(0b00011111& m_word); bitcount+=8;
-              std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rCRCcheck(m_word); bitcount+=8;
+              m_vfatdata->rCRCcheck(m_word>>7);
+	      //std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rCRCcheck(m_word); bitcount+=8;
               std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rHeader(m_word); bitcount+=8;
               if((helper==2||helper==3||helper==6||helper==7)&&(m_word==26||m_word==86)){
                   m_gebdata->v_add(*m_vfatdata);

From e35f0c45b62dd60dc16b6b412b29a7182a922cc9 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 5 Jul 2019 04:59:28 -0500
Subject: [PATCH 17/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index df7b569..24a5048 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -193,6 +193,8 @@ class GEMUnpacker
   private:
     std::FILE *m_file;
     uint64_t m_word;
+    uint8_t m_word8;
+    uint16_t m_word16;	
     uint32_t m_word32;
     bool type;
     AMC13Event * m_AMC13Event;

From c6a2440697afc5814ed75794d50e646c8bc2636c Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Fri, 5 Jul 2019 05:02:33 -0500
Subject: [PATCH 18/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 38 ++++++++++++-------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index 24a5048..3d78ac6 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -112,52 +112,52 @@ class GEMUnpacker
             while((bitcount/64)<m_gebdata- > Vwh()){
               VFATdata * m_vfatdata = new VFATdata();
               if(helper > 8){//PORTION THAT DEALS WITH CALIBRATION MODE
-                  std::fread(&m_word, sizeof(uint8_t), 1, m_file); bitcount+=8;
-                  m_vfatdata->rCH((int) m_word>>7);
-                  m_vfatdata->rEC(0b00000011& m_word);                  
-                  m_vfatdata->rPos(0b00011111& m_word);
+                  std::fread(&m_word8, sizeof(uint8_t), 1, m_file); bitcount+=8;
+                  m_vfatdata->rCH((int) m_word8>>7);
+                  m_vfatdata->rEC(0b00000011& m_word8);                  
+                  m_vfatdata->rPos(0b00011111& m_word8);
                   //ADD METHOD SPECIFICALLY FOR CHANNEL COUNT              
                   m_gebdata->v_add(*m_vfatdata);
                   delete m_vfatdata;
                   continue;
               }
-              std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rPos(0b00011111& m_word); bitcount+=8;
-              m_vfatdata->rCRCcheck(m_word>>7);
+              std::fread(&m_word8, sizeof(uint8_t), 1, m_file); m_vfatdata->rPos(0b00011111& m_word8); bitcount+=8;
+              m_vfatdata->rCRCcheck(m_word8>>7);
 	      //std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rCRCcheck(m_word); bitcount+=8;
-              std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rHeader(m_word); bitcount+=8;
+              std::fread(&m_word8, sizeof(uint8_t), 1, m_file); m_vfatdata->rHeader(m_word8); bitcount+=8;
               if((helper==2||helper==3||helper==6||helper==7)&&(m_word==26||m_word==86)){
                   m_gebdata->v_add(*m_vfatdata);
                   delete m_vfatdata;
                   continue;
               }//Package suppression
 	          if((helper==1||helper==5)&&(mword==26||mword==86)){
-                  std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rEC(m_word); bitcount+=8;
-                  std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rBC(m_word); bitcount+=16;
-                  std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word); bitcount+=16;                
+                  std::fread(&m_word8, sizeof(uint8_t), 1, m_file); m_vfatdata->rEC(m_word8); bitcount+=8;
+                  std::fread(&m_word16, sizeof(uint16_t), 1, m_file); m_vfatdata->rBC(m_word16); bitcount+=16;
+                  std::fread(&m_word16, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word16); bitcount+=16;                
                   m_gebdata->v_add(*m_vfatdata);
                   delete m_vfatdata;
                   continue;
               }//Data Suppression
-              std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rEC(m_word); bitcount+=8;
-              std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rBC(m_word); bitcount+=16;
+              std::fread(&m_word8, sizeof(uint8_t), 1, m_file); m_vfatdata->rEC(m_word8); bitcount+=8;
+              std::fread(&m_word16, sizeof(uint16_t), 1, m_file); m_vfatdata->rBC(m_word16); bitcount+=16;
               if(helper<4){
                   std::fread(&m_word, sizeof(uint64_t), 1, m_file); m_vfatdata->rlsData(m_word); bitcount+=64;
                   std::fread(&m_word, sizeof(uint64_t), 1, m_file); m_vfatdata->rmsData(m_word); bitcount+=64;
-                  std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word); bitcount+=16;
+                  std::fread(&m_word16, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word16); bitcount+=16;
                   m_gebdata->v_add(*m_vfatdata);
                   delete m_vfatdata;
                   continue;
               }
-              std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rcontrolData(m_word); bitcount+=16;
+              std::fread(&m_word16, sizeof(uint16_t), 1, m_file); m_vfatdata->rcontrolData(m_word16); bitcount+=16;
               uint16_t count=0xffff;
-              while (m_word > 0) {
-                  count += m_word & 0bx0000000000000001;
-                  m_word >>= 1;
+              while (m_word16 > 0) {
+                  count += m_word16 & 0bx0000000000000001;
+                  m_word16 >>= 1;
               }
               for(int i=0; i< (int) count;i++){
-                  std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rpacket(m_word,i); bitcount+=8;
+                  std::fread(&m_word8, sizeof(uint8_t), 1, m_file); m_vfatdata->rpacket(m_word8,i); bitcount+=8;
               }
-              std::fread(&m_word, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word); bitcount+=16;                
+              std::fread(&m_word16, sizeof(uint16_t), 1, m_file); m_vfatdata->rcrc(m_word16); bitcount+=16;                
               m_gebdata->v_add(*m_vfatdata);
               delete m_vfatdata;
             }

From de299e4625e44c199decbbb8cc94d6ef43200c17 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Mon, 8 Jul 2019 01:55:35 -0500
Subject: [PATCH 19/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index b25cf45..46adfa8 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -153,8 +153,8 @@ class GEBdata
      */
     void setChamberHeader(uint64_t word)
     {
-      m_Calib=0b0111111 & (word >> 57);
-      m_ZeroSup = 0x00ffffff & (word >> 40);        /*!Zero Suppression*/
+      m_Calib=0b0111111 & (word >> 40);//(Used to be 57)
+      //m_ZeroSup = 0x00ffffff & (word >> 40);        /*!Zero Suppression*/
       m_InputID = 0b00011111 & (word >> 35);        /*!GLIB Input ID*/
       m_Vwh = 0x0fff & (word >> 23);                /*!VFAT word count*///LOOK
       m_ErrorC = 0b0001111111111111 & (word >> 10);    /*!Thirteen Flags*/

From b76c731e6a937029977bc96ea44b12d8d76e0c1c Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@gmail.com>
Date: Mon, 8 Jul 2019 01:58:29 -0500
Subject: [PATCH 20/23] Update GEMAMC13EventFormat.h

---
 gemtreewriter/include/GEMAMC13EventFormat.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gemtreewriter/include/GEMAMC13EventFormat.h b/gemtreewriter/include/GEMAMC13EventFormat.h
index 46adfa8..e288c0b 100644
--- a/gemtreewriter/include/GEMAMC13EventFormat.h
+++ b/gemtreewriter/include/GEMAMC13EventFormat.h
@@ -153,7 +153,7 @@ class GEBdata
      */
     void setChamberHeader(uint64_t word)
     {
-      m_Calib=0b0111111 & (word >> 40);//(Used to be 57)
+      m_Calib=0b01111111 & (word >> 40);//(Used to be 57)
       //m_ZeroSup = 0x00ffffff & (word >> 40);        /*!Zero Suppression*/
       m_InputID = 0b00011111 & (word >> 35);        /*!GLIB Input ID*/
       m_Vwh = 0x0fff & (word >> 23);                /*!VFAT word count*///LOOK

From 64a354c1dac1fd90beadbd551914043db8e36026 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@tamu.edu>
Date: Tue, 9 Jul 2019 07:45:57 -0500
Subject: [PATCH 21/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index 3d78ac6..1c78de3 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -109,7 +109,9 @@ class GEMUnpacker
             
             uint4_t helper=m_amcdata->suppression();
             int bitcount=0;
-            while((bitcount/64)<m_gebdata- > Vwh()){
+            int vfcount=0;
+            while(((bitcount/64)<m_gebdata- > Vwh())&& vfcount<23){
+	      vfcount+=1;
               VFATdata * m_vfatdata = new VFATdata();
               if(helper > 8){//PORTION THAT DEALS WITH CALIBRATION MODE
                   std::fread(&m_word8, sizeof(uint8_t), 1, m_file); bitcount+=8;

From f42d17fdc9b59bf747b541bae08cef730c8502cd Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@tamu.edu>
Date: Tue, 9 Jul 2019 07:56:00 -0500
Subject: [PATCH 22/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index 1c78de3..fcd4397 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -109,12 +109,18 @@ class GEMUnpacker
             
             uint4_t helper=m_amcdata->suppression();
             int bitcount=0;
-            int vfcount=0;
-            while(((bitcount/64)<m_gebdata- > Vwh())&& vfcount<23){
-	      vfcount+=1;
+            //int vfcount=0;//vfcount+=1;
+            while((bitcount/64)<m_gebdata- > Vwh()){
               VFATdata * m_vfatdata = new VFATdata();
+	      std::fread(&m_word8, sizeof(uint8_t), 1, m_file); 
+	      if(m_word8==0b11111111){
+		      while((bitcount/64)<m_gebdata- > Vwh()){
+		      std::fread(&m_word8, sizeof(uint8_t), 1, m_file);bitcount+=8;
+		      }
+		      break;
+	      }    
+	      bitcount+=8;
               if(helper > 8){//PORTION THAT DEALS WITH CALIBRATION MODE
-                  std::fread(&m_word8, sizeof(uint8_t), 1, m_file); bitcount+=8;
                   m_vfatdata->rCH((int) m_word8>>7);
                   m_vfatdata->rEC(0b00000011& m_word8);                  
                   m_vfatdata->rPos(0b00011111& m_word8);
@@ -123,7 +129,7 @@ class GEMUnpacker
                   delete m_vfatdata;
                   continue;
               }
-              std::fread(&m_word8, sizeof(uint8_t), 1, m_file); m_vfatdata->rPos(0b00011111& m_word8); bitcount+=8;
+              m_vfatdata->rPos(0b00011111& m_word8);
               m_vfatdata->rCRCcheck(m_word8>>7);
 	      //std::fread(&m_word, sizeof(uint8_t), 1, m_file); m_vfatdata->rCRCcheck(m_word); bitcount+=8;
               std::fread(&m_word8, sizeof(uint8_t), 1, m_file); m_vfatdata->rHeader(m_word8); bitcount+=8;

From af2e09c625ac79f564a9d6991ba2a31c189ea2e7 Mon Sep 17 00:00:00 2001
From: rodwyer100 <rodwyer100@tamu.edu>
Date: Tue, 9 Jul 2019 08:01:27 -0500
Subject: [PATCH 23/23] Update GEMUnpacker.cc

---
 gemtreewriter/src/common/GEMUnpacker.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gemtreewriter/src/common/GEMUnpacker.cc b/gemtreewriter/src/common/GEMUnpacker.cc
index fcd4397..3b518a3 100644
--- a/gemtreewriter/src/common/GEMUnpacker.cc
+++ b/gemtreewriter/src/common/GEMUnpacker.cc
@@ -111,7 +111,6 @@ class GEMUnpacker
             int bitcount=0;
             //int vfcount=0;//vfcount+=1;
             while((bitcount/64)<m_gebdata- > Vwh()){
-              VFATdata * m_vfatdata = new VFATdata();
 	      std::fread(&m_word8, sizeof(uint8_t), 1, m_file); 
 	      if(m_word8==0b11111111){
 		      while((bitcount/64)<m_gebdata- > Vwh()){
@@ -120,6 +119,7 @@ class GEMUnpacker
 		      break;
 	      }    
 	      bitcount+=8;
+	      VFATdata * m_vfatdata = new VFATdata();
               if(helper > 8){//PORTION THAT DEALS WITH CALIBRATION MODE
                   m_vfatdata->rCH((int) m_word8>>7);
                   m_vfatdata->rEC(0b00000011& m_word8);