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	diff --git a/run.sh b/run.sh
	index 5a885b7..a2f090f 100755
	--- a/run.sh
	+++ b/run.sh
	@@ -1,373 +1,381 @@
	#!/bin/bash

	FILE=""
	FILE_BASENAME=""
	MODULE=""
	LIBERTY_FILE="nem_basic_yosys.lib"
	LIBERTY_USED="3T"
	visualize=0

	# Function to display the menu and get user input
	show_menu() {


	# Define color codes
	GREEN='\033[0;32m'
	YELLOW='\033[1;33m'
	CYAN='\033[0;36m'
	RESET='\033[0m'

	echo "--------------------------------------------------------------"
	echo -e "${CYAN}Current file: $FILE with module: $MODULE${RESET}"
	echo -e "${YELLOW}Please select your options (you can choose multiple options):${RESET}"
	echo
	echo -e "${GREEN}1)${RESET} Synthesize to NEM technology"
	echo -e "${GREEN}2)${RESET} Print initial design"
	echo -e "${GREEN}3)${RESET} Print out NEM optimized design"
	echo -e "${GREEN}4)${RESET} Perform SAT comparison"
	echo -e "${GREEN}5)${RESET} Export FSM as KISS2 format"
	echo -e "${GREEN}6)${RESET} Start shell with modules"
	echo -e "${GREEN}7)${RESET} Switch from normal 3T gate library to new 4T"
	echo -e "${GREEN}8)${RESET} Run series of test and create comparison report"
	echo -e "${GREEN}9)${RESET} Perform MUXIG synthesis run"
	echo -e "${GREEN}10)${RESET} export truth table and MIG run"
	echo -e "${GREEN}11)${RESET} Select a new Verilog file"
	echo -e "${GREEN}0)${RESET} Exit the program"
	echo "--------------------------------------------------------------"
	}

	# Request the file to process
	request_data(){
	echo "-:- Enter the file to map to NEM"
	read -e -p "What is the file name?: " FILE
	read -p "What is the name of the top module? (press ENTER for the same as the file name): " MODULE

	if [ ! -f "$FILE" ]; then
	echo "File not found"
	request_data
	fi

	FILE_BASENAME=$(basename "$FILE" \| cut -d. -f1)
	#echo $FILE_BASENAME

	if [ -z "$MODULE" ]; then
	#echo "setting name equal to that of the file"
	MODULE=$FILE_BASENAME
	fi
	}

	#run a yosys file specified to the function
	run_yosys_file() {
	local yosys_file="$1"
	local depth="$2"
	local additional_yosys_args="$3"

	# Start with basic sed commands
	sed_command=$(sed -e "s\|{{FILE}}\|$FILE\|g" \
	-e "s\|{{FILE_BASENAME}}\|$FILE_BASENAME\|g" \
	-e "s\|{{MODULE}}\|$MODULE\|g" \
	-e "s\|{{LIBERTY_FILE}}\|$LIBERTY_FILE\|g" \
	-e "s\|{{LIBERTY_USED}}\|$LIBERTY_USED\|g"\
	"./yosys/${yosys_file}.ys")

	# Apply additional sed expressions based on DEPTH value
	if [[ $depth -eq 0 ]]; then
	sed_command=$(echo "$sed_command" \| sed -e "/#IF {{DEPTH}}==0/d" \
	-e "/#ELSE/,/#END/d")
	elif [[ $depth -eq 1 ]]; then
	sed_command=$(echo "$sed_command" \| sed -e "/#IF {{DEPTH}}==0/,/#ELSE/d" \
	-e "/#END/d")
	fi

	# Write the result to a temp file and run yosys
	echo "$sed_command" > "./temp/${yosys_file}_temp.ys"
	yosys $additional_yosys_args "./temp/${yosys_file}_temp.ys"
	}

	#Switch between 3T and 4T pass through gates
	switch_liberty() {
	- if [ "$LIBERTY_FILE" == "nem_basic_yosys.lib" ]; then
	+ local override="$1"
	+ if [[ ("$LIBERTY_FILE" == "nem_basic_yosys.lib" && "$override" != "3T") \|\| "$override" == "4T" ]]; then
	LIBERTY_FILE="nem_basic_yosys_extended.lib"
	LIBERTY_USED="4T"
	- echo "Now using extended (4T devices) libary"
	- elif [ "$LIBERTY_FILE" == "nem_basic_yosys_extended.lib" ]; then
	+ echo "Now using extended (4T devices) library"
	+ elif [[ "$LIBERTY_FILE" == "nem_basic_yosys_extended.lib" \|\| "$override" == "3T" ]]; then
	LIBERTY_FILE="nem_basic_yosys.lib"
	LIBERTY_USED="3T"
	- echo "Now using normal libary"
	+ echo "Now using normal library"
	else
	echo "Unknown LIBERTY_FILE value: $LIBERTY_FILE"
	fi
	}

	compare_area() {
	# Extract area values from .stat files
	local area_3T=$(grep "Chip area for module" "./temp/${FILE_BASENAME}_3T.stat" \| awk '{print $6}')
	local area_4T=$(grep "Chip area for module" "./temp/${FILE_BASENAME}_4T.stat" \| awk '{print $6}')
	local area_MUX=$(grep "Chip area for module" "./temp/${FILE_BASENAME}_MUX.stat" \| awk '{print $6}')

	# Calculate ratio as (area_3T / area_4T) * 100
	local ratio_4T=$(echo "($area_4T / $area_3T)" \| bc -l)
	local ratio_MUX=$(echo "($area_MUX / $area_3T)" \| bc -l)

	{
	echo "------------- normal 3T ---------------"
	cat "./temp/${FILE_BASENAME}_3T.stat"
	echo "------------- 4T ---------------"
	cat "./temp/${FILE_BASENAME}_4T.stat"
	echo "------------- Muxig ---------------"
	cat "./temp/${FILE_BASENAME}_MUX.stat"
	echo "------------- Stats ---------------"
	echo "Area 3T: $area_3T"
	echo "Area 4T: $area_4T"
	echo "Ratio 4T->3T: $ratio_4T%"
	echo "Area MUX: $area_MUX"
	echo "Ratio MUX->3T: $ratio_MUX%"
	-
	- ec
	} > "./output/${FILE_BASENAME}.ratio"

	# Output the areas and the ratio
	echo "Area 3T: $area_3T, Area 4T: $area_4T, Ratio 4T->3T: $ratio_4T, Area MUX: $area_MUX, Ratio MUX->3T: $ratio_MUX%"
	}

	create_report() {

	# Output CSV file name
	csv_output="./output/output_report.csv"

	# Clear the CSV file by redirecting an empty string to it
	> "$csv_output"

	# Write the CSV header
	-echo "Module,3T,4T,Ratio" > "$csv_output"
	+echo "Module,3T,4T,Ratio 4T,Mux,Ratio Mux" > "$csv_output"
	# Print the header of the table
	printf "%-20s %-20s %-20s %-20s %-20s %-20s\n" "Module" "3T" "4T" "Ratio 4T" "MUX" "Ratio MUx"
	printf "%-20s %-20s %-20s %-20s %-20s %-20s\n" "-------" "------" "------" "-----" "-----" "-----"

	# Loop through each .ratio file in the directory
	for file in ./output/*.ratio; do
	# Check if the file exists
	if [[ -f "$file" ]]; then
	# Extract the module name
	module_name=$(grep -m 1 -oP '(?<==== ).*(?= ===)' "$file") # Extract the module name

	# Extract areas using grep and sed
	area1=$(grep "Chip area for module" "$file" \| sed -n '1s/.*: //p') # Area 3T
	area2=$(grep "Chip area for module" "$file" \| sed -n '2s/.*: //p') # Area 4T
	area3=$(grep "Chip area for module" "$file" \| sed -n '3s/.*: //p') # Area MUX

	# Extract the ratio
	ratio_4T=$(grep -oP '(?<=Ratio 4T->3T: )[\d.]+' "$file") # Extract the ratio
	ratio_MUX=$(grep -oP '(?<=Ratio MUX->3T: )[\d.]+' "$file") # Extract the ratio
	+ ratio_4T=$(printf "%.5f" "$ratio_4T")
	+ ratio_MUX=$(printf "%.5f" "$ratio_MUX")
	+
	# Append the data to the CSV file
	echo "$module_name,$area1,$area2,$ratio_4T,$area3,$ratio_MUX" >> "$csv_output"

	# Print the results in the table format
	- printf "%-20s %-20s %-20s %-20s\n" "$module_name" "$area1" "$area2" "$ratio"
	+ printf "%-20s %-20s %-20s %-20s %-20s %-20s\n" "$module_name" "$area1" "$area2" "$ratio_4T" "$area3" "$ratio_MUX"
	fi
	done
	}


	#START ACTUAL EXECUTION

	#Check if in menu mode or in CLI mode
	if [ -z "$1" ]; then
	# in menu mode
	request_data
	else

	#in cli mode. Filter through all the parameters
	while getopts ":d:f:m:v:x:r:" opt; do
	case $opt in
	d) # -d option for directory
	file_directory="$OPTARG"
	;;
	f) # -f option for file
	FILE="$OPTARG"
	;;
	m) # -m option for module (requires -f to be set)
	MODULE="$OPTARG"
	;;
	v) # -v visualize before and after synthesis
	echo "found visualize"
	visualize=1
	;;
	x) # -x switch to extended nem liberty file
	echo "switching to 4T libert file"
	switch_liberty
	;;
	r) # -r generate report of output
	echo "generating report"
	create_report
	;;
	\?) # Invalid option
	echo "Invalid option: -$OPTARG" >&2
	usage
	;;
	:) # Missing argument for an option
	echo "Option -$OPTARG requires an argument." >&2
	usage
	;;
	esac
	done

	#running synthesis on al lthe files in the directory
	if [ -n "$file_directory" ]; then
	if [ -d "$file_directory" ]; then
	echo "Directory exists: $file_directory"

	for file in "$file_directory"/*.v; do
	# Check if it's a regular file
	if [ -f "$file" ]; then
	# Use grep to find the line that starts with 'module' and extract the module name
	module_name=$(grep -m 1 -oP '^module\s+\K\w+' "$file")
	- #module_name=
	+
	# If the module name is found, print the file path and the module name
	if [ -n "$module_name" ]; then
	echo "File: $file"
	echo "Module: $module_name"
	echo

	FILE=$file
	FILE_BASENAME=$(basename "$FILE" \| cut -d. -f1)
	- #MODULE=$module_name
	- MODULE=$FILE_BASENAME
	+ MODULE=$module_name

	#synthesise the file
	echo "running sequence of test commands"
	+ switch_liberty "3T"
	run_yosys_file "synth_nem" 0
	- #run_yosys_file "sat_test" 0
	- switch_liberty
	+ run_yosys_file "sat_test" 0
	+ switch_liberty "4T"
	run_yosys_file "synth_nem" 0
	+ run_yosys_file "sat_test" 0
	+ switch_liberty "4T"
	+ run_yosys_file "bruteforce" 0
	+ switch_liberty "3T"
	compare_area
	- switch_liberty
	+
	else
	echo "No module found in file: $file"
	echo
	fi
	fi
	done

	#done with synthesis
	create_report
	exit 0

	else
	echo "Directory does not exist: $file_directory"
	exit 1
	fi
	fi

	#running synthesis on the file requested
	if [ -n "$FILE" ]; then
	if [ -n "$MODULE" ]; then
	if [ -f "$FILE" ]; then
	echo "File exists: $file"
	echo "Module: $module"
	FILE_BASENAME=$(basename "$FILE" \| cut -d. -f1)
	run_yosys_file "synth_nem" 0
	if [ "$visualize" -eq 1 ]; then
	run_yosys_file "visual" 0
	run_yosys_file "visual" 1
	else
	echo "no visualize set"
	fi
	exit 0
	else
	echo "File does not exist: $file"
	exit 1
	fi
	else
	echo "Missing module (-m) for the file (-f)."
	usage
	fi
	fi
	exit 1

	fi


	# Loop to allow multiple selections
	while true; do
	show_menu
	read -p "Enter your choices (e.g., 1 2 3, or 0 to finish): " -a choices

	for choice in "${choices[@]}"; do
	case $choice in
	1)
	echo "performing synthesis"
	run_yosys_file "synth_nem" 0
	;;
	2)
	echo "Plotting the initial design with $FILE and $MODULE"
	run_yosys_file "visual" 0
	;;
	3)
	echo "Plotting the NEM design with $FILE and $MODULE"
	run_yosys_file "visual" 1
	;;
	4)
	echo "Performing SAT test on $FILE and $MODULE"
	run_yosys_file "sat_test" 0
	;;
	5)
	echo "Exporting FSM overview of the design"
	make clean #to make sure no previous .kiss2 file remains
	run_yosys_file "fsm_export" 0

	if [ -f "./temp/${FILE_BASENAME}.kiss2" ]; then
	# If the file exists, run the python script and xdot
	python3 ./yosys/kiss2dot.py ./temp/${FILE_BASENAME}.kiss2 > ./temp/${FILE_BASENAME}.dot
	xdot ./temp/${FILE_BASENAME}.dot
	else
	# If the file doesn't exist, print a message
	echo "Could not detect an FSM in ${MODULE}"
	fi
	;;
	6)
	echo "Plotting the initial design with $FILE and $MODULE"
	make clean #Clean directories
	run_yosys_file "synth_nem" 0
	make all #build plugins
	ls ./plugins/*.so
	run_yosys_file "start_shell" 0 "$(for so_file in ./plugins/*.so; do echo -m "$so_file"; done)" #create a list of all plugins to load
	;;
	7)
	echo "Switching libary"
	switch_liberty
	;;
	8)
	echo "running sequence of test commands"
	+ switch_liberty "3T"
	run_yosys_file "synth_nem" 0
	#run_yosys_file "visual" 1
	- switch_liberty
	+ switch_liberty "4T"
	run_yosys_file "synth_nem" 0
	#run_yosys_file "visual" 1
	run_yosys_file "bruteforce" 0
	compare_area
	+
	;;
	9)
	echo "exporting truth table and running in mockturtle for muxig"
	run_yosys_file "bruteforce" 0
	;;
	10)
	echo "exporting truth table and running in mockturtle for MIG"
	run_yosys_file "bruteforce" 1
	;;
	11)
	echo "requesting new module"
	request_data
	;;
	0)
	echo "exiting"
	break 2
	;;
	*)
	echo "Invalid choice. Please select a number between 1 and 6."
	;;
	esac
	done

	echo
	done
	diff --git a/yosys/bruteforce.ys b/yosys/bruteforce.ys
	index 874e5c4..b9df483 100644
	--- a/yosys/bruteforce.ys
	+++ b/yosys/bruteforce.ys
	@@ -1,48 +1,38 @@
	read_verilog {{FILE}}

	#map to basic cells
	-techmap
	+proc;;
	+techmap;;
	opt;;
	aigmap;;

	splitnets;;
	-show -prefix ./temp/{{MODULE}}_bruteforce_aig_{{LIBERTY_USED}} -color orange t:$_NOT_ -color darkred t:$_AND_ -color purple t:$ge -color darkblue t:$ne -color blue t:$le -color maroon t:$add -enum
	+#show -prefix ./temp/{{MODULE}}_bruteforce_aig_{{LIBERTY_USED}} -color orange t:$_NOT_ -color darkred t:$_AND_ -color purple t:$ge -color darkblue t:$ne -color blue t:$le -color maroon t:$add -enum
	+

	write_blif ./temp/{{FILE_BASENAME}}.blif
	-write_aiger ./temp/{{FILE_BASENAME}}.aig
	+
	+exec -- ./abc/abc -c "read_blif ./temp/{{FILE_BASENAME}}.blif; compress2rs; write_blif ./temp/{{FILE_BASENAME}}_abc.blif"
	#abc -liberty ./nem_liberty/{{LIBERTY_FILE}} -script "+strash; &get -n; collapse; write_eqn ./temp/{{FILE_BASENAME}}.eqn; &write_truths -x ./temp/{{FILE_BASENAME}}.truth"
	delete

	-#IF {{DEPTH}}==0
	-exec -- ./mockturtle/build/experiments/muxig_rewriting ./temp/{{FILE_BASENAME}}.blif 1
	-#ELSE
	-exec -- ./mockturtle/build/experiments/muxig_rewriting ./temp/{{FILE_BASENAME}}.blif 0
	-#END
	+exec -- ./mockturtle/debug/experiments/sim_resubstitution ./temp/{{FILE_BASENAME}}_abc.blif
	+exec -- python3 ./yosys/map_ports.py ./temp/{{FILE_BASENAME}}.blif ./temp/{{FILE_BASENAME}}_abc_mockturtle.blif

	-exec -- python3 ./yosys/map_ports.py ./temp/{{FILE_BASENAME}}.blif ./temp/{{FILE_BASENAME}}_mockturtle.blif
	-
	-read_blif ./temp/mapped_{{FILE_BASENAME}}_mockturtle.blif

	+read_blif ./temp/mapped_{{FILE_BASENAME}}_abc_mockturtle.blif
	rename top {{MODULE}}_nem

	techmap -map ./yosys/mockturtle_map.v
	-
	techmap
	-
	opt_expr

	clean -purge

	-
	-
	-
	abc -liberty ./nem_liberty/{{LIBERTY_FILE}} -script "+attach"

	clean -purge

	-
	-
	-
	write_verilog -selected ./temp/{{FILE_BASENAME}}_nem.v
	#Output stats
	tee -o ./temp/{{FILE_BASENAME}}_MUX.stat stat -liberty ./nem_liberty/{{LIBERTY_FILE}}
	diff --git a/yosys/map_ports.py b/yosys/map_ports.py
	index 228a8f0..e62084b 100644
	--- a/yosys/map_ports.py
	+++ b/yosys/map_ports.py
	@@ -1,63 +1,63 @@
	#!/usr/bin/env python3
	import re
	import sys
	import os

	if(len(sys.argv)!=3):
	sys.exit("Use format: map_ports YOSYS_BLIF_FILE MOCKTURTLE_BLIF_FILE")

	yosys_file = sys.argv[1]
	mockturtle_file = sys.argv[2]

	print("mapping: " + mockturtle_file + " to " + yosys_file)

	os.system('pwd')

	inputVariables = []
	outputVariables = []

	with open(yosys_file, 'r') as infile:
	lines = infile.readlines()


	for line in lines:
	if line.startswith(".inputs"):
	inputs = line.split()
	inputVariables = inputs[1:]

	if line.startswith(".outputs"):
	outputs = line.split()
	outputVariables = outputs[1:]

	print('input variables',inputVariables)
	print('ouput variables',outputVariables)

	replacementList = {}

	for x in range(len(inputVariables)):
	inputReplaceVar = "pi" + str(x + 1)
	replacementList.update({inputReplaceVar:inputVariables[x]})

	for x in range(len(outputVariables)):
	inputReplaceVar = "po" + str(x)
	replacementList.update({inputReplaceVar:outputVariables[x]})

	print('replacement list:',replacementList)

	# construct mapped path.
	mapped_file_parts = mockturtle_file.split('/')
	mapped_file_parts[-1] = "mapped_" + mapped_file_parts[-1]
	mapped_file = "/".join(mapped_file_parts)


	#replace the replacement items in the blif Mockturtle file back to yosys input and outputs
	with open(mockturtle_file, 'r') as mockfile:
	with open(mapped_file, 'w') as outfile:
	for line in mockfile:
	for src, target in replacementList.items():
	line = line.replace(src + " ", target + " ")
	- if(target in outputVariables):
	- line = line.replace(src, target)
	+ if line.endswith(src+'\n'):
	+ line = line[:-len(src)-1] + target + '\n'
	outfile.write(line)

	print("finished mapping ports")
	\ No newline at end of file
	diff --git a/yosys/sat_test.ys b/yosys/sat_test.ys
	index 166bbcb..d92de40 100644
	--- a/yosys/sat_test.ys
	+++ b/yosys/sat_test.ys
	@@ -1,30 +1,33 @@
	# test to check sat comparison.
	echo on

	read_liberty -ignore_miss_func ./nem_liberty/nem_basic_yosys.lib
	design -save lib # save the Liberty library

	read_verilog {{FILE}}
	read_verilog ./temp/{{FILE_BASENAME}}_nem.v

	+
	+
	proc
	-clean
	+clean;;;
	+splitnets -ports;;

	miter -equiv -make_assert {{MODULE}} {{MODULE}}_nem equal

	#show equal

	flatten equal

	clean

	opt -full;;

	techmap -map %lib


	#show -pause equal

	stat equal

	sat -prove-asserts -set-init-zero -tempinduct -verify -show-regs -show-inputs -show-outputs -dump_vcd trace.vcd equal

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