I would first use the "profile" function to check which part of the code is actually taking a long time. Then tackle those lines.
Secondly, maybe some of your for-loops are inevitable, but you can do it more efficiently. One way to do that is reduce the number of iterations you would have to do.
For example -- your big i-for-loop. You are looping your text file, which according to you needs to run 20 million iterations. Consider then, what if you can loop your excel file instead? That only has 800 rows, much less than 20 million. How can modify your code to loop it that way?
Thirdly, you have may conditional assignments within your loop. Instead of doing it item by item inside the loop, think about how you can do this outside the loop in a vectorized form, e.g. use your for-loop to identify those matched_data_indices, then you have a vectorized your assignments:
matched_data_indices; % from loop
flag = isnan(excel_bit(matched_data_inices)) && isnan(excel_signalbyte_2(matched_data_inices));
dec_struct.hex = ...
Lastly, you may not need to do a for-loop to find matching data.
Blessings,
Spencer
