#----------------------------------------------------
#
# Fresnel Free Imaging Script
# for PicoProbe Instrument
# N. J. Zaluzec
# Email: Zaluzec@microscopy.com
# Version 20240820
#
# this is free code to mitigate frensel fringes from the
# condensor apeture in CTEM images 

# See the reference below
# for details. 
#
# Reference:
# Fresnel Free Imaging Mode (FFIM) for Transmission
# Electron Microscopy: A Computationally Mediated Solution
# using Spatio-Temporal Functionalization of the Illumination Optics
# Ref: Microscopy and Microanalysis, 30 (Suppl 1), 2024, 1634–1638 # 
# https://doi.org/10.1093/mam/ozae044.806
#
# Note: Lines # 29,30,39,43,47,76,83 will be vendor specific
#
#----------------------------------------------------


# Import a connection to your microscope control system
# this will be vendor specific python script calls
# check with your instrument vendor for specifics. 

from Vendorscript_tem_connection_client import TemConnection
from Vendorscript_tem_connection_client.allfunctions import *

import time
import math

print("Starting FFIM - Code Courtesy of Nestor Zaluzec")
# these  lines will be vendor specific
# define the instrument 
microscope = TemConnection()

#connect to scope using a Network IP connection
# these  lines will bee vendor specific
microscope.connect("192.168.0.1")

# Get current beam size  
# these  lines will bee vendor specific
beam_size=microscope.beam_diameter

print("Current Beam Diameter : " , beam_size)

StartingBeamDiameter=beam_size  # store this for recall

# define a few parameters 
wait_time=0.001
time.sleep(wait_time)
factor=1
multiplier=.15  #0.15 is default

# this is a small loop that changes the beam diameter
# the larger the number of loops the longer the 
# oscillations will loop and mitigate the fringes

# numberofloops= 10 is a few seconds 100000 is a long time
# try this with  a 1 second detector exposure and then iterate
# as needed to fit your experiment

numberofloops=10; 

for jj in range(0,numberofloops): 
     for j  in range (1,20):
        if (factor>0):
            mfactor=1 + (j)*multiplier/20
        if(factor<0):
            mfactor=1 + (multiplier - (j)*multiplier/20)
        # this changes the beam diameter a small amount
        microscope.beam_diameter=beam_size*(mfactor)
        #this just tells us that something is happening it can be deleted
        print("Iteration, factor, mfactor, Beam Diameter : ",jj, factor, mfactor, microscope.beam_diameter)
     factor=factor*-1
     time.sleep(wait_time)

# All done now  restore original Beam diameter.
microscope.beam_diameter=StartingBeamDiameter

# we are done tell the world

print ("Fresnel Free Done")