#----------------------------------------------------
#
# 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
#
#  This version is for ThermoFisher Spectra UltraX Instruments
#----------------------------------------------------




from autoscript_tem_microscope_client import TemMicroscopeClient
from autoscript_tem_microscope_client.structures import *

import time
import math

#print("Starting blank check")

microscope = TemMicroscopeClient()
microscope.connect("192.168.0.1")

# Set get beam size  (in meters)
beam_size=microscope.optics.beam_diameter
print("Current Beam Diameter : " , beam_size)
StartingBeamDiameter=beam_size
wait_time=0.001
time.sleep(wait_time)
factor=1
multiplier=.15  #0.15 is default
for jj in range(0,10): # ~ runs for about 10 seconds
#for jj in range(0,100000): #runs for a very long time
     for j  in range (1,20):
        if (factor>0):
            mfactor=1 + (j)*multiplier/20
        if(factor<0):
            mfactor=1 + (multiplier - (j)*multiplier/20)
        microscope.optics.beam_diameter=beam_size*(mfactor)
        print("Iteration, factor, mfactor, Beam Diameter : ",jj, factor, mfactor, microscope.optics.beam_diameter)
     factor=factor*-1
     time.sleep(wait_time)

# make sure you restore original Beam diameter.
microscope.optics.beam_diameter=StartingBeamDiameter

# we are done tell the world

print ("Fresnel Free Done")