LCRControllerCode/Dasha_LCRCode.py

# -*- coding: utf-8 -*-
"""
Created on 29.10.2024, 09:00 hrs
LC Controller measurement script
@author: Serdar, adjusted by Lukas and Ryan
"""
############################################
# Packages from Ryan
import re
import math
import threading
import pyvisa
import time
# from pyvisa import ResourceManager, constants
# NOTE: KLCCommandLib64.py must be in the same folder as this script!
try:
    from KLCCommandLib64 import *
except OSError as ex:
    print("Warning:",ex)

V_MAX = 25  # corresponds to the max RMS voltage of 25 V of KLC101 device

############################################

import AMC
import csv
import time
import clr
import sys
import os, glob, string
import spe2py as spe
import spe_loader as sl
import pandas as pd
import time
from System.IO import *
from System import String
import numpy as np
import matplotlib.pyplot as plt
import datetime
from typing import Union

# NOTE: this is possibly not needed, remove later
#First choose your controller
IP_AMC300 = "192.168.1.1"
IP_AMC100 = "192.168.71.100"

# IP = "192.168.1.1"
IP = IP_AMC100

# Import System.IO for saving and opening files
from System.IO import *

from System.Threading import AutoResetEvent

# Import C compatible List and String
from System import String
from System.Collections.Generic import List

# Add needed dll references
sys.path.append(os.environ['LIGHTFIELD_ROOT'])
sys.path.append(os.environ['LIGHTFIELD_ROOT']+"\\AddInViews")
sys.path.append(r'C:\Program Files\Princeton Instruments\LightField\AddInViews')  #I added them by hand -serdar
sys.path.append(r'C:\Program Files\Princeton Instruments\LightField')           #this one also
clr.AddReference('PrincetonInstruments.LightFieldViewV5')
clr.AddReference('PrincetonInstruments.LightField.AutomationV5')
clr.AddReference('PrincetonInstruments.LightFieldAddInSupportServices')
os.environ['LIGHTFIELD_ROOT'] = r'C:\Program Files\Princeton Instruments\LightField'
# PI imports
from PrincetonInstruments.LightField.Automation import Automation
from PrincetonInstruments.LightField.AddIns import ExperimentSettings
from PrincetonInstruments.LightField.AddIns import CameraSettings
#from PrincetonInstruments.LightField.AddIns import DeviceType
from PrincetonInstruments.LightField.AddIns import SpectrometerSettings
from PrincetonInstruments.LightField.AddIns import RegionOfInterest

######################################################################################################### code begins from here #############################################

def set_custom_ROI():
    # Get device full dimensions
    dimensions = experiment.FullSensorRegion()
        
    regions = []
    
    # Add two ROI to regions
    regions.append(
      RegionOfInterest(
          int(dimensions.X), int(dimensions.Y),
          int(dimensions.Width), int(dimensions.Height//4),  # Use // for integer division
          int(dimensions.XBinning), int(dimensions.Height//4)))
    # Set both ROI
    experiment.SetCustomRegions(regions)
    
def experiment_completed(sender, event_args): #callback function which is hooked to event completed, this is the listener
    print("... Acquisition Complete!")
    acquireCompleted.Set() #set the event. This puts the autoresetevent false.(look at .NET library for furher info)

def InitializerFilenameParams():
    experiment.SetValue(ExperimentSettings.FileNameGenerationAttachIncrement, False)
    experiment.SetValue(ExperimentSettings.FileNameGenerationIncrementNumber, 1.0)
    experiment.SetValue(ExperimentSettings.FileNameGenerationIncrementMinimumDigits, 2.0)
    experiment.SetValue(ExperimentSettings.FileNameGenerationAttachDate, False)
    experiment.SetValue(ExperimentSettings.FileNameGenerationAttachTime, False)
    
def AcquireAndLock(name):
    print("Acquiring...", end = "")
    # name += 'Exp{0:06.2f}ms.CWL{1:07.2f}nm'.format(\
                                                   # experiment.GetValue(CameraSettings.ShutterTimingExposureTime)\
                                                   # ,experiment.GetValue(SpectrometerSettings.GratingCenterWavelength))
                                                   
    experiment.SetValue(ExperimentSettings.FileNameGenerationBaseFileName, name) #this creates .spe file with the name
    experiment.Acquire() # this is an ashynrchronus func. 
    acquireCompleted.WaitOne()  
    
def calculate_distance(x1, y1, x2, y2):
    return np.sqrt((x2 - x1)**2 + (y2 - y1)**2)    

def generate_scan_positions(center, range_val, resolution):
    positive_range = np.arange(center, center + range_val + resolution, resolution)   
    return positive_range

def save_as_csv(filename, position_x, position_y):
    file_existance = os.path.isfile(filename)    
    
    with open(filename, 'a', newline = '') as csvfile:
        writer = csv.writer(csvfile)
        
        if not file_existance:
            writer.writerow(['x_coordinates','y_coordinates'])
            
        writer.writerow([position_x, position_y])
                       
# def move_axis(axis, target): 
#     """
#     This function moves an axis to the specified target and stop moving after it is in the really closed
#     vicinity (+- 25nm) of the target (listener hooked to it).
#     """
#     amc.move.setControlTargetPosition(axis, target)
#     amc.control.setControlMove(axis, True)
#     while not (target - 25) < amc.move.getPosition(axis) < (target + 25):
#         time.sleep(0.1)
#     time.sleep(0.15)
#     while not (target - 25) < amc.move.getPosition(axis) < (target + 25):
#         time.sleep(0.1)              
#     amc.control.setControlMove(axis, False)
    
# def move_xy(target_x, target_y): # moving in x and y direction closed to desired position
#     amc.move.setControlTargetPosition(0, target_x)
#     amc.control.setControlMove(0, True)
#     amc.move.setControlTargetPosition(1, target_y)
#     amc.control.setControlMove(1, True)
#     while not (target_x - 25) < amc.move.getPosition(0) < (target_x + 25) and (target_y - 25) < amc.move.getPosition(1) < (target_y + 25):
#         time.sleep(0.1)
#     time.sleep(0.15)
#     while not (target_x - 25) < amc.move.getPosition(0) < (target_x + 25) and (target_y - 25) < amc.move.getPosition(1) < (target_y + 25):
#         time.sleep(0.1)
    
#     amc.control.setControlOutput(0, False)
#     amc.control.setControlOutput(1, False)
  
# intensity_data = []  # To store data from each scan
# data_list = []  

# def move_scan_xy(range_x, range_y, resolution, Settings, baseFileName):
#     """
#     This function moves the positioners to scan the sample with desired ranges and resolution in 2 dimensions.
#     At the end it saves a csv file 

#     Parameters
#     ----------
#     range_x : integer in nm. max value is 5um
#         Scan range in x direction.
#     range_y : integer in nm. max value is 5um
#         Scan range in y direction.
#     resolution : integer in nm. 
#         Room temprature max res is 50nm. In cyrostat (4K) it is 10nm (check the Attocube manual)
#     baseFileName: string. At the end the saved file will be: baseFileName_scan_data.csv and it will be saved to the current directory

#     Returns
#     -------
#     None.

#     """
#     start_time = time.time()
#     axis_x = 0 #first axis 
#     axis_y = 1 #second axis
#     center_x =  amc.move.getPosition(axis_x)
#     center_y =  amc.move.getPosition(axis_y)
#     # #check if the intput range is reasonable
#     # if amc.move.getPosition(axis_x) + range_x >= 5000 or amc.move.getPosition(axis_x)- range_x <= 0 or amc.move.getPosition(axis_y) + range_y >=5000 or amc.move.getPosition(axis_y) - range_y <= 5000 :
#     #     print("scan range is out of range!")
#     #     return
#     # +- range from current positions for x and y directions
    
    
#     array_x = generate_scan_positions(center_x, range_x, resolution)
#     array_y = generate_scan_positions(center_y, range_y, resolution)
#     total_points = len(array_x)*len(array_y)
#     len_y = len(array_y)
#     intensity_data = []  # To store data from each scan
#     data_list = []
#     cwd = os.getcwd() # save original directory
    
#     #This gives a directory, in which the script will save the spectrum of each spot as spe
#     #However, it will open the spectrum, convert it to txt, add it to the intensity_data and delete the spe file
#     temp_folder_path = "C:/Users/localadmin/Desktop/Users/Lukas/2024_02_08_Map_test"
    
#     #scanning loop
#     for i, x_positions in enumerate(array_x):
#         move_axis(axis_x, x_positions)
#         y = False
#         for j, y_positions in enumerate(array_y):
#             move_axis(axis_y, y_positions)
#             #each time when the positioner comes to the beggining of a new line
#             #this if will make the positioner wait a bit longer to really go to the target.
#             if y == False:
#                 move_axis(axis_y, y_positions)
#             y = True                                                               
        
#             #we acquire with the LF 
#             acquire_name_spe = f'{baseFileName}_X{x_positions}_Y{y_positions}'
#             AcquireAndLock(acquire_name_spe) #this creates a .spe file with the scan name.
                        
#             #read the .spe file and get the data as loaded_files
#             cwd = os.getcwd() # save original directory
#             os.chdir(temp_folder_path) #change directory
#             loaded_files = sl.load_from_files([acquire_name_spe + '.spe']) # get the .spe file as a variable
#             os.chdir(cwd) # go back to original directory
            
#             # Delete the created .spe file from acquiring after getting necessary info 
#             spe_file_path = os.path.join(temp_folder_path, acquire_name_spe + '.spe')
#             os.remove(spe_file_path)
            
#             distance = calculate_distance(x_positions, y_positions,amc.move.getPosition(axis_x), amc.move.getPosition(axis_y))            
                                                          
#             points_left = total_points - (i * len_y + (j+1)) + 1
#             print('Points left in the scan: ', points_left)
            
#             #append the intensity data as it is (so after every #of_wl_points, the spectrum of the next point begins)
#             intensity_data.append(loaded_files.data[0][0][0])
            
#             data_list.append({
#                  'position_x': x_positions,
#                  'position_y': y_positions,
#                  'actual_x': amc.move.getPosition(axis_x),
#                  'actual_y': amc.move.getPosition(axis_y),
#                  'distance': distance,                
#             })
  
#     #moves back to starting position
#     move_axis(axis_x, center_x)     
#     move_axis(axis_y, center_y)  
    
#     #prints total time the mapping lasted
#     end_time = time.time()
#     elapsed_time = (end_time - start_time) / 60
#     print('Scan time: ', elapsed_time, 'minutes')
    
#     # df = pd.DataFrame(data_list)
    
#     #save intensity & WL data as .txt
#     os.chdir('C:/Users/localadmin/Desktop/Users/Lukas')
#     # creates new folder for MAP data
#     new_folder_name = "Test_Map_" + f"{datetime.datetime.now().strftime('%Y_%m_%d_%H.%M')}"
#     os.mkdir(new_folder_name)
#     # Here the things will be saved in a new folder under user Lukas !
#     # IMPORTANT last / has to be there, otherwise data cannot be saved and will be lost!!!!!!!!!!!!!!!!
#     os.chdir('C:/Users/localadmin/Desktop/Users/Lukas/'+ new_folder_name)
    
#     intensity_data = np.array(intensity_data) 
#     np.savetxt(Settings + str(center_x) + '_' + str(center_y) + experiment_name +'.txt', intensity_data)
            
#     wl = np.array(loaded_files.wavelength)
#     np.savetxt("Wavelength.txt", wl)

################################################################# RYAN'S FUNCTIONS HERE ##########################################################################################

def polar_to_cartesian(radius, start_angle, end_angle, step_size, clockwise=True):
    # TODO: DOCS
    """Creates a list of discrete cartesian coordinates (x,y), given the radius, start- and end angles, the angle step size, and the direction of rotation. 
    Function then returns a list of two lists: list of angles and list of cartesian coordinates (x,y coordinates in a tuple).

    Args:
        radius (_type_): _description_
        start_angle (_type_): _description_
        end_angle (_type_): _description_
        step_size (_type_): _description_
        clockwise (bool, optional): _description_. Defaults to True.

    Returns:
        _type_: _description_
    """    """"""
    # Initialize lists to hold angles and (x, y) pairs
    angles = []
    coordinates = []

    # Normalize angles to the range [0, 360)
    start_angle = start_angle % 360
    end_angle = end_angle % 360

    if clockwise:
        # Clockwise rotation
        current_angle = start_angle
        while True:
            # Append the current angle to the angles list
            angles.append(current_angle % 360)

            # Convert the current angle to radians
            current_angle_rad = math.radians(current_angle % 360)
            
            # Convert polar to Cartesian coordinates
            x = radius * math.cos(current_angle_rad)
            y = radius * math.sin(current_angle_rad)
            
            # Append the (x, y) pair to the list
            coordinates.append((x, y))

            # Check if we've reached the end_angle (handling wrap-around)  (current_angle - step_size) % 360 == end_angle or
            if current_angle % 360 == end_angle:
                break

            # Decrement the current angle by the step size
            current_angle -= step_size
            if current_angle < 0:
                current_angle += 360
    else:
        # Counterclockwise rotation
        current_angle = start_angle
        while True:
            # Append the current angle to the angles list
            angles.append(current_angle % 360)

            # Convert the current angle to radians
            current_angle_rad = math.radians(current_angle % 360)
            
            # Convert polar to Cartesian coordinates
            x = radius * math.cos(current_angle_rad)
            y = radius * math.sin(current_angle_rad)
            
            # Append the (x, y) pair to the list
            coordinates.append((x, y))

            # Check if we've reached the end_angle (handling wrap-around)  (current_angle + step_size) % 360 == end_angle or
            if current_angle % 360 == end_angle:
                break

            # Increment the current angle by the step size
            current_angle += step_size
            if current_angle >= 360:
                current_angle -= 360

    return [angles, coordinates]


################################################################# DASHA'S CODE HERE ##############################################################################################

# TODO: modify b field scan script for Dasha, to be used for the KLC controller

def LCR_scan_func(handle:int, init_voltage:float, final_voltage:float, 
                res:float, base_file_name='',
                reversescan_bool=False, zerowhenfin_bool=False, loopscan_bool=False)->None:

    def pyramid_list(lst) -> Union[list, np.ndarray]:
        """reverses the list and removes the first element of reversed list. Then, this is appended to
        the end of the original list and returned as the 'pyramid' list.

        Args:
            lst (list or np.ndarray): 
        Raises:
            TypeError: if the input object isn't a list or np.ndarray
        Returns:
            Union[list, np.ndarray]: the pyramid list
        """    ''''''
        if isinstance(lst, list):
            return lst + lst[-2::-1]
        elif isinstance(lst, np.ndarray):
            return np.append(lst, lst[-2::-1])
        else:
            raise TypeError('Please input a list!')
        
    # defines the folder, in which the data from the spectrometer is temporarily stored in
    temp_folder_path = "C:/Users/localadmin/Desktop/Users/Dasha/LCR_temp_dump_folder"
    
    if base_file_name =='':
        base_file_name = datetime.datetime.now().strftime('%Y_%m_%d_%H.%M')

    start_time = time.time()  # start of the scan function

    # if '2101014' in instr_info and (magnet_coil=='y-axis'):  # single power supply
    #     if (min_bval< -BY_MAX) or (max_bval > BY_MAX):
    #         raise ValueError('Input limits exceed that of the magnet By! Please input smaller limits.')
    # elif '2301034' in instr_info:  # dual power supply
    #     if magnet_coil=='z-axis':  # check if its the coils for Bz
    #         if (min_bval < -BZ_MAX) or (max_bval > BZ_MAX):
    #             raise ValueError('Input limits exceed that of the magnet (Bz)! Please input smaller limits.')
    #         write_no_echo(instr, 'CHAN 1')
    #     elif magnet_coil=='x-axis':  # checks limits of Bx
    #         if (min_bval< -BX_MAX) or (max_bval > BX_MAX):
    #             raise ValueError('Input limits exceed that of the magnet Bx! Please input smaller limits.')
    #         write_no_echo(instr, 'CHAN 2')
    # else:
    #     raise ConnectionError('Device is not connected!')

    write_no_echo(instr, f'LLIM {min_bval*10};ULIM {max_bval*10}')  # sets the given limits, must convert to kG for the device to read
    bval_lst = np.arange(min_bval, max_bval + res, res)  # creates list of B values to measure at, with given resolution, in T

    init_lim, subsequent_lim = 'LLIM', 'ULIM'
    init_sweep, subsequent_sweep = 'DOWN', 'UP'
    
    
    # if reverse scan, then flip the values in the b list, and swap the initial limit and sweep conditions
    if reversescan_bool:
        bval_lst = bval_lst[::-1]
        init_lim, subsequent_lim = subsequent_lim, init_lim
        init_sweep, subsequent_sweep = subsequent_sweep, init_sweep

    # creates the pyramid list of B vals if one were to perform a hysteresis measurement 
    if loopscan_bool:
        bval_lst = pyramid_list(bval_lst)

    total_points = len(bval_lst)
    middle_index_bval_lst = total_points // 2 
    intensity_data = []  # To store data from each scan
    cwd = os.getcwd() # save original directory

    # NOTE: helper function for the scanning loop
    def helper_scan_func(idx, bval, instr=instr, init_lim=init_lim, init_sweep=init_sweep,
                         subsequent_lim=subsequent_lim, subsequent_sweep=subsequent_sweep, sleep=5):
        if idx == 0:  # for first iteration, sweep to one of the limits 
            write_no_echo(instr, f'{init_lim} {bval*10}')  # convert back to kG
            write_no_echo(instr, f'SWEEP {init_sweep}')
        else:
            write_no_echo(instr, f'{subsequent_lim} {bval*10}')  # convert back to kG
            write_no_echo(instr, f'SWEEP {subsequent_sweep}')

        actual_bval = sep_num_from_units(query_no_echo(instr, 'IMAG?'))[0]*0.1  # convert kG to T
        print(f'Actual magnet strength: {actual_bval} T,', f'Target magnet strength: {bval} T')

        while abs(actual_bval - bval) > 0.0001:
            time.sleep(5)  # little break
            actual_bval = sep_num_from_units(query_no_echo(instr, 'IMAG?'))[0]*0.1 
                # update the actual bval
            print(f'Actual magnet strength: {actual_bval} T,', f'Target magnet strength: {bval} T')
    
    #scanning loop
    for i, bval in enumerate(bval_lst):

        if not loopscan_bool:
            helper_scan_func(i, bval)
        else:
            if i <= middle_index_bval_lst:
                helper_scan_func(i, bval)
            else:
                helper_scan_func(i, bval, instr=instr, init_lim=subsequent_lim, init_sweep=subsequent_sweep,
                            subsequent_lim=init_lim, subsequent_sweep=init_sweep, sleep=5)
        
        time.sleep(5)
        # we acquire with the LF 
        acquire_name_spe = f'{base_file_name}_{bval}T'
        AcquireAndLock(acquire_name_spe) #this creates a .spe file with the scan name.
                    
        # read the .spe file and get the data as loaded_files
        cwd = os.getcwd() # save original directory
        os.chdir(temp_folder_path) #change directory
        loaded_files = sl.load_from_files([acquire_name_spe + '.spe']) # get the .spe file as a variable
        os.chdir(cwd) # go back to original directory
        
        # Delete the created .spe file from acquiring after getting necessary info 
        spe_file_path = os.path.join(temp_folder_path, acquire_name_spe + '.spe')
        os.remove(spe_file_path)    
                                                        
        points_left = total_points - i - 1
        print('Points left in the scan: ', points_left)
        
        #append the intensity data as it is (so after every #of_wl_points, the spectrum of the next point begins)
        intensity_data.append(loaded_files.data[0][0][0])
    
    #prints total time the mapping lasted
    end_time = time.time()
    elapsed_time = (end_time - start_time) / 60
    print('Scan time: ', elapsed_time, 'minutes')

    write_no_echo(instr, f'LLIM {instr_bsettings[1][0]*10};ULIM {instr_bsettings[2][0]*10}')  # reset the initial limits of the device after the scan

    if zerowhenfin_bool:
        write_no_echo(instr, 'SWEEP ZERO')  # if switched on, discharges the magnet after performing the measurement loop above
    
    #save intensity & WL data as .txt
    os.chdir('C:/Users/localadmin/Desktop/Users/Lukas')
    # creates new folder for MAP data
    new_folder_name = "Test_Map_" + f"{datetime.datetime.now().strftime('%Y_%m_%d_%H.%M')}"
    os.mkdir(new_folder_name)
    # Here the things will be saved in a new folder under user Lukas !
    # IMPORTANT last / has to be there, otherwise data cannot be saved and will be lost!!!!!!!!!!!!!!!!
    os.chdir('C:/Users/localadmin/Desktop/Users/Lukas/'+ new_folder_name)
    
    intensity_data = np.array(intensity_data) 
    np.savetxt(base_file_name + '.txt', intensity_data)
            
    wl = np.array(loaded_files.wavelength)
    np.savetxt("Wavelength.txt", wl)


################################################################# END OF FUNCTION DEFS ###########################################################################################  

# NOTE: RYAN INTRODUCED SOME FUNCTIONS HERE TO PERFORM THE SCAN
try:
    # initialise KLC connection
    # Find devices
    devs = klcListDevices()
    print("Found devices:",devs,"\n")
    if(len(devs)<=0):
        print('There is no device connected')
        sys.exit()
    klc = devs[0]
    serialnumber = klc[0]
    
    # Connect device
    KLC_handle = klcOpen(serialnumber, 115200, 3)
    if(KLC_handle<0):
        print("open ", serialnumber, " failed")
        sys.exit()
    if(klcIsOpen(serialnumber) == 0):
        print("klcIsOpen failed")
        klcClose(KLC_handle)
        sys.exit()
    print("Connected to serial number ", serialnumber)

    # TODO: remove this commented code block later
    # Initialise PYVISA ResourceManager
    # rm = pyvisa.ResourceManager()
    # print(rm.list_resources())  
    # 'ASRL8::INSTR' for dual power supply, 'ASRL9::INSTR' for single power supply (online PC)
    # 'ASRL10::INSTR' for dual power supply, 'ASRL12::INSTR' for single power supply (offline PC)

    auto = Automation(True, List[String]())
    experiment = auto.LightFieldApplication.Experiment
    acquireCompleted = AutoResetEvent(False)

    experiment.Load("Alison_08.07.24")  # NOTE: this should be the 
    experiment.ExperimentCompleted += experiment_completed  # we are hooking a listener.
    # experiment.SetValue(SpectrometerSettings.GratingSelected, '[750nm,1200][0][0]')
    # InitializerFilenameParams()

    # ENTER START AND END VOLTAGES, AS WELL AS VOLTAGE STEP SIZE HERE
    start_voltage = 0
    end_voltage = 0.5
    voltage_stepsize = 0.25

    #Here you can specify the filename of the map e.g. put experiment type, exposure time, used filters, etc....
    experiment_settings = 'PL_SP_700_LP_700_HeNe_52muW_exp_2s_Start_'
    #The program adds the range of the scan as well as the resolution and the date and time of the measurement
    experiment_name = f"{start_voltage}V_to_{end_voltage}V_{voltage_stepsize}V_{datetime.datetime.now().strftime('%Y_%m_%d_%H%M')}"

    # TODO: insert LCR rotation scan function here

    # use this reference code for the LCR scan later on 
    # sweep_b_val(powerbox_dualsupply, set_llim_bval, set_ulim_bval, set_res_bval, 'z-axis',
    #         experiment_settings, base_file_name=experiment_name, zerowhenfin_bool=True, reversescan_bool=False)


except Exception() as e:
    print(e)
finally: 
    #close connection to device
    klcClose(KLC_handle)
    print("Connection closed")