CryostatB-FieldMeasurementScript/20240709SerdarModScript.py

# -*- coding: utf-8 -*-
"""
Created on Fri Dec 22 15:10:10 2023
Lightfield + Positioner 
@author: Serdar, adjusted by Lukas
"""
############################################
# Packages from Ryan
import re
import math
from threading import Thread
import pyvisa
# from pyvisa import ResourceManager, constants

# B Field Limits (in T)
BX_MAX = 1.7
BY_MAX = 1.7
BZ_MAX = 4.0
############################################

import AMC
import csv
import time
import clr
import sys
import os
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


#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 os module
import os, glob, string

# 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
    Path_save = "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(Path_save) #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(Path_save, 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 sep_num_from_units(powerbox_output :str)->list:
    '''
    Receives a string as input and separates the numberic value and unit and returns it as a list.
    
    Parameters
    ----------
    powerbox_output : str
        string output from the attocube powerbox, e.g. 1.35325kG

    Returns
    -------
    list
        list of float value and string (b value and it's units). If string is purely alphabets, then return a single element list

    '''
    match = re.match(r'\s*([+-]?\d*\.?\d+)([A-Za-z]+)', powerbox_output)
    if match:
        numeric_part = float(match.group(1))  # Convert the numeric part to a float
        alphabetic_part = match.group(2)  # Get the alphabetic part
        return [numeric_part, alphabetic_part]
    else:
        return [powerbox_output,]


def query_no_echo(instr:pyvisa.resources.Resource, command:str, sleeptime=0)->str:
    """helper function for the Attocube APS100 that queries a function to the device, removing the echo.

    Args:
        instr (pyvisa.resources.Resource): 
        command (str): commands, can be stringed in series with ; between commands
        sleeptime (float, optional): delay time between commands. Defaults to 0.01.

    Returns:
        str: _description_
    """    ''''''
    try:
        print(f"Sending command: {command}")
        instr.write(command)
        time.sleep(sleeptime)
        echo_response = instr.read()  # Read and discard the echo
        # print(f"Echo response: {echo_response}")
        actual_response = instr.read()  # Read the actual response
        print(f"Actual response: {actual_response}")
        return actual_response
    except pyvisa.VisaIOError as e:
        print(f"Error communicating with instrument: {e}")
        return None


def write_no_echo(instr:pyvisa.resources.Resource, command:str, sleeptime=0)->str:
    """helper function for the Attocube APS100 that writes a function to the device, removing the echo.

    Args:
        instr (pyvisa.resources.Resource): 
        command (str): commands, can be stringed in series with ; between commands
        sleeptime (float, optional): delay time between commands. Defaults to 0.01.

    Returns:
        str: _description_
    """    ''''''
    try:
        print(f"Sending command: {command}")
        instr.write(command)
        time.sleep(sleeptime)  # Give the device some time to process
        try:
            while True:
                echo_response = instr.read()  # Read and discard the echo
                # print(f"Echo response: {echo_response}")
        except pyvisa.VisaIOError as e:
            # Expected timeout after all echoed responses are read
            if e.error_code != pyvisa.constants.VI_ERROR_TMO:
                raise
    except pyvisa.VisaIOError as e:
        print(f"Error communicating with instrument: {e}")


# receive values in units of T, rescale in kg to talk with the power supplyy. 1T = 10kG
# NOTE: removed singlepowersupply_bool, reading serial-nr. of the device instead.
# old save folder: "C:/Users/localadmin/Desktop/Users/Lukas/2024_02_08_Map_test"
def sweep_b_val(instr:pyvisa.resources.Resource, min_bval:float, max_bval:float, 
                res:float, magnet_coil:str, Settings:str, base_file_name='', path_save='',
                reversescan_bool=False, zerowhenfin_bool=False, loopscan_bool=False)->None:
    # TODO: update docs in the end
    """ this function performs a sweep of the B field of the chosen magnet coil. It creates a list o B values from the given min and max values,
    with the given resolution. For each value, a measurement of the spectrum of the probe in the cryostat is made, using the LightField spectrometer.

    Args:
        instr (pyvisa.resources.Resource): chosen power supply device to connect to
        min_bval (float): min B value of the scan (please input in units of Tesla)
        max_bval (float): max B value of the scan (please input in units of Tesla)
        res (float): resolution of the list of B values (please input in units of Tesla)
        magnet_coil (str): select magnet coil to be used. String should be 'x-axis','y-axis' or 'z-axis'.
        Settings (str): experiment settings, included in file name.
        base_file_name (str, optional): base file name. Defaults to ''.
        path_save (str, optional): file path where the file will be saved. Defaults to "C:/Users/localadmin/Desktop/Users/Lukas/2024_02_08_Map_test".
        singlepowersupply_bool (bool, optional): _description_. Defaults to False.
        reversescan_bool (bool, optional): _description_. Defaults to False.
        zerowhenfin_bool (bool, optional): _description_. Defaults to False.

    Raises:
        ValueError: when By limit is exceeded.
        ValueError: when Bz limit is exceeded.
        ValueError: when Bx limit is exceeded.
        ConnectionError: when no device is connected.
    """    ''''''

    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!')
    
    if path_save =='':
        path_save = datetime.datetime.now().strftime("%Y_%m_%d_%H%M_hrs_")
    
    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

    instr_info = query_no_echo(instr, '*IDN?')

    instr_bsettings = list(sep_num_from_units(el) for el in query_no_echo(instr, 'UNITS?;LLIM?;ULIM?').split(';'))  # deliver a 3 element tuple of tuples containing the set unit, llim and ulim 

    if instr_bsettings[0][0] == 'T':
        instr_bsettings[1][0] = instr_bsettings[1][0]*0.1  # rescale kG to T, device accepts values only in kG or A, eventho we set it to T
        instr_bsettings[2][0] = instr_bsettings[2][0]*0.1

    # if singlepowersupply_bool:  # checks limits of Bx or By
    #     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 '1' in query_no_echo(instr, 'CHAN?'):  # 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.')
    # else:  # 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.')
 
    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

    # TODO: unused, see if can remove
    # init_bval = sep_num_from_units(query_no_echo(instr, 'IMAG?'))[0]*0.1  # queries the initial B value of the coil, rescale from kG to T

    init_lim, subsequent_lim = 'LLIM', 'ULIM'
    init_sweep, subsequent_sweep = 'DOWN', 'UP'
    
    ####################################################
    # TODO: decide whether to start at min b val or max b val, depending on which one is nearer, IMPLEMENT THIS LATER
    # nearest_bval = (abs(init_bval - min_bval), abs(init_bval - max_bval))
    # if nearest_bval[0] <= nearest_bval[1]:
    #     reversescan_bool = True
    ####################################################
    
    # 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 init_bval == bval:
        #     # if initial bval is equal to the element of the given iteration from the bval_lst, then commence measuring the spectrum
        #     pass
        # else:

        # NOTE: original code without the loop scan
        ################################################
        # if i == 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')
        ###############################################
        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(path_save) #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(path_save, acquire_name_spe + '.spe')
        os.remove(spe_file_path)    
                                                        
        points_left = total_points - i - 1  # TODO: SEE IF THIS IS CORRECT
        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(Settings + str(min_bval) + 'T_to_' + str(max_bval) + 'T' + experiment_name +'.txt', intensity_data)
            
    wl = np.array(loaded_files.wavelength)
    np.savetxt("Wavelength.txt", wl)


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]


# TODO: write a function that simultaneously controls the two power supplies and perform the rotation of the B-field. => Threading
# in function head should be func(instr1, instr2, args1, kwargs1, args2, kwargs2)
def b_field_rotation(instr1:pyvisa.resources.Resource, instr2:pyvisa.resources.Resource,
                     Babs:float, startangle:float, endangle:float, angle_stepsize:float, clockwise=True, path_save='', base_file_name='', sweepdown=False)->None:
    # TODO: update docs
    """Rotation of the b-field in discrete steps, spectrum is measured at each discrete step in the rotation. Scan angle is 
    defined as the angle between the x-axis and the current B-field vector, i.e., in the anticlockwise direction.

    Args:
        instr1 (pyvisa.resources.Resource): _description_
        instr2 (pyvisa.resources.Resource): _description_
        Babs (float): absolute B-field value in T
        startangle (float): start angle in degrees
        endangle (float): end angle in degrees
        angle_stepsize (float): angle step size in degrees
        clockwise (bool): determines the direction of rotation of the B-field. Defaults to True.
        sweepdown (bool, optional): after finishing the rotation, both B-field components should be set to 0 T. Defaults to False.
    """
    
    def wait_for_b_val_helper_func(instr,):
        pass

    if path_save =='':
        path_save = datetime.datetime.now().strftime("%Y_%m_%d_%H%M_hrs_")  # TODO: add path_save, base_file_name in the function header
    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

    startangle = startangle % 360
    endangle = endangle % 360  # ensures that the angles are within [0,360)

    idnstr1 = query_no_echo(instr1, '*IDN?')
    idnstr2 = query_no_echo(instr1, '*IDN?')

    intensity_data = []  # To store data from each scan
    cwd = os.getcwd() # save original directory

    # TODO: find which one is the dual power supply, then, ramp B_x to Babs value
    if '2301034' in idnstr1: # serial no. the dual power supply
        pass
    elif '2101034' in idnstr2:
        # swap instruments, instr 1 to be the dual power supply (^= x-axis)
        instr1, instr2 = instr2, instr1

    # initialise the sweep angle list as well as the sweep limits and directions for each instrument
    instr1_lim, instr2_lim = 'LLIM', 'ULIM'
    instr1_sweep, instr2_sweep = 'DOWN', 'UP'
    angles, cartesian_coords = polar_to_cartesian(Babs, startangle, endangle, angle_stepsize, clockwise=clockwise)  # create lists of angles and discrete Cartesian coordinates

    if clockwise:  # NOTE: old conditional was:  startangle > endangle      see if this works....
        # reverse sweep limits and directions for the clockwise rotation
        instr1_lim, instr2_lim = instr2_lim, instr1_lim
        instr1_sweep, instr2_sweep = instr2_sweep, instr1_sweep

    # list of rates (with units) for diff ranges of each device, only up to Range 1 for single power supply as that is already
    # the max recommended current. 
    init_range_lst1 = list(sep_num_from_units(el) for el in query_no_echo(instr1, 'RATE? 0;RATE? 1;RATE? 2').split(';'))
    init_range_lst2 = list(sep_num_from_units(el) for el in query_no_echo(instr2, 'RATE? 0;RATE? 1').split(';'))

    min_range_lst = [min(el1[0], el2[0]) for el1,el2 in zip(init_range_lst1, init_range_lst2)]  # min rates for each given range

    # set both devices to the min rates
    write_no_echo(instr1, f'RATE 0 {min_range_lst[0]};RATE 1 {min_range_lst[1]}')
    write_no_echo(instr2, f'RATE 0 {min_range_lst[0]};RATE 1 {min_range_lst[1]}')

    write_no_echo(instr1, f'CHAN 2;ULIM {Babs*10};SWEEP UP')  # sets to B_x, the B_x upper limit and sweeps the magnet field to the upper limit
    print(f'SWEEPING B-X TO {Babs} T NOW')

    # wait for Babs to be reached by the Bx field
    actual_bval = sep_num_from_units(query_no_echo(instr1, 'IMAG?'))[0]*0.1  # convert kG to T
    print(f'Actual magnet strength (Bx): {actual_bval} T,', f'Target magnet strength: {Babs} T')
    while abs(actual_bval - Babs) > 0.0001:
        time.sleep(5)  # little break
        actual_bval = sep_num_from_units(query_no_echo(instr1, 'IMAG?'))[0]*0.1 
        print(f'Actual magnet strength (Bx): {actual_bval} T,', f'Target magnet strength: {Babs} T')

    # TODO: begin the rotation of the B-field, saving the spectrum for each angle, including the start- and end angles
    # NOTE: implement PID control, possibly best option to manage the b field DO THIS LATER ON, WE DO DISCRETE B VALUES RN
    # bug fix for polar_to_cartesian (27.08.2024, 15:52 hrs)
    # TODO: write the for loop for the rotation here, implement threading => create a helper function to enter into the threads
    for idx, angle in enumerate(angles):
        pass
        #     # 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(path_save) #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(path_save, acquire_name_spe + '.spe')
        # os.remove(spe_file_path)    
                                                        
        # points_left = total_points - i - 1  # TODO: SEE IF THIS IS CORRECT
        # 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])

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

# NOTE: RYAN INTRODUCED SOME FUNCTIONS HERE TO PERFORM THE SCAN

# 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)


# Open the connection with the APS100 dual power supply
powerbox_dualsupply = rm.open_resource('ASRL10::INSTR', 
                                        baud_rate=9600,
                                        data_bits=8, 
                                        parity= pyvisa.constants.Parity.none, 
                                        stop_bits= pyvisa.constants.StopBits.one, 
                                        timeout=100)# 5000 ms timeout

# Open the connection with the APS100 dual power supply
powerbox_singlesupply = rm.open_resource('ASRL12::INSTR',
                                        baud_rate=9600,
                                        data_bits=8, 
                                        parity= pyvisa.constants.Parity.none, 
                                        stop_bits= pyvisa.constants.StopBits.one, 
                                        timeout=100)# 5000 ms timeout

write_no_echo(powerbox_dualsupply, 'REMOTE')  # turn on the remote mode
write_no_echo(powerbox_singlesupply, 'REMOTE')  # turn on the remote mode

# TODO: test functionality of the magnet_coil param later on, should work... as this code below is basically implemented inside the scan func.
# select axis for the dual supply, either z-axis(CHAN 1 ^= Supply A) or x-axis(CHAN 2 ^= Supply B)
# write_no_echo(powerbox_dualsupply, 'CHAN 1')

# Setup connection to AMC
amc = AMC.Device(IP)
amc.connect()

# Internally, axes are numbered 0 to 2
amc.control.setControlOutput(0, True)
amc.control.setControlOutput(1, True)


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

experiment.Load("Lukas_experiment_2024_02_06")
experiment.ExperimentCompleted += experiment_completed  # we are hooking a listener.
# experiment.SetValue(SpectrometerSettings.GratingSelected, '[750nm,1200][0][0]')
# InitializerFilenameParams()


#set scan range and resolution in nanometers
range_x = 20000
range_y = 20000
resolution = 1000
# set B-field scan range and resolution (all in T)
set_llim_bval = -0.01
set_ulim_bval = 0.01
set_res_bval = 0.01

#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"{set_llim_bval}T_to_{set_ulim_bval}T_{set_res_bval}T_{datetime.datetime.now().strftime('%Y_%m_%d_%H%M')}"

# this moves the probe in xy-direction and measures spectrum there
# move_scan_xy(range_x, range_y, resolution, experiment_settings, experiment_name)

# perform the B-field measurement for selected axis above
# sweep_b_val(powerbox_dualsupply, set_llim_bval, set_ulim_bval, set_res_bval, experiment_settings, experiment_name)
sweep_b_val(powerbox_dualsupply, set_llim_bval, set_ulim_bval, set_res_bval, 'z-axis',
            experiment_settings, experiment_name, zerowhenfin_bool=True, reversescan_bool=False)

# Internally, axes are numbered 0 to 2

write_no_echo(powerbox_dualsupply, 'LOCAL')  # turn off the remote mode
write_no_echo(powerbox_singlesupply, 'LOCAL')  # turn off the remote mode
# time.sleep(0.5)
powerbox_dualsupply.close()
powerbox_singlesupply.close()