# -*- 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 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 #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=0.01)->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=0.01)->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}") # TODO: implement the reverse scan and zero when finish functionality # receive values in units of T, rescale in kg to talk with the power supplyy. 1T = 10kG def sweep_b_val(instr:pyvisa.resources.Resource, min_bval:float, max_bval:float, res:float, Settings:str, base_file_name='', path_save="C:/Users/localadmin/Desktop/Users/Lukas/2024_02_08_Map_test", singlepowersupply_bool=False, reversescan_bool=False, zerowhenfin_bool=False)->None: """ 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) 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. """ '''''' if base_file_name =='': base_file_name = datetime.datetime.now().strftime('%Y_%m_%d_%H.%M') start_time = time.time() 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 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.') 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_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 total_points = len(bval_lst) intensity_data = [] # To store data from each scan 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 #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: # TODO: improve the conditional block later on... try to shorten the number of conditionals needed/flatten the nested conditionals # else, travel to the lower or higher limit, depending on how far the init val is to each bound, and commence the measurement from there on # if not reversescan_bool: 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') 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') 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) ################################################################# 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 # Open the connection with the APS100 dual power supply powerbox_dualsupply = rm.open_resource('ASRL8::INSTR', baud_rate=9600, # Example baud rate, adjust as needed data_bits=8, parity= pyvisa.constants.Parity.none, stop_bits= pyvisa.constants.StopBits.one, timeout=5000)# 5000 ms timeout write_no_echo(powerbox_dualsupply, 'REMOTE') # turn on the remote mode # 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')}" # # TODO: write the bval scan here # for idx, bval in enumerate(bval_lst): # write_no_echo(powerbox_dualsupply, '') # 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, experiment_settings, experiment_name, singlepowersupply_bool=False, zerowhenfin_bool=True, reversescan_bool=False) # Internally, axes are numbered 0 to 2 write_no_echo(powerbox_dualsupply, 'LOCAL') # turn off the remote mode # time.sleep(0.5) powerbox_dualsupply.close() # TEST COMMIT MAIN BRANCH