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CryostatB-FieldMeasurementS.../20240709SerdarModScript.py

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2024-07-12 14:55:20 +00:00
# -*- 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 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.')
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()
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