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c93d4ff2f7
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78b2aa6ba7
@ -1,33 +0,0 @@
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import re
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import numpy as np
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def sep_num_from_units(powerbox_output :str)->list:
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'''
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Receives a string as input and separates the numberic value and unit and returns it as a list.
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Parameters
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----------
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powerbox_output : str
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string output from the attocube powerbox, e.g. 1.35325kG
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Returns
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-------
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list
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list of float value and string (b value and it's units). If string is purely alphabets, then return a single element list
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'''
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match = re.match(r'\s*([+-]?\d*\.?\d+)([A-Za-z]+)', powerbox_output)
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if match:
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numeric_part = float(match.group(1)) # Convert the numeric part to a float
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alphabetic_part = match.group(2) # Get the alphabetic part
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return [numeric_part, alphabetic_part]
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else:
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return [powerbox_output,]
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angles = [1,2,3]
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print(str(angles[0]) +"\n"+ str(angles[-1]))
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rates_lst = list(sep_num_from_units(el) for el in "0.0kG;1.0kG".split(";"))
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print(rates_lst[1][0])
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File diff suppressed because it is too large
Load Diff
@ -1,355 +0,0 @@
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# -*- coding: utf-8 -*-
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"""
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Created on Fri Dec 22 15:10:10 2023
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Lightfield + Positioner
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@author: Local Admin
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"""
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import AMC
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import csv
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import time
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import clr
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import sys
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import os
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import spe2py as spe
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import spe_loader as sl
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import pandas as pd
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import time
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from System.IO import *
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from System import String
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import numpy as np
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import matplotlib.pyplot as plt
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import datetime
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#First choose your controller
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IP_AMC300 = "192.168.71.101"
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IP_AMC100 = "192.168.71.100"
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# IP = "192.168.1.1"
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IP = IP_AMC300
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# Import os module
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import os, glob, string
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# Import System.IO for saving and opening files
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from System.IO import *
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from System.Threading import AutoResetEvent
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# Import C compatible List and String
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from System import String
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from System.Collections.Generic import List
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# Add needed dll references
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sys.path.append(os.environ['LIGHTFIELD_ROOT'])
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sys.path.append(os.environ['LIGHTFIELD_ROOT']+"\\AddInViews")
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sys.path.append(r'C:\Program Files\Princeton Instruments\LightField\AddInViews') #I added them by hand -serdar
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sys.path.append(r'C:\Program Files\Princeton Instruments\LightField') #this one also
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clr.AddReference('PrincetonInstruments.LightFieldViewV5')
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clr.AddReference('PrincetonInstruments.LightField.AutomationV5')
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clr.AddReference('PrincetonInstruments.LightFieldAddInSupportServices')
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os.environ['LIGHTFIELD_ROOT'] = r'C:\Program Files\Princeton Instruments\LightField'
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# PI imports
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from PrincetonInstruments.LightField.Automation import Automation
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from PrincetonInstruments.LightField.AddIns import ExperimentSettings
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from PrincetonInstruments.LightField.AddIns import CameraSettings
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#from PrincetonInstruments.LightField.AddIns import DeviceType
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from PrincetonInstruments.LightField.AddIns import SpectrometerSettings
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from PrincetonInstruments.LightField.AddIns import RegionOfInterest
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######################################################################################################### code begins from here #############################################
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def set_custom_ROI():
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# Get device full dimensions
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dimensions = experiment.FullSensorRegion()
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regions = []
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# Add two ROI to regions
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regions.append(
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RegionOfInterest(
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int(dimensions.X), int(dimensions.Y),
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int(dimensions.Width), int(dimensions.Height//4), # Use // for integer division
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int(dimensions.XBinning), int(dimensions.Height//4)))
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# Set both ROI
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experiment.SetCustomRegions(regions)
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def experiment_completed(sender, event_args): #callback function which is hooked to event completed, this is the listener
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print("... Acquisition Complete!")
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acquireCompleted.Set() #set the event. This puts the autoresetevent false.(look at .NET library for furher info)
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def InitializerFilenameParams():
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experiment.SetValue(ExperimentSettings.FileNameGenerationAttachIncrement, False)
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experiment.SetValue(ExperimentSettings.FileNameGenerationIncrementNumber, 1.0)
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experiment.SetValue(ExperimentSettings.FileNameGenerationIncrementMinimumDigits, 2.0)
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experiment.SetValue(ExperimentSettings.FileNameGenerationAttachDate, False)
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experiment.SetValue(ExperimentSettings.FileNameGenerationAttachTime, False)
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def AcquireAndLock(name):
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print("Acquiring...", end = "")
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# name += 'Exp{0:06.2f}ms.CWL{1:07.2f}nm'.format(\
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# experiment.GetValue(CameraSettings.ShutterTimingExposureTime)\
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# ,experiment.GetValue(SpectrometerSettings.GratingCenterWavelength))
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experiment.SetValue(ExperimentSettings.FileNameGenerationBaseFileName, name) #this creates .spe file with the name
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experiment.Acquire() # this is an ashynrchronus func.
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acquireCompleted.WaitOne()
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def calculate_distance(x1, y1, x2, y2):
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return np.sqrt((x2 - x1)**2 + (y2 - y1)**2)
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def generate_scan_positions(center, range_val, resolution):
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positive_range = np.arange(center, center + range_val + resolution, resolution)
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return positive_range
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def save_as_csv(filename, position_x, position_y):
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file_existance = os.path.isfile(filename)
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with open(filename, 'a', newline = '') as csvfile:
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writer = csv.writer(csvfile)
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if not file_existance:
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writer.writerow(['x_coordinates','y_coordinates'])
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writer.writerow([position_x, position_y])
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def move_axis(axis, target):
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"""
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This function moves an axis to the specified target and stop moving after it is in the really closed
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vicinity (+- 25nm) of the target (listener hooked to it).
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"""
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amc.move.setControlTargetPosition(axis, target)
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amc.control.setControlMove(axis, True)
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# while not (target - 25) < amc.move.getPosition(axis) < (target + 25):
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# time.sleep(0.1)
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# time.sleep(0.15)
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# while not (target - 25) < amc.move.getPosition(axis) < (target + 25):
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# time.sleep(0.1)
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# amc.control.setControlMove(axis, False)
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def move_xy(target_x, target_y): # moving in x and y direction closed to desired position
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amc.move.setControlTargetPosition(0, target_x)
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amc.control.setControlMove(0, True)
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amc.move.setControlTargetPosition(1, target_y)
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amc.control.setControlMove(1, True)
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while not (target_x - 25) < amc.move.getPosition(0) < (target_x + 25) and (target_y - 25) < amc.move.getPosition(1) < (target_y + 25):
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time.sleep(0.1)
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time.sleep(0.15)
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while not (target_x - 25) < amc.move.getPosition(0) < (target_x + 25) and (target_y - 25) < amc.move.getPosition(1) < (target_y + 25):
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time.sleep(0.1)
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amc.control.setControlOutput(0, False)
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amc.control.setControlOutput(1, False)
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# intensity_data = [] # To store data from each scan
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# data_list = []
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def move_scan_xy(range_x, range_y, resolution, Settings, baseFileName):
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"""
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This function moves the positioners to scan the sample with desired ranges and resolution in 2 dimensions.
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At the end it saves a csv file
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Parameters
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----------
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range_x : integer in nm. max value is 5um
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Scan range in x direction.
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range_y : integer in nm. max value is 5um
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Scan range in y direction.
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resolution : integer in nm.
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Room temprature max res is 50nm. In cyrostat (4K) it is 10nm (check the Attocube manual)
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baseFileName: string. At the end the saved file will be: baseFileName_scan_data.csv and it will be saved to the current directory
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Returns
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-------
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None.
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"""
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start_time = time.time()
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axis_x = 0 #first axis
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axis_y = 1 #second axis
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center_x = amc.move.getPosition(axis_x)
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center_y = amc.move.getPosition(axis_y)
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# #check if the intput range is reasonable
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# 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 :
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# print("scan range is out of range!")
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# return
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# +- range from current positions for x and y directions
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array_x = generate_scan_positions(center_x, range_x, resolution)
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array_y = generate_scan_positions(center_y, range_y, resolution)
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total_points = len(array_x)*len(array_y)
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len_y = len(array_y)
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intensity_data = [] # To store data from each scan
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data_list = []
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cwd = os.getcwd() # save original directory
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#This gives a directory, in which the script will save the spectrum of each spot as spe
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#However, it will open the spectrum, convert it to txt, add it to the intensity_data and delete the spe file
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Path_save = "C:/Users/localadmin/Desktop/Users/Lukas/Map_dump"
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#scanning loop
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for i, x_positions in enumerate(array_x):
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move_axis(axis_x, x_positions)
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y = False
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for j, y_positions in enumerate(array_y):
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move_axis(axis_y, y_positions)
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time.sleep(2)
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if j == 0:
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time.sleep(10)
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#each time when the positioner comes to the beggining of a new line
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#this if will make the positioner wait a bit longer to really go to the target.
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if y == False:
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move_axis(axis_y, y_positions)
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y = True
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#we acquire with the LF
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acquire_name_spe = f'{baseFileName}_X{x_positions}_Y{y_positions}'
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AcquireAndLock(acquire_name_spe) #this creates a .spe file with the scan name.
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#read the .spe file and get the data as loaded_files
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cwd = os.getcwd() # save original directory
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os.chdir(Path_save) #change directory
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loaded_files = sl.load_from_files([acquire_name_spe + '.spe']) # get the .spe file as a variable
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os.chdir(cwd) # go back to original directory
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# Delete the created .spe file from acquiring after getting necessary info
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spe_file_path = os.path.join(Path_save, acquire_name_spe + '.spe')
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os.remove(spe_file_path)
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distance = calculate_distance(x_positions, y_positions,amc.move.getPosition(axis_x), amc.move.getPosition(axis_y))
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points_left = total_points - (i * len_y + (j+1)) + 1
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print('Points left in the scan: ', points_left)
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#append the intensity data as it is (so after every #of_wl_points, the spectrum of the next point begins)
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intensity_data.append(loaded_files.data[0][0][0])
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data_list.append({
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'position_x': x_positions,
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'position_y': y_positions,
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'actual_x': amc.move.getPosition(axis_x),
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'actual_y': amc.move.getPosition(axis_y),
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'distance': distance,
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})
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#moves back to starting position
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move_axis(axis_x, center_x)
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move_axis(axis_y, center_y)
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#prints total time the mapping lasted
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end_time = time.time()
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elapsed_time = (end_time - start_time) / 60
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print('Scan time: ', elapsed_time, 'minutes')
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# df = pd.DataFrame(data_list)
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#save intensity & WL data as .txt
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os.chdir('C:/Users/localadmin/Desktop/Users/Priyanka/2025/stacked_2L/PL_Map_0T/250325')
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# creates new folder for MAP data
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new_folder_name = "PL_Map_By_0T_" + f"{datetime.datetime.now().strftime('%Y_%m_%d_%H.%M')}"
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os.mkdir(new_folder_name)
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# Here the things will be saved in a new folder under user Lukas !
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# IMPORTANT last / has to be there, otherwise data cannot be saved and will be lost!!!!!!!!!!!!!!!!
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os.chdir('C:/Users/localadmin/Desktop/Users/Priyanka/2025/stacked_2L/PL_Map_0T/250325/'+ new_folder_name)
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intensity_data = np.array(intensity_data)
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np.savetxt(Settings + str(center_x) + '_' + str(center_y) + experiment_name +'.txt', intensity_data)
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wl = np.array(loaded_files.wavelength)
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np.savetxt("Wavelength.txt", wl)
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time.sleep(20)
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amc.control.setControlMove(axis_x, False)
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amc.control.setControlMove(axis_y, False)
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# wl.to_csv("wl", index = False)
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# #Plot the scan data
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# plt.figure(figsize=(12, 6))
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# # Plot 1: Target and Actual Positions
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# plt.subplot(1, 2, 1)
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# plt.scatter(df['position_x'], df['position_y'], c='green', label='Target Positions')
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# plt.scatter(df['actual_x'], df['actual_y'], c='red', label='Actual Positions')
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# plt.title('Scan Visualization')
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# plt.xlabel('X Position')
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# plt.ylabel('Y Position')
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# plt.legend()
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# plt.grid(True)
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# #Plot 2: Distance from Target Position
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# mean_distance = df['distance'].mean()
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# plt.subplot(1, 2, 2)
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# plt.plot(df['distance'], label='Distance from Target Position')
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# plt.title(f'Distance from Target Position\nMean Distance: {mean_distance:.2f}')
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# plt.xlabel('Scan Point')
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# plt.ylabel('Distance')
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# plt.subplot(1, 2, 2)
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# plt.hist(df['distance'], bins=30, color='skyblue', edgecolor='black', alpha=0.7)
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# plt.title(f'Distribution of Distance from Target Position\nMean Distance: {mean_distance:.2f} nm')
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# plt.xlabel('Distance')
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# plt.ylabel('Frequency')
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# plt.legend()
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# plt.grid(True)
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# plt.text(0.95, 0.95, f'Herz: {(amc.control.getControlFrequency(0)/1000):.2f} Hz', horizontalalignment='right', verticalalignment='top', transform=plt.gca().transAxes)
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# plt.text(0.95, 0.90, f'Scan Time: {elapsed_time:.2f} mins', horizontalalignment='right', verticalalignment='top', transform=plt.gca().transAxes)
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# plt.text(0.95, 0.05, f"Scan Date: {datetime.datetime.now().strftime('%Y_%m_%d_%H%M')}", horizontalalignment='right', verticalalignment='bottom', transform=plt.gca().transAxes)
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||||||
# plt.legend()
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||||||
# plt.grid(True)
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||||||
# plt.axhline(mean_distance, color='orange', linestyle='--', label=f'Mean Distance: {mean_distance:.2f}')
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||||||
# plt.tight_layout()
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||||||
|
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||||||
# plt.savefig(Settings + str(center_x) + '_' + str(center_y) +'_' + experiment_name + '.png')
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# plt.show()
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||||||
# os.chdir(cwd)
|
|
||||||
|
|
||||||
# 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("2025_02_13_Priyanka_CrSBr")
|
|
||||||
experiment.ExperimentCompleted += experiment_completed # we are hooking a listener.
|
|
||||||
# experiment.SetValue(SpectrometerSettings.GratingSelected, '[750nm,1200][0][0]')
|
|
||||||
# InitializerFilenameParams()
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#set scna range and resolution in nanometers
|
|
||||||
|
|
||||||
range_x = 20000
|
|
||||||
range_y = 20000
|
|
||||||
resolution = 1000
|
|
||||||
|
|
||||||
#Here you can specify the filename of the map e.g. put experiment type, exposure time, used filters, etc....
|
|
||||||
experiment_settings = 'PL_he ne_stacked_2L_G150_P300uW_5s_test_l1_52_l2_260'
|
|
||||||
# experiment_settings = 'DR_NKT_OD2_rep_0.15_600g_cwl_660_exp_3s_Start_'
|
|
||||||
# experiment_settings = 'DR_Halogen_Lamp_lin_b-axis_600g_cwl_910_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"{range_x}nm_{range_y}nm_{resolution}nm_{datetime.datetime.now().strftime('%Y_%m_%d_%H%M')}"
|
|
||||||
|
|
||||||
|
|
||||||
move_scan_xy(range_x, range_y, resolution, experiment_settings, experiment_name)
|
|
||||||
|
|
||||||
# Internally, axes are numbered 0 to 2
|
|
||||||
|
|
||||||
Loading…
x
Reference in New Issue
Block a user