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ABspectro-noadapt.py
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ABspectro-noadapt.py
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import os
import tkinter as tk
from tkinter import filedialog, simpledialog, messagebox
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
from mpl_toolkits.mplot3d import Axes3D
import serial
import serial.tools.list_ports
import time
import seabreeze
seabreeze.use('pyseabreeze')
import seabreeze.spectrometers as sb
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2Tk
os.environ['PYUSB_BACKEND'] = 'libusb'
reference_intensities = np.array([])
reference_wavelengths = np.array([])
all_angles = []
all_transmittances = []
reference_file_path = ""
class SpectrometerApp(tk.Tk):
def __init__(self):
super().__init__()
self.title("ABspectro")
self.geometry("1200x800")
self.spectrometer = None
self.wavelength_min = 200
self.wavelength_max = 850
self.protocol("WM_DELETE_WINDOW", self.on_closing) # Ensure program ends on window close
self.create_widgets()
self.disable_all_buttons()
def on_closing(self):
# Handle the window closing event
if messagebox.askokcancel("Quit", "Do you want to quit?"):
self.quit()
self.destroy()
def create_widgets(self):
# Create control frame for buttons
self.control_frame = tk.Frame(self)
self.control_frame.pack(side=tk.LEFT, fill=tk.Y, padx=10, pady=10)
# Create graph frame for plots
self.graph_frame = tk.Frame(self)
self.graph_frame.pack(side=tk.RIGHT, fill=tk.BOTH, expand=True)
# Create and add buttons
self.spectrometer_button = tk.Button(self.control_frame, text="Choose spectrometer", command=self.choose_spectrometer)
self.spectrometer_button.pack(pady=5)
self.plot_ref_button = tk.Button(self.control_frame, text="Plot reference graph", command=self.plot_reference_and_realtime_measurement)
self.plot_ref_button.pack(pady=5)
self.save_ref_button = tk.Button(self.control_frame, text="Save reference datas", command=self.save_reference_spectrum)
self.save_ref_button.pack(pady=5)
self.plot_trans_button = tk.Button(self.control_frame, text="Plot transmittance graph", command=self.plot_transmittance_graph)
self.plot_trans_button.pack(pady=5)
self.save_trans_button = tk.Button(self.control_frame, text="Save transmittance datas", command=self.save_transmittance_spectrum_as_text)
self.save_trans_button.pack(pady=5)
self.start_motor_button = tk.Button(self.control_frame, text="Start motor (angle measurements)", command=self.start_motor_program)
self.start_motor_button.pack(pady=5)
self.plot_3d_button = tk.Button(self.control_frame, text="Plot 3D graph", command=self.plot_3d_graph)
self.plot_3d_button.pack(pady=5)
self.save_3d_button = tk.Button(self.control_frame, text="Save 3D datas", command=self.save_final_3d_data)
self.save_3d_button.pack(pady=5)
# Create and set up the plot area and the toolbar
self.fig, self.ax = plt.subplots()
self.canvas = FigureCanvasTkAgg(self.fig, master=self.graph_frame)
self.toolbar = NavigationToolbar2Tk(self.canvas, self.graph_frame)
self.toolbar.update()
self.canvas.get_tk_widget().pack(fill=tk.BOTH, expand=True)
self.ani = None
# Create and set up the 3D plot area
self.fig_3d = plt.figure()
self.ax_3d = self.fig_3d.add_subplot(111, projection='3d')
self.canvas_3d = FigureCanvasTkAgg(self.fig_3d, master=self.graph_frame)
def disable_all_buttons(self):
# Disable all buttons initially except Choose Spectrometer
self.plot_ref_button.config(state=tk.DISABLED)
self.save_ref_button.config(state=tk.DISABLED)
self.plot_trans_button.config(state=tk.DISABLED)
self.save_trans_button.config(state=tk.DISABLED)
self.start_motor_button.config(state=tk.DISABLED)
self.plot_3d_button.config(state=tk.DISABLED)
self.save_3d_button.config(state=tk.DISABLED)
def enable_buttons(self, buttons):
# Enable specified buttons
for button in buttons:
button.config(state=tk.NORMAL)
def disable_buttons(self, buttons):
# Disable specified buttons
for button in buttons:
button.config(state=tk.DISABLED)
def choose_spectrometer(self):
# Automatically detect and choose the spectrometer
devices = sb.list_devices()
if len(devices) == 0:
print("No spectrometer was found.")
messagebox.showerror("Error", "No spectrometer detected.")
return
self.spectrometer = sb.Spectrometer(devices[0]) # Automatically choose the first available spectrometer
model = devices[0].model
if model == 'USB2000PLUS':
self.wavelength_min = 200
self.wavelength_max = 850
elif model == 'SR2':
self.wavelength_min = 649
self.wavelength_max = 1300
print(f"Spectrometer {self.spectrometer.model} selected.")
messagebox.showinfo("Information", f"Spectrometer {self.spectrometer.model} selected.")
self.enable_buttons([self.plot_ref_button])
self.disable_buttons([self.spectrometer_button])
def plot_reference_and_realtime_measurement(self):
# Plot the reference graph and start real-time measurement
messagebox.showinfo("Attention", "Adjust the light intensity.")
if not self.spectrometer:
self.choose_spectrometer()
if not self.spectrometer:
return
self.ax.clear()
self.line, = self.ax.plot([], [])
self.ax.set_xlim(self.wavelength_min, self.wavelength_max)
self.ax.set_ylim(0, 65535)
self.ax.set_xlabel('Wavelength (nm)')
self.ax.set_ylabel('Intensity')
self.ax.set_title('Reference Measurement')
self.ani = FuncAnimation(self.fig, self.update_plot, fargs=(self.line,), interval=500, cache_frame_data=False)
self.canvas.draw()
self.enable_buttons([self.save_ref_button])
self.disable_buttons([self.plot_ref_button])
def take_reference_measurement(self):
# Take reference measurement from the spectrometer
global reference_intensities, reference_wavelengths
reference_intensities = self.spectrometer.intensities()
reference_wavelengths = self.spectrometer.wavelengths()
def update_plot(self, frame, line):
# Update the plot in real-time
if self.spectrometer:
wavelengths = self.spectrometer.wavelengths()
intensities = self.spectrometer.intensities()
line.set_data(wavelengths, intensities)
self.ax.relim()
self.ax.autoscale_view()
self.canvas.draw()
return line,
def save_reference_spectrum(self):
# Save the reference spectrum data
global reference_intensities, reference_wavelengths
if not self.spectrometer:
print("No spectrometer available.")
return
self.take_reference_measurement() # Update reference data at the moment of saving
if not len(reference_wavelengths) or not len(reference_intensities):
print("No reference data to save.")
return
root = tk.Tk()
root.withdraw()
reference_file_path = filedialog.asksaveasfilename(defaultextension=".txt", filetypes=[("Text files", "*.txt")], title="Save Reference Data")
if reference_file_path:
try:
with open(reference_file_path, 'w') as file:
file.write("Wavelength\tIntensity\n")
for wavelength, intensity in zip(reference_wavelengths, reference_intensities):
file.write(f"{wavelength}\t{intensity}\n")
print(f"Reference data saved successfully at {reference_file_path}.")
self.enable_buttons([self.plot_trans_button])
self.disable_buttons([self.save_ref_button])
except Exception as e:
print(f"Failed to save reference data: {e}")
def plot_transmittance_graph(self):
# Plot the transmittance graph
messagebox.showinfo("Attention", "Please insert the filter into the setup after pressing OK.")
if not self.spectrometer:
self.choose_spectrometer()
if not self.spectrometer or reference_intensities.size == 0:
print("Reference data is not saved yet.")
return
self.ax.clear()
self.line, = self.ax.plot([], [])
self.ax.set_xlim(self.wavelength_min, self.wavelength_max)
self.ax.set_ylim(0, 1)
self.ax.set_xlabel('Wavelength (nm)')
self.ax.set_ylabel('Transmittance')
self.ax.set_title('Transmittance Measurement')
self.ani = FuncAnimation(self.fig, self.update_transmittance_plot, fargs=(self.line,), interval=500, cache_frame_data=False)
self.canvas.draw()
self.enable_buttons([self.save_trans_button, self.start_motor_button])
self.disable_buttons([self.plot_trans_button])
def update_transmittance_plot(self, frame, line):
# Update the transmittance plot in real-time
if self.spectrometer:
wavelengths = self.spectrometer.wavelengths()
intensities = self.spectrometer.intensities() / reference_intensities
line.set_data(wavelengths, intensities)
self.ax.relim()
self.ax.autoscale_view()
self.canvas.draw()
return line,
def save_transmittance_spectrum_as_text(self):
# Save the transmittance spectrum data
if not self.spectrometer:
print("No spectrometer available.")
return
root = tk.Tk()
root.withdraw()
file_path = filedialog.asksaveasfilename(defaultextension=".txt", filetypes=[("Text files", "*.txt")])
if file_path:
try:
intensities = self.spectrometer.intensities() / reference_intensities
with open(file_path, 'w') as file:
file.write("Wavelength\tTransmittance\n")
for wavelength, transmittance in zip(reference_wavelengths, intensities):
file.write(f"{wavelength}\t{transmittance}\n")
print(f"Transmittance data saved successfully at {file_path}.")
except Exception as e:
print(f"Failed to save transmittance data: {e}")
def start_motor_program(self):
# Start the motor program and save data at each step
lancer_programme_moteur(self.spectrometer)
self.enable_buttons([self.plot_3d_button])
self.disable_buttons([self.start_motor_button])
def plot_3d_graph(self):
# Plot the 3D graph of transmittance vs wavelength and angle
if not len(reference_wavelengths) or not len(all_angles) or not len(all_transmittances):
print("No data to plot.")
return
self.ax_3d.clear()
self.canvas.get_tk_widget().pack_forget() # Hide the 2D plot
self.canvas_3d.get_tk_widget().pack(fill=tk.BOTH, expand=True)
for i, angle in enumerate(all_angles):
self.ax_3d.plot(reference_wavelengths, [angle]*len(reference_wavelengths), all_transmittances[i])
self.ax_3d.set_xlim(self.wavelength_min, self.wavelength_max)
self.ax_3d.set_zlim(0, 1)
self.ax_3d.set_xlabel('Wavelength (nm)')
self.ax_3d.set_ylabel('Angle (degrees)')
self.ax_3d.set_zlabel('Transmittance')
self.ax_3d.set_title('Transmittance Spectrum as a Function of Wavelength and Angle')
self.canvas_3d.draw()
self.enable_buttons([self.save_3d_button])
self.disable_buttons([self.plot_3d_button])
def save_final_3d_data(self):
# Save the final 3D data
if not len(reference_wavelengths) or not len(all_angles) or not len(all_transmittances):
print("No data to save.")
return
root = tk.Tk()
root.withdraw()
final_3d_file_path = filedialog.asksaveasfilename(defaultextension=".txt", filetypes=[("Text files", "*.txt")], title="Save Final 3D Data")
if final_3d_file_path:
try:
with open(final_3d_file_path, 'w') as file:
file.write("Wavelength\tAngle\tTransmittance\n")
for i, angle in enumerate(all_angles):
for wavelength, transmittance in zip(reference_wavelengths, all_transmittances[i]):
file.write(f"{wavelength}\t{angle}\t{transmittance}\n")
print(f"Final 3D datas saved successfully at {final_3d_file_path}.")
except Exception as e:
print(f"Failed to save final 3D data: {e}")
def lancer_programme_moteur(spectrometer):
# Function to run the motor program and save data at each angle
global all_angles, all_transmittances, reference_intensities
print("Starting motor program...")
root = tk.Tk()
root.withdraw()
titre_fichier = simpledialog.askstring("File Title", "Enter the base title for data files:")
if not titre_fichier:
print("File title not provided.")
return
dossier_destination = filedialog.askdirectory()
if not dossier_destination:
print("No folder selected.")
return
# Automatically find the Arduino port
arduino_ports = [p.device for p in serial.tools.list_ports.comports() if 'Arduino' in p.description]
if not arduino_ports:
print("No Arduino was found.")
messagebox.showerror("Error", "No Arduino detected.")
return
port = arduino_ports[0]
try:
ser = serial.Serial(port, 9600)
except serial.SerialException as e:
print(f"Serial port connection error: {e}")
return
def envoyer_commande(direction):
ser.write(direction.encode())
print(f"Command sent: {direction}")
time.sleep(2)
# Save initial position data (0 degree) before moving the motor
save_data(0, spectrometer, titre_fichier, dossier_destination)
angles = [i * 3 for i in range(1, 16)] + [-i * 3 for i in range(1, 16)] # Correct angle order
compteur_fichier = 0 # Start at 0 to properly index angles list
envoyer_commande('S') # Start the motor after the initial measurement
motor_finished = False
while True:
try:
message = ser.readline().strip().decode()
except serial.SerialException as e:
print(f"Serial port read error: {e}")
break
if message:
print("Arduino Message:", message)
if message == 'B' and not motor_finished:
motor_finished = True
break
if message.startswith('Step'):
angle = angles[compteur_fichier]
save_data(angle, spectrometer, titre_fichier, dossier_destination)
compteur_fichier += 1
ser.close()
spectrometer.close()
print("Information")
messagebox.showinfo("Information", "Motor program has finished recording data.")
def save_data(angle, spectrometer, titre_fichier, dossier_destination):
# Save data for each angle step
global reference_intensities
wavelengths = spectrometer.wavelengths()
intensities = spectrometer.intensities()
transmittances = intensities / reference_intensities
all_angles.append(angle)
all_transmittances.append(transmittances)
nom_fichier = f"{titre_fichier}_{angle}deg.txt"
chemin_fichier = os.path.join(dossier_destination, nom_fichier)
try:
with open(chemin_fichier, 'w') as file:
file.write(f"Angle: {angle} degrees\n")
for wavelength, transmittance in zip(wavelengths, transmittances):
file.write(f"{wavelength}\t{transmittance}\n")
print(f"Data saved in {chemin_fichier}")
except Exception as e:
print(f"Failed to save data in {chemin_fichier}: {e}")
if __name__ == "__main__":
app = SpectrometerApp()
app.mainloop()