def animate(i):
spec = Spectrometer.from_first_available()
spec.integration_time_micros(integ)
a = spec.wavelengths()
b = spec.intensities()
a = a[30:] # delete the first pseudo peak
b = b[30:]
if b.max() > 65500:
msg = "Flame is saturated, please reduce integration time"
print(msg)
step = abs(a[1] - a[0])
if wavelength1 is not None:
p = np.where(abs(a - wavelength1) < step)[0][0] # define baseline
a = a[p:]
b = b[p:]
if wavelength2 is not None:
q = np.where(abs(a - wavelength2) < step)[0][0]
a = a[:q]
b = b[:q]
# for i in range(len(b)): #filter out peaks
# if b[i]>3000:
# b[i]=2400
ax1.clear()
ax1.plot(a, b)
plt.title(title)
plt.xlabel('Wavelength, nm')
plt.ylabel('Signal Amplitude, AU')
print(i)
def __init__(self, device_obj=None, **kwargs):
# Yes, I am aware that having a self._device inside the
# Device class can be somewhat confusing
if device_obj is None:
self._device = Spectrometer.from_first_available()
else:
self._device = Spectrometer(device_obj)
def open_spect(t_integracion,logger):
try:
spec = Spectrometer.from_first_available()
#spec = Spectrometer.from_serial_number("S05507")
spec.integration_time_micros(t_integracion)
return spec
except SeaBreezeError as e: # Spectrometer.CalledProcessError as err:
#logger.error("Error conectando el espectrometro",e)
return 0
def open_spect():
try:
spec = Spectrometer.from_first_available()
print("conectando")
return spec
except: #excepcion en caso de que el espectrometro no este conectada
#logger.error("Error conectando el espectrometro")
print("no se pudo conectar")
return 0
def FlameS_save(wavelength1, wavelength2, integ, folder, filename, title):
spec = Spectrometer.from_first_available()
spec.integration_time_micros(integ) #us
a = spec.wavelengths()
b = spec.intensities()
a = a[30:] # delete the first pseudo peak
b = b[30:]
msg = ''
if b.max() > 65500:
msg = "Flame is saturated, please reduce integration time."
print(msg)
step = abs(a[1] - a[0])
if (wavelength1 is not None) and (wavelength2 is not None):
msg = msg + "\nPart of the spectrum is plotted."
print(msg)
if wavelength1 is not None:
p = np.where(abs(a - wavelength1) < step)[0][0] # define baseline
a = a[p:]
b = b[p:]
if wavelength2 is not None:
q = np.where(abs(a - wavelength2) < step)[0][0]
a = a[:q]
b = b[:q]
np.savetxt(folder + '/' + filename + "wl.csv", a,
delimiter=",") # save wavelength
np.savetxt(folder + '/' + filename + ".csv", b,
delimiter=",") # save fluorescen intensity
plt.plot(a, b)
plt.title(title + ' ' + filename)
plt.xlabel('Wavelength, nm')
plt.ylabel('Signal Amplitude, AU')
plt.show()
return msg
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Aug 10 10:27:12 2020
@author: jtm
"""
import pandas as pd
from seabreeze.spectrometers import Spectrometer
from oceanops import dark_measurement
#%% make a df to hold data
# connect to OceanOptics spectrometer
oo = Spectrometer.from_first_available()
data = pd.DataFrame()
it = 10
integration_times = []
while it < oo.integration_time_micros_limits[1]:
integration_times.append(it)
it *= 2
#%% set desired temperature before running this cell
t = oo.f.temperature.temperature_get_all()[0]
cycle = 0
while t < 45.00:
data = data.append(dark_measurement(oo, integration_times))
data['cycle'] = cycle
cycle += 1
t = oo.f.temperature.temperature_get_all()[0]