def connect_spectrometer(self):
if self.spec is None:
devices = sb.list_devices()
self.spec = sb.Spectrometer(devices[0])
self.ui.status_textBrowser.append(
"Ocean Optics Device Connected!\n\n Device:\n\n" +
str(sb.list_devices()[0]))
else:
self.ui.status_textBrowser.append("Already Connected")
def reset(self):
''' This function resets the spectrometer. To make a hardware reset unplug it from the computer and then plug in again. '''
devices = sb.list_devices()
if len(sb.list_devices()) == 0:
print ("No spectrometer is detected!")
return
else:
self.Handle.close()
self.Handle = sb.Spectrometer(devices[0])
self.clear()
def reset(self):
''' This function resets the spectrometer. To make a hardware reset unplug it from the computer and then plug in again. '''
devices = sb.list_devices()
if len(sb.list_devices()) == 0:
print("No spectrometer is detected!")
return
else:
self.Handle.close()
self.Handle = sb.Spectrometer(devices[0])
self.clear()
def __init__(self):
if len(sb.list_devices()) == 0:
print ("No spectrometer is detected!")
return
else:
devices = sb.list_devices()
self.Handle = sb.Spectrometer(devices[0])
print (devices)
print ('Serial number:%s' % self.Handle.serial_number)
print ('Model:%s' % self.Handle.model)
print ('minimum_integration_time_micros: %s microseconds' % self.Handle.minimum_integration_time_micros)
self.clear()
def __init__(self):
if len(sb.list_devices()) == 0:
print("No spectrometer is detected!")
return
else:
devices = sb.list_devices()
self.Handle = sb.Spectrometer(devices[0])
print(devices)
print('Serial number:%s' % self.Handle.serial_number)
print('Model:%s' % self.Handle.model)
print('minimum_integration_time_micros: %s microseconds' %
self.Handle.minimum_integration_time_micros)
self.clear()
def __init__(self):
try:
sb.list_devices()
if len(sb.list_devices()) == 0:
print ("No spectrometer is detected! \n")
self.Error = 1
return
else:
self.detect()
except Exception, e:
if (e.message == 'This should not have happened. Apparently this device has 0 serial number features. The code expects it to have 1 and only 1. Please file a bug report including a description of your device.'):
#print ('Please unplug the spectrometer and then plug again. Then close the python command line and reopen it. Last')
print ('Unplug the spectrometer and then plug again, then close the python command line and reopen it.')
self.Error = 1
return
def animate(frameno, inttime, monitor, prefix):
devices = sb.list_devices()
spec = sb.Spectrometer(devices[0])
spec_model = spec._dev._model
spec.integration_time_micros(inttime)
x = spec.wavelengths()
y = spec.intensities()
line.set_ydata(y) # update the data
ax.set_ylim([min(y[10:]), max(y) * 1.1])
spec.close()
if not monitor:
a = np.column_stack([x, y])
#in np.savetext, using inttime/1000 since the USB2000 uses microseconds, not milliseconds.
if prefix:
filepref = prefix
else:
filepref = "spectrum_data"
np.savetxt("{}_{}.csv".format(filepref, frameno),
a,
delimiter=',',
header="wavelength,intensity",
fmt='%.14f',
comments="#model: {0}\n#integration time: {1} ms\n".format(
spec_model, inttime / 1000))
return line,
def getSpec(typ, intgTime, wl):
devices = sb.list_devices()
if not len(devices):
print("Error: No OceanOptic Device found")
sys.exit(1)
for device in devices:
print(device)
print("getting spectrum")
spec = sb.Spectrometer(devices[0])
print("setting integration time to " + str(intgTime))
spec.integration_time_micros(intgTime)
"""
print("getting wavelengths")
rawWavelengths = spec.wavelengths()
print("getting intensities")
rawIntensities = spec.intensities(correct_dark_counts=False, correct_nonlinearity=False)
"""
spektrum = spec.spectrum()
print("closing Spectroscope")
spec.close()
if typ == 0:
writePlotSpec(spektrum, True)
elif typ == 1:
showWavelength(spektrum, wl)
def detect(self):
try:
devices = sb.list_devices()
sb.Spectrometer(devices[0]).close()
self.Handle = sb.Spectrometer(devices[0])
self.Error = 0
print(devices)
print('Serial number:%s' % self.Handle.serial_number)
print('Model:%s' % self.Handle.model)
print('minimum_integration_time_micros: %s microseconds' %
self.Handle.minimum_integration_time_micros)
self.clear()
self.Error = 0
return
except Exception, e:
if (e.message == 'Device already opened.'):
#print ('Device will be reseted')
#self.reset()
print('Error: ' + e.message)
print('Unplug the spectrometer and then plug again')
elif (e.message == 'Error: Data transfer error'):
print('Error: ' + e.message)
print(
'Please unplug the spectrometer and then plug again. Then close the python command line and reopen it.'
)
#return
else:
print(e.message)
print(
'Please unplug the spectrometer and then plug again. Then close the python command line and reopen it. '
)
#return
self.Error = 1
print('Openning spectrometer failed!')
return
def __init__(self):
# global variables that may or may not be used later on
self.stopped = True
self.ptrn = 0
# get spectrometer going
self.devices = sb.list_devices()
self.spec = sb.Spectrometer(self.devices[0])
self.spec.integration_time_micros(100000)
# initial real and dummy spectra
self.xs = self.spec.wavelengths()
self.ys = self.spec.intensities()
self.xs_roi = np.zeros(300)
self.ys_roi = np.zeros(300)
self.timer = QtCore.QTimer()
# pressure calculation parameters
# lambda zero (ref) is 694.260 based on Ragan et al JAP 72, 5539 (1992) at 295K
self.alpha = 1885
self.beta = 11.0
self.lambda_0_ref = 694.260
self.lambda_0_user = 694.260
self.lambda_0_t_user = 694.260
self.lambda_r1 = 694.260
self.temperature = 295
self.pressure = 0.00
def __init__(self):
# super(CoreData, self).__init__()
# self.curve = gui.pw.plot()
self.vline = pg.InfiniteLine(pos=694.260, angle=90.0, movable=True)
gui.pw.addItem(self.vline)
self.stopped = True
self.ptrn = 0
self.devices = sb.list_devices()
self.spec = sb.Spectrometer(self.devices[0])
self.spec.integration_time_micros(10000)
self.xs = self.spec.wavelengths()
self.ys = self.spec.intensities()
self.xs_roi = np.zeros(300)
self.ys_roi = np.zeros(300)
self.timer = QtCore.QTimer()
# pressure calculation parameters
# lambda zero (ref) is 694.260 based on Ragan et al JAP 72, 5539 (1992) at 295K
self.alpha = 1904
self.beta = 9.5
self.lambda_0_ref = 694.260
self.lambda_0_user = 694.260
self.lambda_0_t_user = 694.260
self.lambda_r1 = 694.260
self.temperature = 295
self.pressure = 0.00
def detect(self):
try:
devices = sb.list_devices()
sb.Spectrometer(devices[0]).close()
self.Handle = sb.Spectrometer(devices[0])
self.Error = 0
print (devices)
print ('Serial number:%s' % self.Handle.serial_number)
print ('Model:%s' % self.Handle.model)
print ('minimum_integration_time_micros: %s microseconds' % self.Handle.minimum_integration_time_micros)
self.clear()
self.Error = 0
return
except Exception, e:
if (e.message == 'Device already opened.'):
#print ('Device will be reseted')
#self.reset()
print ('Error: ' + e.message)
print ('Unplug the spectrometer and then plug again')
elif (e.message == 'Error: Data transfer error'):
print ('Error: ' + e.message)
print ('Please unplug the spectrometer and then plug again. Then close the python command line and reopen it.')
#return
else:
print (e.message)
print ('Please unplug the spectrometer and then plug again. Then close the python command line and reopen it. ')
#return
self.Error = 1
print('Openning spectrometer failed!')
return
def test_crash_may_not_influence_following_tests(backendlified_serial):
devices = list(list_devices())
if len(devices) == 0:
pytest.skip("no supported device connected")
_ = Spectrometer.from_serial_number(backendlified_serial)
raise Exception("crash on purpose")
def test_device_cleanup_on_exit(backendlify):
"""test if opened devices cleanup correctly"""
usb_backend = ""
try:
devices = list_devices()
if len(devices) == 0:
pytest.skip("no supported device connected")
else:
if psb and isinstance(devices[0], psb.SeaBreezeDevice):
# noinspection PyProtectedMember
usb_backend = "_pyusb_backend='{}'".format(
devices[0]._raw_device.pyusb_backend)
del devices
finally:
# noinspection PyProtectedMember
list_devices._api.shutdown()
# noinspection PyProtectedMember
backend_name = backendlify._backend_
cmd = [
"python",
"-c",
"import seabreeze.%s as sb; d = sb.SeaBreezeAPI(%s).list_devices()[0]; d.open()"
% (backend_name, usb_backend),
]
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
assert p.returncode == 0, stderr
def __init__(self):
# super(CoreData, self).__init__()
self.curve = gui.pw.plot()
self.stopped = True
self.ptrn = 0
self.devices = sb.list_devices()
self.spec = sb.Spectrometer(self.devices[0])
self.spec.integration_time_micros(10000)
self.xs = self.spec.wavelengths()
self.ys = self.spec.intensities()
self.timer = QtCore.QTimer()
# pressure calculation parameters
# lambda zero (ref) is 694.260 based on Ragan et al JAP 72, 5539 (1992) at 295K
self.alpha = 1904
self.beta = 9.5
self.lambda_0_ref = 694.260
self.lambda_0_user = 694.260
self.lambda_0_t_user = 694.260
self.lambda_r1 = 694.260
self.temperature = 295
self.pressure = 0.00
def __init__(self):
self.stopped = True
self.ptrn = 0
self.devices = sb.list_devices()
self.spec = sb.Spectrometer(self.devices[0])
self.spec.integration_time_micros(100000)
self.xs = self.spec.wavelengths()
self.ys = self.spec.intensities()
self.xs_roi = np.zeros(300)
self.ys_roi = np.zeros(300)
self.timer = QtCore.QTimer()
# pressure calculation parameters
# lambda zero (ref) is 694.260 based on Ragan et al JAP 72, 5539 (1992) at 295K
self.alpha = 1885
self.beta = 11.0
self.lambda_0_ref = 694.260
self.lambda_0_user = 694.260
self.lambda_0_t_user = 694.260
self.lambda_r1 = 694.260
self.temperature = 295
self.pressure = 0.00
def __init__(self):
# global variables that may or may not be used later on
self.stopped = True
self.ptrn = 0
# get spectrometer going
self.devices = sb.list_devices()
self.spec = sb.Spectrometer(self.devices[0])
self.spec.integration_time_micros(100000)
# initial real and dummy spectra
self.xs = self.spec.wavelengths()
self.ys = self.spec.intensities()
default_zoom = np.abs(self.xs - 694.260).argmin()
self.xs_roi = self.xs[default_zoom - 150:default_zoom + 150]
self.ys_roi = self.ys[default_zoom - 150:default_zoom + 150]
self.timer = QtCore.QTimer()
# pressure calculation parameters
# lambda zero (ref) is 694.260 based on Ragan et al JAP 72, 5539 (1992) at 295K
self.alpha = 1885
self.beta = 11.0
self.lambda_0_ref = 694.260
self.lambda_0_user = 694.260
self.lambda_0_t_user = 694.260
self.lambda_r1 = 694.260
self.temperature = 295
self.pressure = 0.00
def test_read_serial_number(backendlified_serial):
devices = list(list_devices())
if len(devices) == 0:
pytest.skip("no supported device connected")
spec = Spectrometer.from_serial_number(backendlified_serial)
serial = spec.serial_number
assert len(serial) > 0
def test_read_spectrum(backendlified_serial):
devices = list(list_devices())
if len(devices) == 0:
pytest.skip("no supported device connected")
spec = Spectrometer.from_serial_number(backendlified_serial)
arr = spec.spectrum()
assert arr.shape == (2, spec.pixels)
def init_device(self):
# call list of all connected spectrometers
devices = sb.list_devices()
# create object for spectrometers(s)
self.spec = sb.Spectrometer(devices[0])
return self.FLAG_done
def start():
os.system("killall matchbox-keyboard")
global uploadInterval
f = open('config.txt', "r")
conf = [row[0] for row in csv.reader(f, delimiter='\t')]
f.close()
sessionBegin = timeToMinutes(conf[4])
sessionEnd = timeToMinutes(conf[5])
print(sessionBegin)
print(sessionEnd)
uploadInterval = int(conf[6], 10)
print("spectrometer flag is")
print(spectrometerFlag)
durationValue = conf[3]
devices = sb.list_devices()
frame.grid_forget()
if (len(devices) > 0):
spec = sb.Spectrometer(devices[0])
spec.integration_time_micros(int(conf[2], 10))
else:
spec = 0
uploadText = tk.StringVar()
frame3 = Frame(root)
frame3.grid(row=0)
stopButton = Button(frame3, text=" Stop ", command=stop)
stopButton.grid(row=1, column=0)
startButton = Button(frame3, text=" Start ", command=startscan)
startButton.grid(row=1, column=1)
button = Button(frame3, text="QUIT", command=quit)
button.grid(row=1, column=2)
uploadLabel = Label(frame3, textvariable=uploadText)
uploadLabel.grid(row=0, column=4, pady=6)
w0 = Label(frame3, text="Reading in process", font='Helvetica 14 bold')
w0.grid(row=0, pady=6)
root.update()
ftpVar = ftp.get()
ftpUserVar = ftpUser.get()
ftpPassVar = ftpPass.get()
waitTime = 10
print("going into the while loop")
count = 0
while (1):
currentTime = time.localtime().tm_min + time.localtime().tm_hour * 60
print(currentTime)
if (currentTime >= sessionBegin and currentTime <= sessionEnd):
print(" it is looping though")
print(currentTime)
uploadText.set('Time from last upload:' +
str(currentTime - uploadTime))
print(uploadText.get())
scanning(durationValue, spec, currentTime, ftpVar, ftpUserVar,
ftpPassVar) # After 1 second, call scanning
time.sleep(waitTime)
else:
time.sleep(20)
root.update()
def test_list_devices_dont_close_opened_devices():
"""test list_devices() interaction with already opened devices"""
devices = list(list_devices())
if len(devices) == 0:
pytest.skip("no supported device connected")
num_devices = len(devices)
dev = devices[0]
dev.open()
assert dev.is_open is True
devices_2 = list_devices()
assert len(devices_2) == num_devices
# dev.is_open is still True here...
assert dev.is_open is True
# but if we delete the new reference created by the second call to list_devices:
del devices_2
assert dev.is_open is True
def set_spectrometer(self):
spectrometers = sb.list_devices()
for spec in spectrometers:
if str(spec) == self.comboBox.currentText():
try:
self.spectrometer = sb.Spectrometer(spec)
self.alert_message("Connected to: " + str(spec))
except:
pass
def test_max_intensity(backendlified_serial):
devices = list(list_devices())
if len(devices) == 0:
pytest.skip("no supported device connected")
spec = Spectrometer.from_serial_number(backendlified_serial)
value = spec.max_intensity
assert isinstance(value, float)
assert 0 < value < 1e8
def get_spectrometer_list(self):
try:
spectrometers = sb.list_devices()
spectrometer_list = []
for spec in spectrometers:
spectrometer_list.append(str(spec))
except:
spectrometer_list = "No devices found"
return spectrometer_list
def automatic():
global spec
print("automatic mode here we go")
print("spectrometer flag is")
print(spectrometerFlag)
durationValue = duration.get()
calibrateValue = calibration.get()
fillValue = int(fillWait.get())
devices = sb.list_devices()
frame2 = Frame(root, width=450, height=50)
frame2.grid(row=0)
if spectrometerFlag:
spec.integration_time_micros(int(integrationTime.get(), 10))
else:
spec = 0
if calibrateValue:
#code to turn on nitrogen valve
print("turning on valve for nitrogen")
w0 = Label(frame2,
text="Opening valve for Nitrogen Please wait... ",
font='Helvetica 14 bold')
w0.grid(row=0, pady=6)
root.update()
time.sleep(fillValue)
w0.grid_forget()
print("Reading Values")
nitrogenData = getdata(durationValue, spec)
print(nitrogenData)
#code to turn on CO2 valve
print("turning on valve for CO2")
w0 = Label(frame2,
text="Opening valve for CO2 Please wait... ",
font='Helvetica 14 bold')
w0.grid(row=0, pady=6)
root.update()
time.sleep(fillValue)
w0.grid_forget()
print("Reading Values")
secondData = getdata(durationValue, spec)
print(secondData)
alpha = alphaCalculation(nitrogenData, secondData)
#code to turn on air valve
print("turning on valve for air")
w0 = Label(frame2,
text="Opening valve for air Please wait... ",
font='Helvetica 14 bold')
w0.grid(row=0, pady=6)
root.update()
time.sleep(fillValue)
frame2.grid_forget()
print("Reading Values")
measurement(durationValue, spec)
def test_integration_time_limits(backendlified_serial):
devices = list(list_devices())
if len(devices) == 0:
pytest.skip("no supported device connected")
spec = Spectrometer.from_serial_number(backendlified_serial)
low, high = spec.integration_time_micros_limits
assert isinstance(low, int)
assert isinstance(high, int)
assert 0 < low < high < 2**64
def openSpec():
devices = sb.list_devices()
if not len(devices):
print("Error: No OceanOptic Device found")
sys.exit(1)
for device in devices:
print(device)
spec = sb.Spectrometer(devices[0])
return spec
def __init__(self):
try:
sb.list_devices()
if len(sb.list_devices()) == 0:
print("No spectrometer is detected! \n")
self.Error = 1
return
else:
self.detect()
except Exception, e:
if (e.message ==
'This should not have happened. Apparently this device has 0 serial number features. The code expects it to have 1 and only 1. Please file a bug report including a description of your device.'
):
#print ('Please unplug the spectrometer and then plug again. Then close the python command line and reopen it. Last')
print(
'Unplug the spectrometer and then plug again, then close the python command line and reopen it.'
)
self.Error = 1
return
def connect(self):
try:
import seabreeze.spectrometers as sp
self.instrument = sp.Spectrometer(sp.list_devices()[0])
self.name = self.instrument.model
print(self.name)
self.connected = True
except:
print('Spectrometer not connected')
self.name = 'Virtual device'
def connectSpec(self):
try:
devices = sb.list_devices()
self.spec = sb.Spectrometer(devices[0])
self.wav = self.spec.wavelengths()
self.connected = True
return True
except (SeaBreezeError, IndexError):
self.connected = False
return False
def OOinit():
# Init & test spectrometer(s)
# Find spectrometers & print list
devices = sb.list_devices()
print(devices)
# Test spectrometers in the list, 15 frames each
[OO.run(devices, devID=n, frames=15) for n in range(len(devices))]
return devices
def connectOO(self):
devices = sb.list_devices()
self.cam = sb.Spectrometer(devices[0])
self.exp = self.cam.minimum_integration_time_micros / 1000 + 1.0
self.cam.integration_time_micros(self.exp * 1000)
self.expmin, self.expmax, self.expinc = self.exp, 65000, 2
self.satlevel = self.cam._dev.interface._MAX_PIXEL_VALUE
self.wlAxis = self.cam.wavelengths()[sensor_active_pixels[0]:sensor_active_pixels[1]]
self.activeCam = 'OO'
def spectrometerConnect():
devices=sb.list_devices()
print(devices)
if(len(devices)>0):
spectrometerFlag=1
print("Something is connected")
messagebox.showinfo("Detected", "Spectrometer detected :"+str(devices[0]))
return 1
else:
messagebox.showinfo("Error", "No spectrometer detected")
return 0
def __init__(self, int_time=1500):
devices = sb.list_devices() # Find the spectrometer, there is only one
if len(devices) > 1:
print(devices)
if len(devices) < 1:
raise Exception("No spectrometer connected to computer")
self.spec = sb.Spectrometer(devices[0])
self.min_int_time = self.spec.minimum_integration_time_micros
self.wavelengths = self.spec.wavelengths()
self.int_time = int_time
self.set_int_time_ms(int_time)
def connectOO(self):
devices = sb.list_devices()
self.cam = sb.Spectrometer(devices[0])
self.exp = self.cam.minimum_integration_time_micros / 1000 + 1.0
self.cam.integration_time_micros(self.exp * 1000)
self.expmin, self.expmax, self.expinc = self.exp, 65000, 2
self.satlevel = self.cam._dev.interface._MAX_PIXEL_VALUE
self.wlAxis = self.cam.wavelengths(
)[sensor_active_pixels[0]:sensor_active_pixels[1]]
self.activeCam = 'OO'
def connect(self):
self.device = None
try:
devices = list_devices()
except:
devices = list_devices()
for device in devices:
pyusb_device = device._raw_device.pyusb_device
if pyusb_device.idVendor == self.device_id.vid and pyusb_device.idProduct == self.device_id.pid:
self.device = device
if self.device == None:
log.error("Ocean Device: No ocean device found. Returning")
self.message_queue.put_nowait(None)
return False
self.spec = Spectrometer(self.device)
self.settings.eeprom.model = self.device.model
self.settings.eeprom.serial_number = self.device.serial_number
self.settings.eeprom.active_pixels_horizontal = self.device.features[
'spectrometer'][0]._spectrum_num_pixel
self.settings.eeprom.detector = "Ocean" # Ocean API doesn't have access to detector info
return True
def __init__(self):
self.intensities_max = []
self.intensities_min = []
self.intensities_read = []
warnings.filterwarnings('ignore')
devices = sb.list_devices()
self.spec = sb.Spectrometer(devices[0])
self.spec.integration_time_micros(12000)
self.wavelengths = self.spec.wavelengths()
self.percentage_wave = self.wavelengths
def connect(self):
# Open connection to the device:
devices = sb.list_devices()
self.spec = sb.Spectrometer(devices[0])
#Connect settings to hardware:
self.settings.intg_time.connect_to_hardware(
self.spec.integration_time_micros(self.settings['intg_time'] *
1000))
#Take an initial sample of the data.
self.read_from_hardware()
def _init_spectrometer(self):
try:
devices = sb.list_devices()
self._spectrometer = sb.Spectrometer(devices[0])
self._spectrometer.tec_set_temperature_C(-15)
self._spectrometer.tec_set_enable(True)
self._spectrometer.integration_time_micros(100000)
print(self._spectrometer.tec_get_temperature_C())
print("Spectrometer " + str(self._spectrometer.serial_number) + " initialized and working")
except:
#print("Error opening Spectrometer, using Dummy instead")
print("Error accessing Spectrometer")
def Detect ():
devices = sb.list_devices()
print devices
spec = sb.Spectrometer(devices[0])
print 'Serial number:%s' % spec.serial_number
print 'Model:%s' % spec.model
print 'minimum_integration_time_micros:'
spec.minimum_integration_time_micros
spec.trigger_mode(0) #Flushing the stuff down and make the spectrometer ready for next steps!
spec.integration_time_micros(10000)
spec.wavelengths()
Intensities = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
Intensities = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
return spec
def connect_to_spectrometer(intTime=1000000,darkChannel=6,numberOfScans=15):
#connects to first connected spectrometer it finds, takes intTime as integration time in microseconds, darkChannel as
#multiplexer channel that is blocked from all light
#default int time is 1s, channel6 on the multiplexer is blocked off on MC02
#measures dark spectrum
#returns the spectrometer instance, spectrometer wavelengths, and measured dark spectrum
time.sleep(1) # sometimes needs a small delay here...don't know why
devices = sb.list_devices()
#print devices[0] #use this line to print device name
time.sleep(1) #need to wait for a second, otherwise gives error in next step
spec = sb.Spectrometer(devices[0])
spec.integration_time_micros(intTime)
return spec
def performOpen(self, options={}):
"""Perform the operation of opening the instrument connection"""
# init object
self.spec = None
try:
# open connection
devices = sb.list_devices()
# check if devices available
if len(devices) == 0:
# no devices found
raise Exception('No spectrometer found')
elif len(devices) == 1:
# one device, use
self.spec = sb.Spectrometer(devices[0])
else:
# many devices, look for serial
self.spec = sb.Spectrometer.from_serial_number(self.comCfg.address)
except Exception as e:
# re-cast errors as a generic communication error
raise InstrumentDriver.CommunicationError(str(e))
def connect_to_spectrometer(intTime=1000000,darkChannel=6): #connects to first connected spectrometer it finds, takes intTime as integration time in nanoseconds, darkChannel as #multiplexer channel that is blocked from all light #default int time is 1s, channel6 on the multiplexer is blocked off on MC02 #measures dark spectrum #returns the spectrometer instance, spectrometer wavelengths, and measured dark spectrum devices = sb.list_devices() #print devices[0] #use this line to print device name time.sleep(1) #need to wait for a second, otherwise gives error in next step spec = sb.Spectrometer(devices[0]) spec.integration_time_micros(intTime) #actually in nanoseconds not microseconds...WTF mpdll.MPM_SetChannel(darkChannel) time.sleep(1) # have to wait at least 0.5s for multiplexer to switch #averages 15 measurements for the dark backround spectrum darkInt = spec.intensities() for each in range(14): darkInt += spec.intensities() darkInt = darkInt/15.0 return spec, spec.wavelengths(), darkInt
def sample_spectrum(path, logging):
"""Sample the spectrum and store the file locally"""
file_name = get_file_name()
try:
# Get the Spectrometer
devices = sb.list_devices()
spec = sb.Spectrometer(devices[0])
print "[ VISPECS ] Spectrometer:" + spec.model
# Read data
wavelengths = spec.wavelengths()
intensities = spec.intensities()
# Storing in hdf5
spect_file = h5py.File(path + file_name + SPECTRUM_FORMAT, "w")
spect_grp = spect_file.create_group("grp_spectrum")
# Store the pi/system name as an attribute of this group
spect_grp.attrs.__setitem__("attr_system", PI_NAME)
# Store the utc datetime as an attribute of this group
spect_grp.attrs.__setitem__("attr_datetime", DATETIME)
# Dataset for storing the wavelengths
wavelength_dataset = spect_grp.create_dataset("dataset_wavelengths", data=wavelengths)
# Dataset for storing the intensities
intensities_dataset = spect_grp.create_dataset("dataset_intensities", data=intensities)
# Close the spectrum file
spect_file.close()
print "[ VISPECS ] Spectrum file: " + path + file_name + SPECTRUM_FORMAT
logging.info("Spectrum file: " + path + file_name + SPECTRUM_FORMAT)
except Exception as error:
print "[ VISPECS ] Exception when reading spectrum!"
print error
logging.info("Spectrum Exception!: " + repr(error))
def connect_to_spectrometer(intTime=procIntTime,darkChannel=6,numberOfScans=procNumScans):
# connects to first connected spectrometer it finds, takes intTime as integration time in microseconds, darkChannel as
# multiplexer channel that is blocked from all light
# default int time is 1s, channel6 on the multiplexer is blocked off on MC02
# measures dark spectrum
# returns the spectrometer instance, spectrometer wavelengths, and measured dark spectrum
time.sleep(1)
devices = sb.list_devices()
# print devices[0] #use this line to print device name
time.sleep(1) #need to wait for a second, otherwise gives error in next step
try:
spec = sb.Spectrometer(devices[0])
except IndexError:
print 'couldn\'t find spectrometer.'
print 'try unplugging usb cable from spectrometer and restart measurement'
raw_input('press enter to exit')
exit()
spec.integration_time_micros(intTime)
mpdll.MPM_SetChannel(darkChannel)
time.sleep(1) # have to wait at least 0.5s for multiplexer to switch
print 'taking background reading, should take ', str(2*numberOfScans*intTime/(1000000.)),'seconds'
darkInt = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
for each in range(numberOfScans*2 - 1):
darkInt += spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
darkInt = darkInt/float(numberOfScans*2)
wl = spec.wavelengths()
# write darkInt to file in case its needed
if not os.path.isdir(savedir):
os.mkdir(savedir)
if not os.path.isfile(savedir + savedate + ' -- ' + ' OES raw spectra -- Dark Int.csv'):
notWritten = True
while notWritten:
try:
with open(savedir + savedate + ' -- ' + ' OES raw spectra -- Dark Int.csv', 'wb') as csvfile:
spamwriter = csv.writer(csvfile, delimiter=',', quoting=csv.QUOTE_MINIMAL)
spamwriter.writerow(['DateTime']+[eachWL for eachWL in wl])
notWritten = False
except IOError:
print '\n*****************'
print ' raw spectra file (' + savedir + savedate + ' -- ' + ' OES raw spectra -- Dark Int.csv' + ') is open another program, please close it'
print '*****************\n'
time.sleep(5)
notWritten = True
while notWritten:
try:
with open(savedir + savedate + ' -- ' + ' OES raw spectra -- Dark Int.csv', 'ab') as csvfile:
spamwriter = csv.writer(csvfile, delimiter=',', quoting=csv.QUOTE_MINIMAL)
spamwriter.writerow([datetime.strftime(datetime.now(), '%m/%d/%y %H:%M:%S %p')]+[eachInt for eachInt in darkInt])
notWritten = False
except IOError:
print '\n*****************'
print zoneList[each] + ' raw spectra file (' + savedir + savedate + ' -- ' + ' OES raw spectra -- Dark Int.csv' + ') is open another program, please close it'
print '*****************\n'
time.sleep(5)
return spec, spec.wavelengths(), darkInt
import drivers.uc480 as cam
cam480 = cam.uc480()
cam480.connect() # see whether we can connect
sensor_width, _ = cam480.get_sensor_size()
cam480.close()
uc480avail = True
except:
sensor_width = 1024 # some default
uc480avail = False
# import seabreeze module
try:
import seabreeze
seabreeze.use('pyseabreeze')
import seabreeze.spectrometers as sb
if len(sb.list_devices()) == 0: # count connected OOs
raise
sensor_active_pixels = (1, -1)
OOavail = True
except:
OOavail = False
# ---------------------------------------------------------------------------
# main class
class pyUVVIS(wx.Frame):
# initialize the app window
def __init__(self, parent, title):
super(pyUVVIS, self).__init__(parent, title=title, style=wx.DEFAULT_FRAME_STYLE | wx.MAXIMIZE)
while not (instr.timeout == 1 and instr.rigol_quirk == False):
instr.timeout = 1
instr.rigol_quirk = False
idg = ''
while not idg:
try:
idg = instr.ask("*IDN?")
except Exception as e: # USBErrors
print("{} in get_oscilloscope".format(e))
time.sleep(0.4)
print("device info: {}".format(idg))
print("device timeout: {}".format(instr.timeout))
time.sleep(0.5)
## initialize spectrometer
devices = sb.list_devices()
#t_int=12000
t_int=12000*4
print("Available devices {}".format(devices))
spec = sb.Spectrometer(devices[0])
print("Using {}".format(devices[0]))
spec.integration_time_micros(t_int)
print("integratiopn time {} seconds.".format(t_int/1e6))
time.sleep(0.5)
class DummyFile(object):
def write(self, x): pass
def nostdout(func):
def wrapper(*args, **kwargs):
save_stdout = sys.stdout
def __init__(self,device=None,integration_time=20e-3):
if device is None: device = sb.Spectrometer(sb.list_devices()[0])
self.device = device
self.w = device.wavelengths()
self.set_integration_time(integration_time)
