def __init__( self , serialport , romcode = '', label = 'TEMPERATURESENSOR' , plot_title = None , max_buffer_points = 500 , fig_w = 6.5 , fig_h = 5 , has_plot_window = True , has_external_plot_window = None):
'''
temperaturesensor_VIRTUAL.__init__( serialport , romcode, label = 'TEMPERATURESENSOR' , plot_title = None , max_buffer_points = 500 , fig_w = 6.5 , fig_h = 5 , has_plot_window = True , has_external_plot_window = None )
Initialize TEMPERATURESENSOR object (VIRTUAL)
INPUT:
serialport: device name of the serial port for 1-wire connection to the temperature sensor, e.g. serialport = '/dev/ttyUSB3'
romcode: ROM code of the temperature sensor chip (you can find the ROM code using the digitemp program or using the pydigitemp package). If there is only a single temperature sensor connected to the 1-wire bus on the given serial port, romcode can be left empty.
label (optional): label / name of the TEMPERATURESENSOR object (string) for data output. Default: label = 'TEMPERATURESENSOR'
plot_title (optional): title string for use in plot window. If plot_title = None, the sensor label is used. Default: label = None
max_buffer_points (optional): max. number of data points in the PEAKS buffer. Once this limit is reached, old data points will be removed from the buffer. Default value: max_buffer_points = 500
fig_w, fig_h (optional): width and height of figure window used to plot data (inches)
has_external_plot_window (optional): flag to indicate if there is a GUI system that handles the plotting of the data buffer on its own. This flag can be set explicitly to True of False, or can use None to ask for automatic 'on the fly' check if the has_external_plot_window = True or False should be used. Default: has_external_plot_window = None
OUTPUT:
(none)
'''
self._label = label
# Check for has_external_plot_window flag:
if has_external_plot_window is None:
has_external_plot_window = misc.have_external_gui()
# Check plot title:
if plot_title == None:
self._plot_title = self._label
else:
self._plot_title = plot_title
# data buffer for temperature values:
self._tempbuffer_t = numpy.array([])
self._tempbuffer_T = numpy.array([])
self._tempbuffer_unit = ['x'] * 0 # empty list
self._tempbuffer_max_len = max_buffer_points
self._tempbuffer_lastupdate_timestamp = -1
# set up plotting environment
if has_external_plot_window:
# no need to set up plotting
self._has_external_display = True
self._has_display = False
else:
self._has_external_display = False
self._has_display = misc.plotting_setup() # check for graphical environment, import matplotlib
if self._has_display: # prepare plotting environment and figure
import matplotlib.pyplot as plt
# set up plotting environment
self._fig = plt.figure(figsize=(fig_w,fig_h))
t = 'VIRUTAL_TSENSOR'
if self._plot_title:
t = t + ' (' + self._plot_title + ')'
self._fig.canvas.set_window_title(t)
# set up panel for temperature history plot:
self._tempbuffer_ax = plt.subplot(1,1,1)
t = 'TEMPBUFFER'
if self._plot_title:
t = t + ' (' + self._plot_title + ')'
self._tempbuffer_ax.set_title(t,loc="center")
self._tempbuffer_ax.set_xlabel('Time (s)')
self._tempbuffer_ax.set_ylabel('Temperature')
# add (empty) line to plot (will be updated with data later):
self._tempbuffer_ax.plot( [], [] , 'ko-' , markersize = 10 )
# get some space in between panels to avoid overlapping labels / titles
self._fig.tight_layout()
# enable interactive mode:
plt.ion()
self._figwindow_is_shown = False
print ( 'Successfully configured VIRTUAL temperature sensor.' )
def __init__(self,
serialport,
romcode='',
label='TEMPERATURESENSOR',
plot_title=None,
max_buffer_points=500,
fig_w=6.5,
fig_h=5,
has_plot_window=True,
has_external_plot_window=None):
'''
temperaturesensor_MAXIM.__init__( serialport , romcode, label = 'TEMPERATURESENSOR' , plot_title = None , max_buffer_points = 500 , fig_w = 6.5 , fig_h = 5 , has_plot_window = True , has_external_plot_window = None )
Initialize TEMPERATURESENSOR object (MAXIM), configure serial port / 1-wire bus for connection to DS18B20 temperature sensor chip
INPUT:
serialport: device name of the serial port for 1-wire connection to the temperature sensor, e.g. serialport = '/dev/ttyUSB3'
romcode: ROM code of the temperature sensor chip (you can find the ROM code using the digitemp program or using the pydigitemp package). If there is only a single temperature sensor connected to the 1-wire bus on the given serial port, romcode can be left empty.
label (optional): label / name of the TEMPERATURESENSOR object (string) for data output. Default: label = 'TEMPERATURESENSOR'
plot_title (optional): title string for use in plot window. If plot_title = None, the sensor label is used. Default: label = None
max_buffer_points (optional): max. number of data points in the PEAKS buffer. Once this limit is reached, old data points will be removed from the buffer. Default value: max_buffer_points = 500
fig_w, fig_h (optional): width and height of figure window used to plot data (inches)
has_external_plot_window (optional): flag to indicate if there is a GUI system that handles the plotting of the data buffer on its own. This flag can be set explicitly to True of False, or can use None to ask for automatic 'on the fly' check if the has_external_plot_window = True or False should be used. Default: has_external_plot_window = None
OUTPUT:
(none)
'''
self._label = label
# Check for has_external_plot_window flag:
if has_external_plot_window is None:
has_external_plot_window = misc.have_external_gui()
# Check plot title:
if plot_title == None:
self._plot_title = self._label
else:
self._plot_title = plot_title
# data buffer for temperature values:
self._tempbuffer_t = numpy.array([])
self._tempbuffer_T = numpy.array([])
self._tempbuffer_unit = ['x'] * 0 # empty list
self._tempbuffer_max_len = max_buffer_points
self._tempbuffer_lastupdate_timestamp = -1
# set up plotting environment
if has_external_plot_window:
# no need to set up plotting
self._has_external_display = True
self._has_display = False
else:
self._has_external_display = False
self._has_display = misc.plotting_setup(
) # check for graphical environment, import matplotlib
try:
# configure 1-wire bus for communication with MAXIM temperature sensor chip
r = AddressableDevice(
UART_Adapter(serialport)).get_connected_ROMs()
if r is None:
print('Couldn not find any 1-wire devices on ' + serialport)
else:
bus = UART_Adapter(serialport)
if romcode == '':
if len(r) == 1:
# print ('Using 1-wire device ' + r[0] + '\n')
self._sensor = DS18B20(bus)
self._ROMcode = r[0]
else:
print(
'Too many 1-wire devices to choose from! Try again with specific ROM code...'
)
for i in range(1, len(r)):
print('Device ' + i + ' ROM code: ' + r[i - 1] +
'\n')
else:
self._sensor = DS18B20(bus, rom=romcode)
self._ROMcode = romcode
self._UART_locked = False
if self._has_display: # prepare plotting environment and figure
import matplotlib.pyplot as plt
# set up plotting environment
self._fig = plt.figure(figsize=(fig_w, fig_h))
t = 'MAXIM DS1820'
if self._plot_title:
t = t + ' (' + self._plot_title + ')'
self._fig.canvas.set_window_title(t)
# set up panel for temperature history plot:
self._tempbuffer_ax = plt.subplot(1, 1, 1)
t = 'TEMPBUFFER'
if self._plot_title:
t = t + ' (' + self._plot_title + ')'
self._tempbuffer_ax.set_title(t, loc="center")
self._tempbuffer_ax.set_xlabel('Time (s)')
self._tempbuffer_ax.set_ylabel('Temperature')
# add (empty) line to plot (will be updated with data later):
self._tempbuffer_ax.plot([], [], 'ko-', markersize=10)
# get some space in between panels to avoid overlapping labels / titles
self._fig.tight_layout()
# enable interactive mode:
plt.ion()
self._figwindow_is_shown = False
if hasattr(self, '_sensor'):
print(
'Successfully configured DS18B20 temperature sensor (ROM code '
+ self._ROMcode + ')')
else:
self.warning(
'Could not initialize MAXIM DS1820 temperature sensor.')
except:
# print ( '\n**** WARNING: An error occured during configuration of the temperature sensor at serial interface ' + serialport + '. The temperature sensor cannot be used.\n' )
self.warning(
'An error occured during configuration of the temperature sensor at serial interface '
+ serialport + '. The temperature sensor cannot be used.')
def __init__( self , serialport , label = 'PRESSURESENSOR' , plot_title = None , max_buffer_points = 500 , fig_w = 6.5 , fig_h = 5 , has_plot_window = True , has_external_plot_window = None):
'''
pressuresensor_OMEGA.__init__( serialport , label = 'PRESSURESENSOR' , plot_title = None , max_buffer_points = 500 , fig_w = 6.5 , fig_h = 5 , has_plot_window = True , has_external_plot_window = None )
Initialize PRESSURESENSOR object (OMEGA), configure serial port connection
INPUT:
serialport: device name of the serial port, e.g. serialport = '/dev/ttyUSB3'
label (optional): label / name of the PRESSURESENSOR object for data output (string). Default: label = 'PRESSURESENSOR'
plot_title (optional): title string for use in plot window. If plot_title = None, the sensor label is used. Default: label = None
max_buffer_points (optional): max. number of data points in the PEAKS buffer. Once this limit is reached, old data points will be removed from the buffer. Default value: max_buffer_points = 500
fig_w, fig_h (optional): width and height of figure window used to plot data (inches)
has_external_plot_window (optional): flag to indicate if there is a GUI system that handles the plotting of the data buffer on its own. This flag can be set explicitly to True of False, or can use None to ask for automatic 'on the fly' check if the has_external_plot_window = True or False should be used. Default: has_external_plot_window = None
OUTPUT:
(none)
'''
self._label = label
# Check for has_external_plot_window flag:
if has_external_plot_window is None:
has_external_plot_window = misc.have_external_gui()
# Check plot title:
if plot_title == None:
self._plot_title = self._label
else:
self._plot_title = plot_title
# data buffer for PEAK values:
self._pressbuffer_t = numpy.array([])
self._pressbuffer_p = numpy.array([])
self._pressbuffer_unit = ['x'] * 0 # empty list
self._pressbuffer_max_len = max_buffer_points
self._pressbuffer_lastupdate_timestamp = -1
# set up plotting environment
if has_external_plot_window:
# no need to set up plotting
self._has_external_display = True
self._has_display = False
else:
self._has_external_display = False
self._has_display = misc.plotting_setup() # check for graphical environment, import matplotlib
try:
# open and configure serial port for communication with VICI valve (9600 baud, 8 data bits, no parity, 1 stop bit
from pkg_resources import parse_version
if parse_version(serial.__version__) >= parse_version('3.3') :
# open port with exclusive access:
ser = serial.Serial(
port = serialport,
baudrate = 115200,
parity = serial.PARITY_NONE,
stopbits = serial.STOPBITS_ONE,
bytesize = serial.EIGHTBITS,
timeout = 5,
exclusive = True
)
else:
# open port (can't ask for exclusive access):
ser = serial.Serial(
port = serialport,
baudrate = 115200,
parity = serial.PARITY_NONE,
stopbits = serial.STOPBITS_ONE,
bytesize = serial.EIGHTBITS,
timeout = 5
)
ser.flushOutput() # make sure output is empty
time.sleep(0.1)
ser.flushInput() # make sure input is empty
self.ser = ser
self._ser_locked = False
# get serial number of pressure sensor
self.get_serial_lock()
self.ser.write(('SNR\r').encode('utf-8')) # send command with check sum to serial port
ans = self.ser.readline().decode('utf-8') # read response and decode ASCII
ser.flushInput() # make sure input is empty
self.release_serial_lock()
self._serial_number = int(ans.rstrip().split('=')[1]) # parse response to integer number
if self._has_display: # prepare plotting environment and figure
import matplotlib.pyplot as plt
# set up plot figure:
self._fig = plt.figure(figsize=(fig_w,fig_h))
t = 'OMEGA PXM409'
if self._plot_title:
t = t + ' (' + self._plot_title + ')'
self._fig.canvas.set_window_title(t)
# set up panel for pressure history plot:
self._pressbuffer_ax = plt.subplot(1,1,1)
t = 'PRESSBUFFER'
if self._plot_title:
t = t + ' (' + self._plot_title + ')'
self._pressbuffer_ax.set_title(t,loc="center")
self._pressbuffer_ax.set_xlabel('Time (s)')
self._pressbuffer_ax.set_ylabel('Pressure')
# add (empty) line to plot (will be updated with data later):
self._pressbuffer_ax.plot( [], [] , 'ko-' , markersize = 10 )
# get some space in between panels to avoid overlapping labels / titles
self._fig.tight_layout()
# enable interactive mode:
plt.ion()
self._figwindow_is_shown = False
print ('Successfully configured OMEGA pressure sensor with serial number ' + str(self._serial_number) + ' on ' + serialport )
except:
self.warning ( 'An error occured during configuration of the pressure sensor at serial interface ' + serialport + '. The pressure sensor cannot be used.' )
def __init__(self,
serialport=None,
label='MS',
cem_hv=1400,
tune_default_RI=[],
tune_default_RS=[],
max_buffer_points=500,
fig_w=10,
fig_h=8,
peakbuffer_plot_min=0.5,
peakbuffer_plot_max=2,
peakbuffer_plot_yscale='linear',
scan_plot_yscale='linear',
has_plot_window=True,
has_external_plot_window=None):
'''
rgams_SRS_virtual.__init__( serialport , label='MS' , cem_hv = 1400 , tune_default_RI = [] , tune_default_RS = [] , max_buffer_points = 500 , fig_w = 10 , fig_h = 8 , peakbuffer_plot_min=0.5 , peakbuffer_plot_max = 2 , peakbuffer_plot_yscale = 'linear' , scan_plot_yscale = 'linear' , has_plot_window = True , has_external_plot_window = None)
Initialize virtual mass spectrometer (SRS RGA)
INPUT:
serialport (optional): device name of the serial port, e.g. P = '/fake/serialport/to/virtual/rga_MS'
label (optional): label / name of the RGAMS object (string). Default: label = 'MS'
cem_hv (optional): default bias voltage to be used with the electron multiplier (CEM). Default value: cem_hv = 1400 V.
tune_default_RI (optional): default RI parameter value in m/z tuning. Default value: tune_RI = []
tune_default_RS (optional): default RS parameter value in m/z tuning. Default value: tune_RS = []
max_buffer_points (optional): max. number of data points in the PEAKS buffer. Once this limit is reached, old data points will be removed from the buffer. Default value: max_buffer_points = 500
fig_w, fig_h (optional): width and height of figure window used to plot data (inches).
peakbuffer_plot_min, peakbuffer_plot_max (optional): limits of y-axis range in peakbuffer plot (default: peakbuffer_plot_min=0.5 , peakbuffer_plot_max = 2)
peakbuffer_plot_yscale (optional) = y-axis scaling for peakbuffer plot (default: 'linear', use 'log' for log scaling)
scan_plot_yscale (optional) = y-axis scaling for scan plot (default: 'linear', use 'log' for log scaling)
has_plot_window (optional): flag to choose if a plot window should be opened for the rgams_SRS object (default: has_plot_window = True)
has_external_plot_window (optional) = flag to indicate if external plot window is used instead of the "built-in" window. If set to True, this will override the 'has_plot_window' flag (default: has_external_plot_window = False).
OUTPUT:
(none)
'''
# object name label (do this first, so the label/name is set for warning or log messages or exception handling):
self._label = label
# Check for has_external_plot_window flag:
if has_external_plot_window is None:
has_external_plot_window = misc.have_external_gui()
# general parameters:
self._serialport = serialport
if self._serialport is None:
self._serialport = '/there/is/no/serial/port'
self._serial_number = 123456789
self._cem_hv = float(cem_hv)
self._tune_default_RI = tune_default_RI
self._tune_default_RS = tune_default_RS
if not tune_default_RI == []:
self._RI = tune_default_RI
else:
self._RI = -9.0
if not tune_default_RS == []:
self._RS = tune_default_RS
else:
self._RS = 1070.0
self._DI = 116
self._DS = -0.01
self._EE = 70
self._FL = 0.0
self._hasmulti = True
self._mzmax = 200
self._noisefloor = 3
# init MS settings:
self.set_detector('F')
self.filament_off()
# peakbuffer:
self._peakbuffer_t = numpy.array([])
self._peakbuffer_mz = numpy.array([])
self._peakbuffer_intens = numpy.array([])
self._peakbuffer_det = ['x'] * 0 # empty list
self._peakbuffer_unit = ['x'] * 0 # empty list
self._peakbuffer_max_len = max_buffer_points
self._peakbuffer_lastupdate_timestamp = -1
# y-axis range:
self._peakbuffer_plot_min_y = peakbuffer_plot_min
self._peakbuffer_plot_max_y = peakbuffer_plot_max
# y-axis scaling for peakbuffer plot:
self._peakbufferplot_yscale = peakbuffer_plot_yscale
# y-axis scaling for scan plot:
self._scan_yscale = scan_plot_yscale
# mz values and colors (defaults):
self._peakbufferplot_colors = [
(2, 'darkgray'), (4, 'c'), (13, 'darkgray'), (14, 'dimgray'),
(15, 'green'), (16, 'lightcoral'), (28, 'k'), (32, 'r'), (40, 'y'),
(44, 'b'), (84, 'm')
] # default colors for the more common mz values
# set up plotting environment
if has_external_plot_window:
# no need to set up plotting
self._has_external_display = True
self._has_display = False
else:
self._has_external_display = False
self._has_display = misc.plotting_setup(
) # check for graphical environment, import matplotlib
if self._has_display:
# set up plotting environment
import matplotlib.pyplot as plt
self._fig = plt.figure(figsize=(fig_w, fig_h))
t = 'SRS RGA'
if self._label:
t = t + ' (' + self._label + ')'
self._fig.canvas.set_window_title(t)
# set up upper panel for peak history plot:
self._peakbuffer_ax = plt.subplot(2, 1, 1)
self._peakbuffer_ax.set_title('PEAKBUFFER (' + self.label() + ')',
loc="center")
plt.xlabel('Time')
plt.ylabel('Intensity')
# add (empty) line to plot (will be updated with data later):
self._peakbuffer_ax.plot([], [])
self.set_peakbuffer_scale(self._peakbufferplot_yscale)
# set up lower panel for scans:
self._scan_ax = plt.subplot(2, 1, 2)
self._scan_ax.set_title('SCAN (' + self.label() + ')',
loc="center")
plt.xlabel('mz')
plt.ylabel('Intensity')
self.set_scan_scale(self._scan_yscale)
# get some space in between panels to avoid overlapping labels / titles
self._fig.tight_layout(pad=4.0)
self._figwindow_is_shown = False
plt.ion()
self.log(
'Successfully configured virtual SRS RGA MS with serial number ' +
str(self._serial_number) + ' on ' + self._serialport)