def __init__(self, port=None, calib_file=None, calib_cf=[0,1,0], debug=False):
"""calib_file: rontec calibration file, should be like:
#calibration factors
0 0.00410435 1.2e-9
"""
self.sl = Serial(port, baudrate=38400, eol='\r')
self.calib_done = False
self.preset_erange=None
self.live_t = False
self.roi_channel = None
self.type = None
self.times = {}
self.debug = debug
self.roi_dict = {}
#connect to the hardware and make a reset
self.reset(calib_file, calib_cf)
class Rontec:
ERANGE = {0:"10keV", 1:"20keV", 2:"40keV", 3:"80keV"}
MCA_DEFAULTS = {"chmin":0, "chmax":4095}
MCA_ERROR = {0: "General error or buffer overflow",
1: "Unknown command",
2: "Numeric parameter expected",
4: "Boolean parameter expected",
5: "Additional parameter expected",
6: "Unexpected parameter or character",
7: "Illegal numeric value",
8: "Unknown subcommand",
9: "Function not implemented or no hardware support",
13: "Hardware error",
14: "Illegal baud rate"}
def __init__(self, port=None, calib_file=None, calib_cf=[0,1,0], debug=False):
"""calib_file: rontec calibration file, should be like:
#calibration factors
0 0.00410435 1.2e-9
"""
self.sl = Serial(port, baudrate=38400, eol='\r')
self.calib_done = False
self.preset_erange=None
self.live_t = False
self.roi_channel = None
self.type = None
self.times = {}
self.debug = debug
self.roi_dict = {}
#connect to the hardware and make a reset
self.reset(calib_file, calib_cf)
def exit(self):
self.sl.close()
def _check_answer(self, asw, cmd):
if not asw.startswith('!') or asw.startswith('!E'):
e = 'Invalid answer from %s'% cmd
if asw.startswith('!E'):
_,err = asw.split(": ")
e = e+': %s' % Rontec.MCA_ERROR[int(err)]
raise RuntimeError(e)
else:
if self.debug:
print asw
return asw
def _calib_getch(self, energy):
if not self.calib[2]:
if self.calib[1]:
return int((energy - self.calib[0])/self.calib[1])
else:
return 0
cc = 1
print self.calib
if self.calib[1] > 0:
cc = -1
return int((self.calib[1]-cc*math.sqrt(math.pow(self.calib[1], 2)-4*(self.calib[0]-energy)*self.calib[2]))/(2*self.calib[2]))
def _calib_getE(self, chan):
return self.calib[0] + self.calib[1]*chan + self.calib[2]*math.pow(chan,2)
def set_calibration(self, fname=None, calib_cf=None):
"""Set the energy calibration. Give a filename or a list of calibration factors.
Kwargs:
fname (str): optional filename with the calibration factors
calib_cf (list): optional list of calibration factors
Returns:
list. Calibration factors.
Raises:
IOError, ValueError
"""
if fname is None and calib_cf is None:
raise ValueError("Either calibration file or calibration factors must be provided.")
if isinstance(fname, str):
calib_cf = []
try:
f = open(fname)
for line in f:
if not line.startswith('#'):
calib_cf = map(float, line.split())
else:
pass
f.close()
except IOError:
raise IOError('Cannot open %s' % fname)
self.calib = calib_cf
self.calib_done = calib_cf != [0,1,0]
return self.calib
def get_calibration(self):
"""Get the calibration factors list
Returns:
list. Calibration factors.
"""
return self.calib
def reset(self, calib_file=None, calib_cf=[0,1,0]):
"""Reset the controller and sets calibration
Kwargs:
calib_file (str): optional filename with the calibration factors
calib_cf (list): optional list of calibration factors
Returns:
None
Raises:
RuntimeError, IOError, ValueError
"""
self.sl.flush()
#at reset Rontec sends two lines, we want the second one only
asw = str(self.sl.write_readline("$##\r"))
if not asw.__len__():
raise RuntimeError('Invalid answer from reset')
asw = self.sl.readline()
if not asw.__len__():
raise RuntimeError('Invalid answer from reset')
type = asw.split()
try:
type.__len__() > 1
#check if MAX/MMAX...
if type[3] == "MMAX" or type[3] == "XDN":
self.type = 2
elif type[3] == "MAX":
self.type = 1
except Exception:
raise RuntimeError('Invalid answer from reset')
#check if live time accepted - depends on the firmware version
self.sl.flush()
asw = self.sl.write_readline("$LS\r")
try:
self._check_answer(asw, 'reset:livetime')
self.live_t = True
except RuntimeError as e:
print e
self.live_t = False
self.chmin = Rontec.MCA_DEFAULTS["chmin"]
self.chmax = Rontec.MCA_DEFAULTS["chmax"]
if calib_file:
self.set_calibration(calib_file)
else:
self.set_calibration(calib_cf=calib_cf)
self.emin = self._calib_getE(self.chmin)
self.emax = self._calib_getE(self.chmax)
#last but not least - format the reading to be 4 bytes/channel, no clear after reading
self.stop_acq()
self.sl.flush()
asw = str(self.sl.write_readline("$SM 4 0\r"))
self._check_answer(asw, 'reset:set read fromat/mode')
def set_presets(self, **kwargs):
"""Set presets parameters
Keyword Args:
ctime (float): real time [s]
erange (int): the energy range, 0: 10 keV, 1: 20 keV, 2: 40 keV, 3: 80 keV
fname (str): file name (full path) to save the raw data
Returns:
None
"""
if kwargs.has_key("ctime"):
#we want ms or cps - this is the IC/OC counters time(gate)
ms_time = kwargs["ctime"] * 1000
if ms_time < 0.001 or ms_time > 2000:
gate_time = 1000 #1s - we want ICR and OCR in cps
else:
gate_time = ms_time
asw = str(self.sl.write_readline("$CT %u\r" % gate_time))
self._check_answer(asw, 'set_presets: ctime')
self.times["real_time_preset"] = kwargs["ctime"]
self.times["cycle_time_preset"] = gate_time/1000
if kwargs.has_key("erange"):
#set the energy range
if kwargs["erange"] in Rontec.ERANGE:
asw = str(self.sl.write_readline("$SE %d\r" % kwargs["erange"]))
self._check_answer(asw, 'set_presets:erange')
self.preset_erange = kwargs["erange"]
if kwargs.has_key("fname"):
self.fname = kwargs["fname"]
def clear_spectrum(self):
"""Clear the acquired spectrum"""
self.sl.flush()
asw = str(self.sl.write_readline("$CC\r"))
self._check_answer(asw, 'clear_spectrum')
def stop_acq(self):
"""Stop the running acquisition"""
self.sl.flush()
asw = str(self.sl.write_readline("$MP ON\r"))
self._check_answer(asw, 'stop_acq')
def start_acq(self, cnt_time=None):
"""Starts new acquisition. If cnt_time is not specified, counts for preset real time.
Keyword Args:
cnt_time (float, optional): count time in seconds; 0 means to count indefinitely.
Returns:
None
"""
if cnt_time >= 0:
self.set_presets(ctime=cnt_time)
else:
cnt_time = self.times["real_time_preset"]
#cnt_time is in s, firmware needs ms
self.sl.flush()
asw = str(self.sl.write_readline("$MT %d\r" % (cnt_time*1000)))
self._check_answer(asw, 'start_acq')
def set_roi(self, emin, emax, **kwargs):
"""Configure a ROI
Args:
emin (float): energy [keV] or channel number
emax (float): energy [keV] or channel number
Keyword Args:
channel (int): output connector channel number (1-8)
element (str): element name as in periodic table
atomic_nb (int): element atomic number
Returns:
None
Raises:
KeyError
"""
#check if input is energy [keV] or channels
if emax > 80:
self.chmin = emin
self.chmax = emax
if self.calib_done:
self.emin = self._calib_getE(self.chmin)
self.emax = self._calib_getE(self.chmax)
else:
self.emin = emin
self.emax = emax
if self.calib_done:
self.chmin = self._calib_getch(self.emin)
self.chmax = self._calib_getch(self.emax)
if kwargs.has_key("channel") and self.type == 2:
roi_channel = kwargs.get("channel",1)
#test if channel is between 1 and 8
if roi_channel < 1 or roi_channel > 8:
raise KeyError("Channel number is should be between 1 and 8")
self.roi_dict[roi_channel] = "%2.4f(%d) %2.4f(%d)" % (self.emin, self.chmin, self.emax, self.chmax)
roi_str = "$SK %d %d %s %d %d\r" % (roi_channel, kwargs.get("atomic_nb", 34), kwargs.get("element", "Se"), emin*1000, emax*1000)
self.sl.flush()
asw = str(self.sl.write_readline(roi_str))
self._check_answer(asw, 'set_roi')
def clear_roi(self, **kwargs):
"""Clear ROI settings
Keyword Args:
channel (int): optional output connector channel number (1-8)
Returns:
None
"""
self.chmin = Rontec.MCA_DEFAULTS["chmin"]
self.chmax = Rontec.MCA_DEFAULTS["chmax"]
if self.calib_done:
self.emin = self._calib_getE(self.chmin)
self.emax = self._calib_getE(self.chmax)
if kwargs.has_key("channel") and self.type == 2:
self.sl.flush()
roi_channel = kwargs[channel]
asw = str(self.sl.write_readline("$SK %d 0 0 0\r" % roi_channel))
self._check_answer(asw, 'clear_roi')
try:
self.roi_dict.pop(roi_channel)
except KeyError:
pass
def get_roi(self, **kwargs):
"""Get ROI settings
Keyword Args:
channel (int): output connector channel number (1-8)
Returns:
dict. ROI dictionary.
"""
argout = {}
argout["chmin"]= self.chmin
argout["chmax"] = self.chmax
if kwargs.has_key("channel"):
roi_channel = int(kwargs.get("channel"))
#test if channel is between 1 and 8
if roi_channel < 1 or roi_channel > 8:
return argout
else:
roi_channel = 0
if self.type == 2 and roi_channel:
asw = str(self.sl.write_readline("$GK %d\r"% roi_channel))
if self.debug:
print asw
self._check_answer(asw, 'get_roi')
asw = asw[4:]
argout["ext_roi"] = asw
_,_,self.emin,self.emax = asw.split()
self.emin = float(self.emin) / 1000
self.emax = float(self.emax) / 1000
self.roi_dict[roi_channel] = "%2.4f(%d) %2.4f(%d)" % (self.emin, self.chmin, self.emax, self.chmax)
else:
try:
argout.pop("ext_roi")
except KeyError:
pass
if self.calib_done:
argout["chmin"] = self._calib_getch(self.emin)
argout["chmax"] = self._calib_getch(self.emax)
else:
self.emin = self._calib_getE(self.chmin)
self.emax = self._calib_getE(self.chmax)
argout["emin"] = self.emin
argout["emax"] = self.emax
return argout
def get_times(self):
"""Return a dictionary with the preset and elapsed real time [s],
elapsed live time (if possible) [s] and the dead time [%].
Returns:
dict. Times dictionary.
Raises:
RuntimeError
"""
#real time elapsed
self.sl.flush()
asw = str(self.sl.write_readline("$MR\r"))
self._check_answer(asw, 'get_time:real time elapsed')
if self.debug:
print asw
try:
_,rt = asw.split()
#the answer is in ms, we return time in s
self.times["real_time_elapsed"] = float(rt)/1000
if self.times["real_time_preset"]:
self.times["real_time_elapsed"] = self.times["real_time_preset"] - self.times["real_time_elapsed"]
except:
raise RuntimeError('Cannot get the elapsed real time')
#dead time
#get the ICR
self.sl.flush()
asw = str(self.sl.write_readline("$BC\r"))
self._check_answer(asw, 'get_time:ICR')
try:
_,icr = asw.split()
self.times["ICR"] = float(icr)
except:
raise RuntimeError('Cannot get the ICR')
#get the OCR
self.sl.flush()
asw = str(self.sl.write_readline("$NC\r"))
self._check_answer(asw, 'get_time:OCR')
try:
_,ocr = asw.split()
#correct with the cycle time
if ocr > self.times["cycle_time_preset"]:
ocr = float(ocr) - self.times["cycle_time_preset"]
self.times["OCR"] = float(ocr)
except:
raise RuntimeError('Cannot get the OCR')
#calculate the dead time in %
if self.times["ICR"] < 1000 or self.times["ICR"] < self.times["OCR"]:
self.times["dead_time"] = 0
else:
self.times["deat_time"] = ((self.times["ICR"]-self.times["OCR"])/self.times["ICR"])*100.
#live time elapsed
if self.live_t:
self.sl.flush()
asw = str(self.sl.write_readline("$LR\r"))
self._check_answer(asw, 'get_time:live time elapsed')
try:
_,lt = asw.split()
#the answer is in ms, we return time in s
self.times["live_time"] = float(lt)/1000
except:
raise RuntimeError('Cannot get the elapsed live time')
return self.times
def get_presets(self, **kwargs):
"""Get the preset parameters
Keyword Args:
ctime (float): Real time
erange (int): energy range
fname (str): filename where the data are stored
Returns:
dict.
Raises:
RuntimeError
"""
if kwargs.has_key("ctime"):
try:
return self.times["real_time_preset"]
except:
raise RuntimeError('Count time not set')
if kwargs.has_key("erange"):
if self.preset_erange:
return Rontec.ERANGE[self.preset_erange]
else:
self.sl.flush()
asw = str(self.sl.write_readline("$FE\r"))
self._check_answer(asw, 'get_presets:energy range')
try:
_,rr = asw.split()
self.preset_erange = int(rr)
return Rontec.ERANGE[self.preset_erange]
except:
raise RuntimeError('Energy range not set')
def read_roi_data(self, save_data=False):
"""Reads ROI data
Keyword Args:
save_data (bool): save data in the file or not, defaults to False
Returns:
list. Raw data for the predefined ROI channels.
"""
return self.read_raw_data(self.chmin, self.chmax, save_data)
def read_data(self, chmin=0, chmax=4095, calib=False, save_data=False):
"""Reads the data
Keyword Args:
chmin (float): channel number or energy [keV], defaults to 0
chmax (float): channel number or energy [keV], defaults to 4095
calib (bool): use calibration, defaults to False
save_data (bool): save data in the file or not, defaults to False
Returns:
numpy.array. x - channels or energy (if calib=True), y - data.
"""
# the input is energy and the calibration is done
if chmax < 30 and self.calib_done:
chmin = _calib_getch(chmin)
chmax = _calib_getch(chmax)
y = self.read_raw_data(chmin, chmax, save_data)
x = numpy.arange(y.__len__()).astype(numpy.float)
if calib:
x = self.calib[0] + self.calib[1]*x + self.calib[2]*math.pow(x,2)
y = numpy.array(y).astype(numpy.float)
data = numpy.array([x,y])
#data = data.transpose()
return data
def read_raw_data(self, chmin=0, chmax=4095, save_data=False):
"""Reads raw data
Keyword Args:
chmin (int): channel number, defaults to 0
chmax (int): channel number, defaults to 4095
save_data (bool): save data in the file or not, defaults to False
Returns:
list. Raw data.
"""
size = int(chmax - chmin + 1)
#read only what is asked
self.sl.flush()
asw = str(self.sl.write_readline("$SS %d,1,1,%d\r" % (chmin, size)))
self._check_answer(asw, 'read_raw_data:handshake answer reading')
#read again to get the data
raw_data = self.sl.read(size=size*4,timeout=10)
data = ' '.join([ "%02x" % ord(i) for i in raw_data]).split()
if self.debug:
print "read %d characters" % data.__len__()
#we read 4 bytes/ch (hhhhhhhh ........ ........ llllllll)
dd = [int('0x'+i+j+k+l,16) for i,j,k,l in zip(data[::4], data[1::4], data[2::4], data[3::4])]
if save_data:
fd = open(self.fname, "a+")
fd.write("#\n#S 1 mcaacq %d\n" % self.times["real_time_preset"])
if self.calib_done:
fd.write("#@CALIB %g %g %g\n@A" % (self.calib[0], self.calib[1],self.calib[2]))
fd.write(' '.join(map(str, dd)) + "\n")
return dd