def save_data(self, txtfl=None):
"""
Saves all data for that run to a text file
Input textfile for use with run.py UI
"""
if txtfl == None:
txtfl = open(self.filedir + "//voltagedata.txt", 'w')
printfl("txtfl opened, saving...")
txtfl.write(str(self.dta))
txtfl.close()
else:
printfl("saving to txt...")
txtfl.write("Raw data:\n")
txtfl.write(str(self.dta) + "\n")
txtfl.write("Data saved at: %s\n" % timing.log_return())
timing.log("data saved", timing.log_return())
def plot_heights(self, trigger, bins=None, savetxt=False, showimg=False, saveimg=False, txtfl=None):
"""Plots max height of pulses in a histogram"""
if not self.listofpars:
printfl("run fit() first")
else:
def powerfunc(t, tau, A_i, offset, c):
return A_i * ((t - offset) / tau)**2 * math.e**(-(t - offset) / tau + (2 - math.log(4, math.e))) + c
listofmax = []
count = 0
for num in self.listofpars:
if not (2 * num[0] + num[2] < 0 and num[2] < 0): # Ensures that the found point is a max not a min
max1 = powerfunc(2 * num[0] + num[2], *num)
max2 = powerfunc(num[2], *num)
if max1 > max2 and max1 > trigger and max1 < 2**13:
listofmax.append(max1)
count += 1
elif max2 > trigger and max2 < 2**13:
listofmax.append(max2)
count += 1
if showimg == True or saveimg == True:
plt.hist([x * (3.3 / 2**13) * 1000 for x in listofmax], bins)
plt.xlabel("Pulse Height (mV)")
plt.ylabel("# of Pulses")
plt.title("%s Pulses, %s Bins" % (count, bins))
if savetxt == True:
if txtfl == None:
txtfl = open(self.filedir + "//pulseheights.txt", 'w')
printfl("opened txtfl")
txtfl.write(str(listofmax))
txtfl.close()
else:
printfl("saving to txt...")
txtfl.write("Max heights:\n")
txtfl.write(str(listofmax) + "\n")
txtfl.write("Heights saved at: %s\n" % timing.log_return())
if saveimg == True:
plt.savefig(self.filedir + "//heighthist.png")
if showimg == True:
plt.show()
if showimg == True or saveimg == True:
plt.close()
timing.log("histogram created", timing.log_return())
def fit(self, savepars=False, showimg=False, saveimg=False, txtfl=None):
"""
Fits all pulses to a curve and saves the resulting fit parameters if specified. Saves the plot.
"""
printfl("fitting data...")
def powerfunc(t, tau, amplitude, offset, c):
"""The function being used for the fit, identical in all the fitting methods below"""
return amplitude * ((t - offset) / tau)**2 * math.e**(-(t - offset) / tau + (2 - math.log(4, math.e))) + c
count = 0
for i in range(len(self.listofdata)):
x = np.linspace(0, len(self.listofdata[i]), len(self.listofdata[i]))
try:
pars, covariance_matrix = sciopt.curve_fit(powerfunc, x, self.listofdata[i], [1, 100, 0, 284])
self.listofpars.append(pars.tolist())
if showimg == True or saveimg == True:
x = np.linspace(0, len(self.listofdata[i]), 100)
plt.plot(x, [y * (3.3 / 2**13) * 1000 for y in powerfunc(x, *pars)])
#Sometimes curve_fit can't fit
except (RuntimeError, TypeError):
count += 1
if showimg == True or saveimg == True:
plt.xlabel("microsec")
plt.ylabel("mV")
plt.title("%s Pulses" % (len(self.listofdata) - count))
if saveimg == True:
plt.savefig(self.filedir + "//fits.png", dpi=500)
if showimg == True:
plt.show()
if saveimg == True or showimg == True:
plt.close()
if savepars == True:
if txtfl == None:
txtfl = open(self.filedir + "//fitpars.txt", 'w')
printfl("txtfl opened")
txtfl.write(str(self.listofpars))
txtfl.close()
else:
printfl("saving to txt...")
txtfl.write("Parameters:\n")
txtfl.write(str(self.listofpars) + "\n")
txtfl.write("Parameters saved at: %s\n" % timing.log_return())
timing.log("data fitted", timing.log_return())
def splice_data(self, trigger, save=False, txtfl=None):
"""
given a a trigger value, and expected rise/fall times, returns a list of pulses and saves it if specified
input textfile for use with run.py
"""
printfl("splicing data...")
i = 0
while i < len(self.dta) - 1:
if self.dta[i] >= trigger and self.dta[i + 1] >= trigger:
if i - self.rise < 0:
a = 0
else:
a = i - self.rise
if i + self.tail > len(self.dta):
b = len(self.dta)
else:
b = i + self.tail
flag = False
for j in range(len(self.dta[a:b])):
if self.dta[a:b][j] == 0:
flag = True
if a == 0:
i = j + 1
else:
i += j + self.rise + 1
if flag == False:
self.listofdata.append(self.dta[a:b])
i += self.tail
else:
i += 1
if save == True:
if txtfl == None:
txtfl = open(self.filedir + "//pulses.txt", 'w')
printfl("txtfl opened")
txtfl.write(str(self.listofdata))
txtfl.close()
else:
printfl("saving to txt...")
txtfl.write("Pulses:\n")
txtfl.write(str(self.listofdata) + "\n")
txtfl.write("Pulses saved at: %s\n" % timing.log_return())
printfl("%s pulses detected" % len(self.listofdata))
timing.log("data spliced", timing.log_return())
def source(serialportname, chunkSize, nmax):
"""returns voltage data from the serial port, looping forever"""
# Get handle to serial port
s = serial.Serial(serialportname)
print("collecting data...")
curr = 0
while curr < nmax:
data = s.read(chunkSize)
data = np.fromstring(data, dtype=np.uint16)
q.put(data)
curr = curr + 1
timing.log("data collected", timing.log_return())
def plot(self):
"""Plots all pulses together on one graph, then saves it as plot.png"""
printfl("plotting data...")
for item in self.listofdata:
plt.plot([x * (3.3 / 2**13) * 1000 for x in item])
plt.xlabel("microsec")
plt.ylabel("mV")
plt.title("%s Pulses (%s Rise, %s Tail)" % (len(self.listofdata), self.rise, self.tail))
plt.savefig(self.filedir + "//plot.png", dpi=500)
plt.show()
plt.close()
timing.log("data plotted", timing.log_return())
def analyze_secondary(voltages, rise, tail, filedir):
"""Used to perform secondary analysis on already collected data"""
printfl("initalizing object...")
pltr = Plotter(voltages, rise, tail, filedir)
timing.log("object initalized", timing.log_return())
trg = pltr.get_avg() + pltr.get_noise() * 4
printfl("Trigger value:" + str(trg * (3.3 / 2**13) * 1000))
pltr.splice_data(trg)
# Add and remove methods below as needed per run
pltr.fit()
pltr.plot_heights(trg, 100, True, True)
def get_data_from_text(filedir):
"""returns voltage data from a previously saved text file"""
printfl("txtfl open")
txtfl = open(filedir, 'r')
printfl("reading data...")
voltages = txtfl.read().split()
voltagelist = []
printfl("translating data...")
for i in range(len(voltages)):
temp = voltages[i].translate(None, '[],')
if temp == "":
pass
else:
voltagelist.append(float(temp))
timing.log("data read", timing.log_return())
return voltagelist
def get_data(serialportname, loops, chunkSize):
"""returns voltage data from the serial port"""
# Get handle to serial port
s = serial.Serial(serialportname)
printfl("port init")
voltages = []
printfl("collecting data...")
for i in range(loops):
printfl(i)
data = s.read(chunkSize * 2)
data = np.fromstring(data, dtype=np.uint16)
np.set_printoptions(threshold='nan')
voltages.append(0)
voltages += data.tolist()
timing.log("data collected", timing.log_return())
return voltages
def get_data_from_previous_run(filename):
"""function used to read in data from a previously written text file"""
printfl("txtfl open")
textfile = open(filename, 'r')
printfl("reading data...")
while textfile.readline().strip() != 'Raw Data:':
pass
voltages_str = textfile.readline().strip()
voltages = voltages_str.split()
voltagelist = []
printfl("translating data...")
for voltage in voltages:
translated = voltage.translate(None, '[],')
if translated != "" and translated != " ":
voltagelist.append(float(translated))
timing.log("data read", timing.log_return())
return voltagelist
def analyze_default(voltages, rise, tail, filedir):
"""Used to analyze new data from the Arduino"""
printfl("initalizing object...")
pltr = Plotter(voltages, rise, tail, filedir)
timing.log("object initalized", timing.log_return())
pltr.save_data()
printfl("calculating trigger...")
trg = pltr.get_avg() + pltr.get_noise() * 4
printfl("Trigger value:" + str(trg * (3.3 / 2**13) * 1000))
pltr.splice_data(trg)
# Add and remove methods below as needed per run
pltr.plot()
pltr.fit(True, True, True)
pltr.plot_heights(trg, 100, True, True)
folder_dir += "//" + str(crystal_label) + "_" + month_str + "_" + date_str + "_" + year_str + "_" + hour_str\
+ minute_str + "_" + second_str
os.makedirs(folder_dir)
txtfl = open(folder_dir + "//data.txt", 'w')
txtfl.write("crystal: " + crystal_label + "\n")
txtfl.write("loops: %s\n" % loops)
printfl("initalizing object...")
# If specified as default, replace with default values
if rise == "default":
rise = 1
if tail == "default":
tail = 30
pltr = tester.Plotter(get_data(serialportname, loops, chunkSize), rise, tail, folder_dir)
timing.log("object initalized")
txtfl.write("object initalized at: %s\n" % timing.log_return())
# If requested, save raw data to text file
if save_bool == "y":
pltr.save_data(txtfl)
# Uncomment this below if you want the raw data written to a separate text file
# You might want this because for longer loops, raw data can take up a lot of space and make it difficult to
# open the text file
"""
raw_data_txtfl = open(folder_dir + "//raw_data.txt", 'w')
pltr.save_data(raw_data_txtfl)
raw_data_txtfl.close()
"""
printfl("calculating trigger...")
avg = pltr.get_avg(downsample)