def __process_file(self):
""" operations on files """
self.raw = RawDataset(self.filename)
self.step = self.raw.step
self.points = self.raw.points
self.scr = None
# if script is available, get limits according excitation length
if self.raw.scriptable:
self.scr = Script(self.filename)
duration = self.scr.get_excit_duration()
self.start = round(duration / self.step)
self.end = self.points
# if script is not available, fix arbitrary limits
else:
self.start = 0
self.end = self.points
def __process_file(self):
""" operations on files """
self.raw = RawDataset(self.filename)
self.step = self.raw.step
self.points = self.raw.points
self.scr = None
# if script is available, get limits according excitation length
if self.raw.scriptable:
self.scr = Script(self.filename)
duration = self.scr.get_excit_duration()
self.start = round(duration / self.step)
self.end = round(self.points / 2)
# if script is not available, fix arbitrary limits
else:
self.start = 0
self.end = round(self.points / 2)
def get_detect(self):
return self.detectBuffer, self.detection
if __name__ == '__main__':
from pkg.dataset import RawDataset
# filename = "G:\\DATA_PIRENEA_OLD\\DATA_2014\\data140730\\30_07_2014_001.B00"
# NO SCRIPT !!
filename = "G:\\PIRENEA_manips\\2006\\data_2006_06_07\\2006_06_07_002.A00"
filename = "G:\\PIRENEA_manips\\2014\\data_2014_05_12\\2014_05_12_001.B00"
filename = "G:\\PIRENEA_manips\\2014\\data_2014_07_30\\2014_07_30_001.A00"
# filename = "D:\\PIRENEA_manips\\data140515\\15_05_2014_001.A00"
# filename = "G:\\DATA_PIRENEA_OLD\\DATA_2014\\data140515\\15_05_2014_001.A00"
d = RawDataset(filename)
data, step = d.get_science()
print("Number of points: ", len(data))
print("Step time: ", step)
s = Script(filename)
excitBuffer, excitation = s.get_excit()
ejectBuffer, ejection = s.get_eject()
detectBuffer, detection = s.get_detect()
print("ejection", ejection)
print("detection", detection)
for eject in ejectBuffer:
text = ""
for i, element in enumerate(eject):
if i > 0:
text = text + element + " "
class Pipeline(object):
"""
classdocs
"""
def __init__(self, filename=""):
"""
Constructor
"""
self.filename = filename
self.__process_file()
def __process_file(self):
""" operations on files """
self.raw = RawDataset(self.filename)
self.step = self.raw.step
self.points = self.raw.points
self.scr = None
# if script is available, get limits according excitation length
if self.raw.scriptable:
self.scr = Script(self.filename)
duration = self.scr.get_excit_duration()
self.start = round(duration / self.step)
self.end = self.points
# if script is not available, fix arbitrary limits
else:
self.start = 0
self.end = self.points
def process_signal(self,
start=0,
end=0,
hann=False,
half=False,
zero=False,
zero_twice=False):
self.signal = self.raw.truncate(start, end)
if hann:
self.signal = self.raw.hann(self.signal, half=False)
if half:
self.signal = self.raw.hann(self.signal, half=True)
if zero:
dummy = np.zeros(self.points)
if (end > self.points):
end = self.points
dummy[0:(end - start)] = self.signal
self.signal = dummy
if zero_twice:
dummy = np.zeros(self.points * 2)
if (end > self.points):
end = self.points
dummy[0:(end - start)] = self.signal
self.signal = dummy
def process_spectrum(self,
factor=1000.0,
ref_mass=0.0,
cyclo_freq=0.0,
mag_freq=0.0):
# t = time.time()
fs = FrequencySpectrum(self.signal, self.step)
# t1 = time.time() - t
self.spectrum = fs.spectrum * factor
self.freq = fs.freq # in Hz
ms = MassSpectrum(self.freq, ref_mass, cyclo_freq, mag_freq)
self.mass = ms.mass
# def get_excit_duration(self):
# buffer, excitation = self.scr.get_excit()
# if excitation:
# return buffer[0][3]
# else:
# return 0.0
def mass_recalibrate(self, ref_mass=0.0, accuracy=0.1):
# Auto calib
self.ref_mass = ref_mass
self.accuracy = accuracy
if ref_mass > 0.0:
self.ms.basic_recalibrate(self.ref_mass, self.accuracy)
def process_peaks(self, mph=0.0, mpd=0, startx=0.0, endx=0.0):
if mph > 0:
self.mph = mph
if mpd > 0:
self.mpd = mpd
x = self.mass
y = self.spectrum
p = Peaks()
ref = startx + (abs(endx - startx) / 2)
delta = 1.0
mph, mpd, mask = p.prepare_detect(ref, delta, x, y, startx, endx)
# Detect peak on rising edge
edge = 'rising'
# Detect peak greater than threshold
threshold = 0.0
# Don't use default plot
ind = p.detect_peaks(y[mask], self.mph, self.mpd, threshold, edge)
# print("mass =", x[mask][ind])
# print("inten=", y[mask][ind])
self.mph = mph
self.mpd = mpd
self.mask = mask
self.ind = ind
# step = 0.5 524288
filename = "G:\\PIRENEA_manips\\2013\\data_2013_03_22\\2013_03_22_003.A00"
# step = 0.1 262144
filename = "G:\\PIRENEA_manips\\2004\\data_2004_01_06\\2004_01_06_001.A01"
# step = 0.2 524288
filename = "G:\\PIRENEA_manips\\2014\\data_2014_07_30\\2014_07_30_001.A00"
# step = 0.5 524288
filename = "G:\\PIRENEA_manips\\2014\\data_2014_06_26\\2014_06_26_012.A00"
# step = 0.2 524288
filename = "G:\\PIRENEA_manips\\2014\\data_2014_05_12\\2014_05_12_005.E00"
# step = 0.2 524288
filename = "G:\\PIRENEA_manips\\2006\\data_2006_07_26\\2006_07_26_001.A00"
# step = 0.5 524288
filename = "G:\\PIRENEA_manips\\2014\\data_2014_06_26\\2014_06_26_013.A00"
data = RawDataset(filename)
data.hann() # half window
points = len(data.signal)
start = data.start
end = round(points / 2)
data.truncate(start, end)
# data.truncate(data.start*2, round(len(data.signal)/2))
# excit = 1.2 ms / 0.5 micros ==> signal starts after point 2400
signal = data.signal
print("len signal =", len(signal))
# Real FFT on complete signal
step = data.step
print("step=", step)
class Pipeline(object):
"""
classdocs
"""
def __init__(self, filename=""):
"""
Constructor
"""
self.filename = filename
self.__process_file()
def __process_file(self):
""" operations on files """
self.raw = RawDataset(self.filename)
self.step = self.raw.step
self.points = self.raw.points
self.scr = None
# if script is available, get limits according excitation length
if self.raw.scriptable:
self.scr = Script(self.filename)
duration = self.scr.get_excit_duration()
self.start = round(duration / self.step)
self.end = round(self.points / 2)
# if script is not available, fix arbitrary limits
else:
self.start = 0
self.end = round(self.points / 2)
def process_signal(self, start=0, end=0, hann=False, half=False, zero=False, zero_twice=False):
self.signal = self.raw.truncate(start, end)
if hann:
self.signal = self.raw.hann(self.signal, half=False)
if half:
self.signal = self.raw.hann(self.signal, half=True)
if zero:
dummy = np.zeros(self.points)
dummy[0:(end - start)] = self.signal
self.signal = dummy
if zero_twice:
dummy = np.zeros(self.points * 2)
dummy[0:(end - start)] = self.signal
self.signal = dummy
def process_spectrum(self, factor=1000.0, ref_mass=0.0, cyclo_freq=0.0, mag_freq=0.0):
# t = time.time()
fs = FrequencySpectrum(self.signal, self.step)
# t1 = time.time() - t
self.spectrum = fs.spectrum * factor
self.freq = fs.freq # in Hz
ms = MassSpectrum(self.freq, ref_mass, cyclo_freq, mag_freq)
self.mass = ms.mass
# def get_excit_duration(self):
# buffer, excitation = self.scr.get_excit()
# if excitation:
# return buffer[0][3]
# else:
# return 0.0
def mass_recalibrate(self, ref_mass=0.0, accuracy=0.1):
# Auto calib
self.ref_mass = ref_mass
self.accuracy = accuracy
if ref_mass > 0.0:
self.ms.basic_recalibrate(self.ref_mass, self.accuracy)
def process_peaks(self, mph=0.0, mpd=0, startx=0.0, endx=0.0):
if mph > 0:
self.mph = mph
if mpd > 0:
self.mpd = mpd
x = self.mass
y = self.spectrum
p = Peaks()
ref = startx + (abs(endx - startx) / 2)
delta = 1.0
mph, mpd, mask = p.prepare_detect(ref, delta, x, y, startx, endx)
# Detect peak on rising edge
edge = 'rising'
# Detect peak greater than threshold
threshold = 0.0
# Don't use default plot
ind = p.detect_peaks(y[mask], self.mph, self.mpd, threshold, edge)
# print("mass =", x[mask][ind])
# print("inten=", y[mask][ind])
self.mph = mph
self.mpd = mpd
self.mask = mask
self.ind = ind
if __name__ == '__main__':
# from pkg1.dataset import AlyxanRawDataset
from pkg.dataset import RawDataset
import matplotlib.pyplot as plt
""" Prepare Subplots """
fig, (ax1, ax2, ax3) = plt.subplots(3, 1)
# Read PIRENEA signal
filename = "G:\\PIRENEA_manips\\2014\\data_2014_07_30\\2014_07_30_001.A00"
# filename = "D:\\PIRENEA_manips\\data140515\\15_05_2014_001.A00"
# filename = "G:\\DATA_PIRENEA_OLD\\DATA_2014\\data140515\\15_05_2014_001.A00"
filename = "G:\\PIRENEA_manips\\2014\\data_2014_06_26\\2014_06_26_010.A00"
raw = RawDataset(filename)
points = len(raw.signal)
start = raw.start
end = raw.end
step = raw.step
raw.hann()
raw.truncate(start, end)
y1 = raw.signal[start:end]
limit = end - start
y2 = raw.truncated
# y3 = raw.signal[start:]
# y3[end - start:] = 0.0
if __name__ == '__main__':
from pkg.dataset import RawDataset
# filename = "G:\\DATA_PIRENEA_OLD\\DATA_2014\\data140730\\30_07_2014_001.B00"
# NO SCRIPT !!
filename = "G:\\PIRENEA_manips\\2006\\data_2006_06_07\\2006_06_07_002.A00"
filename = "G:\\PIRENEA_manips\\2014\\data_2014_05_12\\2014_05_12_001.B00"
filename = "D:\\PIRENEA\\PIRENEA_manips\\2014\\data_2014_07_30\\2014_07_30_001.A00"
filename = "D:\\PIRENEA\\DATA\\2018\\data_2018_07_20\\P1_2018_07_20_025.A00"
# filename = "D:\\PIRENEA_manips\\data140515\\15_05_2014_001.A00"
# filename = "G:\\DATA_PIRENEA_OLD\\DATA_2014\\data140515\\15_05_2014_001.A00"
filename = "D:\\PIRENEA\\DATA\\2018\\data_2018_07_20\\P1_2018_07_20_025.A00"
d = RawDataset(filename)
s = Script(filename)
excitBuffer, excitation = s.get_excit()
ejectBuffer, ejection = s.get_eject()
detectBuffer, detection = s.get_detect()
print("ejection", ejection)
print("detection", detection)
for eject in ejectBuffer:
text = ""
for i, element in enumerate(eject):
if i > 0:
text = text + element + " "
print("text = ", text)
print("format", "{:.1f}".format(float(eject[3])))
else:
