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#! /usr/bin/env python3
#####################################################################
# This example shows how to handle series data such as z-depth scan #
#####################################################################
# TODO: automatic determination of scan type
import numpy as np
from renishawWiRE import WDFReader
from _path import curdir, imgdir
try:
import matplotlib.pyplot as plt
plot = True
except ImportError:
plot = False
def peak_in_range(spectra, wn, range, method="max", **params):
"""Find the max intensity of peak within range
method can be max, min, or mean
"""
cond = np.where((wn >= range[0]) & (wn <= range[1]))[0]
spectra_cut = spectra[:, cond]
return getattr(np, method)(spectra_cut, axis=1, **params)
def main():
filename = curdir / "spectra_files" / "depth.wdf"
reader = WDFReader(filename)
# A depth scan
assert reader.measurement_type == 2
# For depth scan, xdata is still wavenumber
wn = reader.xdata
spectra = reader.spectra
x = reader.xpos
y = reader.ypos
z = reader.zpos
# print(x, y, z)
# In this example only z is non-zero
assert all([np.all(x == 0), np.all(y == 0), ~np.all(z == 0)])
assert reader.count == z.shape[0]
print(spectra, spectra.shape)
print(reader.count)
# Distance
wn = reader.xdata
spectra = reader.spectra
# Filter blank spectra
cond = np.where(spectra.mean(axis=1) > 0)[0]
z = z[cond]
spectra = spectra[cond, :]
# Data processing
spectra = spectra - spectra.min(axis=1, keepdims=True)
# Simply get accumulated counts between 1560 and 1620 cm^-1
peak_1 = peak_in_range(spectra, wn, range=[1560, 1620])
peak_2 = peak_in_range(spectra, wn, range=[2650, 2750])
ratio = peak_2 / peak_1
if plot is True:
# Level the spectra with baseline intensity
plt.figure(figsize=(6, 4))
plt.plot(z, peak_1 / peak_1.max(), "-o", label="G Peak")
# plt.plot(z, peak_2 / peak_2.max(), label="2D")
# plt.plot(z, ratio, label="2D/G")
plt.xlabel("Z [{0}]".format(str(reader.zpos_unit)))
plt.legend(loc=0)
plt.ylabel("Normed Intensity")
plt.title("Results from depth.wdf")
plt.show(block=False)
plt.pause(3)
plt.savefig(imgdir / "depth.png", dpi=100)
plt.close()
else:
print("Wavenumber is like:", wn)
print("Z-Distance is like:", z)
print("2D/G ratio is like: \n", ratio)
return
if __name__ == "__main__":
main()
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