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include peak detection in scheludko

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François Boulogne 2025-05-21 14:43:20 +02:00
parent 56aac01151
commit ccd1f2c1f0
7 changed files with 100 additions and 82 deletions
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44
check.py
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@ -14,6 +14,7 @@ import matplotlib.pyplot as plt
from optifik.analysis import *
from optifik.auto import auto
from optifik import io
plt.rc('text', usetex=True)
plt.rcParams.update({
@ -25,6 +26,36 @@ plt.rcParams.update({
def play():
##### Chemin du dossier contenant le spectre #####
DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic'))
#SAVE_FOLDER = DATA_FOLDER
# FILE_NAME = '003582.xy' #FFT Exemple -> FFT 3524.51
# FILE_NAME = '000004310.xy' #OOspectro Exemple -> minmax 1338.35
# FILE_NAME = '000005253.xy'#Scheludko 4 pics Exemple -> scheludko ²
# FILE_NAME = '000006544.xy'#Scheludko 2 pics Exemple -> ombre ## Diviser prominence FFT par 2
# FILE_NAME = '000018918.xy' #Scheludko 1 pic max Exemple -> ombre ## Diviser prominence FFT par 2
FILE_NAME = '000004310.xy' #TEST#
spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME)
lambdas, intensities = io.load_spectrum(spectrum_file)
plot_spectrum(lambdas, intensities, title='Raw')
lambdas, intensities = io.load_spectrum(spectrum_file, lambda_min=450)
plot_spectrum(lambdas, intensities, title='Raw, cropped')
smoothed_intensities = smooth_intensities(intensities)
plot_spectrum(lambdas, smoothed_intensities, title='Smoothed')
prominence = 0.02
total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
min_peak_prominence=prominence,
plot=True)
def check_basic():
##### Chemin du dossier contenant le spectre #####
@ -41,7 +72,8 @@ def check_basic():
FILE_NAME = '000004310.xy' #TEST#
auto(DATA_FOLDER, FILE_NAME, plot=False)
spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME)
auto(spectrum_file, plot=False)
def check_SV1():
@ -80,8 +112,9 @@ def check_SV1():
##### Find Peak #####
total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectre_file,
min_peak_prominence=prominence)
total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
min_peak_prominence=prominence,
plot=False)
thickness_minmax = thickness_from_minmax(lambdas,
smoothed_intensities,
@ -99,5 +132,6 @@ def check_SV1():
if __name__ == '__main__':
check_basic()
check_SV1()
#check_basic()
#check_SV1()
play()