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Assesing diad skewness

  • This notebook uses the protocol of DeVitre et al. (in review) to assess diad skewness. This can be useful to identify liquid CO\(_2\) in room temperature diad acqusitions

[1]:

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import DiadFit as pf
pf.__version__

[1]:

'1.0.0'

Set path, and filetype

[2]:

filetype='headless_txt'
import os
spectra_path=os.getcwd()
file_ext='.txt'
exclude_str=['Ne']
Diad_Files=pf.get_files(path=spectra_path,
file_ext=file_ext, exclude_str=exclude_str)

Diad_Files

[2]:

['G170_004_1_4_0.5MW_1800G_45S_5ACC (CRR) (1).txt',
 'G170_004_1_4_0.5MW_1800G_45S_5ACC (CRR).txt',
 'G170_004_2_4_10MW_1800G_5S_1ACC (CRR).txt',
 'G170_004_2_4_10MW_1800G_5S_5ACC (CRR).txt',
 'G170_004_2_4_5MW_1800G_10S_1ACC (CRR).txt',
 'G170_004_2_4_5MW_1800G_10S_3ACC (CRR).txt']

Tweak fit for 1 file before you loop

[3]:

filename=Diad_Files[0]
# Cut off intensity from peak to assess skewness
int_cut_off=0.3
# Calculates absolute skewness, e.g., biggest possible value
skewness='abs'

[4]:

diad1_config=pf.diad1_fit_config(upper_bck_diad1=(1330, 1350))
print(diad1_config)

diad1_fit_config(model_name='PseudoVoigtModel', fit_peaks=2, N_poly_bck_diad1=1, lower_bck_diad1=(1180, 1220), upper_bck_diad1=(1330, 1350), fit_gauss=False, gauss_amp=1000, diad_sigma=0.2, diad_sigma_min_allowance=0.2, diad_sigma_max_allowance=5, diad_prom=100, HB_prom=20, x_range_baseline=75, y_range_baseline=100, dpi=200, x_range_residual=20, return_other_params=False)

Try these parameters for Diad1

[5]:

prominence=10 # prominence for Scipy find peaks
AR_test_diad1=pf.assess_diad1_skewness(config1=diad1_config,
int_cut_off=int_cut_off,
skewness=skewness, path=spectra_path, filename=filename,
filetype=filetype, prominence=prominence)
AR_test_diad1


c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))

[5]:
filename Skewness_diad1 LHS_tie_diad1 RHS_tie_diad1
0 G170_004_1_4_0.5MW_1800G_45S_5ACC (CRR) (1).txt 2.697283 1281.135853 1285.983107 
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_8_3.png

Try these parameters for diad2

[6]:

diad2_config=pf.diad2_fit_config(lower_bck_diad2=(1330, 1360))
print(diad2_config)

diad2_fit_config(model_name='PseudoVoigtModel', fit_peaks=3, N_poly_bck_diad2=1, lower_bck_diad2=(1330, 1360), upper_bck_diad2=(1440, 1470), fit_gauss=False, gauss_amp=1000, diad_sigma=0.2, diad_sigma_min_allowance=0.2, diad_sigma_max_allowance=5, diad_prom=100, HB_prom=20, C13_prom=10, x_range_baseline=75, y_range_baseline=100, plot_figure=True, dpi=200, x_range_residual=20, return_other_params=False)

[7]:

AR_test_diad2=pf.assess_diad2_skewness(config1=diad2_config,
int_cut_off=int_cut_off, prominence=prominence,
skewness=skewness, path=spectra_path, filename=filename,
filetype=filetype)
AR_test_diad2

[7]:
Skewness_diad2 LHS_tie_diad2 RHS_tie_diad2
0 2.037267 1385.54434 1388.961252
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_11_1.png

Now lets loop through all the files

[8]:

df_combo=pf.loop_diad_skewness(Diad_files=Diad_Files,
path=spectra_path, skewness=skewness, prominence=prominence,
filetype=filetype,config_diad1=diad1_config, config_diad2=diad2_config,
int_cut_off=int_cut_off)
df_combo

working on file #0

c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))

working on file #1

c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))

working on file #2

c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))

working on file #3

c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))

working on file #4

c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))

working on file #5

c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))

[8]:
filename Skewness_diad1 Skewness_diad2 LHS_tie_diad1 RHS_tie_diad1 LHS_tie_diad2 RHS_tie_diad2
0 G170_004_1_4_0.5MW_1800G_45S_5ACC (CRR) (1).txt 2.697283 2.037267 1281.135853 1285.983107 1385.544340 1388.961252
0 G170_004_1_4_0.5MW_1800G_45S_5ACC (CRR).txt 2.681303 1.827020 1281.471667 1285.879649 1385.843407 1388.972432
0 G170_004_2_4_10MW_1800G_5S_1ACC (CRR).txt 1.075834 1.167500 1282.302722 1285.784672 1386.324151 1388.747433
0 G170_004_2_4_10MW_1800G_5S_5ACC (CRR).txt 1.036585 1.041332 1281.980476 1285.379321 1386.062816 1388.547589
0 G170_004_2_4_5MW_1800G_10S_1ACC (CRR).txt 1.246673 1.405337 1281.994044 1285.716831 1386.076792 1388.722277
0 G170_004_2_4_5MW_1800G_10S_3ACC (CRR).txt 2.353796 1.616774 1281.763384 1285.284343 1385.944028 1388.778178 
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:1463: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:754: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  posy = float(self.convert_yunits(self._y))
c:\Users\penny\anaconda3\Lib\site-packages\matplotlib\text.py:895: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
  y = float(self.convert_yunits(self._y))
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_14.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_15.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_16.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_17.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_18.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_19.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_20.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_21.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_22.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_23.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_24.png
../../../_images/Examples_Fitting_Fermi_Diads_Example1f_Diad_Peak_Assymetry_Asessing_Diad_Skewness_13_25.png 
[9]:

## This is the outputted data
df_combo

[9]:
filename Skewness_diad1 Skewness_diad2 LHS_tie_diad1 RHS_tie_diad1 LHS_tie_diad2 RHS_tie_diad2
0 G170_004_1_4_0.5MW_1800G_45S_5ACC (CRR) (1).txt 2.697283 2.037267 1281.135853 1285.983107 1385.544340 1388.961252
0 G170_004_1_4_0.5MW_1800G_45S_5ACC (CRR).txt 2.681303 1.827020 1281.471667 1285.879649 1385.843407 1388.972432
0 G170_004_2_4_10MW_1800G_5S_1ACC (CRR).txt 1.075834 1.167500 1282.302722 1285.784672 1386.324151 1388.747433
0 G170_004_2_4_10MW_1800G_5S_5ACC (CRR).txt 1.036585 1.041332 1281.980476 1285.379321 1386.062816 1388.547589
0 G170_004_2_4_5MW_1800G_10S_1ACC (CRR).txt 1.246673 1.405337 1281.994044 1285.716831 1386.076792 1388.722277
0 G170_004_2_4_5MW_1800G_10S_3ACC (CRR).txt 2.353796 1.616774 1281.763384 1285.284343 1385.944028 1388.778178 
[ ]: