linarphy/naroo_reader
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Add peak deletion part

Browse source 
Try to start from the same point for each spectrum by comparing 'ground' part without peaks
This commit is contained in:
linarphy 2023-05-23 11:28:54 +02:00
parent 902259cc2e
commit 3d90b03a6d
No known key found for this signature in database
GPG key ID: 3D4AAAC3AD16E79C
1 changed files with 60 additions and 11 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

71
wavelength_calibration.py
View file

@ -1,8 +1,11 @@
import numpy as np
import scipy.signal as sig
import matplotlib.backends.backend_qtagg as qt
import matplotlib.figure as fig
import utils
rect = [0.125,0.11,0.775,0.77]
calib_top = np.load( 'asset/calib_top.npy' )
calib_down = np.load( 'asset/calib_down.npy' )
reference = np.load( 'asset/reference.npy' )
@ -15,17 +18,6 @@ peaks_reference = utils.retrieve_peaks( reference[1] , window_size = 1 , max_win
polyval = np.polyfit( peaks_calib_top , peaks_reference[ 2 : ] , 1 )
manager = qt.FigureManager(
qt.FigureCanvas(
fig.Figure(
),
),
1,
)
manager.canvas.figure.add_axes( ( 0.05 , 0.15 , 0.9 , 0.7 ) ).plot( peaks_calib_top , np.array( peaks_reference[ 2 : ] ) - np.polyval( polyval , peaks_calib_top ) )
manager.show()
manager.start_main_loop()
peaks_values = [ reference[ 1 , i ] for i in np.array( peaks_reference ).astype( int ) ]
sorting = np.argsort( peaks_values )[ :: -1 ]
wavelength = [ reference[ 0 , i ] for i in np.array( [ peaks_reference[ j ] for j in sorting ] ).astype( int ) ]
@ -34,6 +26,7 @@ polyval_wavelength = np.polyfit( peaks_reference , np.sort( wavelength ) , 1 )
wavelength = np.polyval( polyval_wavelength , np.polyval( polyval , np.arange( 0 , len( mean_calib_top ) , 1 ) ) )
"""
manager = qt.FigureManager(
qt.FigureCanvas(
fig.Figure(
@ -57,3 +50,59 @@ manager.canvas.figure.axes[1].set_title( 'reference' )
manager.show()
manager.start_main_loop()
"""
for peak in np.array( peaks_calib_top ).astype( int ):
first = peak
peak , old = first - 2 , first - 1
while mean_calib_top[ peak ] <= mean_calib_top[ old ]:
old = peak
peak -= 1
mean_calib_top[ peak : first ] = mean_calib_top[ peak ] * np.ones( first - peak )
peak , old = first + 2 , first + 1
while mean_calib_top[ peak ] <= mean_calib_top[ old ]:
old = peak
peak += 1
mean_calib_top[ first : peak ] = mean_calib_top[ peak ] * np.ones( peak - first )
manager = qt.FigureManager(
qt.FigureCanvas(
fig.Figure(
figsize = ( 10 , 5 )
),
),
0,
)
manager.canvas.figure.gca().plot(
mean_calib_top
)
manager.canvas.figure.gca().plot(
sig.medfilt( mean_calib_top , 71 )
)
manager.show()
manager.start_main_loop()
manager = qt.FigureManager(
qt.FigureCanvas(
fig.Figure(),
),
1,
)
signal_calib = sig.convolve(
sig.medfilt( mean_calib_top , 71 ),
np.ones( 50 ),
'same'
)
manager.canvas.figure.gca().plot(
signal
)
manager.canvas.figure.gca().vlines(
[
np.argmin( signal[ 25 : -25 ] )
] ,
np.min( signal[ 25 : -25 ] ),
np.max( signal[ 25 : -25 ] ),
color = 'red' ,
)
manager.show()
manager.start_main_loop()