Update & fix intensity calibration
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78c02df9af
commit
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1 changed files with 89 additions and 22 deletions
109
spectrum.py
109
spectrum.py
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@ -566,7 +566,7 @@ if verbose:
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mean_data = np.mean( data[
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spectrum[ 'y' ][ 'min' ] : spectrum[ 'y' ][ 'max' ],
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spectrum[ 'x' ][ 'min' ] : spectrum[ 'x' ][ 'max' ]
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] , axis = 0 ) - mean_bias
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] , axis = 0 )
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if intensity != None:
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if verbose:
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@ -578,43 +578,110 @@ if intensity != None:
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intensity_stairs = storage[ 'data' ]
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intensity_wavelengths = storage[ 'wavelength' ] * 1e-10
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wavelengths = wavelengths[ # remove wavelengths outside range
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np.where(
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np.logical_and(
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wavelengths > np.min( intensity_wavelengths ),
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wavelengths < np.max( intensity_wavelengths ),
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),
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)
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]
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intensity_wavelengths = intensity_wavelengths[ # remove intensity_wavelengths outside range
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np.where(
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np.logical_and(
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intensity_wavelengths > np.min( wavelengths ),
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intensity_wavelengths < np.max( wavelengths ),
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),
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)
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]
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if len( wavelengths ) == 0:
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raise Exception( 'spectrum.py: spectrum and ETA does not share any common wavelengths' )
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step = 0.2 # depends of ETA source #TODO
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final_intensity = np.zeros( len( wavelengths ) )
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for index in range( len( wavelengths ) ):
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intensity_value = mean_data[ index ]
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intensity_wavelength = wavelengths[ index ]
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intensity_index = utils.near_value(
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intensity_index = utils.near_value( # list of index corresponding to index for intensity_stairs
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intensity_wavelengths,
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intensity_wavelength ,
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)
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if len( intensity_index ) != 1:
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break
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if len( intensity_index ) != 1: # too much or no intensity found near value
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final_intensity[ index ] = - 1
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continue
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intensity_index = intensity_index[0]
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if abs( intensity_wavelength - intensity_wavelengths[ intensity_index ] ) > 5e-10:
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break
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index_stair = np.where(
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indexes_stair_lower = np.where( # stairs lower than intensity value
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intensity_stairs[
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: ,
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intensity_index,
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0 ,
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0
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] < intensity_value
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)
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if len( index_stair[0] ) == 0:
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index_stair = intensity_stairs.shape[0] - 1
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else:
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index_stair = index_stair[0][0]
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)[0]
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stair_before = intensity_stairs[ index_stair , intensity_index , 0 ]
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stair_after = intensity_stairs[ index_stair - 1 , intensity_index , 0 ]
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step = 0.2
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if len( indexes_stair_lower ) == 0: # intensity value outside ETA (below)
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final_intensity[ index ] = 0
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continue
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if len( indexes_stair_lower ) != intensity_stairs.shape[0] - indexes_stair_lower[0]: # stairs intensity does not decrease with index as it should
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# could indicate an artefact in ETA
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indexes_stair_lower = [
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int( np.mean(
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[
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intensity_stairs.shape[0] -
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indexes_stair_lower[0] ,
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len( indexes_stair_lower )
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]
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) )
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]
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indexes_stair_higher = np.where( # stairs higher than intensity value
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intensity_stairs[
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: ,
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intensity_index,
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0
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] > intensity_value
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)[0]
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if len( indexes_stair_higher ) == 0: # intensity value outside ETA (upper)
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final_intensity[ index ] = intensity_stairs.shape[0] * step
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continue
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if len( indexes_stair_higher ) - 1 != indexes_stair_higher[-1]: # stairs intensity does not decrease with index as it should
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indexes_stair_higher = [
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int( np.mean(
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[
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indexes_stair_higher[ - 1 ] ,
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len( indexes_stair_higher ) - 1
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]
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) )
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]
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indexes_stair_higher = [
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indexes_stair_lower[ 0 ] - 1,
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]
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index_stair = {
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'higher': indexes_stair_higher[-1],
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'lower' : indexes_stair_lower[0] ,
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}
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if index_stair[ 'lower' ] - index_stair[ 'higher' ] != 1: # ETA curve should decrease
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raise Exception( 'spectrum.py: given intensity stairs (from ETA) are missformed' )
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stair_intensity = {
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'higher': intensity_stairs[ index_stair[ 'higher' ] , intensity_index , 0 ],
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'lower' : intensity_stairs[ index_stair[ 'lower' ] , intensity_index , 0 ],
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}
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index_polyval = np.polyfit( # fraction stair index from intensity value
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[ stair_before , stair_after ],
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[ index_stair , index_stair - 1 ],
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[ stair_intensity[ 'higher' ] , stair_intensity[ 'lower' ] ],
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[ index_stair[ 'higher' ] , index_stair[ 'lower' ] ],
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1 ,
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)
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true_intensity_value = ( intensity_stairs.shape[0] - np.polyval( index_polyval , intensity_value ) - 1 ) * step
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if true_intensity_value < 0:
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true_intensity_value = 0
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true_intensity_value = ( intensity_stairs.shape[0] - np.polyval( index_polyval , intensity_value ) ) * step
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final_intensity[index] = true_intensity_value
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