Add & Fix final format
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1 changed files with 62 additions and 23 deletions
85
spectrum.py
85
spectrum.py
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@ -7,6 +7,7 @@ import sys
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import shelve
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import pathlib
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from scipy.ndimage import rotate
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from astropy.io import fits
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cache , filename , output , calibration , intensity_calibration , verbose , no_cache = '' , None , None , None , None , False, False
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if len( sys.argv ) < 2:
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@ -107,7 +108,10 @@ if verbose:
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\n===========================================' )
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# TODO: check in advance file to check if exists or writeable
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data = utils.load( filename )
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hdul = fits.open( filename )
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data = hdul[0].data
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head = hdul[0].header
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hdul.close()
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if verbose:
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print( 'data loaded' )
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@ -570,7 +574,7 @@ if intensity != None:
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with shelve.open( str( intensity_file ) ) as storage:
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intensity_stairs = storage[ 'data' ]
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intensity_wavelengths = storage[ 'wavelength' ]
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intensity_wavelengths = storage[ 'wavelength' ] * 1e-10
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final_intensity = np.zeros( len( wavelengths ) )
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for index in range( len( wavelengths ) ):
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@ -580,35 +584,37 @@ if intensity != None:
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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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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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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][-1]
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stair_before = intensity_stairs[ index_stair , intensity_index ]
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stair_after = intensity_stairs[ index_stair - 1 , intensity_index ]
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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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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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start_step = step * ( stairs.shape[0] - index_stair - 1 )
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index_polyval = np.polyfit(
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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_before , stair_after ]
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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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stair_polyval = np.polyfit(
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[ stair_before , stair_after ],
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[ 0 , step ]
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)
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final_intensity[index] = start_step + np.polyval( # the step fraction
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stair_polyval,
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np.polyval( index_polyval , intensity_index ), # the stair "fraction"
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)
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plt.plot( final_intensity )
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plt.show()
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final_intensity[index] = true_intensity_value
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if verbose:
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print( 'intensity calibration finished' )
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@ -621,9 +627,42 @@ if output == None:
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else:
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if verbose:
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print( 'storing result in ' + output )
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output_file = pathlib.Path( output )
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with shelve.open( str( output_file ) ) as output:
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output[ 'data' ] = mean_data
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main_hdu = fits.PrimaryHDU( final_intensity )
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main_hdu.header[ 'CRVAL1' ] = wavelengths[0]
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main_hdu.header[ 'CDELT1' ] = wavelengths[1] - wavelengths[0]
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main_hdu.header[ 'CTYPE1' ] = 'Wavelength'
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main_hdu.header[ 'CUNIT1' ] = 'Angstrom'
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main_hdu.header[ 'OBJNAME' ] = head[ 'OBJECT' ]
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# missing from Naroo
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#main_hdu.header[ 'OBSERVER' ] = head[ '' ]
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#main_hdu.header[ 'DATE-OBS' ] = head| '' ]
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#main_hdu.header[ 'EXPTIME' ] = head[ '' ]
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#main_hdu.header[ 'TELESCOP' ] = head[ '' ]
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#main_hdu.header[ 'INSTRUME' ] = head[ '' ]
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#main_hdu.header[ 'RA' ] = head[ '' ]
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#main_hdu.header[ 'DEC' ] = head[ '' ]
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#main_hdu.header[ 'EQUINOX' ] = head[ '' ]
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#main_hdu.header[ 'MID-HJD' ] = head[ '' ]
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#main_hdu.header[ 'DETNAME' ] = head[ '' ]
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#main_hdu.header[ 'INSTRUME' ] = head[ '' ]
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main_hdu.header[ 'RADECSYS' ] = 'FKS'
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main_hdu.header[ 'OBS-ID' ] = head[ 'OBS_ID' ]
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# BSS keywords
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main_hdu.header[ 'BSS_VHEL' ] = 0
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main_hdu.header[ 'BSS_TELL' ] = 'None'
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main_hdu.header[ 'BSS_COM' ] = 'None'
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# Not understood
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# main_hdu.header[ 'BSS_ORD' ] = ?
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# missing from Naroo
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#main_hdu.header[ 'BSS_INST' ] = head[ '' ]
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#main_hdu.header[ 'BSS_SITE' ] = head[ '' ]
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#main_hdu.header[ 'BSS_LAT' ] = head[ '' ]
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#main_hdu.header[ 'BSS_LONG' ] = head[ '' ]
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#main_hdu.header[ 'BSS_ELEV' ] = head[ '' ]
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hdul = fits.HDUList( [ main_hdu ] )
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hdul.writeto( output , overwrite = True )
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if verbose:
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print( 'output writing finished' )
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print( '===========================================\
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