Add logging & fix
- Add --verbose option - Fix calibration
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parent
d1b02301aa
commit
6eaf141f1f
1 changed files with 93 additions and 11 deletions
104
ETA.py
104
ETA.py
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@ -8,7 +8,7 @@ from scipy.signal import convolve as sp_convolve
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from scipy.signal import find_peaks
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from scipy.ndimage import rotate
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cache , filename , output , calibration = '' , None , None , None
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cache , filename , output , calibration , verbose , no_cache = '' , None , None , None , False , False
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if len( sys.argv ) < 2:
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raise Exception( 'ETA.py: type \'ETA.py -h\' for more information' )
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@ -23,6 +23,8 @@ while i < len( argv ):
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arg = '--help'
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elif arg == '-v':
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arg = '--version'
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elif arg == '-l':
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arg = '--verbose'
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elif arg == '-n':
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arg == '--no-cache'
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elif arg == '-c':
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@ -55,14 +57,17 @@ while i < len( argv ):
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\n -n --no-cache do not use cache and rewrite it\
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\n -o --output output file, default to standard output\
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\n -v --version show version number and quit\
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\n -l --verbose show more information to help debugging\
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\n\
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\nParse a naroo ETA fits' )
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exit()
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elif arg == '--version':
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print( '0.2' )
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exit()
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elif arg == '--verbose':
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verbose = True
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elif arg == '--no-cache':
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cache = '' # hack, empty string mean this dir, so not a file
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no_cache = True
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elif len( arg ) > 8 and arg[ : 8 ] == '--cache=':
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cache = arg[ 8 : ]
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elif len( arg ) > 9 and arg[ : 9 ] == '--output=':
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@ -78,21 +83,39 @@ while i < len( argv ):
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i += 1
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if filename == None:
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raise Exception( 'ETA.py: filename should be given' )
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if verbose:
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cache, filename, output, calibration, verbose
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print( f'ETA.py: launching now with parameters:\
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\n --filename: {filename}\
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\n --cache: {cache} ( default: \'\' )\
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\n --calibration: {calibration} ( default to None )\
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\n --output: {output} ( default to None )\
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\n --verbose: True ( default to False)\
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\n\
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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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if verbose:
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print( 'data loaded' )
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cache_file = pathlib.Path( cache )
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if cache_file.is_file():
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if cache_file.is_file() and not no_cache:
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if verbose:
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print( 'using cache' )
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with shelve.open( str( cache_file ) ) as cache:
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for key in [ 'rotated_data' , 'border' , 'calibrations' ]:
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for key in [ 'data' , 'border' , 'calibrations' ]:
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if key not in cache:
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raise Exception( 'ETA.py: missing data in cache_file' )
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data = cache[ 'data' ]
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border = cache[ 'border' ]
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calibrations = cache[ 'calibrations' ]
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else:
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if verbose:
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print( 'not using cache' )
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print( 'starting first zoom' )
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"""
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find fill points
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"""
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@ -182,6 +205,10 @@ else:
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},
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}
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if verbose:
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print( 'first zoom finished' )
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print( 'starting label deletion' )
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"""
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label deletion
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"""
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@ -227,6 +254,10 @@ else:
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border[ 'x' ][ 'max' ] = label_x[ 'min' ]
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else:
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raise Exception( 'for an unkown reason, label_x[ \'min\' ] > label_x[ \'max\' ]' )
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if verbose:
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print( 'label section deleted' )
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print( 'starting rotation' )
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"""
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Rotation
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@ -281,6 +312,10 @@ else:
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border[ 'y' ][ 'min' ] -= diff_y
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border[ 'y' ][ 'max' ] -= diff_y
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if verbose:
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print( 'rotation finished' )
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print( 'starting isolating calibration' )
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"""
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Calibration
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"""
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@ -351,6 +386,10 @@ else:
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},
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}
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if verbose:
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print( 'calibration lines isolated' )
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print( 'starting curving main ETA' )
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"""
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stripes curves detection
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"""
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@ -393,15 +432,25 @@ else:
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) )
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data[
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calibrations[ 'top' ][ 'y' ][ 'max' ] : calibrations[ 'down' ][ 'y' ][ 'min' ] + np.max( y_diff ),
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calibrations[ 'top' ][ 'y' ][ 'max' ] : calibrations[ 'down' ][ 'y' ][ 'min' ],
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border[ 'x' ][ 'min' ] : border[ 'x' ][ 'max' ]
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] = results
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] = results[
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: results.shape[0] - np.max( y_diff ),
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:
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]
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if verbose:
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print( 'main ETA curved' )
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if not cache_file.exists():
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if verbose:
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print( 'writing result in cache' )
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with shelve.open( str( cache_file ) ) as cache:
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cache[ 'data' ] = data
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cache[ 'border' ] = border
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cache[ 'calibrations'] = calibrations
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if verbose:
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print( 'cache saved' )
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size_x = border[ 'x' ][ 'max' ] - border[ 'x' ][ 'min' ]
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size_y = calibrations[ 'down' ][ 'y' ][ 'min' ] - calibrations[ 'top' ][ 'y' ][ 'max' ]
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@ -409,6 +458,8 @@ size_y = calibrations[ 'down' ][ 'y' ][ 'min' ] - calibrations[ 'top' ][ 'y' ][
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# Calibration
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if calibration != None:
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if verbose:
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print( 'starting calibration' )
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import wavelength_calibration as wave_calib
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peaks_calib = np.loadtxt( calibration ) # sorted list
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peaks_calib = np.sort( peaks_calib )
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@ -464,6 +515,10 @@ if calibration != None:
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diff ,
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3 ,
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)
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if verbose:
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print( 'x pixel to wavelenth calibration finished' )
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print( 'starting y pixel to x pixel calibration' )
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def diff_calc( x , list_y ):
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"""
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@ -498,6 +553,9 @@ if calibration != None:
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calibrations[ 'down' ][ 'x' ][ 'max' ] -= padding
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border[ 'x' ][ 'max' ] -= padding
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if verbose:
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print( 'y to x pixel calibrated' )
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polyval_wavelength = np.polyfit( # x = 0 begins at the start of
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peaks_up , # calibrations[ 'top' ][ 'x' ][ 'min' ]
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peaks_calib,
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@ -511,13 +569,28 @@ if calibration != None:
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1 ,
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)
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)
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if verbose:
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print( 'end of calibration' )
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else:
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if verbose:
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print( 'no calibration' )
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padding = 0
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wavelength = np.arange( size_y )
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if verbose:
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print( 'starting to flatten the ETA' )
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list_ = np.convolve(
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np.gradient(
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np.mean( data , axis = 1 ),
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np.mean(
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data[
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calibrations[ 'top' ][ 'y' ][ 'max' ] : calibrations[ 'down' ][ 'y' ][ 'min' ],
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border[ 'x' ][ 'min' ] : border[ 'x' ][ 'max' ]
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] ,
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axis = 1,
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),
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) ,
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np.ones( 50 ),
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'same' ,
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@ -529,20 +602,29 @@ fall = np.array( [
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] + [
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consecutive[0] + np.argmin(
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list_[ consecutive[0] : consecutive[-1] ]
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) for consecutive in fall
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) for consecutive in fall if len( consecutive ) > 20 # the value might change
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] ).astype( int )
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stairs = np.zeros( ( size_y , size_x ) )
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for x in range( size_x ):
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stairs[ : fall[0] , x ] = 0 # TODO: put the mean
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for i in range( len( fall ) - 1 ):
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stairs[ fall[ i ] : fall[ i + 1 ] , x ] = np.mean( data[ fall[ i ] : fall[ i + 1 ] , x ] )
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stairs[ fall[ i ] : fall[ i + 1 ] , x ] = np.mean( data[
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calibrations[ 'top' ][ 'y' ][ 'max' ] + fall[ i ] : calibrations[ 'top' ][ 'y' ][ 'max' ] + fall[ i + 1 ],
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border[ 'x' ][ 'min' ] + x
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] )
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stairs[ fall[ -1 ] : , x ] = 0
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np.imshow( stairs , aspect = 'auto' )
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np.show()
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if verbose:
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print( 'ETA flattened' )
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print( 'outputting data' )
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if output == None:
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print( stairs )
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else:
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np.savetxt( output , stairs )
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if verbose:
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print( 'output sent' )
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print( '===========================================\
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\nend of ETA.py' )
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