Add logging & fix

- Add --verbose option
- Fix calibration

ETA.py

@@ -8,7 +8,7 @@ from scipy.signal import convolve as sp_convolve
 from scipy.signal import find_peaks
 from scipy.ndimage import rotate
 
-cache , filename , output , calibration = '' , None , None , None
+cache , filename , output , calibration , verbose , no_cache = '' , None , None , None , False , False
 if len( sys.argv ) < 2:
     raise Exception( 'ETA.py: type \'ETA.py -h\' for more information' )
 
@@ -23,6 +23,8 @@ while i < len( argv ):
                 arg = '--help'
             elif arg == '-v':
                 arg = '--version'
+            elif arg == '-l':
+                arg = '--verbose'
             elif arg == '-n':
                 arg == '--no-cache'
             elif arg == '-c':
@@ -55,14 +57,17 @@ while i < len( argv ):
                       \n    -n --no-cache    do not use cache and rewrite it\
                       \n    -o --output      output file, default to standard output\
                       \n    -v --version     show version number and quit\
+                      \n    -l --verbose     show more information to help debugging\
                       \n\
                       \nParse a naroo ETA fits' )
                 exit()
             elif arg == '--version':
                 print( '0.2' )
                 exit()
+            elif arg == '--verbose':
+                verbose = True
             elif arg == '--no-cache':
-                cache = '' # hack, empty string mean this dir, so not a file
+                no_cache = True
             elif len( arg ) > 8 and arg[ : 8 ] == '--cache=':
                 cache = arg[ 8 : ]
             elif len( arg ) > 9 and arg[ : 9 ] == '--output=':
@@ -78,21 +83,39 @@ while i < len( argv ):
     i += 1
 if filename == None:
     raise Exception( 'ETA.py: filename should be given' )
+
+if verbose:
+    cache, filename, output, calibration, verbose
+    print( f'ETA.py: launching now with parameters:\
+           \n    --filename:    {filename}\
+           \n    --cache:       {cache} ( default: \'\' )\
+           \n    --calibration: {calibration} ( default to None )\
+           \n    --output:      {output} ( default to None )\
+           \n    --verbose:     True ( default to False)\
+           \n\
+           \n===========================================' )
 # TODO: check in advance file to check if exists or writeable
 
 data = utils.load( filename )
+if verbose:
+    print( 'data loaded' )
 
 cache_file = pathlib.Path( cache )
 
-if cache_file.is_file():
+if cache_file.is_file() and not no_cache:
+    if verbose:
+        print( 'using cache' )
     with shelve.open( str( cache_file ) ) as cache:
-        for key in [ 'rotated_data' , 'border' , 'calibrations' ]:
+        for key in [ 'data' , 'border' , 'calibrations' ]:
             if key not in cache:
                 raise Exception( 'ETA.py: missing data in cache_file' )
         data         = cache[     'data'     ]
         border       = cache[    'border'    ]
         calibrations = cache[ 'calibrations' ]
 else:
+    if verbose:
+        print( 'not using cache' )
+        print( 'starting first zoom' )
     """
     find fill points
     """
@@ -182,6 +205,10 @@ else:
         },
     }
 
+    if verbose:
+        print( 'first zoom finished' )
+        print( 'starting label deletion' )
+
     """
     label deletion
     """
@@ -228,6 +255,10 @@ else:
     else:
         raise Exception( 'for an unkown reason, label_x[ \'min\' ] > label_x[ \'max\' ]' )
     
+    if verbose:
+        print( 'label section deleted' )
+        print( 'starting rotation' )
+
     """
     Rotation
     """
@@ -281,6 +312,10 @@ else:
     border[ 'y' ][ 'min' ] -= diff_y
     border[ 'y' ][ 'max' ] -= diff_y
 
+    if verbose:
+        print( 'rotation finished' )
+        print( 'starting isolating calibration' )
+
     """
     Calibration
     """
@@ -351,6 +386,10 @@ else:
         },
     }
 
+    if verbose:
+        print( 'calibration lines isolated' )
+        print( 'starting curving main ETA' )
+
     """
     stripes curves detection
     """
@@ -393,15 +432,25 @@ else:
         ) )
 
     data[
-        calibrations[ 'top' ][ 'y' ][ 'max' ] : calibrations[ 'down' ][ 'y' ][ 'min' ] + np.max( y_diff ),
+        calibrations[ 'top' ][ 'y' ][ 'max' ] : calibrations[ 'down' ][ 'y' ][ 'min' ],
         border[ 'x' ][ 'min' ] : border[ 'x' ][ 'max' ]
-    ] = results
+    ] = results[
+        : results.shape[0] - np.max( y_diff ),
+        :
+    ]
+
+    if verbose:
+        print( 'main ETA curved' )
 
     if not cache_file.exists():
+        if verbose:
+            print( 'writing result in cache' )
         with shelve.open( str( cache_file ) ) as cache:
             cache[ 'data'   ]      = data
             cache[ 'border' ]      = border
             cache[ 'calibrations'] = calibrations
+        if verbose:
+            print( 'cache saved' )
 
 size_x = border[ 'x' ][ 'max' ]                 - border[ 'x' ][ 'min' ]
 size_y = calibrations[ 'down' ][ 'y' ][ 'min' ] - calibrations[ 'top' ][ 'y' ][ 'max' ]
@@ -409,6 +458,8 @@ size_y = calibrations[ 'down' ][ 'y' ][ 'min' ] - calibrations[ 'top' ][ 'y' ][
 # Calibration
 
 if calibration != None:
+    if verbose:
+        print( 'starting calibration' )
     import wavelength_calibration as wave_calib
     peaks_calib = np.loadtxt( calibration ) # sorted list
     peaks_calib = np.sort( peaks_calib )
@@ -465,6 +516,10 @@ if calibration != None:
         3       ,
     )
     
+    if verbose:
+        print( 'x pixel to wavelenth calibration finished' )
+        print( 'starting y pixel to x pixel calibration'   )
+
     def diff_calc( x , list_y ):
         """
         give "good" x list for a given x and y
@@ -498,6 +553,9 @@ if calibration != None:
     calibrations[ 'down' ][ 'x' ][ 'max' ] -= padding
     border[ 'x' ][ 'max' ]                 -= padding
 
+    if verbose:
+        print( 'y to x pixel calibrated' )
+
     polyval_wavelength = np.polyfit( # x = 0 begins at the start of
         peaks_up   ,                 # calibrations[ 'top' ][ 'x' ][ 'min' ]
         peaks_calib,
@@ -511,13 +569,28 @@ if calibration != None:
             1             ,
         )
     )
+
+    if verbose:
+        print( 'end of calibration' )
+
 else:
+    if verbose:
+        print( 'no calibration' )
     padding    = 0
     wavelength = np.arange( size_y )
 
+if verbose:
+    print( 'starting to flatten the ETA' )
+
 list_ = np.convolve(
     np.gradient(
-        np.mean( data , axis = 1 ),
+        np.mean(
+            data[
+                calibrations[ 'top' ][ 'y' ][ 'max' ] : calibrations[ 'down' ][ 'y' ][ 'min' ],
+                border[ 'x' ][ 'min' ] : border[ 'x' ][ 'max' ]
+            ]       ,
+            axis = 1,
+        ),
     )            ,
     np.ones( 50 ),
     'same'       ,
@@ -529,20 +602,29 @@ fall = np.array( [
     ] + [
     consecutive[0] + np.argmin(
         list_[ consecutive[0] : consecutive[-1] ]
-    ) for consecutive in fall
+    ) for consecutive in fall if len( consecutive ) > 20 # the value might change
 ] ).astype( int )
 
 stairs = np.zeros( ( size_y , size_x ) )
 for x in range( size_x ):
     stairs[ : fall[0] , x ] = 0 # TODO: put the mean
     for i in range( len( fall ) - 1 ):
-        stairs[ fall[ i ] : fall[ i + 1 ] , x ] = np.mean( data[ fall[ i ] : fall[ i + 1 ] , x ] )
+        stairs[ fall[ i ] : fall[ i + 1 ] , x ] = np.mean( data[
+            calibrations[ 'top' ][ 'y' ][ 'max' ] + fall[ i ] : calibrations[ 'top' ][ 'y' ][ 'max' ] + fall[ i + 1 ],
+            border[ 'x' ][ 'min' ] + x
+        ] )
     stairs[ fall[ -1 ] : , x ] = 0
 
-np.imshow( stairs , aspect = 'auto' )
+if verbose:
-np.show()
+    print( 'ETA flattened' )
+    print( 'outputting data' )
 
 if output == None:
     print( stairs )
 else:
     np.savetxt( output , stairs )
+
+if verbose:
+    print( 'output sent' )
+    print( '===========================================\
+          \nend of ETA.py' )