Add calibration (WIP)

- Fix command parser
- Add --calibration option
- Add calibration (WIP)

ETA.py

@@ -8,12 +8,13 @@ from scipy.signal import convolve as sp_convolve
 from scipy.signal import find_peaks
 from scipy.ndimage import rotate
 
-cache , filename , output = '' , None , None
+cache , filename , output , calibration = '' , None , None , None
 if len( sys.argv ) < 2:
     raise Exception( 'ETA.py: type \'ETA.py -h\' for more information' )
 
-for i in range( 1 , len( sys.argv ) ):
+argv , i = sys.argv[ 1 : ] , 0
-    arg = sys.argv[ i ]
+while i < len( argv ):
+    arg = argv[ i ]
     if arg[0] == '-':
         if len( arg ) < 2:
             raise Exception( 'ETA.py: unknown argument, type \'ETA.py -h\' for more information' )
@@ -27,23 +28,33 @@ for i in range( 1 , len( sys.argv ) ):
             elif arg == '-c':
                 if i == len( sys.argv ) - 1:
                     raise Exception( 'ETA.py: cache have to take a value' )
-                arg[ i + 1 ] == '--cache=' + arg[ i + 1 ]
+                argv[ i + 1 ] = '--cache=' + argv[ i + 1 ]
+                i += 1
                 continue
             elif arg == '-o':
                 if i == len( sys.argv ) - 1:
                     raise Exception( 'ETA.py: output have to take a value' )
-                arg[ i + 1 ] == '--output=' + arg[ i + 1 ]
+                argv[ i + 1 ] = '--output=' + argv[ i + 1 ]
+                i += 1
+                continue
+            elif arg == '-a':
+                if i == len( sys.argv ) - 1:
+                    raise Exception( 'ETA.py: calibration have to take a value' )
+                argv[ i + 1 ] = '--calibration=' + argv[ i + 1 ]
+                i += 1
                 continue
             else:
                 raise Exception( 'ETA.py: unknown argument "' + arg + '", type \'ETA.py -h\' for more information' )
         if arg[1] == '-': # not elif because arg can change after last if
             if arg == '--help':
                 print( 'ETA.py [options...] filename\
-                      \n    -h --help     show this help and quit\
+                      \n    -a --calibration calibration file, default to no calibration.\
-                      \n    -v --version  show version number and quit\
+                      \n                     No calibration means no wavelength interpolation\
-                      \n    -n --no-cache do not use cache and rewrite it\
+                      \n    -c --cache       use given cache\
-                      \n    -c --cache    use given cache\
+                      \n    -h --help        show this help and quit\
-                      \n    -o --output   output file, default to standard output\
+                      \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\
                       \nParse a naroo ETA fits' )
                 exit()
@@ -56,14 +67,18 @@ for i in range( 1 , len( sys.argv ) ):
                 cache = arg[ 8 : ]
             elif len( arg ) > 9 and arg[ : 9 ] == '--output=':
                 output = arg[ 9 : ]
+            elif len( arg ) > 14 and arg[ : 14 ] == '--calibration=':
+                calibration = arg[ 14 : ]
             else:
                 raise Exception( 'ETA.py: unknown argument "' + arg + '", type \'ETA.py -h\' for more information' )
         else:
             raise Exception( 'ETA.py: this exception should never be raised' )
     else:
         filename = arg
+    i += 1
 if filename == None:
     raise Exception( 'ETA.py: filename should be given' )
+# TODO: check in advance file to check if exists or writeable
 
 data = utils.load( filename )
 
@@ -366,6 +381,28 @@ else:
             cache[ 'calibrations']  = calibrations
             cache[ 'stripes' ]      = stripes
 
+# Calibration
+
+if calibration != None:
+    calib_peaks   = np.loadtxt( calibration )
+    mean_calib_up = np.mean( data[
+        calibrations[ 'top' ][ 'y' ][ 'min' ] : calibrations[ 'top' ][ 'y' ][ 'max' ],
+        border[ 'x' ][ 'min' ] : border[ 'x' ][ 'max' ]
+    ] , axis = 0 )
+    mean_calib_up -= np.min( mean_calib_up )
+    mean_calib_up /= np.max( mean_calib_up )
+
+    peaks_up = find_peaks( mean_calib_up , height = 0.6 )[0] + border[ 'x' ][ 'min' ]
+
+    if len( peaks_up ) != len( calib_peaks ):
+        print( calib_peaks , peaks_up )
+        print( len( calib_peaks ) , len( peaks_up ) )
+        plt.plot( mean_calib_up )
+        plt.show()
+        exit()
+    polyval = np.polyfit( peaks_up , calib_peaks , 1 )
+    print( polyval )
+
 # First deformation
 
 list_ = data[
@@ -398,7 +435,7 @@ fall = np.array( [
 stairs = np.zeros_like( results )
 for x in range( size ):
     stairs[ : , x ] = results[ : , x ] # can be modified, but no used anymore so it's fine
-    stairs[ : fall[0] , x ] = 0
+    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( stairs[ fall[ i ] : fall[ i + 1 ] ] )
     stairs[ fall[ -1 ] : , x ] = 0