Update to support i18n & logging
- Add --log-file option - Add internationalization support with gettext - Add logging featur - Remove verbosity flag - Update string formatting - Fix Plate::set_border method
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1 changed files with 126 additions and 40 deletions
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@ -1,7 +1,13 @@
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from numpy import ndarray, argmax, max, quantile, arange, where, convolve, ones
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from numpy import ndarray, gradient, ones, argmax, arange, arctan, tan
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from scipy.optimize import curve_fit
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from scipy.signal import convolve
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from cv2 import getRotationMatrix2D, warpAffine, INTER_NEAREST
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from classes.science.border import Border
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from function.utils import find_point, fill
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from function.fit import linear
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from logging import getLogger
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from gettext import gettext as _
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class Plate:
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"""
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@ -10,15 +16,17 @@ class Plate:
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def __init__( self , data ):
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if not isinstance( data , ndarray ):
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raise TypeError( 'data must be a ndarray' )
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raise TypeError( _( 'data must be a ndarray' ) )
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if len( data.shape ) != 2:
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raise ValueError( _( 'data must be a 2d matrix' ) )
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self.data = data
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self.set_border()
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def set_border( self , factor = 10 ):
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def set_border( self ):
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"""
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Set current border (without area outside the plate)
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"""
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compressed = self.compress( factor )
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compressed , factor = self.compress()
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points = self.get_points( compressed )
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self.border = Border()
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@ -39,24 +47,45 @@ class Plate:
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taken_points = fill(
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compressed,
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point ,
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1000 , # intensity threshold
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2000 , # intensity threshold
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)
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x = [ taken_point[1] for taken_point in taken_points ]
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y = [ taken_point[0] for taken_point in taken_points ]
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if max( x ) < x_half:
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if self.border.x.min < max( x ):
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self.border.x.min = max( x ) # biggest min
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elif min( x ) > x_half: # elif to only accept one side
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if self.border.x.max > min( x ):
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self.border.x.max = min( x ) # smallest max
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elif max( y ) < y_half:
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if self.border.y.min < max( y ):
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self.border.y.min = max( y ) # same
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elif min( y ) > y_half:
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if self.border.y.max > min( y ):
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self.border.y.max = min( y ) # same
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"""
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matrix = ones( compressed.shape )
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for taken_point in taken_points:
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matrix[ taken_point[0] , taken_point[1] ] = 0
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import matplotlib.pyplot as plt
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plt.plot(
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[ point[1] ] ,
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[ point[0] ] ,
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linestyle = '' ,
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marker = 'x' ,
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markersize = 15 ,
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markeredgecolor = 'red',
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markeredgewidth = 5 ,
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)
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plt.imshow( compressed , aspect = 'auto' )
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plt.imshow( matrix , aspect = 'auto' , alpha = 0.5 )
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plt.show()
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"""
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if len( x ) > 5 and len( y ) > 5:
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if max( x ) < x_half:
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if self.border.x.min < max( x ):
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self.border.x.min = max( x ) # biggest min
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elif min( x ) > x_half:
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# elif to only accept one side
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if self.border.x.max > min( x ):
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self.border.x.max = min( x ) # smallest max
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elif max( y ) < y_half:
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if self.border.y.min < max( y ):
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self.border.y.min = max( y ) # same
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elif min( y ) > y_half:
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if self.border.y.max > min( y ):
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self.border.y.max = min( y ) # same
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offset = 3
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@ -116,36 +145,93 @@ class Plate:
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return first_column + last_column + first_line + last_line
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def compress( self , factor ):
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def compress( self ):
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"""
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Compress the plate data to fit the biggest dimension in a 1000
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pixels axis and the smallest in a 100 pixels axis at minimum.
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Return the compressed data and the compression factor used.
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"""
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min_factor = max( self.data.shape ) // 1000 # min factor to have a side
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# with a maximum of 1000 pixels
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max_factor = min( self.data.shape ) // 100 # max factor to have
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# a side with a minimum of 100 pixel
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if min_factor < max_factor:
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factor = int( mean( ( max_factor , min_factor ) ) )
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else: # the smallest side will be less than 100 pixels with the
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# minimum compression factor
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logger = getLogger( 'naroo reader' )
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logger.warning(
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_( (
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'slow compression: ratio between height and width'
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' is greater than 10 ({ratio:.2f})'
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) ).format(
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ratio = max( self.size() ) / min( self.size() )
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)
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)
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factor = max_factor
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return self.data[
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: : factor,
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: : factor,
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]
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] , factor
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def middle( self ):
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"""
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Get coordinate of center
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"""
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return (
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self.size()[0] // 2,
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self.size()[1] // 2,
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)
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def rotate( self ):
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"""
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Auto-rotate to be vertically and horizontally aligned
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"""
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maxes = max(
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self.data[ self.border.slice() ],
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axis = 0 ,
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)
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indexes = where(
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maxes > quantile( maxes , 0.5 )
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indexes_max = argmax(
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convolve(
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self.data[
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1 * self.border.y.size() // 4:
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3 * self.border.y.size() // 4,
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1 * self.border.x.size() // 4:
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3 * self.border.x.size() // 4
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] ,
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ones( ( 500 , 1 ) ),
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'valid' ,
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) ,
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axis = 0,
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)
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abciss = arange(
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self.border.x.min,
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self.border.x.max
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)[ indexes ]
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indexes_max = argmax(
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self.data[ self.border.slice() ],
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axis = 0 ,
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)[ indexes ]
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indexes_max = convolve(
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indexes_max ,
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ones( 100 ) ,
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'same' ,
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) / 100
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import matplotlib.pyplot as plt
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plt.plot( abciss , indexes_max )
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plt.show()
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1 * self.border.x.size() // 4,
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3 * self.border.x.size() // 4
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)
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fit_result = curve_fit(
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linear ,
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abciss ,
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indexes_max,
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)[0]
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angle = arctan( fit_result[0] ) # rad
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diff = int( # adjust height border
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tan( angle ) * ( self.border.x.size() )
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)
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rotation_matrix = getRotationMatrix2D(
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self.middle(),
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angle ,
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1 ,
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)
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self.data = warpAffine(
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self.data ,
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rotation_matrix,
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self.size() ,
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flags = INTER_NEAREST,
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)
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self.border.y.min -= diff
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self.border.y.max -= diff
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def size( self ):
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"""
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get plate size
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"""
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return self.data.shape
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