Calculate sig.py
Jump to navigation
Jump to search
#!/usr/bin/env python
from pycharm import pymfg
from copy import deepcopy
#================================================================
def main():
feature_lists = LoadFeatureLists()
full_list = "\n"
full_list = full_list.join( feature_lists )
original = pymfg.ImageMatrix()
original.OpenImage("Y24-2-2_GREEN.tif", 0, None, 0, 0)
im_cache = {}
im_cache[ " " ] = original
global global_AllAlgorithms
global global_AllTransforms
global_AllAlgorithms = LoadFeatureAlgorithms()
global_AllTransforms = LoadFeatureTransforms()
feature_groups = []
for feature_group_str in full_list.splitlines():
feature_groups.append( ParseFeatureString( feature_group_str ) )
print "{} feature groups".format( len( feature_groups ) )
feature_names = []
signatures = []
for fg in feature_groups:
print "Group {}".format(fg.Name)
feature_vector = fg.CalculateFeatures( im_cache )
count = 0
for value in feature_vector:
feature_names.append( fg.Name + " [{}]".format( count ) )
signatures.append( value )
count += 1
WriteFeaturesToSigFile( "pychrm_calculated.sig", feature_names, signatures )
#================================================================
class FeatureGroup:
"""
Attributes Name, Alg and Tforms are string representations, not links to the object
"""
Name = ""
Alg = None
Tforms = []
def __init__( self, name_str = "", algorithm = None, tform_list = [] ):
self.Name = name_str
self.Alg = algorithm
self.Tforms = tform_list
def CalculateFeatures( self, cached_pixel_planes ):
"""Returns a tuple with the features"""
pixel_plane = None
try:
pixel_plane = RetrievePixelPlane( cached_pixel_planes, self.Tforms )
except:
raise
return global_AllAlgorithms[ self.Alg ].calculate( pixel_plane )
#================================================================
def RetrievePixelPlane( image_matrix_cache, tform_list ):
"""
Returns the image matrix prescribed in tform_list
If it laready exists in cache just return
If it doesn't exist calculates it
Recurses through the compound transform chain in tform_list
"""
requested_transform = " "
requested_transform.join( tform_list )
if requested_transform in image_matrix_cache:
return image_matrix_cache[ requested_transform ]
# Required transform isn't in the cache, gotta make it
# Pop transforms off the end sequentially and check to see if
# lower-level transforms have already been calculated and stored in cache
# Can't begin if there isn't at least the raw (untransformed) pixel plane
# already stored in the cache
if image_matrix_cache is None or len(image_matrix_cache) == 0:
raise ValueError( "Can't calculate features: couldn't find the original pixel plane" +\
"to calculate features {}.".format( self.Name ) )
sublist = deepcopy( tform_list )
top_level_transform_name = sublist.pop()
intermediate_pixel_plane = RetrievePixelPlane( image_matrix_cache, sublist )
tformed_pp = global_AllTransforms[ top_level_transform_name ].transform( intermediate_pixel_plane )
image_matrix_cache[ requested_transform ] = tformed_pp
return tformed_pp
#================================================================
def ParseFeatureString( name ):
"""Takes a string input, parses, and returns an instance of a FeatureGroup class"""
#TBD: make a member function of the FeatureGroup
# get the algorithm
string_rep = name.rstrip( ")" )
parsed = string_rep.split( ' (' )
alg = parsed[0]
if alg not in global_AllAlgorithms:
raise KeyError( "Don't know about a feature algorithm with the name {}".format(alg) )
tform_list = parsed[1:]
try:
tform_list.remove( "" )
except ValueError:
pass
if len(tform_list) != 0:
for tform in tform_list:
if tform not in global_AllTransforms:
raise KeyError( "Don't know about a transform named {}".format(tform) )
return FeatureGroup( name, alg, tform_list )
#================================================================
def WriteFeaturesToSigFile( file_name, feature_names, signatures ):
"""Write a sig file."""
with open( file_name, "w" ) as out_file:
if len( feature_names ) != len( signatures ):
raise ValueError( "Internal error: Can't write sig file: # of feature names " +\
"({}) doesn't match # signatures ({})".format( len( feature_names ), len( signatures ) ) )
for i in range( 0, len( feature_names ) ):
out_file.write( "{val:0.5f} {name}\n".format( val=signatures[i], name=feature_names[i] ) )
#================================================================
def LoadFeatureAlgorithms():
out = {}
out[ 'Chebyshev Coefficients' ] = pymfg.ChebyshevCoefficients()
out[ 'Chebyshev-Fourier Coefficients' ] = pymfg.ChebyshevFourierCoefficients()
out[ 'Zernike Coefficients' ] = pymfg.ZernikeCoefficients()
out[ 'Haralick Textures' ] = pymfg.HaralickTextures()
out[ 'Multiscale Histograms' ] = pymfg.MultiscaleHistograms()
out[ 'Tamura Textures' ] = pymfg.TamuraTextures()
out[ 'Comb Moments' ] = pymfg.CombFirstFourMoments()
out[ 'Radon Coefficients' ] = pymfg.RadonCoefficients()
out[ 'Fractal Features' ] = pymfg.FractalFeatures()
out[ 'Pixel Intensity Statistics' ] = pymfg.PixelIntensityStatistics()
out[ 'Edge Features' ] = pymfg.EdgeFeatures()
out[ 'Object Features' ] = pymfg.ObjectFeatures()
out[ 'Gabor Textures' ] = pymfg.GaborTextures()
out[ 'Gini Coefficient' ] = pymfg.GiniCoefficient()
return out
#================================================================
def LoadFeatureTransforms():
out = {}
out[ 'Fourier' ] = pymfg.FourierTransform()
out[ 'Chebyshev' ] = pymfg.ChebyshevTransform()
out[ 'Wavelet' ] = pymfg.WaveletTransform()
out[ 'Edge' ] = pymfg.EdgeTransform()
out[ 'Color' ] = pymfg.ColorTransform()
out[ 'Hue' ] = pymfg.HueTransform()
return out
#================================================================
def LoadFeatureLists():
small = """Chebyshev Coefficients ()
Chebyshev Coefficients (Fourier ())
Chebyshev-Fourier Coefficients ()
Chebyshev-Fourier Coefficients (Fourier ())
Comb Moments ()
Comb Moments (Chebyshev ())
Comb Moments (Chebyshev (Fourier ()))
Comb Moments (Fourier ())
Comb Moments (Wavelet ())
Comb Moments (Wavelet (Fourier ()))
Edge Features ()
Gabor Textures ()
Haralick Textures ()
Haralick Textures (Chebyshev ())
Haralick Textures (Chebyshev (Fourier ()))
Haralick Textures (Fourier ())
Haralick Textures (Wavelet ())
Haralick Textures (Wavelet (Fourier ()))
Multiscale Histograms ()
Multiscale Histograms (Chebyshev ())
Multiscale Histograms (Chebyshev (Fourier ()))
Multiscale Histograms (Fourier ())
Multiscale Histograms (Wavelet ())
Multiscale Histograms (Wavelet (Fourier ()))
Object Features ()
Radon Coefficients ()
Radon Coefficients (Chebyshev ())
Radon Coefficients (Chebyshev (Fourier ()))
Radon Coefficients (Fourier ())
Tamura Textures ()
Tamura Textures (Chebyshev ())
Tamura Textures (Chebyshev (Fourier ()))
Tamura Textures (Fourier ())
Tamura Textures (Wavelet ())
Tamura Textures (Wavelet (Fourier ()))
Zernike Coefficients ()
Zernike Coefficients (Fourier ())"""
large = """Chebyshev Coefficients (Chebyshev ())
Chebyshev Coefficients (Edge ())
Chebyshev Coefficients (Fourier (Edge ()))
Chebyshev Coefficients (Fourier (Wavelet ()))
Chebyshev Coefficients (Wavelet ())
Chebyshev Coefficients (Wavelet (Edge ()))
Chebyshev-Fourier Coefficients (Chebyshev ())
Chebyshev-Fourier Coefficients (Edge ())
Chebyshev-Fourier Coefficients (Fourier (Edge ()))
Chebyshev-Fourier Coefficients (Fourier (Wavelet ()))
Chebyshev-Fourier Coefficients (Wavelet ())
Chebyshev-Fourier Coefficients (Wavelet (Edge ()))
Comb Moments (Chebyshev (Wavelet ()))
Comb Moments (Edge ())
Comb Moments (Fourier (Chebyshev ()))
Comb Moments (Fourier (Edge ()))
Comb Moments (Fourier (Wavelet ()))
Comb Moments (Wavelet (Edge ()))
Fractal Features ()
Fractal Features (Chebyshev ())
Fractal Features (Chebyshev (Fourier ()))
Fractal Features (Chebyshev (Wavelet ()))
Fractal Features (Edge ())
Fractal Features (Fourier ())
Fractal Features (Fourier (Chebyshev ()))
Fractal Features (Fourier (Edge ()))
Fractal Features (Fourier (Wavelet ()))
Fractal Features (Wavelet ())
Fractal Features (Wavelet (Edge ()))
Fractal Features (Wavelet (Fourier ()))
Gini Coefficient ()
Gini Coefficient (Chebyshev ())
Gini Coefficient (Chebyshev (Fourier ()))
Gini Coefficient (Chebyshev (Wavelet ()))
Gini Coefficient (Edge ())
Gini Coefficient (Fourier ())
Gini Coefficient (Fourier (Chebyshev ()))
Gini Coefficient (Fourier (Edge ()))
Gini Coefficient (Fourier (Wavelet ()))
Gini Coefficient (Wavelet ())
Gini Coefficient (Wavelet (Edge ()))
Gini Coefficient (Wavelet (Fourier ()))
Haralick Textures (Chebyshev (Wavelet ()))
Haralick Textures (Edge ())
Haralick Textures (Fourier (Chebyshev ()))
Haralick Textures (Fourier (Edge ()))
Haralick Textures (Fourier (Wavelet ()))
Haralick Textures (Wavelet (Edge ()))
Multiscale Histograms (Chebyshev (Wavelet ()))
Multiscale Histograms (Edge ())
Multiscale Histograms (Fourier (Chebyshev ()))
Multiscale Histograms (Fourier (Edge ()))
Multiscale Histograms (Fourier (Wavelet ()))
Multiscale Histograms (Wavelet (Edge ()))
Pixel Intensity Statistics ()
Pixel Intensity Statistics (Chebyshev ())
Pixel Intensity Statistics (Chebyshev (Fourier ()))
Pixel Intensity Statistics (Chebyshev (Wavelet ()))
Pixel Intensity Statistics (Edge ())
Pixel Intensity Statistics (Fourier ())
Pixel Intensity Statistics (Fourier (Chebyshev ()))
Pixel Intensity Statistics (Fourier (Edge ()))
Pixel Intensity Statistics (Fourier (Wavelet ()))
Pixel Intensity Statistics (Wavelet ())
Pixel Intensity Statistics (Wavelet (Edge ()))
Pixel Intensity Statistics (Wavelet (Fourier ()))
Radon Coefficients (Chebyshev (Wavelet ()))
Radon Coefficients (Edge ())
Radon Coefficients (Fourier (Chebyshev ()))
Radon Coefficients (Fourier (Edge ()))
Radon Coefficients (Fourier (Wavelet ()))
Radon Coefficients (Wavelet ())
Radon Coefficients (Wavelet (Edge ()))
Radon Coefficients (Wavelet (Fourier ()))
Tamura Textures (Chebyshev (Wavelet ()))
Tamura Textures (Edge ())
Tamura Textures (Fourier (Chebyshev ()))
Tamura Textures (Fourier (Edge ()))
Tamura Textures (Fourier (Wavelet ()))
Tamura Textures (Wavelet (Edge ()))
Zernike Coefficients (Chebyshev ())
Zernike Coefficients (Edge ())
Zernike Coefficients (Fourier (Edge ()))
Zernike Coefficients (Fourier (Wavelet ()))
Zernike Coefficients (Wavelet ())
Zernike Coefficients (Wavelet (Edge ()))"""
return small, large
#================================================================
if __name__=="__main__":
main()
