def apply( self, img, target_header=None,
interpolation='linear', gaussian_parameter=1.0 ):
"""
Apply.
"""
if not isinstance( img, irtk.Image ):
# point transformation
pt = np.array(img, dtype='float64', copy=True)
if len(pt.shape) == 1:
tmp_pt = np.hstack((pt,[1])).astype('float64')
return np.dot( self.matrix(), tmp_pt )[:3]
else:
pt = _irtk.transform_points( self.matrix(), pt )
return pt
# tmp_pt = np.hstack((pt,[[1]]*pt.shape[0])).astype('float64')
# return np.transpose( np.dot( self.matrix(),
# np.transpose(tmp_pt) ) )[:,:3]
# if target_header is None:
# target_header = img.get_header()
if target_header is None:
(x_min, y_min, z_min, x_max, y_max, z_max ) = img.bbox(world=True)
corners = [[x_min, y_min, z_min],
[x_max, y_min, z_min],
[x_min, y_max, z_min],
[x_min, y_min, z_max],
[x_max, y_max, z_min],
[x_min, y_max, z_max],
[x_max, y_min, z_max],
[x_max, y_max, z_max]]
corners = self.apply( corners )
x_min, y_min, z_min = corners.min(axis=0)
x_max, y_max, z_max = corners.max(axis=0)
res = img.header['pixelSize'][0]
pixelSize = [res, res, res, 1]
origin = [ x_min + (x_max+1 - x_min)/2,
y_min + (y_max+1 - y_min)/2,
z_min + (z_max+1 - z_min)/2,
img.header['origin'][3] ]
dim = [ (x_max+1 - x_min)/res,
(y_max+1 - y_min)/res,
(z_max+1 - z_min)/res,
1 ]
target_header = irtk.new_header( pixelSize=pixelSize, origin=origin, dim=dim)
if isinstance( target_header, irtk.Image ):
target_header = target_header.get_header()
data = img.get_data('float32','cython')
new_data = _irtk.transform_rigid( self.tx, self.ty, self.tz,
self.rx, self.ry, self.rz,
data,
img.get_header(),
target_header,
interpolation,
gaussian_parameter )
return irtk.Image( new_data, target_header )
def apply( self, img, target_header=None,
interpolation='linear', gaussian_parameter=1.0 ):
"""
Apply.
"""
if not isinstance( img, irtk.Image ):
# point transformation
pt = np.array(img, dtype='float64', copy=True)
if len(pt.shape) == 1:
tmp_pt = np.hstack((pt,[1])).astype('float64')
return np.dot( self.matrix(), tmp_pt )[:3]
else:
pt = _irtk.transform_points( self.matrix(), pt )
return pt
# tmp_pt = np.hstack((pt,[[1]]*pt.shape[0])).astype('float64')
# return np.transpose( np.dot( self.matrix(),
# np.transpose(tmp_pt) ) )[:,:3]
# if target_header is None:
# target_header = img.get_header()
if target_header is None:
(x_min, y_min, z_min, x_max, y_max, z_max ) = img.bbox(world=True)
corners = [[x_min, y_min, z_min],
[x_max, y_min, z_min],
[x_min, y_max, z_min],
[x_min, y_min, z_max],
[x_max, y_max, z_min],
[x_min, y_max, z_max],
[x_max, y_min, z_max],
[x_max, y_max, z_max]]
corners = self.apply( corners )
x_min, y_min, z_min = corners.min(axis=0)
x_max, y_max, z_max = corners.max(axis=0)
res = img.header['pixelSize'][0]
pixelSize = [res, res, res, 1]
origin = [ x_min + (x_max+1 - x_min)/2,
y_min + (y_max+1 - y_min)/2,
z_min + (z_max+1 - z_min)/2,
img.header['origin'][3] ]
dim = [ (x_max+1 - x_min)/res,
(y_max+1 - y_min)/res,
(z_max+1 - z_min)/res,
1 ]
target_header = irtk.new_header( pixelSize=pixelSize, origin=origin, dim=dim)
if isinstance( target_header, irtk.Image ):
target_header = target_header.get_header()
data = img.get_data('float32','cython')
new_data = _irtk.transform_rigid( self.tx, self.ty, self.tz,
self.rx, self.ry, self.rz,
data,
img.get_header(),
target_header,
interpolation,
gaussian_parameter )
return irtk.Image( new_data, target_header )
def WorldToImage( self, pt ):
"""
Returns integers
"""
tmp_pt = np.array( pt, dtype='float64' ).copy()
if len(tmp_pt.shape) == 1:
tmp_pt = np.hstack((tmp_pt,[1])).astype('float64')
return np.rint( np.dot( self.W2I, tmp_pt )[:3] ).astype('int32')
else:
tmp_pt = np.rint( _irtk.transform_points( self.W2I, tmp_pt ) ).astype('int32')
return tmp_pt
def WorldToImage(self, pt):
"""
Returns integers
"""
tmp_pt = np.array(pt, dtype='float64').copy()
if len(tmp_pt.shape) == 1:
tmp_pt = np.hstack((tmp_pt, [1])).astype('float64')
return np.rint(np.dot(self.W2I, tmp_pt)[:3]).astype('int32')
else:
tmp_pt = np.rint(_irtk.transform_points(self.W2I,
tmp_pt)).astype('int32')
return tmp_pt
def WorldToImage(self, pt):
"""
Returns integers
"""
# make sure I2W an W2I are up-to-date
self.__updateMatrix()
tmp_pt = np.array(pt, dtype='float64').copy()
if len(tmp_pt.shape) == 1:
tmp_pt = np.hstack((tmp_pt, [1])).astype('float64')
return np.rint(np.dot(self.W2I, tmp_pt)[:3]).astype('int32')
else:
tmp_pt = np.rint(_irtk.transform_points(self.W2I,
tmp_pt)).astype('int32')
return tmp_pt
def ImageToWorld(self, pt):
"""
BEWARE: images are indexed as img[t,z,y,x],
so for instance:
Examples
--------
>>> tx,ty,tz = img.ImageToWorld( [(img.shape[2]-1)/2,(img.shape[1]-1)/2,(img.shape[0]-1)/2] )
"""
tmp_pt = np.array(pt, dtype='float64').copy()
if len(tmp_pt.shape) == 1:
tmp_pt = np.hstack((tmp_pt, [1])).astype('float64')
return np.dot(self.I2W, tmp_pt)[:3]
else:
tmp_pt = _irtk.transform_points(self.I2W, tmp_pt)
return tmp_pt
def ImageToWorld( self, pt ):
"""
BEWARE: images are indexed as img[t,z,y,x],
so for instance:
Examples
--------
>>> tx,ty,tz = img.ImageToWorld( [(img.shape[2]-1)/2,(img.shape[1]-1)/2,(img.shape[0]-1)/2] )
"""
tmp_pt = np.array( pt, dtype='float64' ).copy()
if len(tmp_pt.shape) == 1:
tmp_pt = np.hstack((tmp_pt,[1])).astype('float64')
return np.dot( self.I2W, tmp_pt )[:3]
else:
tmp_pt = _irtk.transform_points( self.I2W, tmp_pt )
return tmp_pt
