def img_to_tex_vert_coords(self, imgcoords):
vertcoords = img_to_ras_coords(imgcoords, self.affine)
if self.convention == 'LAS':
vertcoords = ras_to_las_coords(vertcoords)
texcoords = img_to_tex_coords(imgcoords, self.data.shape)
vertcoords = vertcoords - self.centershift
if self.post_mat is not None:
vertcoords = vertcoords.T
vertcoords1 = np.vstack((vertcoords, np.ones(vertcoords.shape[1])))
vertcoords1 = np.dot(self.post_mat, vertcoords1)
vertcoords = vertcoords1[:-1, :].T
return texcoords, vertcoords
def img_to_tex_vert_coords(self, imgcoords):
vertcoords = img_to_ras_coords(imgcoords, self.affine)
if self.convention == 'LAS':
vertcoords = ras_to_las_coords(vertcoords)
texcoords = img_to_tex_coords(imgcoords, self.data.shape)
vertcoords = vertcoords - self.centershift
if self.post_mat is not None:
vertcoords = vertcoords.T
vertcoords1 = np.vstack((vertcoords,
np.ones(vertcoords.shape[1])))
vertcoords1 = np.dot(self.post_mat, vertcoords1)
vertcoords = vertcoords1[:-1, :].T
return texcoords, vertcoords
def __init__(self, name, data, affine, convention='RAS', post_mat=None):
""" Volume Slicer
Parameters
----------
name : str
data : array, (X, Y, Z) or (X, Y, Z, 3) or (X, Y, Z, 4)
affine : array, shape (4, 4)
convention : str,
'LAS' or 'RAS'
post_mat : array, shape (4, 4)
"""
self.name = name
self.data = data
self.affine = affine
self.convention = convention
self.post_mat = post_mat
self.tex = Texture3D('Buzz', self.data, self.affine, interp='linear')
self.vertices = self.tex.vertices
self.visible = True
self.I, self.J, self.K = self.data.shape[:3]
self.i, self.j, self.k = self.I/2, self.J/2, self.K/2
self.centershift = img_to_ras_coords(
np.array([[self.I/2., self.J/2., self.K/2.]]),
affine)
if self.convention == 'LAS':
self.centershift = ras_to_las_coords(self.centershift)
self.texcoords_i, self.vertcoords_i = self.slicecoords_i()
self.texcoords_j, self.vertcoords_j = self.slicecoords_j()
self.texcoords_k, self.vertcoords_k = self.slicecoords_k()
self.show_i = True
self.show_j = True
self.show_k = True
def __init__(self, name, data, affine, convention='RAS', post_mat=None):
""" Volume Slicer
Parameters
----------
name : str
data : array, (X, Y, Z) or (X, Y, Z, 3) or (X, Y, Z, 4)
affine : array, shape (4, 4)
convention : str,
'LAS' or 'RAS'
post_mat : array, shape (4, 4)
"""
self.name = name
self.data = data
self.affine = affine
self.convention = convention
self.post_mat = post_mat
self.tex = Texture3D('Buzz', self.data, self.affine, interp='linear')
self.vertices = self.tex.vertices
self.visible = True
self.I, self.J, self.K = self.data.shape[:3]
self.i, self.j, self.k = self.I / 2, self.J / 2, self.K / 2
self.centershift = img_to_ras_coords(
np.array([[self.I / 2., self.J / 2., self.K / 2.]]), affine)
if self.convention == 'LAS':
self.centershift = ras_to_las_coords(self.centershift)
self.texcoords_i, self.vertcoords_i = self.slicecoords_i()
self.texcoords_j, self.vertcoords_j = self.slicecoords_j()
self.texcoords_k, self.vertcoords_k = self.slicecoords_k()
self.show_i = True
self.show_j = True
self.show_k = True
