utils¶
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Apply affine matrix aff to points pts. |
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Change the vertices order of a given triangle. |
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Access colors from actor which uses polydata. |
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Compute Bounds of actor. |
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Return corrected triangles. |
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Get actor from a vtkPolyData. |
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Get actor from a vtkPolyDataMapper. |
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Get actor from a vtkPolyData. |
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Get the bounding box sizes of an actor. |
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Return Bounds of actor. |
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Construct a XY-grid based on the cells content shape. |
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Get points color (ndarrays Nx3 int) from a vtk polydata. |
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Convert vtk polydata to a list of lines ndarrays. |
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Get vertices normal (ndarrays Nx3 int) from a vtk polydata. |
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Get triangles (ndarrays Nx3 int) from a vtk polydata. |
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Get vertices (ndarrays Nx3 int) from a vtk polydata. |
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Get vtkPolyDataMapper from a vtkPolyData. |
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Create colors for streamlines to be used in actor.line. |
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Create a vtkPolyData with lines and colors. |
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Map the input array to new coordinates by interpolation. |
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Evaluate the input_array data at the given indices using trilinear interpolation. |
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Normalize a numpy array of 3 component vectors shape=(N, 3). |
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Calculate normals from vertices and faces. |
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Convert numpy array to a vtk cell array. |
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Convert Numpy color array to a vtk color array. |
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Convert a numpy array to a VTK matrix. |
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Convert Numpy points array to a vtk points array. |
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Transform a vtksource to glyph. |
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RGB or RGBA images to VTK arrays. |
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Rotate actor around axis by angle. |
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Set Generic input function which takes into account VTK 5 or 6. |
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Set polydata colors with a numpy array (ndarrays Nx3 int). |
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Set polydata normals with a numpy array (ndarrays Nx3 int). |
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Set polydata triangles with a numpy array (ndarrays Nx3 int). |
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Set polydata vertices with a numpy array (ndarrays Nx3 int). |
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Create a shallow copy of a given vtkObject object. |
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Determine the winding order of a given set of vertices and a triangle. |
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Update actor. |
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Generate and update polydata normals. |
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Access to vertices from actor. |
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Convert VTK matrix to numpy array. |
apply_affine¶
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fury.utils.apply_affine(aff, pts)[source]¶ Apply affine matrix aff to points pts.
Returns result of application of aff to the right of pts. The coordinate dimension of pts should be the last. For the 3D case, aff will be shape (4,4) and pts will have final axis length 3 - maybe it will just be N by 3. The return value is the transformed points, in this case:: res = np.dot(aff[:3,:3], pts.T) + aff[:3,3:4] transformed_pts = res.T This routine is more general than 3D, in that aff can have any shape (N,N), and pts can have any shape, as long as the last dimension is for the coordinates, and is therefore length N-1.
- Parameters
aff ((N, N) array-like) – Homogenous affine, for 3D points, will be 4 by 4. Contrary to first appearance, the affine will be applied on the left of pts.
pts ((.., N-1) array-like) – Points, where the last dimension contains the coordinates of each point. For 3D, the last dimension will be length 3.
- Returns
transformed_pts – transformed points
- Return type
(.., N-1) array
Notes
Copied from nibabel to remove dependency.
Examples
>>> aff = np.array([[0,2,0,10],[3,0,0,11],[0,0,4,12],[0,0,0,1]]) >>> pts = np.array([[1,2,3],[2,3,4],[4,5,6],[6,7,8]]) >>> apply_affine(aff, pts) array([[14, 14, 24], [16, 17, 28], [20, 23, 36], [24, 29, 44]]...) Just to show that in the simple 3D case, it is equivalent to: >>> (np.dot(aff[:3,:3], pts.T) + aff[:3,3:4]).T array([[14, 14, 24], [16, 17, 28], [20, 23, 36], [24, 29, 44]]...) But `pts` can be a more complicated shape: >>> pts = pts.reshape((2,2,3)) >>> apply_affine(aff, pts) array([[[14, 14, 24], [16, 17, 28]], [[20, 23, 36], [24, 29, 44]]]...)
change_vertices_order¶
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fury.utils.change_vertices_order(triangle)[source]¶ Change the vertices order of a given triangle.
- Parameters
triangle (ndarray, shape(1, 3)) – array of 3 vertices making up a triangle
- Returns
new_triangle – new array of vertices making up a triangle in the opposite winding order of the given parameter
- Return type
ndarray, shape(1, 3)
colors_from_actor¶
compute_bounds¶
fix_winding_order¶
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fury.utils.fix_winding_order(vertices, triangles, clockwise=False)[source]¶ Return corrected triangles.
Given an ordering of the triangle’s three vertices, a triangle can appear to have a clockwise winding or counter-clockwise winding. Clockwise means that the three vertices, in order, rotate clockwise around the triangle’s center.
- Parameters
vertices (ndarray) – array of vertices corresponding to a shape
triangles (ndarray) – array of triangles corresponding to a shape
clockwise (bool) – triangle order type: clockwise (default) or counter-clockwise.
- Returns
corrected_triangles – The corrected order of the vert parameter
- Return type
ndarray
get_actor_from_polydata¶
get_actor_from_polymapper¶
get_actor_from_primitive¶
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fury.utils.get_actor_from_primitive(vertices, triangles, colors=None, normals=None, backface_culling=True)[source]¶ Get actor from a vtkPolyData.
- Parameters
vertices ((Mx3) ndarray) – XYZ coordinates of the object
triangles ((Nx3) ndarray) – Indices into vertices; forms triangular faces.
colors ((Nx3) or (Nx4) ndarray) – RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1] N is equal to the number of vertices.
normals ((Nx3) ndarray) – normals, represented as 2D ndarrays (Nx3) (one per vertex)
backface_culling (bool) – culling of polygons based on orientation of normal with respect to camera. If backface culling is True, polygons facing away from camera are not drawn. Default: True
- Returns
actor
- Return type
actor
get_bounding_box_sizes¶
get_bounds¶
get_grid_cells_position¶
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fury.utils.get_grid_cells_position(shapes, aspect_ratio=1.7777777777777777, dim=None)[source]¶ Construct a XY-grid based on the cells content shape.
This function generates the coordinates of every grid cell. The width and height of every cell correspond to the largest width and the largest height respectively. The grid dimensions will automatically be adjusted to respect the given aspect ratio unless they are explicitly specified.
The grid follows a row-major order with the top left corner being at coordinates (0,0,0) and the bottom right corner being at coordinates (nb_cols*cell_width, -nb_rows*cell_height, 0). Note that the X increases while the Y decreases.
- Parameters
shapes (list of tuple of int) – The shape (width, height) of every cell content.
aspect_ratio (float (optional)) – Aspect ratio of the grid (width/height). Default: 16:9.
dim (tuple of int (optional)) – Dimension (nb_rows, nb_cols) of the grid, if provided.
- Returns
3D coordinates of every grid cell.
- Return type
ndarray
get_polydata_colors¶
get_polydata_lines¶
get_polydata_normals¶
get_polydata_triangles¶
get_polydata_vertices¶
get_polymapper_from_polydata¶
line_colors¶
lines_to_vtk_polydata¶
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fury.utils.lines_to_vtk_polydata(lines, colors=None)[source]¶ Create a vtkPolyData with lines and colors.
- Parameters
lines (list) – list of N curves represented as 2D ndarrays
colors (array (N, 3), list of arrays, tuple (3,), array (K,)) – If None or False, a standard orientation colormap is used for every line. If one tuple of color is used. Then all streamlines will have the same colour. If an array (N, 3) is given, where N is equal to the number of lines. Then every line is coloured with a different RGB color. If a list of RGB arrays is given then every point of every line takes a different color. If an array (K, 3) is given, where K is the number of points of all lines then every point is colored with a different RGB color. If an array (K,) is given, where K is the number of points of all lines then these are considered as the values to be used by the colormap. If an array (L,) is given, where L is the number of streamlines then these are considered as the values to be used by the colormap per streamline. If an array (X, Y, Z) or (X, Y, Z, 3) is given then the values for the colormap are interpolated automatically using trilinear interpolation.
- Returns
poly_data (vtkPolyData)
color_is_scalar (bool, true if the color array is a single scalar) – Scalar array could be used with a colormap lut None if no color was used
map_coordinates¶
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fury.utils.map_coordinates(input, coordinates, output=None, order=3, mode='constant', cval=0.0, prefilter=True)[source]¶ Map the input array to new coordinates by interpolation.
The array of coordinates is used to find, for each point in the output, the corresponding coordinates in the input. The value of the input at those coordinates is determined by spline interpolation of the requested order.
The shape of the output is derived from that of the coordinate array by dropping the first axis. The values of the array along the first axis are the coordinates in the input array at which the output value is found.
- Parameters
input (array_like) – The input array.
coordinates (array_like) – The coordinates at which input is evaluated.
output (array or dtype, optional) – The array in which to place the output, or the dtype of the returned array. By default an array of the same dtype as input will be created.
order (int, optional) – The order of the spline interpolation, default is 3. The order has to be in the range 0-5.
mode ({'reflect', 'constant', 'nearest', 'mirror', 'wrap'}, optional) –
The mode parameter determines how the input array is extended beyond its boundaries. Default is ‘constant’. Behavior for each valid value is as follows:
- ’reflect’ (d c b a | a b c d | d c b a)
The input is extended by reflecting about the edge of the last pixel.
- ’constant’ (k k k k | a b c d | k k k k)
The input is extended by filling all values beyond the edge with the same constant value, defined by the cval parameter.
- ’nearest’ (a a a a | a b c d | d d d d)
The input is extended by replicating the last pixel.
- ’mirror’ (d c b | a b c d | c b a)
The input is extended by reflecting about the center of the last pixel.
- ’wrap’ (a b c d | a b c d | a b c d)
The input is extended by wrapping around to the opposite edge.
cval (scalar, optional) – Value to fill past edges of input if mode is ‘constant’. Default is 0.0.
prefilter (bool, optional) – Determines if the input array is prefiltered with spline_filter before interpolation. The default is True, which will create a temporary float64 array of filtered values if order > 1. If setting this to False, the output will be slightly blurred if order > 1, unless the input is prefiltered, i.e. it is the result of calling spline_filter on the original input.
- Returns
map_coordinates – The result of transforming the input. The shape of the output is derived from that of coordinates by dropping the first axis.
- Return type
ndarray
See also
spline_filter(),geometric_transform(),scipy.interpolate()Examples
>>> from scipy import ndimage >>> a = np.arange(12.).reshape((4, 3)) >>> a array([[ 0., 1., 2.], [ 3., 4., 5.], [ 6., 7., 8.], [ 9., 10., 11.]]) >>> ndimage.map_coordinates(a, [[0.5, 2], [0.5, 1]], order=1) array([ 2., 7.])
Above, the interpolated value of a[0.5, 0.5] gives output[0], while a[2, 1] is output[1].
>>> inds = np.array([[0.5, 2], [0.5, 4]]) >>> ndimage.map_coordinates(a, inds, order=1, cval=-33.3) array([ 2. , -33.3]) >>> ndimage.map_coordinates(a, inds, order=1, mode='nearest') array([ 2., 8.]) >>> ndimage.map_coordinates(a, inds, order=1, cval=0, output=bool) array([ True, False], dtype=bool)
map_coordinates_3d_4d¶
normalize_v3¶
normals_from_v_f¶
numpy_to_vtk_cells¶
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fury.utils.numpy_to_vtk_cells(data, is_coords=True)[source]¶ Convert numpy array to a vtk cell array.
- Parameters
data (ndarray) – points coordinate or connectivity array (e.g triangles).
is_coords (ndarray) – Select the type of array. default: True.
- Returns
vtk_cell – connectivity + offset information
- Return type
vtkCellArray
numpy_to_vtk_colors¶
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fury.utils.numpy_to_vtk_colors(colors)[source]¶ Convert Numpy color array to a vtk color array.
- Parameters
colors (ndarray) –
- Returns
vtk_colors
- Return type
vtkDataArray
Notes
If colors are not already in UNSIGNED_CHAR you may need to multiply by 255.
Examples
>>> import numpy as np >>> from fury.utils import numpy_to_vtk_colors >>> rgb_array = np.random.rand(100, 3) >>> vtk_colors = numpy_to_vtk_colors(255 * rgb_array)
numpy_to_vtk_matrix¶
numpy_to_vtk_points¶
repeat_sources¶
rgb_to_vtk¶
rotate¶
set_input¶
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fury.utils.set_input(vtk_object, inp)[source]¶ Set Generic input function which takes into account VTK 5 or 6.
- Parameters
vtk_object (vtk object) –
inp (vtkPolyData or vtkImageData or vtkAlgorithmOutput) –
- Returns
- Return type
vtk_object
Notes
- This can be used in the following way::
from fury.utils import set_input poly_mapper = set_input(vtk.vtkPolyDataMapper(), poly_data)
set_polydata_colors¶
set_polydata_normals¶
set_polydata_triangles¶
set_polydata_vertices¶
shallow_copy¶
triangle_order¶
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fury.utils.triangle_order(vertices, faces)[source]¶ Determine the winding order of a given set of vertices and a triangle.
- Parameters
vertices (ndarray) – array of vertices making up a shape
faces (ndarray) – array of triangles
- Returns
order – If the order is counter clockwise (CCW), returns True. Otherwise, returns False.
- Return type