TriMesh¶
-
class
menpo.shape.
TriMesh
(points, trilist=None, copy=True)[source]¶ Bases:
PointCloud
A
PointCloud
with a connectivity defined by a triangle list. These are designed to be explicitly 2D or 3D.Parameters: - points (
(n_points, n_dims)
ndarray) – The array representing the points. - trilist (
(M, 3)
ndarray orNone
, optional) – The triangle list. If None, a Delaunay triangulation of the points will be used instead. - copy (bool, optional) – If
False
, the points will not be copied on assignment. Any trilist will also not be copied. In general this should only be used if you know what you are doing.
-
_view_2d
(figure_id=None, new_figure=False, image_view=True, render_lines=True, line_colour='r', line_style='-', line_width=1.0, render_markers=True, marker_style='o', marker_size=20, marker_face_colour='k', marker_edge_colour='k', marker_edge_width=1.0, render_axes=True, axes_font_name='sans-serif', axes_font_size=10, axes_font_style='normal', axes_font_weight='normal', axes_x_limits=None, axes_y_limits=None, figure_size=(10, 8), label=None)[source]¶ Visualization of the TriMesh in 2D.
Returns: - figure_id (object, optional) – The id of the figure to be used.
- new_figure (bool, optional) –
If
True
, a new figure is created. - image_view (bool, optional) –
If
True
the TriMesh will be viewed as if it is in the image coordinate system. - render_lines (bool, optional) –
If
True
, the edges will be rendered. - line_colour (See Below, optional) –
The colour of the lines.
Example options:
{r, g, b, c, m, k, w} or (3, ) ndarray
- line_style (
{-, --, -., :}
, optional) – The style of the lines. - line_width (float, optional) – The width of the lines.
- render_markers (bool, optional) –
If
True
, the markers will be rendered. - marker_style (See Below, optional) –
The style of the markers. Example options
{., ,, o, v, ^, <, >, +, x, D, d, s, p, *, h, H, 1, 2, 3, 4, 8}
- marker_size (int, optional) – The size of the markers in points^2.
- marker_face_colour (See Below, optional) –
The face (filling) colour of the markers.
Example options
{r, g, b, c, m, k, w} or (3, ) ndarray
- marker_edge_colour (See Below, optional) –
The edge colour of the markers.
Example options
{r, g, b, c, m, k, w} or (3, ) ndarray
- marker_edge_width (float, optional) – The width of the markers’ edge.
- render_axes (bool, optional) –
If
True
, the axes will be rendered. - axes_font_name (See Below, optional) –
The font of the axes.
Example options
{serif, sans-serif, cursive, fantasy, monospace}
- axes_font_size (int, optional) – The font size of the axes.
- axes_font_style ({
normal
,italic
,oblique
}, optional) – The font style of the axes. - axes_font_weight (See Below, optional) –
The font weight of the axes.
Example options
{ultralight, light, normal, regular, book, medium, roman, semibold, demibold, demi, bold, heavy, extra bold, black}
- axes_x_limits ((float, float) tuple or
None
, optional) – The limits of the x axis. - axes_y_limits ((float, float) tuple or
None
, optional) – The limits of the y axis. - figure_size ((float, float) tuple or
None
, optional) – The size of the figure in inches. - label (str, optional) – The name entry in case of a legend.
Returns: viewer ( PointGraphViewer2d
) – The viewer object.
-
_view_landmarks_2d
(group=None, with_labels=None, without_labels=None, figure_id=None, new_figure=False, image_view=True, render_lines=True, line_colour=None, line_style='-', line_width=1, render_markers=True, marker_style='o', marker_size=20, marker_face_colour=None, marker_edge_colour=None, marker_edge_width=1.0, render_numbering=False, numbers_horizontal_align='center', numbers_vertical_align='bottom', numbers_font_name='sans-serif', numbers_font_size=10, numbers_font_style='normal', numbers_font_weight='normal', numbers_font_colour='k', render_legend=False, legend_title='', legend_font_name='sans-serif', legend_font_style='normal', legend_font_size=10, legend_font_weight='normal', legend_marker_scale=None, legend_location=2, legend_bbox_to_anchor=(1.05, 1.0), legend_border_axes_pad=None, legend_n_columns=1, legend_horizontal_spacing=None, legend_vertical_spacing=None, legend_border=True, legend_border_padding=None, legend_shadow=False, legend_rounded_corners=False, render_axes=False, axes_font_name='sans-serif', axes_font_size=10, axes_font_style='normal', axes_font_weight='normal', axes_x_limits=None, axes_y_limits=None, figure_size=(10, 8))¶ Visualize the landmarks. This method will appear on the Image as
view_landmarks
if the Image is 2D.Parameters: - group (str or``None`` optional) – The landmark group to be visualized. If
None
and there are more than one landmark groups, an error is raised. - with_labels (
None
or str or list of str, optional) – If notNone
, only show the given label(s). Should not be used with thewithout_labels
kwarg. - without_labels (
None
or str or list of str, optional) – If notNone
, show all except the given label(s). Should not be used with thewith_labels
kwarg. - figure_id (object, optional) – The id of the figure to be used.
- new_figure (bool, optional) – If
True
, a new figure is created. - image_view (bool, optional) – If
True
the PointCloud will be viewed as if it is in the image coordinate system. - render_lines (bool, optional) – If
True
, the edges will be rendered. - line_colour (See Below, optional) –
The colour of the lines. Example options:
{r, g, b, c, m, k, w} or (3, ) ndarray
- line_style (
{-, --, -., :}
, optional) – The style of the lines. - line_width (float, optional) – The width of the lines.
- render_markers (bool, optional) – If
True
, the markers will be rendered. - marker_style (See Below, optional) –
The style of the markers. Example options
{., ,, o, v, ^, <, >, +, x, D, d, s, p, *, h, H, 1, 2, 3, 4, 8}
- marker_size (int, optional) – The size of the markers in points^2.
- marker_face_colour (See Below, optional) –
The face (filling) colour of the markers. Example options
{r, g, b, c, m, k, w} or (3, ) ndarray
- marker_edge_colour (See Below, optional) –
The edge colour of the markers. Example options
{r, g, b, c, m, k, w} or (3, ) ndarray
- marker_edge_width (float, optional) – The width of the markers’ edge.
- render_numbering (bool, optional) – If
True
, the landmarks will be numbered. - numbers_horizontal_align (
{center, right, left}
, optional) – The horizontal alignment of the numbers’ texts. - numbers_vertical_align (
{center, top, bottom, baseline}
, optional) – The vertical alignment of the numbers’ texts. - numbers_font_name (See Below, optional) –
The font of the numbers. Example options
{serif, sans-serif, cursive, fantasy, monospace}
- numbers_font_size (int, optional) – The font size of the numbers.
- numbers_font_style (
{normal, italic, oblique}
, optional) – The font style of the numbers. - numbers_font_weight (See Below, optional) –
The font weight of the numbers. Example options
{ultralight, light, normal, regular, book, medium, roman, semibold, demibold, demi, bold, heavy, extra bold, black}
- numbers_font_colour (See Below, optional) –
The font colour of the numbers. Example options
{r, g, b, c, m, k, w} or (3, ) ndarray
- render_legend (bool, optional) – If
True
, the legend will be rendered. - legend_title (str, optional) – The title of the legend.
- legend_font_name (See below, optional) –
The font of the legend. Example options
{serif, sans-serif, cursive, fantasy, monospace}
- legend_font_style (
{normal, italic, oblique}
, optional) – The font style of the legend. - legend_font_size (int, optional) – The font size of the legend.
- legend_font_weight (See Below, optional) –
The font weight of the legend. Example options
{ultralight, light, normal, regular, book, medium, roman, semibold, demibold, demi, bold, heavy, extra bold, black}
- legend_marker_scale (float, optional) – The relative size of the legend markers with respect to the original
- legend_location (int, optional) –
The location of the legend. The predefined values are:
‘best’ 0 ‘upper right’ 1 ‘upper left’ 2 ‘lower left’ 3 ‘lower right’ 4 ‘right’ 5 ‘center left’ 6 ‘center right’ 7 ‘lower center’ 8 ‘upper center’ 9 ‘center’ 10 - legend_bbox_to_anchor ((float, float) tuple, optional) – The bbox that the legend will be anchored.
- legend_border_axes_pad (float, optional) – The pad between the axes and legend border.
- legend_n_columns (int, optional) – The number of the legend’s columns.
- legend_horizontal_spacing (float, optional) – The spacing between the columns.
- legend_vertical_spacing (float, optional) – The vertical space between the legend entries.
- legend_border (bool, optional) – If
True
, a frame will be drawn around the legend. - legend_border_padding (float, optional) – The fractional whitespace inside the legend border.
- legend_shadow (bool, optional) – If
True
, a shadow will be drawn behind legend. - legend_rounded_corners (bool, optional) – If
True
, the frame’s corners will be rounded (fancybox). - render_axes (bool, optional) – If
True
, the axes will be rendered. - axes_font_name (See Below, optional) –
The font of the axes. Example options
{serif, sans-serif, cursive, fantasy, monospace}
- axes_font_size (int, optional) – The font size of the axes.
- axes_font_style (
{normal, italic, oblique}
, optional) – The font style of the axes. - axes_font_weight (See Below, optional) –
The font weight of the axes. Example options
{ultralight, light, normal, regular, book, medium, roman, semibold,demibold, demi, bold, heavy, extra bold, black}
- axes_x_limits ((float, float) tuple or
None
optional) – The limits of the x axis. - axes_y_limits ((float, float) tuple or
None
optional) – The limits of the y axis. - figure_size ((float, float) tuple or
None
optional) – The size of the figure in inches.
Raises: ValueError
– If bothwith_labels
andwithout_labels
are passed.ValueError
– If the landmark manager doesn’t contain the provided group label.
- group (str or``None`` optional) – The landmark group to be visualized. If
-
as_pointgraph
(copy=True, skip_checks=False)[source]¶ Converts the TriMesh to a
PointUndirectedGraph
.Parameters: - copy (bool, optional) – If
True
, the graph will be a copy. - skip_checks (bool, optional) – If
True
, no checks will be performed.
Returns: pointgraph (
PointUndirectedGraph
) – The point graph.- copy (bool, optional) – If
-
as_vector
(**kwargs)¶ Returns a flattened representation of the object as a single vector.
Returns: vector ((N,) ndarray) – The core representation of the object, flattened into a single vector. Note that this is always a view back on to the original object, but is not writable.
-
boundary_tri_index
()[source]¶ Boolean index into triangles that are at the edge of the TriMesh
Returns: boundary_tri_index ( (n_tris,)
ndarray) – For each triangle (ABC), returns whether any of it’s edges is not also an edge of another triangle (and so this triangle exists on the boundary of the TriMesh)
-
bounding_box
()¶ Return a bounding box from two corner points as a directed graph. The the first point (0) should be nearest the origin. In the case of an image, this ordering would appear as:
0<--3 | ^ | | v | 1-->2
In the case of a pointcloud, the ordering will appear as:
3<--2 | ^ | | v | 0-->1
Returns: bounding_box ( PointDirectedGraph
) – The axis aligned bounding box of the PointCloud.
-
bounds
(boundary=0)¶ The minimum to maximum extent of the PointCloud. An optional boundary argument can be provided to expand the bounds by a constant margin.
Parameters: boundary (float) – A optional padding distance that is added to the bounds. Default is 0
, meaning the max/min of tightest possible containing square/cube/hypercube is returned.Returns: - min_b (
(n_dims,)
ndarray) – The minimum extent of thePointCloud
and boundary along each dimension - max_b (
(n_dims,)
ndarray) – The maximum extent of thePointCloud
and boundary along each dimension
- min_b (
-
centre
()¶ The mean of all the points in this PointCloud (centre of mass).
Returns: centre ( (n_dims)
ndarray) – The mean of this PointCloud’s points.
-
centre_of_bounds
()¶ The centre of the absolute bounds of this PointCloud. Contrast with
centre()
, which is the mean point position.Returns: centre ( n_dims
ndarray) – The centre of the bounds of this PointCloud.
-
copy
()¶ Generate an efficient copy of this object.
Note that Numpy arrays and other
Copyable
objects onself
will be deeply copied. Dictionaries and sets will be shallow copied, and everything else will be assigned (no copy will be made).Classes that store state other than numpy arrays and immutable types should overwrite this method to ensure all state is copied.
Returns: type(self)
– A copy of this object
-
distance_to
(pointcloud, **kwargs)¶ Returns a distance matrix between this PointCloud and another. By default the Euclidean distance is calculated - see scipy.spatial.distance.cdist for valid kwargs to change the metric and other properties.
Parameters: pointcloud ( PointCloud
) – The second pointcloud to compute distances between. This must be of the same dimension as this PointCloud.Returns: distance_matrix ( (n_points, n_points)
ndarray) – The symmetric pairwise distance matrix between the two PointClouds s.t.distance_matrix[i, j]
is the distance between the i’th point of this PointCloud and the j’th point of the input PointCloud.
-
edge_indices
()[source]¶ An unordered index into points that rebuilds the edges of this
TriMesh
.Note that there will be two edges present in cases where two triangles ‘share’ an edge. Consider
unique_edge_indices()
for a single index for each physical edge on theTriMesh
.Returns: edge_indices ( (n_tris * 3, 2)
ndarray) – For each triangle (ABC), returns the pair of point indices that rebuild AB, AC, BC. All edge indices are concatenated for a total ofn_tris * 3
edge_indices. The ordering is done so that all AB vectors are first in the returned list, followed by BC, then CA.
-
edge_lengths
()[source]¶ The length of each edge in this
TriMesh
.Note that there will be two edges present in cases where two triangles ‘share’ an edge. Consider
unique_edge_indices()
for a single index for each physical edge on theTriMesh
. The ordering matches the case for edges and edge_indices.Returns: edge_lengths ( (n_tris * 3, )
ndarray) – Scalar euclidean lengths for each edge in thisTriMesh
.
-
edge_vectors
()[source]¶ A vector of edges of each triangle face.
Note that there will be two edges present in cases where two triangles ‘share’ an edge. Consider
unique_edge_vectors()
for a single vector for each physical edge on theTriMesh
.Returns: edges ( (n_tris * 3, n_dims)
ndarray) – For each triangle (ABC), returns the edge vectors AB, BC, CA. All edges are concatenated for a total ofn_tris * 3
edges. The ordering is done so that all AB vectors are first in the returned list, followed by BC, then CA.
-
from_mask
(mask)[source]¶ A 1D boolean array with the same number of elements as the number of points in the TriMesh. This is then broadcast across the dimensions of the mesh and returns a new mesh containing only those points that were
True
in the mask.Parameters: mask ( (n_points,)
ndarray) – 1D array of booleansReturns: mesh ( TriMesh
) – A new mesh that has been masked.
-
from_vector
(vector)¶ Build a new instance of the object from it’s vectorized state.
self
is used to fill out the missing state required to rebuild a full object from it’s standardized flattened state. This is the default implementation, which is which is adeepcopy
of the object followed by a call tofrom_vector_inplace()
. This method can be overridden for a performance benefit if desired.Parameters: vector ( (n_parameters,)
ndarray) – Flattened representation of the object.Returns: object ( type(self)
) – An new instance of this class.
-
from_vector_inplace
(vector)¶ Updates the points of this PointCloud in-place with the reshaped points from the provided vector. Note that the vector should have the form
[x0, y0, x1, y1, ....., xn, yn]
for 2D.Parameters: vector ( (n_points,)
ndarray) – The vector from which to create the points’ array.
-
h_points
()¶ Convert poincloud to a homogeneous array:
(n_dims + 1, n_points)
Type: type(self)
-
has_nan_values
()¶ Tests if the vectorized form of the object contains
nan
values or not. This is particularly useful for objects with unknown values that have been mapped tonan
values.Returns: has_nan_values (bool) – If the vectorized object contains nan
values.
-
mean_edge_length
(unique=True)[source]¶ The mean length of each edge in this
TriMesh
.Parameters: unique (bool, optional) – If True
, each shared edge will only be counted once towards the average. If false, shared edges will be counted twice.Returns: mean_edge_length ( float
) – The mean length of each edge in thisTriMesh
-
mean_tri_area
()[source]¶ The mean area of each triangle face in this
TriMesh
.Returns: mean_tri_area ( float
) – The mean area of each triangle face in thisTriMesh
Raises: ValueError
– If mesh is not 3D
-
norm
(**kwargs)¶ Returns the norm of this PointCloud. This is a translation and rotation invariant measure of the point cloud’s intrinsic size - in other words, it is always taken around the point cloud’s centre.
By default, the Frobenius norm is taken, but this can be changed by setting kwargs - see
numpy.linalg.norm
for valid options.Returns: norm (float) – The norm of this PointCloud
-
range
(boundary=0)¶ The range of the extent of the PointCloud.
Parameters: boundary (float) – A optional padding distance that is used to extend the bounds from which the range is computed. Default is 0
, no extension is performed.Returns: range ( (n_dims,)
ndarray) – The range of thePointCloud
extent in each dimension.
-
tojson
()[source]¶ Convert this
TriMesh
to a dictionary representation suitable for inclusion in the LJSON landmark format. Note that this enforces a simpler representation, and as such is not suitable for a permanent serialization of aTriMesh
(to be clear,TriMesh
‘s serialized as part of a landmark set will be rebuilt as aPointUndirectedGraph
).Returns: json (dict) – Dictionary with points
andconnectivity
keys.
-
tri_areas
()[source]¶ The area of each triangle face.
Returns: areas ( (n_tris,)
ndarray) – Area of each triangle, ordered as the trilist isRaises: ValueError
– If mesh is not 2D or 3D
-
tri_normals
()[source]¶ Compute the triangle face normals from the current set of points and triangle list. Only valid for 3D dimensional meshes.
Returns: normals ( (n_tris, 3)
ndarray) – Normal at each triangle face.Raises: ValueError
– If mesh is not 3D
-
unique_edge_indicies
()[source]¶ An unordered index into points that rebuilds the unique edges of this
TriMesh
.Note that each physical edge will only be counted once in this method (i.e. edges shared between neighbouring triangles are only counted once not twice). The ordering should be considered random.
Returns: unique_edge_indicies ( (n_unique_edges, 2)
ndarray) – Return a point index that rebuilds all edges present in thisTriMesh
only once.
-
unique_edge_lengths
()[source]¶ The length of each edge in this
TriMesh
.Note that each physical edge will only be counted once in this method (i.e. edges shared between neighbouring triangles are only counted once not twice). The ordering should be considered random.
Returns: edge_lengths ( (n_tris * 3, )
ndarray) – Scalar euclidean lengths for each edge in thisTriMesh
.
-
unique_edge_vectors
()[source]¶ An unordered vector of unique edges for the whole
TriMesh
.Note that each physical edge will only be counted once in this method (i.e. edges shared between neighbouring triangles are only counted once not twice). The ordering should be considered random.
Returns: unique_edge_vectors ( (n_unique_edges, n_dims)
ndarray) – Vectors for each unique edge in thisTriMesh
.
-
vertex_normals
()[source]¶ Compute the per-vertex normals from the current set of points and triangle list. Only valid for 3D dimensional meshes.
Returns: normals ( (n_points, 3)
ndarray) – Normal at each point.Raises: ValueError
– If mesh is not 3D
-
view_widget
(browser_style='buttons', figure_size=(10, 8), style='coloured')[source]¶ Visualization of the TriMesh using the
visualize_pointclouds
widget.Parameters: - browser_style ({
'buttons'
,'slider'
}, optional) – It defines whether the selector of the objects will have the form of plus/minus buttons or a slider. - figure_size ((int, int) tuple, optional) – The initial size of the rendered figure.
- style ({
'coloured'
,'minimal'
}, optional) – If'coloured'
, then the style of the widget will be coloured. Ifminimal
, then the style is simple using black and white colours.
- browser_style ({
-
has_landmarks
¶ Whether the object has landmarks.
Type: bool
-
landmarks
¶ The landmarks object.
Type: LandmarkManager
-
n_dims
¶ The number of dimensions in the pointcloud.
Type: int
-
n_landmark_groups
¶ The number of landmark groups on this object.
Type: int
-
n_parameters
¶ The length of the vector that this object produces.
Type: int
-
n_points
¶ The number of points in the pointcloud.
Type: int
-
n_tris
¶ The number of triangles in the triangle list.
Type: int
- points (