PointDirectedGraph¶
-
class
menpo.shape.
PointDirectedGraph
(points, adjacency_array, copy=True)[source]¶ Bases:
PointGraph
,DirectedGraph
Class for defining a directed graph with geometry.
Parameters: - points (
(n_points, n_dims)
ndarray) – The array representing the points. - adjacency_array (
(n_edges, 2, )
ndarray) –The adjacency array of the graph, i.e. an array containing the sets of the graph’s edges. The numbering of vertices is assumed to start from 0. For example
|-->0<--| adjacency_array = ndarray([[1, 0], | | [2, 0], | | [1, 2], 1<----->2 [2, 1], | | [1, 3], v v [2, 4], 3------>4 [3, 4], | [3, 5]]) v 5
- copy (bool, optional) – If
False
, theadjacency_list
will not be copied on assignment.
Raises: ValueError
– A point for each graph vertex needs to be passed. Got {n_points} points instead of {n_vertices}.-
_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)¶ Visualization of the pointgraph 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 PointGraph 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_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.
-
bounding_box
()¶ Return the bounding box of this PointCloud as a directed graph. The the first point (0) will be nearest the origin for an axis aligned Pointcloud. In the case of an image, this ordering would appear as:
0<--3 | ^ | | v | 1-->2
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.
-
children
(vertex)¶ Returns the children of the selected vertex.
Parameters: vertex (int) – The selected vertex. Returns: children (list) – The list of children. Raises: ValueError
– The vertex must be between 0 and {n_vertices-1}.
-
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.
-
find_all_paths
(start, end, path=[])¶ Returns a list of lists with all the paths (without cycles) found from start vertex to end vertex.
Parameters: - start (int) – The vertex from which the paths start.
- end (int) – The vertex from which the paths end.
- path (list, optional) – An existing path to append to.
Returns: paths (list of list) – The list containing all the paths from start to end.
-
find_path
(start, end, path=None)¶ Returns a list with the first path (without cycles) found from start vertex to end vertex.
Parameters: - start (int) – The vertex from which the path starts.
- end (int) – The vertex from which the path ends.
- path (list, optional) – An existing path to append to.
Returns: path (list) – The path’s vertices.
-
find_shortest_path
(start, end, path=None)¶ Returns a list with the shortest path (without cycles) found from start vertex to end vertex.
Parameters: - start (int) – The vertex from which the path starts.
- end (int) – The vertex from which the path ends.
- path (list, optional) – An existing path to append to.
Returns: path (list) – The shortest path’s vertices.
-
from_mask
(mask)[source]¶ A 1D boolean array with the same number of elements as the number of points in the PointDirectedGraph. This is then broadcast across the dimensions of the PointDirectedGraph and returns a new PointDirectedGraph containing only those points that were
True
in the mask.Parameters: mask ( (n_points,)
ndarray) – 1D array of booleansReturns: pointgraph ( PointDirectedGraph
) – A new pointgraph that has been masked.Raises: ValueError
– Mask must have same number of points as pointgraph.
-
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.
-
get_adjacency_matrix
()¶ Returns the Adjacency Matrix of the graph, i.e. the boolean ndarray that is
True
andFalse
if there is an edge connecting the two vertices or not respectively.Type: (n_vertices, n_vertices, )
ndarray
-
h_points
()¶ Convert poincloud to a homogeneous array:
(n_dims + 1, n_points)
Type: type(self)
-
has_cycles
()¶ Whether the graph has at least on cycle.
Returns: has_cycles (bool) – True
if it has at least one cycle.
-
is_edge
(parent, child)¶ Returns whether there is an edge between the provided vertices.
Parameters: - parent (int) – The first selected vertex which is considered as the parent.
- child (int) – The second selected vertex which is considered as the child.
Returns: is_edge (bool) – True if there is an edge.
Raises: ValueError
– The vertex must be in the range[0, n_vertices - 1]
.
-
is_tree
()¶ Checks if the graph is tree.
Returns: is_true (bool) – If the graph is a tree.
-
n_children
(vertex)¶ Returns the number of children of the selected vertex.
Parameters: vertex (int) – The selected vertex. Returns: n_children (int) – The number of children. Raises: ValueError
– The vertex must be in the range[0, n_vertices - 1]
.
-
n_parent
(vertex)¶ Returns the number of parents of the selected vertex.
Parameters: vertex (int) – The selected vertex. Returns: n_parent (int) – The number of parents. Raises: ValueError
– The vertex must be in the range[0, n_vertices - 1]
.
-
n_paths
(start, end)¶ Returns the number of all the paths (without cycles) existing from start vertex to end vertex.
Parameters: - start (int) – The vertex from which the paths start.
- end (int) – The vertex from which the paths end.
Returns: paths (int) – The paths’ numbers.
-
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
-
parent
(vertex)¶ Returns the parents of the selected vertex.
Parameters: vertex (int) – The selected vertex. Returns: parent (list) – The list of parents. Raises: ValueError
– The vertex must be in the range[0, n_vertices - 1]
.
-
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.
-
relative_location_edge
(parent, child)[source]¶ Returns the relative location between the provided vertices. That is if vertex j is the parent and vertex i is its child and vector l denotes the coordinates of a vertex, then
l_i - l_j = [[x_i], [y_i]] - [[x_j], [y_j]] = = [[x_i - x_j], [y_i - y_j]]
Parameters: - parent (int) – The first selected vertex which is considered as the parent.
- child (int) – The second selected vertex which is considered as the child.
Returns: relative_location (
(2,)
ndarray) – The relative location vector.Raises: ValueError
– Verticesparent
andchild
are not connected with an edge.
-
relative_locations
()[source]¶ Returns the relative location between the vertices of each edge. If vertex j is the parent and vertex i is its child and vector l denotes the coordinates of a vertex, then:
l_i - l_j = [[x_i], [y_i]] - [[x_j], [y_j]] = = [[x_i - x_j], [y_i - y_j]]
Returns: relative_locations ( (n_vertexes, 2)
ndarray) – The relative locations vector.
-
tojson
()¶ Convert this
PointGraph
to a dictionary representation suitable for inclusion in the LJSON landmark format.Returns: json (dict) – Dictionary with points
andconnectivity
keys.
-
view_widget
(popup=False, browser_style='buttons', figure_size=(10, 8))¶ Visualization of the PointGraph using the
visualize_pointclouds
widget.Parameters: - popup (bool, optional) – If
True
, the widget will be rendered in a popup window. - browser_style (
{buttons, slider}
, optional) – It defines whether the selector of the PointGraph 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.
- popup (bool, optional) – If
-
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_edges
¶ Returns the number of the graph edges.
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_vertices
¶ Returns the number of the graph vertices.
Type: int
- points (