PointCloud¶

class
menpo.shape.
PointCloud
(points, copy=True)[source]¶ Bases:
Shape
An Ndimensional point cloud. This is internally represented as an ndarray of shape
(n_points, n_dims)
. This class is important for dealing with complex functionality such as viewing and representing metadata such as landmarks.Currently only 2D and 3D pointclouds are viewable.
 Parameters
points (
(n_points, n_dims)
ndarray) – The array representing the points.copy (bool, optional) – If
False
, the points will not be copied on assignment. Note that this will miss out on additional checks. Further note that we still demand that the array is Ccontiguous  if it isn’t, a copy will be generated anyway. 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_markers=True, marker_style='o', marker_size=5, marker_face_colour='r', marker_edge_colour='k', marker_edge_width=1.0, render_numbering=False, numbers_horizontal_align='center', numbers_vertical_align='bottom', numbers_font_name='sansserif', numbers_font_size=10, numbers_font_style='normal', numbers_font_weight='normal', numbers_font_colour='k', render_axes=True, axes_font_name='sansserif', axes_font_size=10, axes_font_style='normal', axes_font_weight='normal', axes_x_limits=None, axes_y_limits=None, axes_x_ticks=None, axes_y_ticks=None, figure_size=(7, 7), label=None, **kwargs)[source]¶ Visualization of the PointCloud 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 PointCloud will be viewed as if it is in the image coordinate system.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.
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, sansserif, 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_axes (bool, optional) – If
True
, the axes will be rendered.axes_font_name (See Below, optional) – The font of the axes. Example options
{serif, sansserif, 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 or (float, float) or
None
, optional) – The limits of the x axis. If float, then it sets padding on the right and left of the PointCloud as a percentage of the PointCloud’s width. If tuple or list, then it defines the axis limits. IfNone
, then the limits are set automatically.axes_y_limits ((float, float) tuple or
None
, optional) – The limits of the y axis. If float, then it sets padding on the top and bottom of the PointCloud as a percentage of the PointCloud’s height. If tuple or list, then it defines the axis limits. IfNone
, then the limits are set automatically.axes_x_ticks (list or tuple or
None
, optional) – The ticks of the x axis.axes_y_ticks (list or tuple or
None
, optional) – The ticks 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_markers=True, marker_style='s', marker_size=7, marker_face_colour='k', marker_edge_colour='k', marker_edge_width=1.0, render_lines_lms=True, line_colour_lms=None, line_style_lms='', line_width_lms=1, render_markers_lms=True, marker_style_lms='o', marker_size_lms=5, marker_face_colour_lms=None, marker_edge_colour_lms=None, marker_edge_width_lms=1.0, render_numbering=False, numbers_horizontal_align='center', numbers_vertical_align='bottom', numbers_font_name='sansserif', numbers_font_size=10, numbers_font_style='normal', numbers_font_weight='normal', numbers_font_colour='k', render_legend=False, legend_title='', legend_font_name='sansserif', 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='sansserif', axes_font_size=10, axes_font_style='normal', axes_font_weight='normal', axes_x_limits=None, axes_y_limits=None, axes_x_ticks=None, axes_y_ticks=None, figure_size=(7, 7))[source]¶ Visualize the landmarks. This method will appear on the PointCloud as
view_landmarks
. 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_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.
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_lines_lms (bool, optional) – If
True
, the edges of the landmarks will be rendered.line_colour_lms (See Below, optional) –
The colour of the lines of the landmarks. Example options:
{r, g, b, c, m, k, w} or (3, ) ndarray
line_style_lms (
{, , ., :}
, optional) – The style of the lines of the landmarks.line_width_lms (float, optional) – The width of the lines of the landmarks.
render_markers – If
True
, the markers of the landmarks will be rendered.marker_style –
The style of the markers of the landmarks. Example options
{., ,, o, v, ^, <, >, +, x, D, d, s, p, *, h, H, 1, 2, 3, 4, 8}
marker_size – The size of the markers of the landmarks in points.
marker_face_colour –
The face (filling) colour of the markers of the landmarks. Example options
{r, g, b, c, m, k, w} or (3, ) ndarray
marker_edge_colour –
The edge colour of the markers of the landmarks. Example options
{r, g, b, c, m, k, w} or (3, ) ndarray
marker_edge_width – The width of the markers’ edge of the landmarks.
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, sansserif, 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, sansserif, 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, sansserif, 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 or (float, float) or
None
, optional) – The limits of the x axis. If float, then it sets padding on the right and left of the PointCloud as a percentage of the PointCloud’s width. If tuple or list, then it defines the axis limits. IfNone
, then the limits are set automatically.axes_y_limits ((float, float) tuple or
None
, optional) – The limits of the y axis. If float, then it sets padding on the top and bottom of the PointCloud as a percentage of the PointCloud’s height. If tuple or list, then it defines the axis limits. IfNone
, then the limits are set automatically.axes_x_ticks (list or tuple or
None
, optional) – The ticks of the x axis.axes_y_ticks (list or tuple or
None
, optional) – The ticks of the y axis.figure_size ((float, float) tuple or
None
optional) – The size of the figure in inches.
 Raises
ValueError – If both
with_labels
andwithout_labels
are passed.ValueError – If the landmark manager doesn’t contain the provided group label.

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
()[source]¶ Return a bounding box from two corner points as a directed graph. In the case of a 2D pointcloud, 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
In the case of a 3D pointcloud, the first point (0) should be the near closest to the origin and the second point is the far opposite corner.
 Returns
bounding_box (
PointDirectedGraph
) – The axis aligned bounding box of the PointCloud.

bounds
(boundary=0)[source]¶ 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 dimensionmax_b (
(n_dims,)
ndarray) – The maximum extent of thePointCloud
and boundary along each dimension

centre
()[source]¶ 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
()[source]¶ 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.

constrain_to_bounds
(bounds)[source]¶ Returns a copy of this PointCloud, constrained to lie exactly within the given bounds. Any points outside the bounds will be ‘snapped’ to lie exactly on the boundary.
 Parameters
bounds (
(n_dims, n_dims)
tuple of scalars) – The bounds to constrain this pointcloud within. Returns
constrained (
PointCloud
) – The constrained 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)[source]¶ 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.

from_mask
(mask)[source]¶ A 1D boolean array with the same number of elements as the number of points in the PointCloud. This is then broadcast across the dimensions of the PointCloud and returns a new PointCloud containing only those points that were
True
in the mask. Parameters
mask (
(n_points,)
ndarray) – 1D array of booleans Returns
pointcloud (
PointCloud
) – A new pointcloud that has been masked. Raises
ValueError – Mask must have same number of points as pointcloud.

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)¶ Deprecated. Use the nonmutating API,
from_vector
.For internal usage in performancesensitive spots, see _from_vector_inplace()
 Parameters
vector (
(n_parameters,)
ndarray) – Flattened representation of this object

h_points
()[source]¶ 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.

classmethod
init_2d_grid
(shape, spacing=None)[source]¶ Create a pointcloud that exists on a regular 2D grid. The first dimension is the number of rows in the grid and the second dimension of the shape is the number of columns.
spacing
optionally allows the definition of the distance between points (uniform over points). The spacing may be different for rows and columns. Parameters
shape (tuple of 2 int) – The size of the grid to create, this defines the number of points across each dimension in the grid. The first element is the number of rows and the second is the number of columns.
spacing (int or tuple of 2 int, optional) – The spacing between points. If a single int is provided, this is applied uniformly across each dimension. If a tuple is provided, the spacing is applied nonuniformly as defined e.g.
(2, 3)
gives a spacing of 2 for the rows and 3 for the columns.
 Returns
shape_cls (type(cls)) – A PointCloud or subclass arranged in a grid.

classmethod
init_from_depth_image
(depth_image)[source]¶ Return a 3D point cloud from the given depth image. The depth image is assumed to represent height/depth values and the XY coordinates are assumed to unit spaced and represent image coordinates. This is particularly useful for visualising depth values that have been recovered from images.
 Parameters
depth_image (
Image
or subclass) – A single channel image that contains depth values  as commonly returned by RGBD cameras, for example. Returns
depth_cloud (
type(cls)
) – A new 3D PointCloud with unit XY coordinates and the given depth values as Z coordinates.

norm
(**kwargs)[source]¶ 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)[source]¶ 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
PointCloud
to a dictionary representation suitable for inclusion in the LJSON landmark format. Returns
json (dict) – Dictionary with
points
keys.

with_dims
(dims)[source]¶ Return a copy of this shape with only particular dimensions retained.
 Parameters
dims (valid numpy array slice) – The slice that will be used on the dimensionality axis of the shape under transform. For example, to go from a 3D shape to a 2D one, [0, 1] could be provided or np.array([True, True, False]).
 Returns
copy of self, with only the requested dims

property
has_landmarks
¶ Whether the object has landmarks.
 Type
bool

property
landmarks
¶ The landmarks object.
 Type

property
lms
¶ Deprecated. Maintained for compatibility, will be removed in a future version. Returns a copy of this object, which previously would have held the ‘underlying’
PointCloud
subclass. Type
self

property
n_dims
¶ The number of dimensions in the pointcloud.
 Type
int

property
n_landmark_groups
¶ The number of landmark groups on this object.
 Type
int

property
n_parameters
¶ The length of the vector that this object produces.
 Type
int

property
n_points
¶ The number of points in the pointcloud.
 Type
int