Using the shapes layer#

In this document, you will learn about the napari Shapes layer, including how to display and edit shapes like rectangle, ellipses, polygons, paths, and lines. You will also understand how to add a shapes layer and edit it from the GUI and from the console.

When to use the shapes layer#

The Shapes layer allows you to display a list of an NxD arrays, where each array corresponds to one shape, specified by N points in D coordinates. You can adjust the position, size, face color, edge color, and opacity of all the shapes independently, both programmatically and from the GUI.

A simple example#

You can create a new viewer and add a list of shapes in one go using the napari.view_shapes method, or if you already have an existing viewer, you can add shapes to it using viewer.add_shapes. The api of both methods is the same. In these examples we’ll mainly use add_shapes to overlay shapes onto on an existing image.

In this example, we will overlay some shapes on the image of a photographer:

import napari
import numpy as np
from skimage import data

# create the list of polygons
triangle = np.array([[11, 13], [111, 113], [22, 246]])

person = np.array([[505, 60], [402, 71], [383, 42], [251, 95], [212, 59],
                   [131, 137], [126, 187], [191, 204], [171, 248], [211, 260],
                   [273, 243], [264, 225], [430, 173], [512, 160]])

building = np.array([[310, 382], [229, 381], [209, 401], [221, 411],
                     [258, 411], [300, 412], [306, 435], [268, 434],
                     [265, 454], [298, 461], [307, 461], [307, 507],
                     [349, 510], [352, 369], [330, 366], [330, 366]])

polygons = [triangle, person, building]

# add the image
viewer = napari.view_image(data.camera(), name='photographer')

# add the polygons
shapes_layer = viewer.add_shapes(polygons, shape_type='polygon', edge_width=5,
                          edge_color='coral', face_color='royalblue')
Hide code cell source 
from napari.utils import nbscreenshot

nbscreenshot(viewer, alt_text="Shapes overlaid on image")
Shapes overlaid on image

Arguments of view_shapes and add_shapes#

view_shapes() and add_shapes() accept the same layer-creation parameters.

Hide code cell content 
help(napari.view_shapes)

Help on function view_shapes in module napari.view_layers:

view_shapes(data=None, *, ndim=None, features=None, feature_defaults=None, properties=None, property_choices=None, text=None, shape_type='rectangle', edge_width=1, edge_color='#777777', edge_color_cycle=None, edge_colormap='viridis', edge_contrast_limits=None, face_color='white', face_color_cycle=None, face_colormap='viridis', face_contrast_limits=None, z_index=0, name=None, metadata=None, scale=None, translate=None, rotate=None, shear=None, affine=None, opacity=0.7, blending='translucent', visible=True, cache=True, experimental_clipping_planes=None, title='napari', ndisplay=2, order=(), axis_labels=(), show=True) -> napari.viewer.Viewer
    Create a viewer and add a shapes layer.
    
    Parameters
    ----------
    data : list or array
        List of shape data, where each element is an (N, D) array of the
        N vertices of a shape in D dimensions. Can be an 3-dimensional
        array if each shape has the same number of vertices.
    ndim : int
        Number of dimensions for shapes. When data is not None, ndim must be D.
        An empty shapes layer can be instantiated with arbitrary ndim.
    features : dict[str, array-like] or Dataframe-like
        Features table where each row corresponds to a shape and each column
        is a feature.
    feature_defaults : dict[str, Any] or Dataframe-like
        The default value of each feature in a table with one row.
    properties : dict {str: array (N,)}, DataFrame
        Properties for each shape. Each property should be an array of length N,
        where N is the number of shapes.
    property_choices : dict {str: array (N,)}
        possible values for each property.
    text : str, dict
        Text to be displayed with the shapes. If text is set to a key in properties,
        the value of that property will be displayed. Multiple properties can be
        composed using f-string-like syntax (e.g., '{property_1}, {float_property:.2f}).
        A dictionary can be provided with keyword arguments to set the text values
        and display properties. See TextManager.__init__() for the valid keyword arguments.
        For example usage, see /napari/examples/add_shapes_with_text.py.
    shape_type : string or list
        String of shape shape_type, must be one of "{'line', 'rectangle',
        'ellipse', 'path', 'polygon'}". If a list is supplied it must be
        the same length as the length of `data` and each element will be
        applied to each shape otherwise the same value will be used for all
        shapes.
    edge_width : float or list
        Thickness of lines and edges. If a list is supplied it must be the
        same length as the length of `data` and each element will be
        applied to each shape otherwise the same value will be used for all
        shapes.
    edge_color : str, array-like
        If string can be any color name recognized by vispy or hex value if
        starting with `#`. If array-like must be 1-dimensional array with 3
        or 4 elements. If a list is supplied it must be the same length as
        the length of `data` and each element will be applied to each shape
        otherwise the same value will be used for all shapes.
    edge_color_cycle : np.ndarray, list
        Cycle of colors (provided as string name, RGB, or RGBA) to map to edge_color if a
        categorical attribute is used color the vectors.
    edge_colormap : str, napari.utils.Colormap
        Colormap to set edge_color if a continuous attribute is used to set face_color.
    edge_contrast_limits : None, (float, float)
        clims for mapping the property to a color map. These are the min and max value
        of the specified property that are mapped to 0 and 1, respectively.
        The default value is None. If set the none, the clims will be set to
        (property.min(), property.max())
    face_color : str, array-like
        If string can be any color name recognized by vispy or hex value if
        starting with `#`. If array-like must be 1-dimensional array with 3
        or 4 elements. If a list is supplied it must be the same length as
        the length of `data` and each element will be applied to each shape
        otherwise the same value will be used for all shapes.
    face_color_cycle : np.ndarray, list
        Cycle of colors (provided as string name, RGB, or RGBA) to map to face_color if a
        categorical attribute is used color the vectors.
    face_colormap : str, napari.utils.Colormap
        Colormap to set face_color if a continuous attribute is used to set face_color.
    face_contrast_limits : None, (float, float)
        clims for mapping the property to a color map. These are the min and max value
        of the specified property that are mapped to 0 and 1, respectively.
        The default value is None. If set the none, the clims will be set to
        (property.min(), property.max())
    z_index : int or list
        Specifier of z order priority. Shapes with higher z order are
        displayed ontop of others. If a list is supplied it must be the
        same length as the length of `data` and each element will be
        applied to each shape otherwise the same value will be used for all
        shapes.
    name : str
        Name of the layer.
    metadata : dict
        Layer metadata.
    scale : tuple of float
        Scale factors for the layer.
    translate : tuple of float
        Translation values for the layer.
    rotate : float, 3-tuple of float, or n-D array.
        If a float convert into a 2D rotation matrix using that value as an
        angle. If 3-tuple convert into a 3D rotation matrix, using a yaw,
        pitch, roll convention. Otherwise assume an nD rotation. Angles are
        assumed to be in degrees. They can be converted from radians with
        np.degrees if needed.
    shear : 1-D array or n-D array
        Either a vector of upper triangular values, or an nD shear matrix with
        ones along the main diagonal.
    affine : n-D array or napari.utils.transforms.Affine
        (N+1, N+1) affine transformation matrix in homogeneous coordinates.
        The first (N, N) entries correspond to a linear transform and
        the final column is a length N translation vector and a 1 or a napari
        `Affine` transform object. Applied as an extra transform on top of the
        provided scale, rotate, and shear values.
    opacity : float
        Opacity of the layer visual, between 0.0 and 1.0.
    blending : str
        One of a list of preset blending modes that determines how RGB and
        alpha values of the layer visual get mixed. Allowed values are
        {'opaque', 'translucent', and 'additive'}.
    visible : bool
        Whether the layer visual is currently being displayed.
    cache : bool
        Whether slices of out-of-core datasets should be cached upon retrieval.
        Currently, this only applies to dask arrays.
        title : string, optional
        The title of the viewer window. By default 'napari'.
    ndisplay : {2, 3}, optional
        Number of displayed dimensions. By default 2.
    order : tuple of int, optional
        Order in which dimensions are displayed where the last two or last
        three dimensions correspond to row x column or plane x row x column if
        ndisplay is 2 or 3. By default None
    axis_labels : list of str, optional
        Dimension names. By default they are labeled with sequential numbers
    show : bool, optional
        Whether to show the viewer after instantiation. By default True.
    
    
    Returns
    -------
    viewer : :class:`napari.Viewer`
        The newly-created viewer.

Shapes data#

The input data to the shapes layer must be a list of NxD numpy array, with each array containing the coordinates of the N vertices in D dimensions that make up the shape. The ordering of these dimensions is the same as the ordering of the dimensions for image layers. This list of arrays is always accessible through the layer.data property and will grow or shrink as new shapes are either added or deleted. By storing data as a list of arrays it is possible for each shape to have a different number of vertices in it. This is especially useful when drawing polygons or paths.

Adding different shape types#

Right now the shapes layer supports 5 types of shapes, Lines, Rectangles, Ellipses, Polygons, and Paths. When adding new data can set the shape type through the shape_type keyword argument, as either a single shape type if all the shapes to be added have the same type or as a list of shape types if some of the shapes have different types. The actual shape types of all the shapes is accessible through the layer.shape_types property. Selecting different shape creation tools will cause shapes of the different types to be added.

Lines consist of two vertices representing the end points of the line. The line creation tool can be selected from the layer control panel or by pressing the L key when the shapes layer is selected. When adding a new line the first click will coordinates of the first endpoint and the second click will mark the coordinates of the second endpoint. You’ll then be able to add another line.

Rectangles can be added using two vertices representing the corners of the rectangle for axis aligned rectangle, or using four corners so that non-axis aligned rectangle can be represented too. Internally we use the four vertex representation so we can always support rotated rectangles. The rectangle creation tool can be selected from the layer control panel or by pressing the R key when the shapes layer is selected. When adding a rectangle you must click and drag the rectangle to have the desired shape. When you release the mouse the rectangle will be completed and you’ll then be able to add another one. If you just make a single click then a rectangle of default size will be created centered on that click.

Ellipses can be added using either two vectors, one representing the center position of the ellipse and the other representing the radii of the ellipse in all dimensions for an axis aligned ellipse, or by using the four corners of the ellipse bounding box for a non-axis aligned ellipse. Internally we use the four vertex representation so we can always support rotated ellipses. The ellipse creation tool can be selected from the layer control panel or by pressing the E key when the shapes layer is selected. When adding an ellipse you must click and drag the ellipse to have the desired shape. When you release the mouse the ellipse will be completed and you’ll then be able to add another one. If you just make a single click then an ellipse of default size will be created centered on that click.

Polygons can be added using an array of N vertices. Polygons are closed by default, and so you don’t also need to include the first point at the end of the array. The order of the vertices will determine the triangulation of the polygon, which can be non-convex, but cannot have holes. For drawing polygons, multiple tools can be used. The polygon creation tool can be selected from the layer control panel or by pressing the P key when the shapes layer is selected. When adding a polygon each click will add a vertex at the clicked location. To finish drawing a polygon you must click theescape key, which will add a final vertex at the current mouse position and complete the polygon. You’ll then be able to start adding another one.

Polygons can also be created with the polygon lasso creation tool, which can be found in the layer control panel or by pressing shift+P. The tool can be used to draw complex Polygons with the mouse or tablet. When using the mouse, the sequence of events to draw a polygon is as follows:

  1. Click mouse (left-click) to begin drawing.

  2. Move mouse — without holding down the mouse button — to draw the polygon.

  3. Click mouse (left-click) or press escape to end drawing—the polygon will auto-complete.

The polygon lasso tool can also be used to draw Polygons using a tablet. In this case, drawing the polygon is started by touching the tablet screen with the tablet stylus and drawing will continue for as long as the pencil is moved while touching the tablet screen. Note that similar behavior is also available when using a macOS trackpad, using three-finger drag mode.
For both modes, vertices are added only if the vertex to be added is at a certain number of screen pixels away from the previous vertex. This value can be adjusted in the settings in napari by going to File -> Preferences (or control + shift + P), then in the menu on the left-clicking on Experimental and then adjusting the value of Minimum distance threshold of shapes lasso tool. The default is 10 and can be any integer higher than 0 and lower than 50. As with the polygon creation tool drawing the shape can also be finished by pressing the escape key.

After finishing drawing a polygon using the polygon lasso tool, an implementation of the Ramer–Douglas–Peucker algorithm is applied to reduce the number of vertices that make up the shape, while preserving its contours. The aggressiveness with which the algorithm reduces the number of vertices of the polygon is determined by an epsilon parameter, which is a perpendicular distance threshold. Any vertices beyond the threshold will be preserved, so if epsilon is set to 0, no vertices will be removed. With increasing values of epsilon, more and more vertices will be removed. The value of epsilon can be set in napari by going to File -> Preferences (or control + shift + P), then in the menu on the left-clicking on Experimental and then adjusting the value of RDP epsilon. The default value is 0.5 and cannot set lower than 0.

Paths are like polygons but are not closed or filled in. They can also be added using an array of N vertices. The path creation tool can be selected from the layer control panel or by pressing the T key when the shapes layer is selected. When adding a path each click will add a vertex at the clicked location. To finish drawing a path you must click the escape key, which will add a final vertex at the current mouse position and complete the path. You’ll then be able to start adding another one.

When using the shapes addition or editing tools the pan and zoom functionality of the viewer canvas is disabled and you can edit the layer. You can temporarily re-enable pan and zoom by pressing and holding the spacebar. This feature can be useful if you want to move around the shapes layer as you edit it.

Adding new shapes#

You can add new shapes to an existing Shapes layer programmatically by using the add method, which allows you to pass in a shape_type list when you have mixed shape data.

import napari
import numpy as np
from skimage import data

# add the image
viewer = napari.view_image(data.camera(), name='photographer')

# create a triangle
triangle = np.array([[11, 13], [111, 113], [22, 246]])

# create an ellipse
ellipse = np.array([[59, 222], [110, 289], [170, 243], [119, 176]])

# put both shapes in a list
mixed_shapes = [triangle, ellipse]

# add an empty shapes layer
shapes_layer = viewer.add_shapes()

# add mixed shapes using the `add` method
shapes_layer.add(
  mixed_shapes,
  shape_type=['polygon', 'ellipse'],
  edge_width=5,
  edge_color='coral',
  face_color='royalblue'
)
Hide code cell source 
from napari.utils import nbscreenshot

nbscreenshot(viewer, alt_text="Add new shapes to an existing shapes layer")
Add new shapes to an existing shapes layer

Finally, each shape type has its own convenience method for adding new shapes to a layer. Their arguments are identical to those of the add method, but they do not take a shape_type.

import napari
import numpy as np
from skimage import data

# add the image
viewer = napari.view_image(data.camera(), name='photographer')

# create some ellipses
ellipse = np.array([[59, 222], [110, 289], [170, 243], [119, 176]])

ellipse2 = np.array([[165, 329], [165, 401], [234, 401], [234, 329]])

# put both shapes in a list
ellipses = [ellipse, ellipse2]

# add an empty shapes layer
shapes_layer = viewer.add_shapes()

# add ellipses using their convenience method
shapes_layer.add_ellipses(
  ellipses,
  edge_width=5,
  edge_color='coral',
  face_color='royalblue'
)
Hide code cell source 
from napari.utils import nbscreenshot

nbscreenshot(viewer, alt_text="Add new ellipses to an existing shapes layer using the specific method for this layer type")
Add new ellipses to an existing shapes layer using the specific method for this layer type

Creating a new shapes layer#

As you can add new shapes to a shapes layer using the various shape creation tools, it is possible to create a brand-new empty shapes layers by clicking the new shapes layer button above the layers list. The shape of the shapes layer is defined by the shapes inside it, and so as you add new shapes the shape will adjust as needed. The dimension of the new shapes layer will default to the largest dimension of any layer currently in the viewer, or to 2 if no other layers are present in the viewer.

Non-editable mode#

If you want to disable editing of the shapes layer you can set the editable property of the layer to False.

As note in the section on 3D rendering, when using 3D rendering the shapes layer is not editable.

3D rendering of shapes#

All our layers can be rendered in both 2D and 3D mode, and one of our viewer buttons can toggle between each mode. The number of dimensions sliders will be 2 or 3 less than the total number of dimensions of the layer. See for example the examples/nD_shapes.py to see shapes in both 2D and 3D:

Note though that when entering 3D rendering mode the shape editing tools are all disabled. Those options are only supported when viewing a layer using 2D rendering.

Also note that for a multidimensional shape to be displayed on a given view slice all of its non-displayed coordinates must match the coordinates of that view slice, i.e. the shape must be entirely defined within that plane.

For paths that are defined by coordinates spanning more than two dimensions, it is possible to visualize them as 3D cylinders, see for example the examples/3D_paths.py

image: 3D paths

Note

Right now, it is not possible to display 3D cuboids or 3D spheroids, but will be supporting those options soon.

Pan and zoom mode#

The default mode of the shapes layer is to support panning and zooming, as in the image layer. This mode is represented by the magnifying glass in the layers control panel, and while it is selected editing the layer is not possible. Continue reading to learn how to use some of the editing modes. You can always return to pan and zoom mode by pressing the Z key when the shapes layer is selected.

Selecting, resizing, moving, and deleting shapes#

New shapes can be added using one of the 5 shape creation tools, for Lines, Rectangles, Ellipses, Polygons, and Paths. For more information on the different shape types see the shape types section.

You can select a shape by clicking on it using the shape selection tool, which can be selected by clicking on it in the layer controls panel or by pressing the S key when the shapes layer is selected. Once selected you can move the shape by dragging it. You can also resize the shape by clicking and dragging on one of the handles along the edge of the shape bounding box. You can also rotate the shape by clicking and dragging on the rotation handle above the shape bounding box.

When resizing a layer if you hold down the shift key the aspect ratio of the shape will lock and you can continue to resize the shape now with a fixed aspect ratio.

You can select multiple shapes by continuing to shift click on additional shapes after the first, or by dragging a bounding box around the shapes you want to select.

You can select all the shapes in the currently viewed slice by clicking the A key if you are in select mode.

Once selected you can delete the selected shapes by clicking on the delete button in the layer controls panel or pressing the delete key.

For example see below:

Adding, moving, and deleting individual vertices#

You can move individual vertices by entering the direct selection mode by either clicking on the direct select tool in the layer controls panel or pressing the D key while the shapes layer is selected. To move a vertex, you can click and drag it to its new position.

You can add vertices to a selected shape using the vertex addition tool which can be selected either clicking on the vertex addition tool in the layer controls panel or pressing the I key while the shapes layer is selected.

You can delete vertices to a selected shape using the vertex deletion tool which can be selected either clicking on the vertex deletion tool in the layer controls panel or pressing the X key while the shapes layer is selected.

For example see below:

Changing shape edge and face colors#

Individual shapes can each have different edge and face colors. You can initially set these colors by providing a list of colors to the edge_color or face_color keyword arguments respectively, or you can edit them from the GUI. The colors of each of the shapes are available as lists under the layer.edge_color and layer.face_color properties. These properties are different from the layer.current_edge_color and layer.current_face_color properties that will determine the color of the next shape to be added or any currently selected shapes.

To change the shape color properties from the GUI you must first select the shape whose properties you want to change, otherwise you will just be initializing the property for the next shape you add.

Changing shape edge widths#

Individual shapes can each have different edge widths. You can initially set the edge widths by providing a list of values to the edge_width keyword arguments respectively, or you can edit them from the GUI. The widths of each of the shapes are available as a list under the layer.edge_width property. Similar to the edge and face colors, these property is different from the layer.current_edge_width property that will determine the edge width of the next shape to be added or any currently selected shapes.

To change the edge with property from the GUI you must first select the shape whose properties you want to change, otherwise you will just be initializing the property for the next shape you add.

Layer ordering#

You can adjust the ordering of shapes in the layer by selecting shapes and then clicking the move to front or move to back buttons. You can get the ordering of all the shapes using the layer.z_indices property. You can also set the initial ordering of shapes by passing a list to the layer.z_index property.

Copying and pasting shapes#

It is possible to copy and paste any selected shapes using the ctrl-C and ctrl-V keybindings respectively. If you have a multidimensional shapes layer you can copy shapes from one slice to another by pasting them into the new slice. The coordinates of the shapes in the visible dimensions will be in the same place on the new slice as in the old slice, but the rest of the coordinates will be updated with the new slice values.

Shapes layer opacity#

The opacity value applies to all shapes. You can initialize the shape opacities using the opacity keyword argument which accepts a single opacity value that will be applied globally. You can then access the opacity using the layer.opacity property. In order to adjust the opacity of individual shapes you need to adjust the alpha value in the layer.edge_color and layer.face_color properties.

Putting it all together#

Here you can see an example of adding, selecting, and editing shapes and change their properties: