napari.layers.Tracks¶
-
class
napari.layers.Tracks(data, *, properties=None, graph=None, tail_width=2, tail_length=30, name=None, metadata=None, scale=None, translate=None, rotate=None, shear=None, affine=None, opacity=1, blending='additive', visible=True, colormap='turbo', color_by='track_id', colormaps_dict=None)[source]¶ Bases:
napari.layers.base.base.LayerTracks layer.
- Parameters
data (array (N, D+1)) – Coordinates for N points in D+1 dimensions. ID,T,(Z),Y,X. The first axis is the integer ID of the track. D is either 3 or 4 for planar or volumetric timeseries respectively.
properties (dict {str: array (N,)}, DataFrame) – Properties for each point. Each property should be an array of length N, where N is the number of points.
graph (dict {int: list}) – Graph representing associations between tracks. Dictionary defines the mapping between a track ID and the parents of the track. This can be one (the track has one parent, and the parent has >=1 child) in the case of track splitting, or more than one (the track has multiple parents, but only one child) in the case of track merging. See examples/tracks_3d_with_graph.py
color_by (str) – Track property (from property keys) by which to color vertices.
tail_width (float) – Width of the track tails in pixels.
tail_length (float) – Length of the track tails in units of time.
colormap (str) – Default colormap to use to set vertex colors. Specialized colormaps, relating to specified properties can be passed to the layer via colormaps_dict.
colormaps_dict (dict {str: napari.utils.Colormap}) – Optional dictionary mapping each property to a colormap for that property. This allows each property to be assigned a specific colormap, rather than having a global colormap for everything.
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 lenght N translation vector and a 1 or a napari AffineTransform object. If provided then translate, scale, rotate, and shear values are ignored.
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.
Methods
Attributes
-
property
affine¶ Affine transform.
- Type
napari.utils.transforms.Affine
-
bind_key(key, func=<object object>, *, overwrite=False)¶ Bind a key combination to a keymap.
- Parameters
keymap (dict of str: callable) – Keymap to modify.
key (str or ..) – Key combination.
...acts as a wildcard if no key combinations can be matched in the keymap (this will overwrite all key combinations further down the lookup chain).func (callable, None, or ..) – Callable to bind to the key combination. If
Noneis passed, unbind instead....acts as a blocker, effectively unbinding the key combination for all keymaps further down the lookup chain.overwrite (bool, keyword-only, optional) – Whether to overwrite the key combination if it already exists.
- Returns
unbound – Callable unbound by this operation, if any.
- Return type
callable or None
Notes
Key combinations are represented in the form
[modifier-]key, e.g.a,Control-c, orControl-Alt-Delete. Valid modifiers are Control, Alt, Shift, and Meta.Letters will always be read as upper-case. Due to the native implementation of the key system, Shift pressed in certain key combinations may yield inconsistent or unexpected results. Therefore, it is not recommended to use Shift with non-letter keys. On OSX, Control is swapped with Meta such that pressing Command reads as Control.
Special keys include Shift, Control, Alt, Meta, Up, Down, Left, Right, PageUp, PageDown, Insert, Delete, Home, End, Escape, Backspace, F1, F2, F3, F4, F5, F6, F7, F8, F9, F10, F11, F12, Space, Enter, and Tab
Functions take in only one argument: the parent that the function was bound to.
By default, all functions are assumed to work on key presses only, but can be denoted to work on release too by separating the function into two statements with the yield keyword:
@viewer.bind_key('h') def hello_world(viewer): # on key press viewer.status = 'hello world!' yield # on key release viewer.status = 'goodbye world :('
To create a keymap that will block others,
bind_key(..., ...)`.
-
property
blending¶ Determines how RGB and alpha values get mixed.
- Blending.OPAQUE
Allows for only the top layer to be visible and corresponds to depth_test=True, cull_face=False, blend=False.
- Blending.TRANSLUCENT
Allows for multiple layers to be blended with different opacity and corresponds to depth_test=True, cull_face=False, blend=True, blend_func=(‘src_alpha’, ‘one_minus_src_alpha’).
- Blending.ADDITIVE
Allows for multiple layers to be blended together with different colors and opacity. Useful for creating overlays. It corresponds to depth_test=False, cull_face=False, blend=True, blend_func=(‘src_alpha’, ‘one’).
- Type
Blending mode
-
property
coordinates¶ Cursor position in data coordinates.
-
property
current_time¶ current time according to the first dimension
-
property
cursor_size¶ Size of cursor if custom. None yields default size.
- Type
int | None
-
property
extent¶ Extent of layer in data and world coordinates.
- Return type
Extent
-
get_message()¶ Generate a status message based on the coordinates and value
- Returns
msg – String containing a message that can be used as a status update.
- Return type
string
-
get_status(position=None, *, world=False)¶ Status message of the data at a coordinate position.
- Parameters
- Returns
msg – String containing a message that can be used as a status update.
- Return type
string
-
get_value(position=None, *, world=False)¶ Value of the data at a position.
-
property
graph¶ Graph representing associations between tracks.
-
property
loaded¶ Return True if this layer is fully loaded in memory.
This base class says that layers are permanently in the loaded state. Derived classes that do asynchronous loading can override this.
- Return type
-
property
properties¶ Properties for each track.
-
property
properties_to_color_by¶ track properties that can be used for coloring etc…
-
refresh(event=None)¶ Refresh all layer data based on current view slice.
-
property
rotate¶ Rotation matrix in world coordinates.
- Type
array
-
save(path, plugin=None)¶ Save this layer to
pathwith default (or specified) plugin.- Parameters
path (str) – A filepath, directory, or URL to open. Extensions may be used to specify output format (provided a plugin is available for the requested format).
plugin (str, optional) – Name of the plugin to use for saving. If
Nonethen all plugins corresponding to appropriate hook specification will be looped through to find the first one that can save the data.
- Returns
File paths of any files that were written.
- Return type
list of str
-
property
shear¶ Sheer matrix in world coordinates.
- Type
array
-
property
thumbnail¶ Integer array of thumbnail for the layer
- Type
array
-
property
track_colors¶ return the vertex colors according to the currently selected property
- Return type
-
property
use_fade¶ toggle whether we fade the tail of the track, depending on whether the time dimension is displayed
- Return type