traccuracy
package description.
Subpackages
Package Contents
Classes
An enum containing standard flags that are used to |
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An enum containing standard flags that are used to annotate the nodes |
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A directed graph representing a tracking solution where edges go forward in time. |
Functions
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Compute given metrics on data using the given matcher. |
- traccuracy.run_metrics(gt_data: traccuracy._tracking_graph.TrackingGraph, pred_data: traccuracy._tracking_graph.TrackingGraph, matcher: traccuracy.matchers._base.Matcher, metrics: list[traccuracy.metrics._base.Metric]) list[dict] [source]
Compute given metrics on data using the given matcher.
The returned result dictionary will contain all metrics computed by the given Metric classes, as well as general summary numbers e.g. false positive/false negative detection and edge counts.
- Parameters:
gt_data (traccuracy.TrackingGraph) – ground truth graph and optionally segmentation
pred_data (traccuracy.TrackingGraph) – predicted graph and optionally segmentation
matcher (Matcher) – instantiated matcher object
metrics (List[Metric]) – list of instantiated metrics objects to compute
- Returns:
List of dictionaries with one dictionary per Metric object
- Return type:
List[Dict]
- class traccuracy.EdgeFlag[source]
An enum containing standard flags that are used to annotate the edges of a TrackingGraph. If a graph already has annotations using these strings before becoming a TrackingGraph, this will likely ruin metrics computation!
- TRUE_POS = 'is_tp'
- FALSE_POS = 'is_fp'
- FALSE_NEG = 'is_fn'
- INTERTRACK_EDGE = 'is_intertrack_edge'
- WRONG_SEMANTIC = 'is_wrong_semantic'
- class traccuracy.NodeFlag[source]
An enum containing standard flags that are used to annotate the nodes of a TrackingGraph. Note that the user specified frame and location attributes are also valid node attributes that will be stored on the graph and should not overlap with these values. Additionally, if a graph already has annotations using these strings before becoming a TrackingGraph, this will likely ruin metrics computation!
- TRUE_POS = 'is_tp'
- FALSE_POS = 'is_fp'
- FALSE_NEG = 'is_fn'
- NON_SPLIT = 'is_ns'
- TP_DIV = 'is_tp_division'
- FP_DIV = 'is_fp_division'
- FN_DIV = 'is_fn_division'
- classmethod has_value(value)[source]
Check if a value is one of the enum’s values. This can be used to check if other graph annotation strings are colliding with our reserved strings.
- Parameters:
value – Check if the enum contains this value.
- Returns:
- True if the value is already in the enum’s values,
false otherwise
- Return type:
bool
- class traccuracy.TrackingGraph(graph: networkx.DiGraph, segmentation: numpy.ndarray | None = None, frame_key: str = 't', label_key: str = 'segmentation_id', location_keys: tuple[str, Ellipsis] = ('x', 'y'), name: str | None = None)[source]
A directed graph representing a tracking solution where edges go forward in time.
Nodes represent cell detections and edges represent links between detections in the same track. Nodes in the graph must have an attribute that represents time frame (default to ‘t’) and location (defaults to ‘x’ and ‘y’). As in networkx, every cell must have a unique id, but these can be of any (hashable) type.
We provide common functions for accessing parts of the track graph, for example all nodes in a certain frame, or all previous or next edges for a given node. Additional functionality can be accessed by querying the stored networkx graph with native networkx functions.
Currently it is assumed that the structure of the networkx graph as well as the time frame and location of each node is not mutated after construction, although non-spatiotemporal attributes of nodes and edges can be modified freely.
- start_frame
int, the first frame with a node in the graph
- end_frame
int, the end of the span of frames containing nodes (one frame after the last frame that contains a node)
- nodes_by_frame
dict of int -> node_id Maps from frames to all node ids in that frame
- frame_key
str The name of the node attribute that corresponds to the frame of the node. Defaults to “t”.
- location_keys
list of str Keys used to access the location of the cell in space.
- property nodes: networkx.classes.reportviews.NodeView
Get all the nodes in the graph, along with their attributes.
- Returns:
Provides set-like operations on the nodes as well as node attribute lookup.
- Return type:
NodeView
- property edges: networkx.classes.reportviews.OutEdgeView
Get all the edges in the graph, along with their attributes.
- Returns:
- Provides set-like operations on the edge-tuples as well as edge attribute
lookup.
- Return type:
OutEdgeView
- get_location(node_id: Hashable) list[float] [source]
Get the spatial location of the node with node_id using self.location_keys.
- Parameters:
node_id (hashable) – The node_id to get the location of
- Returns:
A list of location values in the same order as self.location_keys
- Return type:
list of float
- get_nodes_with_flag(flag: NodeFlag) set[Hashable] [source]
Get all nodes with specified NodeFlag set to True.
- Parameters:
flag (traccuracy.NodeFlag) – the node flag to query for
- Returns:
- An iterable of node_ids which have the given flag
and the value is True.
- Return type:
(List(hashable))
- get_edges_with_flag(flag: EdgeFlag) set[tuple[Hashable, Hashable]] [source]
Get all edges with specified EdgeFlag set to True.
- Parameters:
flag (traccuracy.EdgeFlag) – the edge flag to query for
- Returns:
- An iterable of edge ids which have the given flag
and the value is True.
- Return type:
(List(hashable))
- get_divisions() list[Hashable] [source]
Get all nodes that have at least two edges pointing to the next time frame
- Returns:
a list of node ids for nodes that have more than one child
- Return type:
list of hashable
- get_merges() list[Hashable] [source]
Get all nodes that have at least two incoming edges from the previous time frame
- Returns:
a list of node ids for nodes that have more than one parent
- Return type:
list of hashable
- get_connected_components() list[TrackingGraph] [source]
Get a list of TrackingGraphs, each corresponding to one track (i.e., a connected component in the track graph).
- Returns:
A list of TrackingGraphs, one for each track.
- get_subgraph(nodes: Iterable[Hashable]) TrackingGraph [source]
Returns a new TrackingGraph with the subgraph defined by the list of nodes
- Parameters:
nodes (list) – List of node ids to use in constructing the subgraph
- set_flag_on_node(_id: Hashable, flag: NodeFlag, value: bool = True) None [source]
Set an attribute flag for a single node. If the id is not found in the graph, a KeyError will be raised. If the flag already exists, the existing value will be overwritten.
- Parameters:
_id (Hashable) – The node id on which to set the flag.
flag (traccuracy.NodeFlag) – The node flag to set. Must be of type NodeFlag - you may not not pass strings, even if they are included in the NodeFlag enum values.
value (bool, optional) – Flags can only be set to True or False. Defaults to True.
- Raises:
KeyError if the provided id is not in the graph. –
ValueError if the provided flag is not a NodeFlag –
- set_flag_on_all_nodes(flag: NodeFlag, value: bool = True) None [source]
Set an attribute flag for all nodes in the graph. If the flag already exists, the existing values will be overwritten.
- Parameters:
flag (traccuracy.NodeFlag) – The node flag to set. Must be of type NodeFlag - you may not not pass strings, even if they are included in the NodeFlag enum values.
value (bool, optional) – Flags can only be set to True or False. Defaults to True.
- Raises:
ValueError if the provided flag is not a NodeFlag. –
- set_flag_on_edge(_id: tuple[Hashable, Hashable], flag: EdgeFlag, value: bool = True) None [source]
Set an attribute flag for an edge. If the flag already exists, the existing value will be overwritten.
- Parameters:
ids (tuple[Hashable]) – The edge id or list of edge ids to set the attribute for. Edge ids are a 2-tuple of node ids.
flag (traccuracy.EdgeFlag) – The edge flag to set. Must be of type EdgeFlag - you may not pass strings, even if they are included in the EdgeFlag enum values.
value (bool) – Flags can only be set to True or False. Defaults to True.
- Raises:
KeyError if edge with _id not in graph. –
- set_flag_on_all_edges(flag: EdgeFlag, value: bool = True) None [source]
Set an attribute flag for all edges in the graph. If the flag already exists, the existing values will be overwritten.
- Parameters:
flag (traccuracy.EdgeFlag) – The edge flag to set. Must be of type EdgeFlag - you may not not pass strings, even if they are included in the EdgeFlag enum values.
value (bool, optional) – Flags can only be set to True or False. Defaults to True.
- Raises:
ValueError if the provided flag is not an EdgeFlag. –
- get_tracklets(include_division_edges: bool = False) list[TrackingGraph] [source]
Gets a list of new TrackingGraph objects containing all tracklets of the current graph.
Tracklet is defined as all connected components between divisions (daughter to next parent). Tracklets can also start or end with a non-dividing cell.
- Parameters:
include_division_edges (bool, optional) – If True, include edges at division.