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Merge pull request #937 from AFM-SPM/ns-rse/919-numpydoc-validate-nod…
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…estats
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@ns-rse
ns-rse authored Oct 9, 2024
2 parents c45ace6 + c657bc5 commit 3327404
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Showing 2 changed files with 33 additions and 38 deletions.
1 change: 0 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -278,7 +278,6 @@ exclude = [ # don't report on objects that match any of these regex
"\\.__repr__$",
"^test_",
"^conftest",
"^nodestats",
"^tracingfuncs",
"^conf$",
"^theme",
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70 changes: 33 additions & 37 deletions topostats/tracing/nodestats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,8 @@ class nodeStats:
The length over which to join skeletal intersections to be counted as one crossing.
node_joining_length : float
The distance over which to join nearby odd-branched nodes.
node_extend_dist : float
The distance under which to join odd-branched node regions.
branch_pairing_length : float
The length from the crossing point to pair and trace, obtaining FWHM's.
pair_odd_branches : bool
Expand Down Expand Up @@ -142,6 +144,8 @@ def __init__(
The length over which to join skeletal intersections to be counted as one crossing.
node_joining_length : float
The distance over which to join nearby odd-branched nodes.
node_extend_dist : float
The distance under which to join odd-branched node regions.
branch_pairing_length : float
The length from the crossing point to pair and trace, obtaining FWHM's.
pair_odd_branches : bool
Expand Down Expand Up @@ -528,9 +532,6 @@ def analyse_nodes(self, max_branch_length: float = 20) -> None:
----------
max_branch_length : float
The side length of the box around the node to analyse (in nm).
test_run : bool, optional
Flag to determine whether to run in test mode, if enabled, it will pickle objects to
files, by default False.
"""
# Get coordinates of nodes
# This is a numpy array of coords, shape Nx2
Expand Down Expand Up @@ -687,24 +688,24 @@ def add_branches_to_labelled_image(
----------
branch_under_over_order : npt.NDArray[np.int32]
The order of the branches.
matched_branches: dict[int, dict[str, MatchedBranch]]
matched_branches : dict[int, dict[str, MatchedBranch]]
Dictionary where the key is the index of the pair and the value is a dictionary containing the following
keys:
- "ordered_coords" : npt.NDArray[np.int32].
- "heights" : npt.NDArray[np.number]. Heights of the branches.
- "distances" :
- "fwhm" : npt.NDArray[np.number]. Full width half maximum of the branches.
masked_image: dict[int, dict[str, npt.NDArray[np.bool_]]]
masked_image : dict[int, dict[str, npt.NDArray[np.bool_]]]
Dictionary where the key is the index of the pair and the value is a dictionary containing the following
keys:
- "avg_mask" : npt.NDArray[np.bool_]. Average mask of the branches.
branch_start_coords: npt.NDArray[np.int32]
branch_start_coords : npt.NDArray[np.int32]
An Nx2 numpy array of the coordinates of the branches connected to the node.
ordered_branches: list[npt.NDArray[np.int32]]
ordered_branches : list[npt.NDArray[np.int32]]
List of numpy arrays of ordered branch coordinates.
pairs: npt.NDArray[np.int32]
pairs : npt.NDArray[np.int32]
Nx2 numpy array of pairs of branches that are matched through a node.
average_trace_advised: bool
average_trace_advised : bool
Flag to determine whether to use the average trace.
image_shape : tuple[int]
The shape of the image, to create a mask from.
Expand Down Expand Up @@ -760,7 +761,8 @@ def analyse_node_branches(
npt.NDArray[np.int32],
np.float64 | None,
]:
"""Analyse the branches of a single node.
"""
Analyse the branches of a single node.
Parameters
----------
Expand All @@ -769,28 +771,24 @@ def analyse_node_branches(
reduced_node_area : npt.NDArray[np.int32]
An NxM numpy array of the node in question and the branches connected to it.
Node is marked by 3, and branches by 1.
branch_start_coords: npt.NDArray[np.int32]
branch_start_coords : npt.NDArray[np.int32]
An Nx2 numpy array of the coordinates of the branches connected to the node.
max_length_px : np.int32
The maximum length in pixels to traverse along while ordering.
reduced_skeleton_graph: nx.classes.graph.Graph
reduced_skeleton_graph : nx.classes.graph.Graph
The graph representation of the reduced node area.
image: npt.NDArray[np.number]
image : npt.NDArray[np.number]
The full image of the grain.
average_trace_advised: bool
average_trace_advised : bool
Flag to determine whether to use the average trace.
node_coord: tuple[np.int32, np.int32]
node_coord : tuple[np.int32, np.int32]
The node coordinates.
filename: str
The filename of the image.
pair_odd_branches : bool
Whether to try and pair odd-branched nodes.
test_run: bool
Flag to determine whether to run in test mode, if enabled, it will pickle objects to files.
resolution_threshold: np.float64
filename : str
The filename of the image.
resolution_threshold : np.float64
The resolution threshold below which to warn the user that the node is difficult to analyse.
node_number: int
The node number.
Returns
-------
Expand Down Expand Up @@ -885,19 +883,19 @@ def join_matching_branches_through_node(
Parameters
----------
pairs: npt.NDArray[np.int32]
pairs : npt.NDArray[np.int32]
Nx2 numpy array of pairs of branches that are matched through a node.
ordered_branches: list[npt.NDArray[np.int32]]
ordered_branches : list[npt.NDArray[np.int32]]
List of numpy arrays of ordered branch coordinates.
reduced_skeleton_graph: nx.classes.graph.Graph
reduced_skeleton_graph : nx.classes.graph.Graph
Graph representation of the skeleton.
image: npt.NDArray[np.number]
image : npt.NDArray[np.number]
The full image of the grain.
average_trace_advised: bool
average_trace_advised : bool
Flag to determine whether to use the average trace.
node_coords: tuple[np.int32, np.int32]
node_coords : tuple[np.int32, np.int32]
The node coordinates.
filename: str
filename : str
The filename of the image.
Returns
Expand Down Expand Up @@ -1011,7 +1009,6 @@ def get_ordered_branches_and_vectors(
-------
tuple[list[npt.NDArray[np.int32]], list[npt.NDArray[np.int32]]]
A tuple containing a list of ordered branches and a list of vectors.
"""
ordered_branches = []
vectors = []
Expand Down Expand Up @@ -1232,7 +1229,8 @@ def gaussian(x: npt.NDArray, h: float, mean: float, sigma: float):

@staticmethod
def interpolate_between_yvalue(x: npt.NDArray, y: npt.NDArray, yvalue: float) -> float:
"""Calculate the x value between the two points either side of yvalue in y.
"""
Calculate the x value between the two points either side of yvalue in y.
Parameters
----------
Expand Down Expand Up @@ -1816,18 +1814,14 @@ def minimum_crossing_confs(node_dict: dict) -> None | float:
def compile_metrics(self) -> None:
"""
Add the number of crossings, average and minimum crossing confidence to the metrics dictionary.
Returns
-------
None
"""
self.metrics["num_crossings"] = (self.node_centre_mask == 3).sum()
self.metrics["avg_crossing_confidence"] = nodeStats.average_crossing_confs(self.node_dicts)
self.metrics["min_crossing_confidence"] = nodeStats.minimum_crossing_confs(self.node_dicts)


def nodestats_image(
image: npt.NPArray,
image: npt.NDArray,
disordered_tracing_direction_data: dict,
filename: str,
pixel_to_nm_scaling: float,
Expand All @@ -1854,11 +1848,13 @@ def nodestats_image(
The length over which to join skeletal intersections to be counted as one crossing.
node_joining_length : float
The distance over which to join nearby odd-branched nodes.
node_extend_dist : float
The distance under which to join odd-branched node regions.
branch_pairing_length : float
The length from the crossing point to pair and trace, obtaining FWHM's.
pair_odd_branches : bool
Whether to try and pair odd-branched nodes.
Pad width : int
pad_width : int
The number of edge pixels to pad the image by.
Returns
Expand Down

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