shape_metric
Compute a set of shape metrics for every row of the gdf.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gdf
|
GeoDataFrame
|
The input GeoDataFrame. |
required |
metrics
|
Tuple[str, ...]
|
A Tuple/List of shape metrics. |
required |
parallel
|
bool
|
Flag whether to use parallel apply operations when computing the diversities. |
True
|
num_processes
|
int
|
The number of processes to use when parallel=True. If -1, this will use all available cores. |
1
|
col_prefix
|
str
|
Prefix for the new column names. |
None
|
create_copy
|
bool
|
Flag whether to create a copy of the input gdf or not. |
True
|
Note
Allowed shape metrics are:
area
perimeter
major_axis_len
minor_axis_len
major_axis_angle
minor_axis_angle
compactness
circularity
convexity
solidity
elongation
eccentricity
fractal_dimension
sphericity
shape_index
rectangularity
squareness
equivalent_rectangular_index
Raises:
Type | Description |
---|---|
ValueError
|
If an illegal metric is given. |
Returns:
Type | Description |
---|---|
GeoDataFrame
|
gpd.GeoDataFrame: The input geodataframe with computed shape metric columns added. |
Examples:
>>> from histolytics.utils.gdf import set_uid
>>> from histolytics.data import cervix_nuclei
>>> from histolytics.spatial_geom.shape_metrics import shape_metric
>>>
>>> # input data
>>> nuc = cervix_nuclei()
>>> nuc = set_uid(nuc)
>>>
>>> # Calculate shape metrics
>>> nuc = shape_metric(nuc, metrics=["eccentricity", "solidity"])
>>> print(nuc.head(3))
geometry class_name uid uid
0 POLYGON ((940.01 5570.02, 939.01 5573, 939 559... connective 0
1 POLYGON ((906.01 5350.02, 906.01 5361, 908.01 ... connective 1
2 POLYGON ((866 5137.02, 862.77 5137.94, 860 513... squamous_epithel 2
eccentricity solidity
uid
0 0.960195 0.989154
1 0.041712 1.000000
2 0.610266 0.996911
Source code in src/histolytics/spatial_geom/shape_metrics.py
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