wsireg.reg_shapes package

Submodules

wsireg.reg_shapes.reg_shapes module

class wsireg.reg_shapes.reg_shapes.RegShapes(shape_data=None, itk_point_transforms=None, source_res=1, target_res=1, **kwargs)

Bases: object

Class that holds and manages shape data and it’s transformations in the registration graph

Parameters:

• shape_data (list) – list of np.ndarrays of shape data str - file path to GeoJSON file containing shape data np.ndarray - single shape

• itk_point_transforms (list) – list of ITK point transforms, appropriately inverted where non-linear. Usually generated on-the-fly when points are transformed from wsireg transformation data

• source_res (float) – isotropic image resolution of the source image in the registration stack, i.e., resolution of the image to which shape data is associated

• target_res (float) – isotropic image resolution of the target image in the registration stack usually generated on-the-fly when points are transformed from wsireg transformation data

• kwargs – keyword arguments passed to wsireg.utils.tform_utils.shape_reader (shape_name, shape_type)

shape_data

list of np.ndarrays of shape data str - file path to GeoJSON file containing shape data np.ndarray - single shape

Type:

list of shape data

shape_data_gj

shape data in geoJSON dicts

Type:

list of geoJSON shape data

transformed_shape_data

numpy shape data that as been tranformed

Type:

list of shape data

itk_point_transforms

list of ITK point transforms, appropriately inverted where non-linear. Usually generated on-the-fly when points are transformed from wsireg transformation data

Type:

list

source_res

isotropic image resolution of the source image in the registration stack, i.e., resolution of the image to which shape data is associated

Type:

float

target_res

isotropic image resolution of the target image in the registration stack usually generated on-the-fly when points are transformed from wsireg transformation data

Type:

float

add_shapes(shape_data, **kwargs)

Add shapes via shape_reader, will extend current shape list rather than overwrite it

Parameters:

• shape_data – list of np.ndarrays of shape data str - file path to GeoJSON file containing shape data np.ndarray - single shape

• kwargs – keyword arguments passed to wsireg.utils.tform_utils.shape_reader (shape_name, shape_type)

draw_mask(output_size: Tuple[int, int], transformed: bool = False, labels: bool = False) → ndarray

Draw a binary or label mask using shape data.

Parameters:

• output_size (tuple of int) – size of mask in in tuple(x,y)

• transformed (bool) – Whether to write transformed shapes to mask or original shapes

• labels (bool) – Whether to write each mask instance as a label (1-n_shapes) or to write all as binary (255)

Returns:

mask – Drawn mask at set output size

Return type:

np.ndarray

property n_shapes

Number of shapes loaded

save_shape_data(output_fp: str | Path, transformed: bool = True) → str

Save shape file to GeoJSON on disk.

Parameters:

• output_fp (str) – path to the .json file where shape data will be saved

• transformed (bool) – save the transformed shape data or shape data as currently help in memory

Returns:

output_fp – Path to the saved file

Return type:

str

scale_shapes(scale_factor: int | float)

Scale coordinates of list of shape data by scale_factor

Parameters:

scale_factor (float, int) – isotropic scaling factor for the coordinates

property shape_names

list of GeoJSON shape names in shape data

property shape_types

List of GeoJSON shape types in shape data

transform_shapes(transformations: str | Path | dict | RegTransformSeq, px_idx: bool = True, output_idx: bool = True)

Transform shapes using transformations data from wsireg

Parameters:

• transformations – RegTransformSeq parsable object

• px_idx (bool) – whether shape points are specified in physical coordinates (i.e., microns) or in pixel indices

• output_idx (bool) – whether transformed shape points should be output in physical coordinates (i.e., microns) or in pixel indices

update_shapes(imported_shapes: List[Dict[str, ndarray | str]])

Extend list of shape data with new shape data

Parameters:

imported_shapes (list of shape data) – Shapes to add in numpy format

update_shapes_gj(imported_shapes: List[Dict[Any, Any]])

Extend list of shape data with new shape data in geoJSON.

Parameters:

imported_shapes (list of shape data) – Shapes to add in geoJSON format