`spateo.digitization.grid`#

Written by @Jinerhal, adapted by @Xiaojieqiu.

Module Contents#

Functions#

`digitize`(→ None)	Calculate the "heat" for a closed area of interests by solving a PDE, partial differential equation, the heat
`gridit`(→ None)	Segment the area of interests into specific layer/column number, according to precomputed digitization heat

spateo.digitization.grid.digitize(adata: spateo.digitization.utils.AnnData, ctrs: spateo.digitization.utils.Tuple, ctr_idx: int, pnt_xy: spateo.digitization.utils.Tuple[int, int], pnt_Xy: spateo.digitization.utils.Tuple[int, int], pnt_xY: spateo.digitization.utils.Tuple[int, int], pnt_XY: spateo.digitization.utils.Tuple[int, int], spatial_key: str = 'spatial', dgl_layer_key: str = 'digital_layer', dgl_column_key: str = 'digital_column', max_itr: int = 100000.0, lh: float = 1, hh: float = 100) → None[source]#

Calculate the “heat” for a closed area of interests by solving a PDE, partial differential equation, the heat: equation. Boundary conditions are defined upon four user provided coordinates that set the direction of heat diffusion. The value of “heat” will be used for define different spatial layers, domains and grids.

Parameters:

adata: The adata object to digitize.
ctrs: Contours generated by cv2.findContours.
ctr_idx: The index of the contour of interests.
pnt_xy: Corner point to define an area of interest. pnt_xy corresponds to the point with minimal layer and minimal column value.
pnt_Xy: Corner point corresponds to the point with maximal column value but minimal layer value.
pnt_xY: Corner point corresponds to the point with minimal column value but maximal layer value.
pnt_XY: Corner point corresponds to the point with maximal layer and maximal columns value.
spatial_key: The key name in adata.obsm of the spatial coordinates. Default to “spatial”.
dgl_layer_key: The key name in adata.obs to store layer digital-heat (temperature). Default to “digital_layer”.
dgl_column_key: The key name to store column digital-heat (temperature).
max_itr: Maximum number of iterations dedicated to solving the heat equation.
lh: lowest digital-heat (temperature). Defaults to 1.
hh: highest digital-heat (temperature). Defaults to 100.

Returns:

dgl_layer_key: The key in adata.obs points to the values of layer digital-heat (temperature).
dgl_column_key: The key in adata.obs points to the values of column digital-heat (temperature).

Return type:

Nothing but update the adata object with the following keys in .obs

spateo.digitization.grid.gridit(adata: spateo.digitization.utils.AnnData, layer_num: int, column_num: int, lh: float = 1, hh: float = 100, dgl_layer_key: str = 'digital_layer', dgl_column_key: str = 'digital_column', layer_border_width: int = 2, column_border_width: int = 2, layer_label_key: str = 'layer_label', column_label_key: str = 'column_label', grid_label_key: str = 'grid_label') → None[source]#

Segment the area of interests into specific layer/column number, according to precomputed digitization heat value.