dummy-spatialdata 0.1.5

A package for creating arbitrary spatialdata for testing purposes.

dummy-spatialdata

Allows generating dummy spatialdata objects, which can be useful for testing purposes.

Installation

pip install dummy-spatialdata

Example usage

dummy-spatialdata is compatible with both spatialdata == 0.5.0 (zarr v2) and 0.7.2 (zarr v3)

Thus please use

1. conda create --name dummy_sd_env python==3.12 spatialdata==0.7.2 or
2. conda create --name dummy_sd_env_05 python==3.12 spatialdata==0.5.0 setuptools==75.8.0

from dummy_spatialdata import generate_dataset
import dummy_anndata
import spatialdata_plot as sdp 
import spatialdata as sd
import matplotlib.pyplot as plt
import anndata as ad

# generate anndata
adata = dummy_anndata.generate_dataset(n_obs=12, n_vars=20)

# generate spatialdata
sdata = generate_dataset(
    images = [
        {'type': 'rgb', 'scale_factors': [2,2,2], 'coordinate_system': 'global'},
        {'type': 'grayscale', 'coordinate_system': 'global'},
    ],
    labels = [
        {'n': 12, 'scale_factors': [2,2,3], 'coordinate_system': 'global2'},
        {'n': 12, 'coordinate_system': 'global2'},
    ], 
    shapes = [
        {'n': 12, 'type': 'circle', 'coordinate_system': 'global'},
        {'n': 20, 'type': 'circle'},
    ],
    points = [
        {'n': 12}
    ],
    tables = [
        {'table': adata, 'element': 'shape', 'element_index': 0}
    ],
    coordinate_systems = {
        'global': {'transformations': ['affine'], 'shape': {'x': 2000, 'y': 2000}},
        'global2': {'transformations': ['scale', 'translation'], 'shape':{'x': 500, 'y': 500}}
    },
    SEED=13
)
sdata

SpatialData object
├── Images
│     ├── 'image_0': DataTree[cyx] (3, 2000, 2000), (3, 1000, 1000), (3, 500, 500), (3, 250, 250)
│     └── 'image_1': DataTree[cyx] (1, 2000, 2000)
├── Labels
│     ├── 'label_0': DataTree[yx] (500, 500), (250, 250), (125, 125), (41, 41)
│     └── 'label_1': DataTree[yx] (500, 500)
├── Points
│     └── 'point_0': DataFrame with shape: (<Delayed>, 2) (2D points)
├── Shapes
│     ├── 'shape_0': GeoDataFrame shape: (12, 2) (2D shapes)
│     └── 'shape_1': GeoDataFrame shape: (20, 2) (2D shapes)
└── Tables
      └── 'table_0': AnnData (12, 20)
with coordinate systems:
    ▸ 'global', with elements:
        image_0 (Images), image_1 (Images), shape_0 (Shapes)
    ▸ 'global2', with elements:
        label_0 (Labels), label_1 (Labels)
    ▸ 'point_0', with elements:
        point_0 (Points)
    ▸ 'shape_1', with elements:
        shape_1 (Shapes)

You can plot the demo data now!

sdata.pl.render_images('image_0').pl.render_shapes('shape_0', color='Gene001', table_name = 'table_0', table_layer = 'float_matrix').pl.show(coordinate_systems = 'global')