art

art#

Utilities for artistic visualizations created from scPortrait datasets.

Artistic visualizations created from scPortrait datasets.

scportrait.art.create_h5sc_collage(master_png: str | PathLike[str], h5sc_path: str | PathLike[str], colors: ndarray, *, grid_width: int, n_samples_per_color: int = 200, crop_size: int = 200, channel_indices: slice = slice(2, 6, None), dataset_key: str = 'obsm/single_cell_images', edge_fraction_threshold: float | None = 0.2, random_seed: int | None = 492755, max_cell_uses: int = 1, master_batch_size: int = 128, tile_batch_size: int = 10000, output_path: str | PathLike[str] | None = None) → Any#

Create a photomosaic from colorized h5sc single-cell images.

Parameters:

  • master_png – PNG image to recreate as a collage.

  • h5sc_path – An h5sc file or a directory containing *.h5sc or *.h5 files.

  • colors – RGB colors of shape (n_colors, 3) in the 0–255 range.

  • grid_width – Number of mosaic tiles across the output.

  • n_samples_per_color – Unique cells sampled per color and input h5 file.

  • crop_size – Side length of each centered square crop in pixels.

  • channel_indices – Channels combined into each colorized tile.

  • dataset_key – HDF5 dataset containing images shaped (cell, channel, y, x). Defaults to the standardized scPortrait h5sc location.

  • edge_fraction_threshold – Discard tiles with a greater nonzero edge fraction. Set to None to keep every tile.

  • random_seed – Seed used for reproducible cell sampling; set to None for random sampling.

  • max_cell_uses – Maximum number of times a colorized channel/cell tile may appear in the mosaic.

  • master_batch_size – Number of master cells processed per MPS calculation batch.

  • tile_batch_size – Number of source tiles processed per MPS calculation batch.

  • output_path – Optional path where the completed collage is saved.

Returns:

The image result returned by phomo.Mosaic.build.

Example

```python from scportrait.art import create_h5sc_collage

result = create_h5sc_collage(

master_png=”master.png”, h5sc_path=”cells/”, colors=[[179, 38, 42], [47, 85, 154]], grid_width=60, output_path=”mosaic.png”,

)#