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Streaming writers for persisting tile-level predictions. Provides a PredictionWriter protocol and three concrete implementations (ZarrWriter, HDF5Writer, NPZWriter) that save per-tile outputs and metadata to disk in a memory-efficient way. Zarr and HDF5 writers stream results row-by-row so that the full output tensor never needs to reside in memory. The NPZ writer accumulates results in Python lists and flushes on close.

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OutputFormat

Supported on-disk formats for prediction output.

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PredictionWriter

Abstract base for streaming prediction writers.

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open

Pre-allocates storage once the embedding dim is known.
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int
required
Total number of tiles to be written.
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int
required
Dimensionality of each prediction vector.

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write

Writes a single tile’s model response.
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ModelResponse
required
The model response to persist.

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set_thumbnail

Stores a slide thumbnail image.
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NDArray
required
RGB image array of shape (H, W, 3).

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set_metadata

Stores slide-level metadata alongside the arrays.
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dict[str, Any]
required
Key-value pairs (slide_name, tile_size, etc.).

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set_tissue_mask

Stores the tissue mask used during extraction.
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NDArray
required
Binary mask array of shape (H, W), dtype uint8.

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set_gene_names

Stores input and output gene name lists. Default implementation is a no-op. Subclasses that support gene annotation should override this.
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list[str] | None
Ordered Ensembl IDs for bulk RNA input.
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list[str] | None
Ordered Ensembl IDs for predicted output.

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close

Flushes and finalises the output file.

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ZarrWriter

Streams tile predictions into a Zarr directory store.

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open

Pre-allocates Zarr datasets for outputs, coordinates, and tissue ratios.
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int
required
Total number of tiles to be written.
​
int
required
Dimensionality of each prediction vector.

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write

Writes a single tile response into the Zarr datasets.
​
ModelResponse
required
The model response to persist.

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set_thumbnail

Stores a slide thumbnail as a Zarr dataset.
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NDArray
required
RGB image array of shape (H, W, 3).

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set_metadata

Stores metadata as Zarr root attributes.
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dict[str, Any]
required
Key-value pairs (slide_name, tile_size, etc.).

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set_tissue_mask

Stores the tissue mask as a Zarr dataset.
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NDArray
required
Binary mask array of shape (H, W), dtype uint8.

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set_gene_names

Stores gene name arrays as Zarr string datasets.
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list[str] | None
Ordered Ensembl IDs for bulk RNA input.
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list[str] | None
Ordered Ensembl IDs for predicted output.

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close

Logs output path (Zarr stores are flushed on write).

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HDF5Writer

Streams tile predictions into an HDF5 file.

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open

Opens the HDF5 file and pre-allocates datasets.
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int
required
Total number of tiles to be written.
​
int
required
Dimensionality of each prediction vector.

​
write

Writes a single tile response into the HDF5 datasets.
​
ModelResponse
required
The model response to persist.

​
set_thumbnail

Stores a slide thumbnail as an HDF5 dataset.
​
NDArray
required
RGB image array of shape (H, W, 3).

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set_metadata

Stores metadata as HDF5 file-level attributes.
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dict[str, Any]
required
Key-value pairs (slide_name, tile_size, etc.).

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set_tissue_mask

Stores the tissue mask as an HDF5 dataset.
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NDArray
required
Binary mask array of shape (H, W), dtype uint8.

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set_gene_names

Stores gene name arrays as HDF5 string datasets.
​
list[str] | None
Ordered Ensembl IDs for bulk RNA input.
​
list[str] | None
Ordered Ensembl IDs for predicted output.

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close

Closes the HDF5 file handle and flushes to disk.

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NPZWriter

Accumulates tile predictions in memory, saves as compressed npz.

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open

Allocates in-memory arrays for accumulating results.
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int
required
Total number of tiles to be written.
​
int
required
Dimensionality of each prediction vector.

​
write

Writes a single tile response into the in-memory arrays.
​
ModelResponse
required
The model response to persist.

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set_thumbnail

Stores the slide thumbnail for later NPZ serialization.
​
NDArray
required
RGB image array of shape (H, W, 3).

​
set_metadata

Stores metadata for later NPZ serialization.
​
dict[str, Any]
required
Key-value pairs (slide_name, tile_size, etc.).

​
set_tissue_mask

Stores the tissue mask for later NPZ serialization.
​
NDArray
required
Binary mask array of shape (H, W), dtype uint8.

​
set_gene_names

Stores gene name lists for later NPZ serialization.
​
list[str] | None
Ordered Ensembl IDs for bulk RNA input.
​
list[str] | None
Ordered Ensembl IDs for predicted output.

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close

Flushes all accumulated arrays to a compressed .npz file.

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create_writer

Creates a writer for the requested format.
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OutputFormat
required
Output format.
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Path
required
Destination file or directory path.
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PredictionWriter
An initialised (but not yet opened) PredictionWriter.