stitching_orchestrator

class StitchingProcessor(sample_manager: SampleManager, cfg_coordinator: ConfigCoordinator)

Bases: PipelineOrchestrator

This class is used to manage the stitching process Handle image stitching operations. Manage stitching configurations and processes.

align_channel_rigid(channel, _force=False)

channel_was_stitched_rigid(channel)

convert_tiles(*args, _force=False, **kwargs)

convert_tiles_channel(channel, _force=False)

copy_or_stack(channel)

Copy or stack or convert to npy the channel data in case there is no X/Y tiling

Parameters:

channel (str) – The channel to copy or stack

create_layout_from_ome(channel: str) → None

Build and persist a real WobblyLayout for ‘channel’ from OME TileConfiguration. Marks the channel as ‘use_existing_layout’ so rigid placement can be skipped.

get_stitching_order(strict=False)

Returns a list of trees (each tree is a list of channels in hierarchical order). Raises a ValueError if any channel is unreachable or if there is a cycle.

get_wobbly_layout(channel, overlaps=None)

overlay_layout_plane(layout)

Overlays the sources to check their placement.

Arguments

layoutLayout class

The layout with the sources to overlay.

Returns

imagearray

A color image.

place_layout_rigid(channel)

plot_layout(channel, asset_sub_type='aligned_axis')

plot_stitching_results(channels=None, mode='side-by-side', parent=None)

prepare_all_channels_raw_data(force: bool = False) → list[str]

Prepare all pipeline-ready channels that don’t yet have their working asset. Tiled channels → convert tiles to npy. Non-tiled → stack/copy to stitched volume. Idempotent unless force=True.

Parameters:

force (bool) – If True, re-prepare even if the working asset already exists.

Returns

list[str]

Channel names that were prepared.

setup(sample_manager: SampleManager | None = None, convert_tiles: bool = False)

Attach a sample manager and mark this processor as ready.

Parameters:

sample_manager (SampleManager, optional) – If provided, replaces the currently stored sample manager. When None, the previously stored instance is reused.

Raises:

ValueError – If the config section identified by config_name is absent.

stack_columns(channel)

stitch()

stitch_channel_wobbly(*args, _force=False, **kwargs)

stitch_overlay(channel, color=True)

This creates a dumb overlay of the tiles i.e. only using the fixed guess overlap

Parameters:

• channel

• color

Returns

np.array(dtype=uint8)

The overlay image

config_name = 'stitching'

property n_rigid_steps_to_run

property n_wobbly_steps_to_run