BioFormatsVirtualSetupLoader¶

class io.loaders.BioFormatsVirtualSetupLoader¶

Bases: io.loaders.BaseImageLoader

BIOFORMATSVIRTUALSETUPLOADER - Virtual-mode setup loader for BioFormats datasets.

Wraps BioFormatsStdLoader and adapts it for virtual stacking mode: loadMetadata delegates entirely to BioFormatsStdLoader (series selection dialog, pixel-size extraction, etc.) loadImages does NOT read pixel data; instead returns the file path(s) as a cell array and stores the Virtual struct in imginfo{“Virtual”} so that MibVirtualImage.initialize can wire it up.

Relationship to BioFormatsVirtualLoader

These two classes serve different phases of the virtual dataset lifecycle:

BioFormatsVirtualSetupLoader - runs ONCE when the user opens a file. Phase : dataset initialisation (MibModel.loadImages) Job : parse metadata, build the Virtual struct, return file paths. Reads pixels? No. Lifetime: discarded after open; implements BaseImageLoader. Created by: LoaderFactory

BioFormatsVirtualLoader - runs on EVERY slice request during session. Phase : on-demand pixel reading (MibVirtualImage.getDataVirt) Job : open Memoizer reader, call bfGetPlane per channel. Reads pixels? Yes. Lifetime: cached in MibVirtualImage.loaders{} for the session. Created by: MibVirtualImage.getOrCreateLoader (lazily, per file)

Usage example:

loader = io.loaders.BioFormatsVirtualSetupLoader(options);
[imginfo, files] = loader.loadMetadata({'stack.czi'}, options);
[img, imginfo] = loader.loadImages(files, imginfo, options);
% img is {'C:\data\stack.czi'} and imginfo{"Virtual"} holds the struct

Constructor Summary

BioFormatsVirtualSetupLoader(options)¶

BIOFORMATSVIRTUALSETUPLOADER - Create a virtual-mode BioFormats setup loader.

Syntax:

obj = BioFormatsVirtualSetupLoader(options)

Input Arguments:

• options - (optional) [struct] options passed to BioFormatsStdLoader

Output Arguments:

• obj - [BioFormatsVirtualSetupLoader] new loader instance

Property Summary

innerLoader¶

Method Summary

loadImages(files, imginfo, options)¶

LOADIMAGES - Virtual-mode image setup - does NOT load pixel data.

Syntax:

[img, imginfo] = obj.loadImages(files, imginfo, options)

Returns the file path(s) as a cell array (consumed by MibVirtualImage.initialize as obj.data{}) and populates imginfo{“Virtual”} with the struct fields required by MibVirtualImage.

Input Arguments:

• files - [struct array] per-file metadata from loadMetadata

• imginfo - [dictionary] image metadata from loadMetadata

• options (optional) - [struct] unused in virtual mode

Output Arguments:

• img - [nFiles x 1 cell] cell array of original file paths

• imginfo - [dictionary] updated dictionary; imginfo{"Virtual"} is added with fields:

  • .objectType - [cell] 'bioformats' per file

  • .seriesName - [cell] 1-based series index per file

  • .slicesPerFile - [numeric] z-slice count per file

  • .filenames - [cell] original file paths (before multi-series rename)

  • .readerId - [totalZ x 1 numeric] maps each slice index to its source file index

loadMetadata(filenames, options)¶

LOADMETADATA - Delegate metadata loading to BioFormatsStdLoader unchanged.

Syntax:

[imginfo, files] = obj.loadMetadata(filenames, options)

Input Arguments:

• filenames - [cell] cell array of file paths to load

• options - [struct] loader options

Output Arguments:

• imginfo - [dictionary] image metadata dictionary

• files - [struct array] per-file metadata; each element has fields:

  • .origFilename - [char] path to the actual file

  • .seriesName - [numeric] 1-based series index

  • .noLayers - [numeric] number of z-slices in this series

  • .color - [numeric] number of colour channels