Seed class for lazy on-disk QPTIFF access — QPTIFFArraySeed-class • bgnormR

An S4 class that satisfies the DelayedArray seed contract, enabling lazy, block-based processing of large Akoya PhenoCycler-Fusion QPTIFF images. Each channel (TIFF page) is read from disk only when data for that channel is actually requested by the DelayedArray framework.

Called internally by the DelayedArray framework. Reads only the requested channels and the spatial region specified by index from disk, keeping memory use proportional to the data actually needed.

Usage

# S4 method for class 'QPTIFFArraySeed'
dim(x)

# S4 method for class 'QPTIFFArraySeed'
dimnames(x)

# S4 method for class 'QPTIFFArraySeed'
type(x)

# S4 method for class 'QPTIFFArraySeed'
extract_array(x, index)

Arguments

x: A QPTIFFArraySeed.
index: List of length 3. Each element is either NULL (all indices for that dimension) or a sorted integer vector of 1-based indices.

Value

An ordinary array with dimensions c(length(i_rows), length(i_cols), length(i_channels)).

Details

Internally the seed reads the full TIFF/BigTIFF directory chain at construction time (fast: only header bytes, no pixel data) and stores tile/strip layout metadata for each channel page. Pixel data is fetched per-tile (when the image is tiled) or per-strip with DEFLATE/zlib decompression handled by R's built-in memDecompress. Unsupported compression types fall back to tiff::readTIFF.

Do not construct this class directly; use read_qptiff(path, lazy = TRUE).

Slots

filepath: Absolute path to the QPTIFF file.
.dim: Integer vector [H, W, C].
.dimnames: List of dimnames; element 3 holds channel names.
page_layouts: List of per-channel page layout objects (one per channel) each containing the TIFF structural metadata needed to fetch that page.
dtype: Character, "integer" (raw 16-bit values 0-65535) or "double" (normalised to [0, 1]).
metadata: List; rich QPI metadata as returned by .parse_qpi_xml.
level: Integer; pyramid resolution level (1 = full resolution).