quadsv.comparators.grid

quadsv.comparators.grid#

ComparatorGrid — cross-sample pattern comparison on a list of spatialdata.SpatialData (regular rasterized bins, FFT backend).

Classes#

ComparatorGrid

Cross-sample pattern comparison on regular bins via FFT + SpatialData.

Module Contents#

class quadsv.comparators.grid.ComparatorGrid(samples, *, bins, table_name, col_key, row_key, value_key=None, gene_names=None, feature_mode='radial', n_radial_bins=30, fft_solver='rfft2', workers=None, spacing=None, freq_edges=None, presence_threshold=0.0, fft_chunk_size=256)[source]#

Bases: quadsv.comparators.base._ComparatorBase

Cross-sample pattern comparison on regular bins via FFT + SpatialData.

Accepts a list of spatialdata.SpatialData (one per sample). For each sample, spatialdata.rasterize_bins() turns the designated bin shape + table into a dense (n_genes, ny, nx) image, which is then fed to the batched 2D FFT. All samples are expected to share the same rasterization schema (bins / table_name / col_key / row_key / value_key) — this mirrors DetectorGrid.

Parameters:

  • samples (sequence of spatialdata.SpatialData)

  • bins (str) – SpatialElement key for the bin shapes in each sdata.

  • table_name (str) – Table key in each sdata.tables.

  • col_key (str) – Column / row-index columns in the table’s .obs.

  • row_key (str) – Column / row-index columns in the table’s .obs.

  • value_key (str, optional) – Expression column in .obs; defaults to None (rasterizes counts / presence directly off .X).

  • gene_names (sequence of str, optional) – If None, inferred from the first sample’s table. All samples must share var_names.

  • fft_chunk_size (int, default 256) – Genes per batched scipy.fft call on the rasterized block. Keeps transient memory bounded at O(ny · nx · chunk · 8 B). The raster itself is still built once per sample (full (n_genes, ny, nx) footprint is unavoidable on SpatialData).

  • feature_mode (str) – See _ComparatorBase.

  • n_radial_bins (int) – See _ComparatorBase.

  • fft_solver (str) – See _ComparatorBase.

  • workers (int | None) – See _ComparatorBase.

  • freq_edges (ndarray | None) – See _ComparatorBase.

  • presence_threshold (float) – See _ComparatorBase.

  • spacing (tuple[float, float] | None)

Notes

The comparator carries no design / contrast state — supply the cross-sample contrast directly to test_diff_freq() / test_diff_expr(). A single fitted comparator can therefore serve any number of unrelated comparisons on the same spectra.

feature_mode = 'radial'[source]#
freq_edges = None[source]#
gene_names[source]#
samples[source]#
Contents