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SGE Reorientation (sge_orientate)

Overview

sge_orientate rotates and flips an SGE to match the desired image orientation.

Requirements

Actions

Rotations are clockwise; flips are applied after rotation.

Example Usage

Below is an example with 90 degree rotation and a horizontal flip.

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OUT_PREFIX=r90_hflip                # Replace r90_hflip with your prefix
cartloader sge_orientate  \
    --in-transcript /path/to/transcripts.unsorted.tsv.gz \
    --in-feature  /path/to/feature.clean.tsv.gz \
    --in-minmax /path/to/coordinate_minmax.tsv \
    --out-transcript /path/to/${OUT_PREFIX}.transcripts.unsorted.tsv.gz \
    --out-feature /path/to/${OUT_PREFIX}.feature.clean.tsv.gz \
    --out-minmax  /path/to/${OUT_PREFIX}.coordinate_minmax.tsv \
    --rotate 90 \
    --flip-horizontal

Parameters

Input/Output Parameters

  • --in-transcript (str): Path to input transcript SGE TSV (gzipped).
  • --in-feature (str): Path to input feature TSV (gzipped).
  • --in-minmax (str): Path to input coordinate min/max TSV.
  • --out-transcript (str): Output path for oriented transcript SGE TSV (gzipped).
  • --out-feature (str): Output path for feature TSV (copied from input).
  • --out-minmax (str): Output path for oriented min/max TSV.

Key Parameters

  • --rotate (90|180|270): Rotate clockwise (applied before flips).
  • --flip-vertical (flag): Flip vertically (flipped along the Y-axis; applied after rotation).
  • --flip-horizontal (flag): Flip horizontally (flipped along the X-axis; applied after rotation).
  • --chunk-size (int, default: 1_000_000): Rows per chunk when processing the transcript TSV.

Output

An output SGE matrix after orientation.