kemal
c0d556d4af
- signal/normalization/numerics.py: vendor percentile, trimmean, MAD sigma (old/new), bisquare robust fits, float32/float64 typing and sequential sums reproduced exactly (ported from gtc2vcf, MIT) - signal/normalization/fit.py: outlier removal, offset, rotation, shear, scale, nn12/rr12, single-channel model for small Infinium I bins, exact and binned nearest-neighbour sweeps; vendor quirks marked QUIRK - signal/normalization/apply.py: affine transform and theta/R - pipeline/normalize.py + CLI `simurg normalize` - oracle GTCs rebuilt with -ffp-contract=off (aarch64 gcc fuses a*b+c by default, shifting the last bits); the old FMA oracle differed by <=4 ULP Result: transforms bit-identical to the oracle for all 36 GSA samples x 48 bins, for both normalization versions (3456/3456 bins, 0 ULP).
37 lines
1.3 KiB
Python
37 lines
1.3 KiB
Python
"""Phase P2 acceptance on P0 data: raw X/Y and control intensities assembled from IDATs equal the arrays stored
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in oracle GTCs (TOC 1000/1001, 500/501). The same check on vendor GTCs runs in scripts/validate_p1_large.py --p2.
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"""
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from __future__ import annotations
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import numpy as np
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import pytest
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from tests.conftest import GSA_BPM, GSA_IDATS, ORACLE_GTCS, need
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from simurg.formats.bpm import read_bpm
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from simurg.formats.gtc import read_gtc
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from simurg.formats.idat import read_idat
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from simurg.signal.raw_xy import LocusMapCache, assemble_raw_xy, check_coverage
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pytestmark = pytest.mark.data
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def test_raw_xy_equals_oracle_gtcs() -> None:
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need(GSA_BPM, GSA_IDATS, ORACLE_GTCS)
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m = read_bpm(GSA_BPM)
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cache = LocusMapCache(m)
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gtcs = sorted(ORACLE_GTCS.glob("*.gtc"))
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assert gtcs
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for g in gtcs:
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sid = g.stem
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chip = sid.split("_")[0]
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grn = read_idat(GSA_IDATS / chip / f"{sid}_Grn.idat")
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red = read_idat(GSA_IDATS / chip / f"{sid}_Red.idat")
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assert check_coverage(grn, m)[0] == 1.0
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raw = assemble_raw_xy(grn, red, m, cache=cache)
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ref = read_gtc(g)
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assert np.array_equal(raw.raw_x, ref.raw_x), sid
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assert np.array_equal(raw.raw_y, ref.raw_y), sid
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assert np.array_equal(raw.controls_x, ref.controls_x), sid
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assert np.array_equal(raw.controls_y, ref.controls_y), sid
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