Thomas Ales
007089dd48
- pyproject.toml replaces sras_viewer_requirements.txt (same pins) and adds a dev extra with pytest. - tools/test_refactor.py, test_alignment.py, test_gui.py become tests/test_compute.py, tests/test_alignment.py, tests/test_gui.py with assertions preserved verbatim. test_gui.py stays one ordered integration sequence over a shared module-scoped window. - check_equivalence.py: drop the dead pre-refactor monolith shim (and the _compute_angle_alignment alias it consumed), extend the pad sweep to (1, 2, 4, 8, 40), add legacy-v4 and big-endian int16 legs (new bps=2 option in make_test_sras) so the padded FFT path and the >i2 memmap path are in the baseline before the FFT rewrite. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
278 lines
13 KiB
Python
278 lines
13 KiB
Python
"""Behavioural tests for the compute/format layer.
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Covers what the golden-hash harness can't: the v6->v7 cache round-trip
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(including block carry-forward), parallel-vs-serial identity, the no-mask
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fast path, and the ROI bounding-box mask optimisation.
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"""
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import subprocess
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import sys
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from pathlib import Path
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import numpy as np
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import sras_compute as compute
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from sras_compute import (
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cache_file, compute_dc_image, compute_rf_image, dc_image_mv,
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)
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from sras_format import CH3_IDX, CH4_IDX, SrasFile, adc_to_mv
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import tools.make_test_sras as gen
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REPO = Path(__file__).resolve().parent.parent
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def test_cache_roundtrip(tmp_path):
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"""v6 -> v7 for DC, then FFT, asserting the first block survives the
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second write (the carry-forward path in write_v7_cache)."""
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path = tmp_path / "roundtrip.sras"
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gen.write(path, n_angles=3, seed=1, samples_per_frame=64)
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src = SrasFile(str(path))
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assert src.version == 6, f"got v{src.version}"
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expect_dc3 = [dc_image_mv(src, a, CH3_IDX) for a in range(src.n_angles)]
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expect_dc4 = [dc_image_mv(src, a, CH4_IDX) for a in range(src.n_angles)]
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expect_fft = [compute_rf_image(src, a, dc_threshold_mv=None, apply_bg_sub=True)
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for a in range(src.n_angles)]
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err = cache_file(str(path), "dc", True)
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assert err == "", err
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after_dc = SrasFile(str(path))
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assert after_dc.version == 7, f"got v{after_dc.version}"
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assert all(x is not None for x in after_dc.precomputed_dc3_mv)
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assert all(np.allclose(after_dc.precomputed_dc3_mv[a], expect_dc3[a], atol=1e-4)
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for a in range(after_dc.n_angles))
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assert all(np.allclose(after_dc.precomputed_dc4_mv[a], expect_dc4[a], atol=1e-4)
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for a in range(after_dc.n_angles))
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assert all(x is None for x in after_dc.precomputed_freq_mhz), "no fft block yet"
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assert (after_dc.precomputed_dc3_mv[0].dtype == np.float32
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and after_dc.precomputed_dc3_mv[0].dtype.byteorder in ("=", "|")), \
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"cached images are native float32"
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assert after_dc.precomputed_dc3_mv[0].flags.writeable
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err = cache_file(str(path), "fft", True)
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assert err == "", err
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both = SrasFile(str(path))
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assert all(x is not None for x in both.precomputed_freq_mhz)
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assert all(np.allclose(both.precomputed_freq_mhz[a], expect_fft[a], atol=1e-3)
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for a in range(both.n_angles))
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assert all(np.allclose(both.precomputed_dc3_mv[a], expect_dc3[a], atol=1e-4)
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for a in range(both.n_angles)), \
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"DC block carried forward through the FFT write"
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assert both.precomputed_bg_sub is True
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# The fast path must reproduce a fresh compute, and masking must still
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# apply on top of a cached (unmasked) image.
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fresh = SrasFile(str(path))
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fresh.precomputed_freq_mhz = [None] * fresh.n_angles
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dc4 = dc_image_mv(both, 0, CH4_IDX)
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thr = float(np.median(dc4))
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assert np.allclose(
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compute_rf_image(both, 0, dc_threshold_mv=None, apply_bg_sub=True),
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compute_rf_image(fresh, 0, dc_threshold_mv=None, apply_bg_sub=True),
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atol=1e-3), "cached fast path == fresh compute (unmasked)"
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assert np.allclose(
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compute_rf_image(both, 0, dc_threshold_mv=thr, apply_bg_sub=True),
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compute_rf_image(fresh, 0, dc_threshold_mv=thr, apply_bg_sub=True),
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atol=1e-3), "cached fast path == fresh compute (masked)"
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# Waveform data must be byte-identical to the pre-cache file.
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orig = tmp_path / "roundtrip_orig.sras"
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gen.write(orig, n_angles=3, seed=1, samples_per_frame=64)
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o, n = SrasFile(str(orig)), SrasFile(str(path))
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assert all(np.array_equal(np.asarray(o.data[a]), np.asarray(n.data[a]))
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for a in range(o.n_angles)), \
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"waveform data untouched by the cache write"
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def test_partial_v7_cache(tmp_path):
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"""Only some angles cached: uncached angles must compute, not read zeros.
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This is the v5 bug the ragged normalisation fixed, checked via v7."""
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path = tmp_path / "partial.sras"
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gen.write(path, n_angles=3, seed=2, samples_per_frame=64)
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src = SrasFile(str(path))
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expected = [compute_rf_image(src, a, dc_threshold_mv=None, apply_bg_sub=True)
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for a in range(src.n_angles)]
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partial = [expected[0], None, expected[2]] # angle 1 deliberately absent
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src.write_v7_cache(new_freq_mhz=partial, new_bg_sub=True)
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reread = SrasFile(str(path))
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assert reread.precomputed_freq_mhz[1] is None
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assert (reread.precomputed_freq_mhz[0] is not None
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and reread.precomputed_freq_mhz[2] is not None)
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img1 = compute_rf_image(reread, 1, dc_threshold_mv=None, apply_bg_sub=True)
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assert np.any(img1 != 0) and np.allclose(img1, expected[1], atol=1e-3), \
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"uncached angle computes rather than returning zeros"
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def test_parallel_identity(tmp_path, monkeypatch):
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"""Forcing 1 worker vs many must give identical output — catches
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chunk-boundary and race bugs."""
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path = tmp_path / "parallel.sras"
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# Many rows, so the row loop actually splits into several chunks.
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n_rows, n_frames, spf = 48, 9, 256
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gen.write(path, n_angles=1, seed=3, samples_per_frame=spf,
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geometry=[(n_rows, n_frames)])
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sras = SrasFile(str(path))
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# Shrink the budget so chunk_rows collapses to 1 and every row is
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# its own chunk — the worst case for boundary bugs.
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monkeypatch.setattr(compute, "_TOTAL_BYTES_BUDGET", 8 * n_frames * spf * 4)
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monkeypatch.setattr(compute, "_MAX_WORKERS", 1)
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dc_serial = compute_dc_image(sras, 0, CH4_IDX)
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rf_serial = compute_rf_image(sras, 0, dc_threshold_mv=None, apply_bg_sub=True)
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dc4 = adc_to_mv(dc_serial, *sras.cal(CH4_IDX))
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thr = float(np.median(dc4))
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rf_masked_serial = compute_rf_image(sras, 0, dc_threshold_mv=thr,
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apply_bg_sub=True)
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chunk_rows, n_workers = compute._plan_chunks(
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n_rows, n_frames, spf, live_multiplier=compute._FFT_LIVE_MULTIPLIER)
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assert n_workers == 1, f"serial plan uses 1 worker (chunk_rows={chunk_rows})"
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assert chunk_rows < n_rows, \
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f"work actually splits into multiple chunks ({chunk_rows} of {n_rows} rows)"
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monkeypatch.setattr(compute, "_MAX_WORKERS", 8)
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chunk_rows, n_workers = compute._plan_chunks(
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n_rows, n_frames, spf, live_multiplier=compute._FFT_LIVE_MULTIPLIER)
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assert n_workers > 1, \
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f"parallel plan uses >1 worker (chunk_rows={chunk_rows} workers={n_workers})"
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dc_par = compute_dc_image(sras, 0, CH4_IDX)
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rf_par = compute_rf_image(sras, 0, dc_threshold_mv=None, apply_bg_sub=True)
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rf_masked_par = compute_rf_image(sras, 0, dc_threshold_mv=thr, apply_bg_sub=True)
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assert np.array_equal(dc_serial, dc_par), "dc image identical"
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assert np.array_equal(rf_serial, rf_par), "rf image identical (unmasked)"
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assert np.array_equal(rf_masked_serial, rf_masked_par), \
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"rf image identical (masked)"
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def test_nomask_equals_low_threshold(tmp_path):
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"""dc_threshold_mv=None must equal a threshold below every pixel, while
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skipping the CH4 read."""
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path = tmp_path / "nomask.sras"
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gen.write(path, n_angles=2, seed=4, samples_per_frame=128)
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sras = SrasFile(str(path))
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for a in range(sras.n_angles):
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none_img = compute_rf_image(sras, a, dc_threshold_mv=None, apply_bg_sub=True)
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low_img = compute_rf_image(sras, a, dc_threshold_mv=-1e9, apply_bg_sub=True)
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assert np.array_equal(none_img, low_img), \
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f"angle {a}: None == -1e9 threshold"
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assert len(np.unique(none_img)) > 1, \
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f"angle {a}: image is degenerate ({len(np.unique(none_img))} unique)"
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def test_roi_mask():
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"""The bbox-restricted mask must equal a full-grid point-in-polygon test."""
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from matplotlib.path import Path as MplPath
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from sras_viewer import RoiQuad
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rng = np.random.default_rng(0)
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x = np.linspace(-2.0, 3.0, 137)
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y = np.linspace(1.0, 4.0, 91)
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cases = {
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"axis-aligned rect": np.array([[0.0, 1.5], [1.0, 1.5], [1.0, 3.0], [0.0, 3.0]]),
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"skewed quad": np.array([[-0.5, 1.2], [1.7, 1.9], [1.2, 3.4], [-1.0, 2.6]]),
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"entirely outside": np.array([[8.0, 8.0], [9.0, 8.0], [9.0, 9.0], [8.0, 9.0]]),
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"covers whole grid": np.array([[-9.0, -9.0], [9.0, -9.0], [9.0, 9.0], [-9.0, 9.0]]),
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"straddles left edge": np.array([[-4.0, 2.0], [0.5, 2.0], [0.5, 3.0], [-4.0, 3.0]]),
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}
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for _ in range(5):
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cases[f"random {_}"] = rng.uniform([-2.5, 0.5], [3.5, 4.5], size=(4, 2))
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for name, pts in cases.items():
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roi = RoiQuad(pts)
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fast = roi.mask_for_grid(x, y)
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X, Y = np.meshgrid(x.astype(np.float64), y.astype(np.float64))
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slow = MplPath(pts).contains_points(
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np.column_stack([X.ravel(), Y.ravel()])).reshape(X.shape)
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assert np.array_equal(fast, slow), f"{name} ({int(slow.sum())} px inside)"
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# Descending y axis (images are stored top-down in some scans).
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roi = RoiQuad(cases["skewed quad"])
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y_desc = y[::-1]
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fast = roi.mask_for_grid(x, y_desc)
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X, Y = np.meshgrid(x.astype(np.float64), y_desc.astype(np.float64))
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slow = MplPath(cases["skewed quad"]).contains_points(
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np.column_stack([X.ravel(), Y.ravel()])).reshape(X.shape)
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assert np.array_equal(fast, slow), "descending y axis"
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def test_legacy_parse(tmp_path):
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"""v2-v4 parsing against known written data."""
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for version in (2, 3, 4):
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path = tmp_path / f"legacy_v{version}.sras"
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meta = gen.write_legacy(path, version=version, n_angles=2, n_rows=4,
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n_frames=12, samples_per_frame=32, seed=version)
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s = SrasFile(str(path))
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assert s.version == version, f"got v{s.version}"
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assert list(s.n_rows) == [4, 4] and list(s.n_frames) == [12, 12], \
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f"rows={list(s.n_rows)} frames={list(s.n_frames)}"
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assert all(np.array_equal(np.asarray(s.data[a]), meta["data"][a])
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for a in range(s.n_angles)), \
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f"v{version} waveform data matches what was written"
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assert (s.background is not None) == (version >= 4), \
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f"v{version} background {'present' if version >= 4 else 'absent'}"
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assert (isinstance(s.precomputed_freq_mhz, list)
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and len(s.precomputed_freq_mhz) == s.n_angles), \
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f"v{version} precomputed stores are ragged lists"
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# DC image must equal a direct mean of the known input.
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expect = meta["data"][0][:, CH3_IDX, :, :].astype(np.float64).mean(axis=-1)
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assert np.allclose(compute_dc_image(s, 0, CH3_IDX), expect, atol=1e-3), \
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f"v{version} DC image equals a direct mean"
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def test_sras_average(tmp_path):
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"""The sras_average.py CLI: frame averaging with remainder handling."""
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src = tmp_path / "legacy_v4.sras"
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meta = gen.write_legacy(src, version=4, n_angles=2, n_rows=4, n_frames=12,
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samples_per_frame=32, seed=4)
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dst = tmp_path / "legacy_v4_avg.sras"
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proc = subprocess.run(
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[sys.executable, str(REPO / "sras_average.py"), str(src), str(dst), "--n", "4"],
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capture_output=True, text=True, cwd=REPO)
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assert proc.returncode == 0, (proc.stderr or proc.stdout).strip()[-200:]
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avg = SrasFile(str(dst))
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assert avg.version == 4
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assert list(avg.n_frames) == [3, 3], f"{list(avg.n_frames)}"
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assert (avg.n_angles == 2 and list(avg.n_rows) == [4, 4]
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and avg.n_channels == meta["n_channels"])
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assert np.allclose(avg.ch_ymult_mv, SrasFile(str(src)).ch_ymult_mv), \
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"calibration preserved"
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assert np.array_equal(avg.background, SrasFile(str(src)).background), \
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"background preserved"
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src_data = meta["data"]
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expect0 = src_data[0][:, :, 0:4, :].astype(np.float32).mean(axis=2).astype(np.int16)
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assert np.array_equal(np.asarray(avg.data[0])[:, :, 0, :], expect0), \
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"first averaged group equals the mean of its 4 source frames"
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# Remainder handling: 12 frames / 5 -> 2 full groups + 1 partial.
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dst2 = tmp_path / "legacy_v4_avg5.sras"
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subprocess.run([sys.executable, str(REPO / "sras_average.py"),
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str(src), str(dst2), "--n", "5"],
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capture_output=True, text=True, cwd=REPO)
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assert list(SrasFile(str(dst2)).n_frames) == [3, 3], \
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"partial trailing group kept by default"
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dst3 = tmp_path / "legacy_v4_avg5d.sras"
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subprocess.run([sys.executable, str(REPO / "sras_average.py"),
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str(src), str(dst3), "--n", "5", "--discard-remainder"],
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capture_output=True, text=True, cwd=REPO)
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assert list(SrasFile(str(dst3)).n_frames) == [2, 2], \
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"--discard-remainder drops the partial group"
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def test_unsupported_version_reported(tmp_path):
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"""cache_file must report, not raise, for a file it can't handle."""
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bogus = tmp_path / "bogus.sras"
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bogus.write_bytes(b"SRAS" + bytes([99]) + b"\x00" * 200)
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err = cache_file(str(bogus), "dc", True)
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assert err, "bad version returns an error string"
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missing = cache_file(str(tmp_path / "does_not_exist.sras"), "dc", True)
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assert missing, "missing file returns an error string"
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