Merge the Documents/sras-viewer working copy into this repo
The two clones had diverged from origin/main (191d1b8) and both had
grown uncommitted work. This merges the other clone's three commits and
reconciles four conflicting files.
Both clones independently grew a feature called "batch export", but they
are different sweeps and both are kept:
- BatchExportWorker (this clone) — every angle x channel of the one open
file, fixed colorbar per channel, under a new Export menu.
- BatchExportImagesWorker (other clone) — the current view across many
selected files, process-pooled, under Convert.
Conflict resolutions of note:
- sras_average.py: the other clone's memory-bounded rewrite had silently
reverted this clone's float32 -> int16 accumulator fix, which exists to
keep averaged output from landing 1 ADC count off the original tool.
Kept the rewrite, re-applied the fix, and corrected the two docstrings
that still claimed float32.
- tests/test_compute.py: kept the other clone's meta["waveforms"] key
(meta["data"] no longer exists for this fixture and would KeyError)
and its laser_freq_hz assertions, plus this clone's int16 expectation
and its dropped subprocess returncode assertions.
- ComputeWorker: row_avg_n and min_freq_mhz were added independently on
either side; both are now threaded through.
- compute_rf_image's `exact` parameter is gone, removed by the other
clone's PyFFTW peak-search rewrite. It had no remaining callers.
Verified: 149 passed with a complete dependency set. The failures seen
with this clone's own .venv are a missing scikit-image, which predates
this merge and reproduces identically on the pre-merge commit.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
This commit is contained in:
Thomas Ales [M S E]
+296
-4
@@ -90,7 +90,7 @@ def no_fft(monkeypatch):
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"""Make any real FFT work loud: returns a list that stays empty unless a
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peak search actually runs."""
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calls = []
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for name in ("_peak_bins_direct", "_peak_bins_zoom"):
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for name in ("_peak_bins",):
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original = getattr(compute, name)
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def spy(*args, _f=original, **kwargs):
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@@ -147,7 +147,7 @@ def test_cache_is_stored_at_the_configured_pad(tmp_path, pad):
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gen.write(path, n_angles=2, seed=13, samples_per_frame=256)
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spf = SrasFile(str(path)).samples_per_frame
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assert cache_file(str(path), "fft", True, "scipy", 0, pad) == ""
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assert cache_file(str(path), "fft", True, 0, pad) == ""
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sras = SrasFile(str(path))
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assert sras.precomputed_pad_factor == pad, "pad factor survives the round trip"
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@@ -180,12 +180,18 @@ def test_cach_v1_reads_as_natural_resolution(tmp_path):
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# Rewrite the tail as a genuine CACH v1 block (old header, no pad field).
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v2 = SrasFile(str(path))
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freq, entries = v2.precomputed_freq_mhz, list(range(v2.n_angles))
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tail_offset = v2._cache_tail_offset()
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payload = struct.pack(fmt.CACH_HDR_FMT, fmt.CACH_MAGIC, 1, fmt.CACH_FLAG_FFT)
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payload += struct.pack(fmt.SFFT_HDR_FMT_V1, fmt.SFFT_MAGIC,
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fmt.SFFT_FLAG_BG_SUB, len(entries))
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for a in entries:
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payload += struct.pack(">H", a) + freq[a].astype(">f4").tobytes()
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head = path.read_bytes()[:v2._cache_tail_offset()]
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# Windows refuses to truncate a file with a live mapping (write_bytes
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# opens 'wb'), and every SrasFile holds its waveform memmaps for life —
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# drop the instance first. The parsed freq arrays are plain copies and
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# stay usable.
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del v2
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head = path.read_bytes()[:tail_offset]
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path.write_bytes(head + payload)
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v1 = SrasFile(str(path))
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@@ -493,12 +499,16 @@ def test_cach_v1_backward_compat_defaults_row_avg_n_zero(tmp_path):
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v2 = SrasFile(str(path))
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freq, entries = v2.precomputed_freq_mhz, list(range(v2.n_angles))
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tail_offset = v2._cache_tail_offset()
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payload = struct.pack(fmt.CACH_HDR_FMT, fmt.CACH_MAGIC, 1, fmt.CACH_FLAG_FFT)
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payload += struct.pack(fmt.SFFT_HDR_FMT_V1, fmt.SFFT_MAGIC,
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fmt.SFFT_FLAG_BG_SUB, len(entries))
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for a in entries:
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payload += struct.pack(">H", a) + freq[a].astype(">f4").tobytes()
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head = path.read_bytes()[:v2._cache_tail_offset()]
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# See test_cach_v1_reads_as_natural_resolution: release the memmaps
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# before write_bytes truncates, or Windows raises EINVAL.
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del v2
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head = path.read_bytes()[:tail_offset]
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path.write_bytes(head + payload)
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v1 = SrasFile(str(path))
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@@ -510,6 +520,288 @@ def test_cach_v1_backward_compat_defaults_row_avg_n_zero(tmp_path):
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"a v1 tail (predating this feature) can never satisfy a row-averaged request"
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# ---------------------------------------------------------------------------
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# Min peak frequency floor: serve-time masking, on-disk provenance, batch
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# ---------------------------------------------------------------------------
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def _biting_floor(stored: np.ndarray) -> float:
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"""A floor that zeroes some-but-not-all of *stored*'s positive peaks:
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the median distinct positive value, so pixels below it get masked and
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pixels at/above it survive (the mask is a strict <)."""
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positive = np.unique(stored[stored > 0])
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assert len(positive) >= 2, "fixture must have varied peak frequencies"
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return float(positive[len(positive) // 2])
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def test_stored_image_served_with_raised_floor_masked(rig, no_fft):
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"""The core of the 5 m/s bug fix: a floor above the stored one (here 0)
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is re-applied when the stored image is served — pixels whose stored
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peak falls below it come back as the 0.0 invalid sentinel, everything
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else passes through, and no FFT runs. Both directly through
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cached_rf_image and through compute_rf_image's fast path."""
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assert rig.sras.precomputed_min_freq_mhz == 0.0, "batched without a floor"
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stored = rig.sras.precomputed_freq_mhz[0]
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floor = _biting_floor(stored)
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expect = np.where(stored < floor, np.float32(0.0), stored)
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img = cached_rf_image(rig.sras, 0, None, apply_bg_sub=True,
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min_freq_mhz=floor)
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assert img is not None, "an equal-or-higher floor is servable"
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assert np.array_equal(img, expect)
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assert (img == 0).any() and (img > 0).any(), \
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"the floor bites some pixels but not all"
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via_compute = compute_rf_image(rig.sras, 0, dc_threshold_mv=None,
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apply_bg_sub=True, min_freq_mhz=floor)
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assert np.array_equal(via_compute, expect), \
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"compute_rf_image's fast path applies the same serve-time mask"
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assert not no_fft, f"serving + masking must not run an FFT: {no_fft}"
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def test_min_freq_floor_round_trips_and_gates_serving(tmp_path):
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"""cache_file records the floor in the SFFT header and the accept rule
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is asymmetric: an equal-or-higher request is servable, a lower one is
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refused (the stored search never looked below its floor). 20.1 pins the
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fixed-point kHz encoding — a float32 header field would read back as
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20.10000038…, above the requested 20.1, and mismatch forever."""
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path = tmp_path / "floor_roundtrip.sras"
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gen.write(path, n_angles=2, seed=31, samples_per_frame=128)
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floor = 20.1
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assert cache_file(str(path), "fft", True, min_freq_mhz=floor) == ""
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sras = SrasFile(str(path))
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assert sras.precomputed_min_freq_mhz == floor, "exact fixed-point round-trip"
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assert all(((img == 0) | (img >= floor)).all()
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for img in sras.precomputed_freq_mhz), \
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"no stored peak below the floor"
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def reasons(f):
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return compute.cache_mismatch_reasons(
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sras, n_fft=None, apply_bg_sub=True, row_avg_n=0, min_freq_mhz=f)
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assert reasons(floor) == []
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assert reasons(floor + 5.0) == [], "a higher request is servable (masked)"
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low = reasons(0.0)
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assert low and "min-peak-freq floor" in low[0], \
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"a lower request cannot be answered by the stored search"
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assert cached_rf_image(sras, 0, None, apply_bg_sub=True) is None, \
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"default floor-0 request refused against a floored store"
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assert cached_rf_image(sras, 0, None, apply_bg_sub=True,
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min_freq_mhz=floor) is not None
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def test_batch_recompute_resolves_not_masks(tmp_path, no_fft):
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"""Re-batching an already-cached file at a raised floor must run the
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real FFT and store re-resolved peaks — never let compute_rf_image's
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fast path serve the file's own stale cache back to it and bake the
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masked copy in as if it were a recompute (silent, permanent data
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loss: a masked pixel's true above-floor peak is unrecoverable)."""
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path = tmp_path / "rebatch.sras"
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gen.write(path, n_angles=2, seed=32, samples_per_frame=256)
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assert cache_file(str(path), "fft", True) == ""
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first = SrasFile(str(path))
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n_angles = first.n_angles
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# On the header's kHz grid up front (as the spinbox value would be), so
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# the recorded floor reads back equal — cache_file quantizes whatever it
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# is given, and this test wants that to be the identity.
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floor = round(_biting_floor(first.precomputed_freq_mhz[0]) * 1000) / 1000.0
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bites = [img < floor for img in first.precomputed_freq_mhz]
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assert bites[0].any(), "the floor must actually bite this fixture"
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# What a real floored compute gives, from a view blinded to the cache.
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first.precomputed_freq_mhz = [None] * n_angles
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expected = [compute_rf_image(first, a, dc_threshold_mv=None,
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apply_bg_sub=True, min_freq_mhz=floor)
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for a in range(n_angles)]
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del first # release memmaps before cache_file rewrites the tail
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no_fft.clear()
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assert cache_file(str(path), "fft", True, min_freq_mhz=floor) == ""
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assert no_fft, "the re-batch ran a real FFT"
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after = SrasFile(str(path))
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assert after.precomputed_min_freq_mhz == floor
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for a in range(n_angles):
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assert np.array_equal(after.precomputed_freq_mhz[a], expected[a]), \
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f"angle {a}: stored image is a real floored recompute"
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assert (after.precomputed_freq_mhz[a][bites[a]] >= floor).all(), \
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f"angle {a}: bitten pixels re-resolved above the floor, not zeroed"
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def test_min_freq_carries_forward_through_dc_write(tmp_path):
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"""A later DC-only write must leave the FFT block's recorded floor
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untouched, like row_avg_n and pad_factor."""
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path = tmp_path / "floor_carry.sras"
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gen.write(path, n_angles=2, seed=33, samples_per_frame=128)
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assert cache_file(str(path), "fft", True, min_freq_mhz=75.0) == ""
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assert cache_file(str(path), "dc", True) == ""
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after = SrasFile(str(path))
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assert after.precomputed_min_freq_mhz == 75.0, \
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"floor survives a DC-only write"
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def test_cach_v3_backward_compat_defaults_floor_zero(tmp_path):
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"""A v3 CACH tail predates the min peak frequency floor entirely (no
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min_freq_khz field) — readers must still parse it in full, treating it
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as floor 0: servable as-is at floor 0, and serve-maskable at any higher
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one. This is what protects existing real-world v7 caches from silently
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becoming unusable after the v4 bump ships."""
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path = tmp_path / "v3_floor.sras"
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gen.write(path, n_angles=2, seed=34, samples_per_frame=128)
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assert cache_file(str(path), "fft", True) == ""
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# Rewrite the tail as a genuine CACH v3 block (no min_freq field).
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v4 = SrasFile(str(path))
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freq, entries = v4.precomputed_freq_mhz, list(range(v4.n_angles))
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tail_offset = v4._cache_tail_offset()
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payload = struct.pack(fmt.CACH_HDR_FMT, fmt.CACH_MAGIC, 3, fmt.CACH_FLAG_FFT)
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payload += struct.pack(fmt.SFFT_HDR_FMT_V3, fmt.SFFT_MAGIC,
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fmt.SFFT_FLAG_BG_SUB, len(entries), 0, 1)
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for a in entries:
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payload += struct.pack(">H", a) + freq[a].astype(">f4").tobytes()
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# See test_cach_v1_reads_as_natural_resolution: release the memmaps
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# before write_bytes truncates, or Windows raises EINVAL.
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del v4
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head = path.read_bytes()[:tail_offset]
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path.write_bytes(head + payload)
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v3 = SrasFile(str(path))
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assert v3.precomputed_min_freq_mhz == 0.0
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assert v3.precomputed_pad_factor == 1 and v3.precomputed_bg_sub is True
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assert all(np.array_equal(v3.precomputed_freq_mhz[a], freq[a])
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for a in entries), "v3 images read back unchanged"
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assert cached_rf_image(v3, 0, None, apply_bg_sub=True) is not None
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floor = _biting_floor(freq[0])
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served = cached_rf_image(v3, 0, None, apply_bg_sub=True,
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min_freq_mhz=floor)
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assert served is not None
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assert np.array_equal(served,
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np.where(freq[0] < floor, np.float32(0.0), freq[0]))
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def test_min_freq_validation(tmp_path):
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path = tmp_path / "floor_bad.sras"
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gen.write(path, n_angles=1, seed=35, samples_per_frame=64)
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assert cache_file(str(path), "fft", True, min_freq_mhz=-1.0), \
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"negative floor must be an error, not a write"
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assert cache_file(str(path), "fft", True, min_freq_mhz=float("nan")), \
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"NaN floor must be an error, not a write"
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sras = SrasFile(str(path))
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with pytest.raises(ValueError):
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sras.write_v7_cache(new_min_freq_mhz=-0.5)
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def test_viewer_reapplies_floor_to_stored_images_without_computing(
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rig, no_fft, monkeypatch):
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"""The session-cache poisoning bug behind the '95 MHz peak but 5 m/s'
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report: changing 'Min peak freq' against a stored cache used to re-file
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the identical un-floored image under a key claiming the new floor — the
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UI looked updated, the pixels weren't. Now the floor really is
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re-applied on serve (masked, still no compute), and clearing it
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restores the unmasked image, still without computing."""
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app = QApplication.instance() or QApplication([]) # noqa: F841
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win = SrasViewerWindow()
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win.show()
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dispatched = []
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original_start = type(win)._start_compute
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monkeypatch.setattr(type(win), "_start_compute",
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lambda self: (dispatched.append(self.spin_angle.value()),
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original_start(self))[1])
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try:
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win._load_file(str(rig.path))
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assert wait_until(lambda: win._sras is not None), "file loaded"
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assert wait_until(lambda: all((a, CH4_IDX) in win._dc_cache
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for a in range(rig.n_angles))), \
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"DC precompute finished"
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win.combo_channel.setCurrentIndex(CH1_IDX)
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assert wait_until(lambda: win._current_ch == CH1_IDX), "CH1 displayed"
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assert np.allclose(win._current_image, rig.fresh[0], atol=1e-3)
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# Round to the spinbox's 3-decimal granularity; the chosen bin value
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# still survives its own (strict-<) floor after rounding down.
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floor = round(_biting_floor(rig.fresh[0]), 3)
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expect = np.where(rig.fresh[0] < floor, np.float32(0.0), rig.fresh[0])
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dispatched.clear()
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no_fft.clear()
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win.spin_min_freq_mhz.setValue(floor)
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win._on_min_freq_changed()
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pump(120)
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assert np.allclose(win._current_image, expect, atol=1e-3), \
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"raised floor re-masks the stored image on serve"
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assert (win._current_image == 0).any() and (win._current_image > 0).any()
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assert dispatched == [] and not no_fft, \
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f"re-masked serve needs no compute (jobs={dispatched}, fft={no_fft})"
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key = (0, win.spin_threshold_mv.value(), win.spin_min_freq_mhz.value())
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assert key in win._fft_cache
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assert np.allclose(win._fft_cache[key], expect, atol=1e-3), \
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"the session cache holds the value its key claims"
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win.spin_min_freq_mhz.setValue(0.0)
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win._on_min_freq_changed()
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pump(120)
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assert np.allclose(win._current_image, rig.fresh[0], atol=1e-3), \
|
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"clearing the floor restores the unmasked stored image"
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assert dispatched == [] and not no_fft
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finally:
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win.close()
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pump(300)
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|
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def test_viewer_batch_fft_records_the_floor(tmp_path, no_fft, monkeypatch):
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"""Convert → Batch Compute FFT with a floor set: the live spinbox value
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reaches cache_file, lands in the reloaded file's provenance and the
|
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info panel, and the viewer then serves the floored cache without
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recomputing — the tooltip's promised remedy, end to end."""
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path = tmp_path / "floor_gui.sras"
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gen.write(path, n_angles=2, seed=36, samples_per_frame=256)
|
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|
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app = QApplication.instance() or QApplication([]) # noqa: F841
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win = SrasViewerWindow()
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win.show()
|
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|
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dispatched = []
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original_start = type(win)._start_compute
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monkeypatch.setattr(type(win), "_start_compute",
|
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lambda self: (dispatched.append(self.spin_angle.value()),
|
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original_start(self))[1])
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try:
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win._load_file(str(path))
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assert wait_until(lambda: win._sras is not None), "file loaded"
|
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assert wait_until(lambda: all((a, CH4_IDX) in win._dc_cache
|
||||
for a in range(win._sras.n_angles))), \
|
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"DC precompute finished"
|
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|
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floor = 100.0
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win.spin_min_freq_mhz.setValue(floor)
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with patch("sras_viewer.main_window.QFileDialog.getOpenFileNames",
|
||||
return_value=([str(path)], "")):
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win._on_batch_compute("fft")
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assert wait_until(lambda: not win._job_running("batch"), 60000), "batch ran"
|
||||
assert wait_until(lambda: win._sras is not None
|
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and win._sras.version == 7), "file reloaded as v7"
|
||||
pump(200)
|
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assert win._sras.precomputed_min_freq_mhz == floor, \
|
||||
"the viewer's floor reached the stored provenance"
|
||||
assert "floor ≥ 100 MHz" in win.lbl_frame_warn.text()
|
||||
|
||||
no_fft.clear()
|
||||
dispatched.clear()
|
||||
win.combo_channel.setCurrentIndex(CH1_IDX)
|
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assert wait_until(lambda: win._current_ch == CH1_IDX), "CH1 displayed"
|
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pump(120)
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assert dispatched == [] and not no_fft, \
|
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f"floored cache serves the view directly (jobs={dispatched}, fft={no_fft})"
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img = win._current_image
|
||||
assert ((img == 0) | (img >= floor)).all(), \
|
||||
"no displayed peak below the floor"
|
||||
finally:
|
||||
win.close()
|
||||
pump(300)
|
||||
|
||||
|
||||
def test_viewer_batch_row_average_dispatch(tmp_path, monkeypatch, no_fft):
|
||||
"""Driving the new 'Batch Compute Row-Averaged FFT and Store' action
|
||||
end-to-end through the real menu handler: dialog values reach the
|
||||
|
||||
Reference in New Issue
Block a user