specmod 0.2.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (62) hide show
  1. specmod/__init__.py +17 -0
  2. specmod/_vendor/__init__.py +21 -0
  3. specmod/_vendor/qiinv.py +243 -0
  4. specmod/acquire.py +358 -0
  5. specmod/api.py +480 -0
  6. specmod/cli.py +139 -0
  7. specmod/config/__init__.py +44 -0
  8. specmod/config/layers.py +168 -0
  9. specmod/config/provenance.py +77 -0
  10. specmod/config/sections.py +385 -0
  11. specmod/config/serialize.py +58 -0
  12. specmod/core/__init__.py +41 -0
  13. specmod/core/bandwidth.py +187 -0
  14. specmod/core/collection.py +549 -0
  15. specmod/core/noise.py +478 -0
  16. specmod/core/scalogram.py +234 -0
  17. specmod/core/spectrum.py +326 -0
  18. specmod/core/units.py +116 -0
  19. specmod/datasets.py +316 -0
  20. specmod/distance.py +190 -0
  21. specmod/exceptions.py +58 -0
  22. specmod/fitting/__init__.py +58 -0
  23. specmod/fitting/base.py +50 -0
  24. specmod/fitting/event.py +284 -0
  25. specmod/fitting/guess.py +170 -0
  26. specmod/fitting/spectrum.py +330 -0
  27. specmod/io.py +241 -0
  28. specmod/magnitude.py +312 -0
  29. specmod/picks/__init__.py +182 -0
  30. specmod/picks/base.py +250 -0
  31. specmod/picks/delimited.py +224 -0
  32. specmod/picks/events.py +157 -0
  33. specmod/picks/resolution.py +149 -0
  34. specmod/picks/snuffler.py +92 -0
  35. specmod/pipeline.py +280 -0
  36. specmod/plotting.py +203 -0
  37. specmod/preprocess.py +554 -0
  38. specmod/smoothing/__init__.py +50 -0
  39. specmod/smoothing/base.py +56 -0
  40. specmod/smoothing/konno_ohmachi.py +83 -0
  41. specmod/smoothing/log_bins.py +171 -0
  42. specmod/sources/__init__.py +65 -0
  43. specmod/sources/attenuation.py +110 -0
  44. specmod/sources/composite.py +135 -0
  45. specmod/sources/motion.py +40 -0
  46. specmod/sources/source.py +147 -0
  47. specmod/spreading.py +209 -0
  48. specmod/staged.py +523 -0
  49. specmod/tables.py +110 -0
  50. specmod/transforms/__init__.py +50 -0
  51. specmod/transforms/base.py +242 -0
  52. specmod/transforms/cwt.py +219 -0
  53. specmod/transforms/fft.py +157 -0
  54. specmod/transforms/multitaper.py +357 -0
  55. specmod/transforms/prieto.py +272 -0
  56. specmod/transforms/quadratic.py +221 -0
  57. specmod/utils.py +305 -0
  58. specmod-0.2.0.dist-info/METADATA +294 -0
  59. specmod-0.2.0.dist-info/RECORD +62 -0
  60. specmod-0.2.0.dist-info/WHEEL +4 -0
  61. specmod-0.2.0.dist-info/entry_points.txt +2 -0
  62. specmod-0.2.0.dist-info/licenses/LICENSE +21 -0
@@ -0,0 +1,234 @@
1
+ """The time-frequency surface a CWT produces, and the QC it makes possible.
2
+
3
+ A :class:`Scalogram` is deliberately *not* an amplitude spectrum. Its ``power``
4
+ is ``|W(a,b)|**2`` in the L2-Morlet convention, which carries units of
5
+ ``[signal]**2 * time`` — documented, but not comparable to a Fourier amplitude
6
+ spectrum and not something to fit a source model to.
7
+
8
+ The conversion happens in exactly one place, :meth:`Scalogram.time_average`,
9
+ which applies the ``C_delta`` and ``dj*dt`` bridge and returns an ordinary
10
+ :class:`~specmod.core.spectrum.Spectrum`. One normalisation path, one test. A
11
+ second "already normalised" surface would be a second thing to get wrong.
12
+
13
+ References
14
+ ----------
15
+ Torrence, C. and Compo, G.P. (1998). A practical guide to wavelet analysis.
16
+ *Bulletin of the American Meteorological Society* 79(1), 61-78.
17
+ """
18
+
19
+ from __future__ import annotations
20
+
21
+ from dataclasses import dataclass, field
22
+ from types import MappingProxyType
23
+ from typing import Any
24
+
25
+ import numpy as np
26
+ from numpy.typing import NDArray
27
+
28
+ from .spectrum import Spectrum
29
+ from .units import AmplitudeKind, Motion
30
+
31
+ __all__ = ["Scalogram", "ScalogramQC"]
32
+
33
+
34
+ @dataclass(frozen=True)
35
+ class ScalogramQC:
36
+ """Quality checks a time-frequency surface makes possible.
37
+
38
+ An amplitude-only signal-to-noise test cannot see any of these: it collapses
39
+ the time axis before looking. Every field is computed and recorded rather
40
+ than acted on — a trace is never silently dropped, the numbers travel with
41
+ the result so they can be filtered downstream.
42
+ """
43
+
44
+ #: Lowest frequency with usable coverage outside the cone of influence.
45
+ #: Window length imposes this limit and nothing else in the pipeline
46
+ #: enforces it, so a short window can otherwise report usable bandwidth
47
+ #: where the transform has no support.
48
+ lowest_resolved_frequency: float
49
+
50
+ #: Fraction of the window free of edge effects, per frequency, summarised
51
+ #: as the median across the band.
52
+ median_coi_coverage: float
53
+
54
+ #: Normalised Gini coefficient of energy over time, in ``[0, 1]``. Near 0
55
+ #: is stationary; near 1 means essentially all the energy is in a handful
56
+ #: of samples, which is a glitch rather than an arrival.
57
+ temporal_concentration: float
58
+
59
+ #: Ratio of spectral energy in the first half of the window to the second.
60
+ #: Far from 1 suggests coda contamination, a second arrival, or a window
61
+ #: that started late.
62
+ half_window_ratio: float
63
+
64
+ def to_dict(self) -> dict[str, float]:
65
+ """Flat mapping, for landing in a results table as columns."""
66
+ return {
67
+ "qc_lowest_resolved_frequency": self.lowest_resolved_frequency,
68
+ "qc_median_coi_coverage": self.median_coi_coverage,
69
+ "qc_temporal_concentration": self.temporal_concentration,
70
+ "qc_half_window_ratio": self.half_window_ratio,
71
+ }
72
+
73
+
74
+ @dataclass(frozen=True)
75
+ class Scalogram:
76
+ """Full time-frequency surface from a continuous wavelet transform.
77
+
78
+ Parameters
79
+ ----------
80
+ time
81
+ Sample times, shape ``(n_times,)``.
82
+ freq
83
+ Fourier-equivalent frequencies, shape ``(n_scales,)``. These are true
84
+ Fourier frequencies via the analytic Morlet relation, not scales, so the
85
+ axis means the same thing as an FFT's.
86
+ power
87
+ ``|W(a,b)|**2``, shape ``(n_scales, n_times)``.
88
+ scales
89
+ Wavelet scales in seconds, shape ``(n_scales,)``. Needed by the
90
+ normalisation bridge, which divides by scale.
91
+ coi
92
+ Longest resolvable period at each time, shape ``(n_times,)``. A
93
+ frequency is inside the cone of influence where ``1/freq > coi``.
94
+ c_delta
95
+ Reconstruction constant for the wavelet actually used. Computed rather
96
+ than tabulated, so a non-default ``omega0`` stays correct.
97
+ dj
98
+ Spacing of the log-scale grid, in octaves.
99
+ """
100
+
101
+ time: NDArray[np.float64]
102
+ freq: NDArray[np.float64]
103
+ power: NDArray[np.float64]
104
+ scales: NDArray[np.float64]
105
+ coi: NDArray[np.float64]
106
+ c_delta: float
107
+ dj: float
108
+ dt: float
109
+ motion: Motion
110
+ meta: MappingProxyType[str, Any] = field(
111
+ default_factory=lambda: MappingProxyType({})
112
+ )
113
+
114
+ def __post_init__(self) -> None:
115
+ for name in ("time", "freq", "power", "scales", "coi"):
116
+ array = getattr(self, name)
117
+ array.setflags(write=False)
118
+
119
+ @property
120
+ def duration(self) -> float:
121
+ return float(self.time.size * self.dt)
122
+
123
+ def coi_mask(self) -> NDArray[np.bool_]:
124
+ """``True`` where a coefficient is free of edge effects."""
125
+ period = 1.0 / self.freq
126
+ return period[:, None] <= self.coi[None, :]
127
+
128
+ def coi_coverage(self) -> NDArray[np.float64]:
129
+ """Fraction of the window free of edge effects, per frequency.
130
+
131
+ This is the number that says whether a window is long enough to
132
+ constrain the low-frequency plateau, which is what sets ``Omega``.
133
+ """
134
+ coverage: NDArray[np.float64] = self.coi_mask().mean(axis=1)
135
+ return coverage
136
+
137
+ def time_average(self, *, mask_coi: bool = True) -> Spectrum:
138
+ """Collapse to an ordinary amplitude spectrum.
139
+
140
+ Applies the Torrence & Compo normalisation so that the result satisfies
141
+ the same Parseval contract as every other estimator: summing the
142
+ wavelet power over scales, weighted by ``dj*dt/C_delta`` and divided by
143
+ scale, returns the record's energy.
144
+
145
+ Parameters
146
+ ----------
147
+ mask_coi
148
+ Exclude coefficients inside the cone of influence and rescale by
149
+ the surviving fraction. Without this a short window reads low at
150
+ low frequency — precisely the band that constrains ``Omega``.
151
+ """
152
+ freq, scales = self.freq, self.scales
153
+ if mask_coi:
154
+ valid = self.coi_mask()
155
+ counts = valid.sum(axis=1)
156
+ # A scale with no edge-free sample is not measured by this record.
157
+ # Dropping it is the honest answer: emitting zero would read as "no
158
+ # energy here" rather than "no measurement here", and would take a
159
+ # log-space fit to -inf. The axis therefore depends on record
160
+ # length, exactly as the cone of influence says it must.
161
+ usable = counts > 0
162
+ if not usable.any():
163
+ raise ValueError(
164
+ f"No frequency in {freq.min():.3g}-{freq.max():.3g} Hz is "
165
+ f"free of edge effects over a {self.duration:.3g} s record. "
166
+ f"The window is too short for this scale range; raise "
167
+ f"f_min, lengthen the window, or pass mask_coi=False to "
168
+ f"accept edge-contaminated coefficients."
169
+ )
170
+ freq, scales = freq[usable], scales[usable]
171
+ counts = counts[usable]
172
+ summed = (self.power * valid).sum(axis=1)[usable]
173
+ # Rescale the survivors up to the full window length, so masking
174
+ # changes the variance of the estimate rather than its level.
175
+ summed = summed * self.time.size / counts
176
+ else:
177
+ summed = self.power.sum(axis=1)
178
+
179
+ # Torrence & Compo eq. 14: the scale sum of |W|**2 / s, times
180
+ # dj*dt/C_delta, recovers the variance. Multiplying by dt again turns
181
+ # variance into energy, matching sum(x**2)*dt.
182
+ energy_per_scale = summed / scales * (self.dj * self.dt / self.c_delta)
183
+ energy_per_scale = energy_per_scale * self.dt
184
+
185
+ # The scale grid is logarithmic, so each frequency bin subtends
186
+ # df = f * ln(2) * dj. Spreading each scale's energy over its own bin
187
+ # gives a density on a frequency axis.
188
+ bin_width = freq * np.log(2.0) * self.dj
189
+ psd = energy_per_scale / (bin_width * self.duration)
190
+
191
+ # Ascending frequency, matching every other estimator's axis.
192
+ order = np.argsort(freq)
193
+ spectrum = Spectrum(
194
+ freq=np.ascontiguousarray(freq[order]),
195
+ amp=np.ascontiguousarray(psd[order]),
196
+ motion=self.motion,
197
+ kind=AmplitudeKind.PSD,
198
+ duration=self.duration,
199
+ sampling_rate=1.0 / self.dt,
200
+ meta=MappingProxyType({**dict(self.meta), "coi_masked": mask_coi}),
201
+ )
202
+ return spectrum.to_kind(AmplitudeKind.FAS)
203
+
204
+ def qc(self) -> ScalogramQC:
205
+ """Compute the §4.4.2 checks."""
206
+ coverage = self.coi_coverage()
207
+ resolved = self.freq[coverage > 0.5]
208
+ lowest = float(resolved.min()) if resolved.size else float(self.freq.max())
209
+
210
+ # Energy over time, summed across the band, as a Gini coefficient.
211
+ over_time = self.power.sum(axis=0)
212
+ total = float(over_time.sum())
213
+ if total > 0:
214
+ sorted_energy = np.sort(over_time)
215
+ n = sorted_energy.size
216
+ index = np.arange(1, n + 1)
217
+ gini = float(
218
+ (2.0 * (index * sorted_energy).sum()) / (n * sorted_energy.sum())
219
+ - (n + 1.0) / n
220
+ )
221
+ else:
222
+ gini = 0.0
223
+
224
+ half = self.time.size // 2
225
+ first = float(self.power[:, :half].sum())
226
+ second = float(self.power[:, half:].sum())
227
+ ratio = first / second if second > 0 else np.inf
228
+
229
+ return ScalogramQC(
230
+ lowest_resolved_frequency=lowest,
231
+ median_coi_coverage=float(np.median(coverage)),
232
+ temporal_concentration=gini,
233
+ half_window_ratio=ratio,
234
+ )
@@ -0,0 +1,326 @@
1
+ """The :class:`Spectrum` container.
2
+
3
+ Immutable, self-describing, and normalisation-aware. Every operation returns a
4
+ new object rather than mutating in place, so a spectrum cannot be silently
5
+ integrated twice — the pre-refactor ``Spectrum.integrate()`` mutated, and its
6
+ only inverse was ``differentiate()``, which is neither exact nor recorded.
7
+ """
8
+
9
+ from __future__ import annotations
10
+
11
+ from collections.abc import Mapping
12
+ from dataclasses import dataclass, field, replace
13
+ from types import MappingProxyType
14
+ from typing import Any
15
+
16
+ import numpy as np
17
+ from numpy.typing import NDArray
18
+
19
+ from .units import AmplitudeKind, Motion
20
+
21
+ __all__ = ["Spectrum"]
22
+
23
+ #: Tolerance on the derived sample count. ``duration`` is ``n * dt`` and
24
+ #: ``sampling_rate`` is ``1 / dt``, so their product is ``n`` exactly up to
25
+ #: floating-point representation — anything further out is a real mismatch,
26
+ #: not rounding.
27
+ _SAMPLE_COUNT_TOL = 1e-6
28
+
29
+
30
+ def _validate_record_geometry(
31
+ freq: NDArray[np.float64], duration: float, sampling_rate: float
32
+ ) -> None:
33
+ """Check the three quantities every correction is built on agree.
34
+
35
+ Sample count, duration and sampling rate are not independent: ``duration =
36
+ n * dt`` and ``sampling_rate = 1 / dt``, so any two determine the third and
37
+ the frequency axis they imply. Every normalisation in this package — the
38
+ ``2T`` between amplitude and power, the fold at DC and Nyquist, the taper
39
+ corrections, the wavelet scale grid — is a function of them.
40
+
41
+ That makes an inconsistent triple the most dangerous thing a caller can
42
+ construct: it produces a spectrum that is wrong by a clean factor
43
+ everywhere, which looks like a plausible spectrum and survives every check
44
+ that inspects shape rather than scale. Catching it here is cheap; catching
45
+ it downstream has historically meant noticing that a magnitude looks odd.
46
+ """
47
+ implied = duration * sampling_rate
48
+ if abs(implied - round(implied)) > _SAMPLE_COUNT_TOL * max(1.0, implied):
49
+ raise ValueError(
50
+ f"duration={duration} s at {sampling_rate} Hz implies "
51
+ f"{implied} samples, which is not a whole number. These are not "
52
+ f"independent: duration = n_samples / sampling_rate. One of them "
53
+ f"is wrong, and every amplitude conversion depends on both."
54
+ )
55
+
56
+ if freq.size == 0:
57
+ return
58
+ if freq[0] < 0.0:
59
+ raise ValueError(f"frequencies must be non-negative, got {freq.min()}")
60
+ if freq.size > 1 and not np.all(np.diff(freq) > 0):
61
+ raise ValueError(
62
+ "freq must be strictly increasing; band() and the smoothers both "
63
+ "assume it, and an unsorted axis integrates to nonsense"
64
+ )
65
+
66
+ nyquist = sampling_rate / 2.0
67
+ if freq[-1] > nyquist * (1.0 + 1e-9):
68
+ raise ValueError(
69
+ f"frequency axis reaches {freq[-1]} Hz but the Nyquist frequency "
70
+ f"for {sampling_rate} Hz sampling is {nyquist} Hz. Either "
71
+ f"sampling_rate is wrong or the axis does not belong to this "
72
+ f"record; energy() would silently integrate over a band the "
73
+ f"record cannot represent."
74
+ )
75
+
76
+
77
+ @dataclass(frozen=True)
78
+ class Spectrum:
79
+ """A one-sided spectrum that knows its own units.
80
+
81
+ Parameters
82
+ ----------
83
+ freq
84
+ Frequency axis in Hz, strictly increasing, excluding DC by default.
85
+ amp
86
+ Amplitude in whatever :attr:`kind` declares.
87
+ motion
88
+ Ground-motion domain.
89
+ kind
90
+ What ``amp`` represents.
91
+ duration
92
+ **Physical** record duration in seconds, ``n_samples * dt``. Carried
93
+ explicitly because every conversion between kinds needs it and it
94
+ cannot be recovered from ``len(freq)`` once padding is involved.
95
+ sampling_rate
96
+ Samples per second of the source record, in Hz.
97
+ meta
98
+ Arbitrary trace metadata. Stored read-only so a shared mapping cannot be
99
+ mutated through one spectrum and observed through another.
100
+ """
101
+
102
+ freq: NDArray[np.float64]
103
+ amp: NDArray[np.float64]
104
+ motion: Motion
105
+ kind: AmplitudeKind
106
+ duration: float
107
+ sampling_rate: float
108
+ meta: Mapping[str, Any] = field(default_factory=dict)
109
+
110
+ def __post_init__(self) -> None:
111
+ freq = np.ascontiguousarray(self.freq, dtype=np.float64)
112
+ amp = np.ascontiguousarray(self.amp, dtype=np.float64)
113
+ if freq.ndim != 1 or amp.ndim != 1:
114
+ raise ValueError("freq and amp must be one-dimensional")
115
+ if freq.shape != amp.shape:
116
+ raise ValueError(
117
+ f"freq and amp must be the same length, got "
118
+ f"{freq.shape[0]} and {amp.shape[0]}"
119
+ )
120
+ if self.duration <= 0:
121
+ raise ValueError(f"duration must be positive, got {self.duration}")
122
+ if self.sampling_rate <= 0:
123
+ raise ValueError(
124
+ f"sampling_rate must be positive, got {self.sampling_rate}"
125
+ )
126
+ _validate_record_geometry(freq, self.duration, self.sampling_rate)
127
+ freq.setflags(write=False)
128
+ amp.setflags(write=False)
129
+ object.__setattr__(self, "freq", freq)
130
+ object.__setattr__(self, "amp", amp)
131
+ object.__setattr__(self, "motion", Motion(self.motion))
132
+ object.__setattr__(self, "kind", AmplitudeKind(self.kind))
133
+ object.__setattr__(self, "meta", MappingProxyType(dict(self.meta)))
134
+
135
+ def __reduce__(self) -> tuple[Any, tuple[Any, ...]]:
136
+ """Rebuild through ``__init__`` rather than by restoring ``__dict__``.
137
+
138
+ ``meta`` is a :class:`~types.MappingProxyType`, which is the right
139
+ thing for an immutable spectrum and **is not picklable**. Without this
140
+ the whole container tree — a ``SpectrumPair``, a ``SpectrumSet``, an
141
+ event — could not be written to disk at all, which was found the moment
142
+ the legacy pickle I/O was removed and there was nothing left to
143
+ persist a result with.
144
+
145
+ Reconstructing through the constructor also re-freezes the arrays.
146
+ ``numpy`` restores a pickled array as writeable, so a spectrum
147
+ round-tripped by any other route would come back mutable and quietly
148
+ lose the guarantee it exists to make.
149
+ """
150
+ return (
151
+ self.__class__,
152
+ (
153
+ self.freq,
154
+ self.amp,
155
+ self.motion,
156
+ self.kind,
157
+ self.duration,
158
+ self.sampling_rate,
159
+ dict(self.meta),
160
+ ),
161
+ )
162
+
163
+ # ------------------------------------------------------------------ units
164
+
165
+ @property
166
+ def unit(self) -> str:
167
+ """Unit string, e.g. ``m/s*s`` for a velocity FAS."""
168
+ return self.kind.unit(self.motion)
169
+
170
+ @property
171
+ def n_samples(self) -> int:
172
+ """Samples in the source record, ``duration * sampling_rate``.
173
+
174
+ The third of the triple, derived rather than stored so it cannot
175
+ disagree with the other two. Validated on construction — see
176
+ :func:`_validate_record_geometry` for why that matters.
177
+
178
+ Note this is the *record* length, not ``len(freq)``. Zero-padding
179
+ changes the second and not the first, and confusing them is the §2.2
180
+ bug.
181
+ """
182
+ return round(self.duration * self.sampling_rate)
183
+
184
+ @property
185
+ def nyquist(self) -> float:
186
+ return self.sampling_rate / 2.0
187
+
188
+ @property
189
+ def frequency_resolution(self) -> float:
190
+ """``1/T`` — the narrowest frequency difference the record can resolve.
191
+
192
+ This is the low-frequency floor the SNR bandwidth search must respect;
193
+ nothing enforced it before, so a short window could report usable
194
+ bandwidth below what it could physically resolve.
195
+ """
196
+ return 1.0 / self.duration
197
+
198
+ def to_kind(self, kind: AmplitudeKind | str) -> Spectrum:
199
+ """Convert between FAS, MAGNITUDE, PSD and ASD.
200
+
201
+ Conversions go via FAS rather than being enumerated pairwise, so the
202
+ factors of ``2T`` and of the fold each live in exactly one place.
203
+
204
+ ``MAGNITUDE`` is the conversion to reach for when reading a long-period
205
+ level: ``Omega`` is defined on ``|X|``, not on the folded ``FAS``, and
206
+ the two differ by two. Asking for it by name is the point — the factor
207
+ is easy to apply by hand and easy to apply twice, or not at all.
208
+ """
209
+ target = AmplitudeKind(kind)
210
+ if target is self.kind:
211
+ return self
212
+ fas = self._to_fas()
213
+ if target is AmplitudeKind.FAS:
214
+ return fas
215
+ if target is AmplitudeKind.MAGNITUDE:
216
+ # Undo the fold: FAS carries the negative-frequency half, |X| does not.
217
+ return replace(fas, amp=fas.amp / self._fold_factor(), kind=target)
218
+ two_t = 2.0 * self.duration
219
+ if target is AmplitudeKind.PSD:
220
+ amp = fas.amp**2 / two_t
221
+ else: # ASD
222
+ amp = fas.amp / np.sqrt(two_t)
223
+ return replace(fas, amp=amp, kind=target)
224
+
225
+ def _fold_factor(self) -> NDArray[np.float64]:
226
+ """Per-bin ratio between the folded ``FAS`` and the unfolded ``|X|``.
227
+
228
+ Two everywhere except DC and Nyquist, which have no negative-frequency
229
+ twin to fold in — a real signal's transform is conjugate-symmetric, and
230
+ those two bins are their own mirror image. A blanket factor of two is
231
+ therefore wrong at both ends, by exactly two.
232
+
233
+ **Parity matters here.** An ``rfft`` of an even-length record ends
234
+ exactly on Nyquist; an odd-length one ends half a bin below it, at
235
+ ``fs/2 * (n-1)/n``, and that bin *does* have a twin and *is* folded. So
236
+ which bins are special depends on the record length as well as on
237
+ ``drop_dc``, and is read off the axis rather than assumed.
238
+
239
+ The tolerance is derived from the axis's own bin spacing rather than
240
+ being a fixed relative one. For an odd-length record the top bin sits
241
+ ``df/2`` below Nyquist, and ``df`` shrinks as the record lengthens — so
242
+ a fixed ``rtol`` eventually swallows the gap and folds that bin wrongly.
243
+ With ``numpy``'s default it does so from about 200000 samples, which at
244
+ 1000 Hz is a 200 s record. Scaling with ``df`` keeps the two cases
245
+ separated at any length.
246
+ """
247
+ factor = np.full(self.freq.shape, 2.0)
248
+ if self.freq.size == 0:
249
+ return factor
250
+ # A hundredth of the narrowest spacing: far tighter than the df/2 gap
251
+ # that separates an odd-length top bin from Nyquist, and far looser
252
+ # than floating-point error on an even-length one, which lands exactly.
253
+ spacing = float(np.min(np.diff(self.freq))) if self.freq.size > 1 else 0.0
254
+ tol = 0.01 * spacing if spacing > 0 else 1e-12
255
+ factor[self.freq < tol] = 1.0
256
+ factor[np.abs(self.freq - self.nyquist) < tol] = 1.0
257
+ return factor
258
+
259
+ def _to_fas(self) -> Spectrum:
260
+ if self.kind is AmplitudeKind.FAS:
261
+ return self
262
+ if self.kind is AmplitudeKind.MAGNITUDE:
263
+ return replace(
264
+ self, amp=self.amp * self._fold_factor(), kind=AmplitudeKind.FAS
265
+ )
266
+ two_t = 2.0 * self.duration
267
+ if self.kind is AmplitudeKind.PSD:
268
+ amp = np.sqrt(self.amp * two_t)
269
+ else: # ASD
270
+ amp = self.amp * np.sqrt(two_t)
271
+ return replace(self, amp=amp, kind=AmplitudeKind.FAS)
272
+
273
+ def to_motion(self, motion: Motion | str) -> Spectrum:
274
+ """Integrate or differentiate to another ground-motion domain.
275
+
276
+ Multiplies by ``(2*pi*f)`` per order of differentiation. Only valid on
277
+ an amplitude-like kind, so a PSD is converted to FAS, transformed, and
278
+ converted back — squaring the frequency factor would otherwise be
279
+ silently wrong.
280
+ """
281
+ target = Motion(motion)
282
+ if target is self.motion:
283
+ return self
284
+ if self.kind is not AmplitudeKind.FAS:
285
+ return self.to_kind(AmplitudeKind.FAS).to_motion(target).to_kind(self.kind)
286
+ order = target.derivative_order - self.motion.derivative_order
287
+ factor = (2.0 * np.pi * self.freq) ** order
288
+ return replace(self, amp=self.amp * factor, motion=target)
289
+
290
+ # ------------------------------------------------------------- operations
291
+
292
+ def band(self, fmin: float | None = None, fmax: float | None = None) -> Spectrum:
293
+ """Restrict to a frequency band, inclusive of both bounds."""
294
+ mask = np.ones(self.freq.shape, dtype=bool)
295
+ if fmin is not None:
296
+ mask &= self.freq >= fmin
297
+ if fmax is not None:
298
+ mask &= self.freq <= fmax
299
+ if not mask.any():
300
+ raise ValueError(
301
+ f"No samples in band [{fmin}, {fmax}] Hz; spectrum spans "
302
+ f"[{self.freq[0]:.4g}, {self.freq[-1]:.4g}] Hz."
303
+ )
304
+ return replace(self, freq=self.freq[mask], amp=self.amp[mask])
305
+
306
+ def energy(self) -> float:
307
+ """Total signal energy, ``sum(x^2) * dt``, recovered from the spectrum.
308
+
309
+ This is the quantity Parseval's theorem ties to the time domain, and it
310
+ is what the cross-estimator normalisation test asserts. For a one-sided
311
+ FAS the two-sided integral folds to ``integral of A^2 / 2 df``.
312
+ """
313
+ fas = self.to_kind(AmplitudeKind.FAS)
314
+ return float(np.trapezoid(fas.amp**2 / 2.0, fas.freq))
315
+
316
+ def __len__(self) -> int:
317
+ return int(self.freq.size)
318
+
319
+ def __repr__(self) -> str:
320
+ sid = self.meta.get("id", "")
321
+ where = f" {sid}" if sid else ""
322
+ return (
323
+ f"Spectrum({self.kind.value}, {self.motion.value},{where} "
324
+ f"n={len(self)}, {self.freq[0]:.3g}-{self.freq[-1]:.3g} Hz, "
325
+ f"T={self.duration:.4g} s, [{self.unit}])"
326
+ )
specmod/core/units.py ADDED
@@ -0,0 +1,116 @@
1
+ """Physical units and domains, as types rather than conventions.
2
+
3
+ The pre-refactor code tracked none of this. A ``Spectrum`` did not know whether
4
+ it held power or amplitude, nor whether it was in displacement, velocity or
5
+ acceleration; that lived in ``Models.MOTION``, a module global read at import
6
+ time which the user had to keep in sync by hand with however many times they
7
+ had called ``.inte()`` or ``.diff()``. Getting it wrong returned a wrong seismic
8
+ moment with no error anywhere.
9
+
10
+ Making both a typed attribute turns those silent factor errors into exceptions.
11
+
12
+ Conventions
13
+ -----------
14
+ The canonical amplitude kind is the **folded** one-sided Fourier amplitude
15
+ spectrum (:attr:`AmplitudeKind.FAS`), in units of ``[signal] * s``. "Folded"
16
+ means the negative-frequency half has been added in, so ``FAS = 2|X|`` where
17
+ ``X`` is the Fourier transform. That is what makes energy recoverable by
18
+ integrating over non-negative frequencies alone, and it is why every estimator
19
+ here can be held to one Parseval check.
20
+
21
+ **It is not the quantity the source model is written in.** Omega, the
22
+ long-period spectral level, is the plateau of ``|X|`` — at zero frequency
23
+ ``|X(0)| = |integral u dt|``, which is what ``M0`` is proportional to. Reading
24
+ ``FAS`` as Omega puts ``M0`` out by two, which is 0.2 magnitude units. Use
25
+ :attr:`AmplitudeKind.MAGNITUDE` for that, and let :meth:`Spectrum.to_kind`
26
+ apply the factor rather than doing it by hand.
27
+
28
+ Relationships between the kinds, for a record of duration ``T``:
29
+
30
+ ============= ======================== ==================================
31
+ Kind Units From FAS ``A``
32
+ ============= ======================== ==================================
33
+ ``FAS`` ``[x] * s`` --
34
+ ``MAGNITUDE`` ``[x] * s`` ``|X| = A / 2``
35
+ ``PSD`` ``[x]^2 / Hz`` ``P = A^2 / (2 T)``
36
+ ``ASD`` ``[x] / sqrt(Hz)`` ``D = A / sqrt(2 T)``
37
+ ============= ======================== ==================================
38
+
39
+ Parseval takes a different form in each amplitude convention, which is the
40
+ whole reason both are named here rather than left to the caller::
41
+
42
+ E = integral A**2 / 2 df (FAS, folded)
43
+ E = 2 * integral |X|**2 df (MAGNITUDE, unfolded)
44
+
45
+ ``T`` is the **physical record duration**, ``n_samples * dt``. It is never
46
+ inferred from the length of the frequency axis: zero-padding changes that length
47
+ while leaving the duration alone, which is precisely how the old
48
+ ``psd_to_amp`` acquired a padding-dependent error.
49
+ """
50
+
51
+ from __future__ import annotations
52
+
53
+ from enum import StrEnum
54
+
55
+ __all__ = ["AmplitudeKind", "Motion"]
56
+
57
+
58
+ class Motion(StrEnum):
59
+ """Ground-motion domain of a time series or spectrum."""
60
+
61
+ DISPLACEMENT = "displacement"
62
+ VELOCITY = "velocity"
63
+ ACCELERATION = "acceleration"
64
+
65
+ @property
66
+ def derivative_order(self) -> int:
67
+ """Order of time differentiation relative to displacement.
68
+
69
+ Converting between domains multiplies the spectrum by ``(2*pi*f)`` per
70
+ order, so the difference of two orders gives the exponent directly.
71
+ """
72
+ return {"displacement": 0, "velocity": 1, "acceleration": 2}[self.value]
73
+
74
+ @property
75
+ def unit(self) -> str:
76
+ """SI unit of the time-domain signal."""
77
+ return {"displacement": "m", "velocity": "m/s", "acceleration": "m/s^2"}[
78
+ self.value
79
+ ]
80
+
81
+
82
+ class AmplitudeKind(StrEnum):
83
+ """What the amplitude axis of a spectrum represents."""
84
+
85
+ #: Folded one-sided Fourier amplitude spectrum, ``2|X|``, in ``[x] * s``.
86
+ #: Energy is ``integral(FAS**2 / 2) df``. The default, because it is the
87
+ #: convention in which one Parseval check covers every estimator.
88
+ FAS = "fas"
89
+ #: Unfolded Fourier transform magnitude, ``|X| = |rfft(x)| * dt``, in
90
+ #: ``[x] * s``. **This is the one Omega is defined in**, and the one to
91
+ #: read a long-period spectral level off. Energy is
92
+ #: ``2 * integral(|X|**2) df``.
93
+ MAGNITUDE = "magnitude"
94
+ #: One-sided power spectral density, ``[x]^2 / Hz``.
95
+ PSD = "psd"
96
+ #: One-sided amplitude spectral density, ``[x] / sqrt(Hz)``.
97
+ ASD = "asd"
98
+
99
+ @property
100
+ def is_amplitude(self) -> bool:
101
+ """Whether this kind scales linearly with the record.
102
+
103
+ The distinction that matters for :meth:`Spectrum.to_motion`: applying
104
+ a ``2*pi*f`` factor to a squared quantity is wrong by ``2*pi*f`` again.
105
+ """
106
+ return self in (AmplitudeKind.FAS, AmplitudeKind.MAGNITUDE, AmplitudeKind.ASD)
107
+
108
+ def unit(self, motion: Motion) -> str:
109
+ """Full unit string for this kind in a given motion domain."""
110
+ base = motion.unit
111
+ return {
112
+ "fas": f"{base}*s",
113
+ "magnitude": f"{base}*s",
114
+ "psd": f"({base})^2/Hz",
115
+ "asd": f"{base}/sqrt(Hz)",
116
+ }[self.value]