jerlov 0.1.1__tar.gz

jerlov-0.1.1/LICENSE

@@ -0,0 +1,201 @@
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jerlov-0.1.1/NOTICE

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+jerlov
+Copyright 2026 T. Ishibashi
+
+This product includes data derived from:
+
+  Williamson, C. A. and Hollins, R. C. (2022), "Dataset to accompany paper:
+  Measured inherent optical properties of Jerlov water types", figshare,
+  https://doi.org/10.6084/m9.figshare.20290782 (Version 3).
+  (c) Crown copyright (2022), Dstl. Licensed under the Open Government
+  Licence v3.0: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3
+
+Coefficient tables are additionally derived from the publications listed in
+DATA.md, which records the provenance of every value.

jerlov-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: jerlov
+Version: 0.1.1
+Summary: Inherent optical properties of Jerlov water types, with provenance
+Author: T. Ishibashi
+License-Expression: Apache-2.0
+Keywords: ocean optics,Jerlov water types,inherent optical properties
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy>=1.22
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == "plot"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: build
+Requires-Dist: openpyxl; extra == "build"
+Requires-Dist: colour-science; extra == "build"
+Dynamic: license-file
+
+# jerlov
+
+Inherent optical properties of the Jerlov optical water types, with
+provenance.
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.22321312.svg)](https://doi.org/10.5281/zenodo.22321312)
+
+https://github.com/tishibashi-cpu/jerlov
+
+*Working name; not yet released.*
+
+Every coefficient carries the source it came from. Values that a published
+table got wrong are flagged rather than quietly repaired, and quantities that
+the data do not determine are refused rather than guessed.
+
+```python
+import jerlov
+
+w = jerlov.water("III")          # Williamson & Hollins (2022) by default
+w.a(550), w.b(550), w.c(550)
+```
+
+## Why the source is part of the API
+
+The same Jerlov water type has different coefficients in different papers, and
+the differences are not small. Solonenko & Mobley (2015) obtained a and b by
+inverting Kd; Williamson & Hollins (2022) measured them. At 510 nm their
+scattering coefficients differ by up to a factor of 2.6.
+
+The equations differ too. Both papers use the scattering model of Haltrin
+(1999), but with different constants: Haltrin's Eq. (6) gives a
+small-particle coefficient of 1.151302, and Solonenko & Mobley print and
+compute with 1.513. Reproducing a published table therefore needs that
+paper's own constant, so constants are attached to sources.
+
+## What this package will not do
+
+- **Extrapolate.** Asking for a wavelength outside the data raises.
+- **Fill a gap.** Where a published value is wrong and could not be
+  recovered, the value is NaN and stays NaN through interpolation.
+- **Supply bb.** The backscattering coefficient is not determined by the
+  Jerlov classification. Deriving it from the particle concentrations of the
+  two sources gives answers differing by up to a factor of 31, so
+  `Water.bb` requires an explicit `backscatter_ratio`.
+
+## Provenance warnings
+
+Interpolating across a value that a paper got wrong gives a number that looks
+no different from a sound one. `ProvenanceWarning` is the only thing that
+tells them apart.
+
+```python
+>>> w = jerlov.water("5C", source="solonenko2015")
+>>> w.b(650)
+ProvenanceWarning: b for Jerlov 5C rests on flagged values:
+reconstructed at 650 nm. ...
+```
+
+`Water.caveats()` returns everything known to be doubtful about that water.
+
+## Sources
+
+| key | a, b from | types | range |
+|---|---|---|---|
+| `williamson2022` | measurement | IB-5C | 300-800 nm |
+| `solonenko2015` | inversion of Kd | I-9C | 300-700 nm |
+| `jerlov1976` | Kd only | I-9C | 300-715 nm |
+| `austin1986` | Kd only, replacement values | I-1C | 350-700 nm |
+
+`jerlov.SOURCES` holds the full citation, DOI and caveats for each.
+
+## Looking at something through water
+
+For a horizontal path, the observed radiance splits into the target's light
+that survived and the light the water added along the way:
+
+```python
+import numpy as np, jerlov
+
+wl   = np.arange(450., 651., 50.)
+iops = jerlov.water("III")
+kd   = jerlov.water("III", source="austin1986")
+
+scene = jerlov.Scene.at_depth(iops, 10.0, np.ones_like(wl), wl, kd=kd)
+b_inf = jerlov.veiling_radiance_estimate(
+    iops, scene.downwelling, wl, backscatter_ratio=0.015
+)
+
+obs = scene.observe(np.full_like(wl, 0.8), distance_m=5.0,
+                    veiling_radiance=b_inf)
+obs.direct, obs.veiling, obs.radiance
+obs.veiling_fraction        # how much of what you see is just water
+obs.contrast(background)    # against another target down the same path
+```
+
+`veiling_radiance` has no default. B_inf depends on the backscattering
+coefficient and the phase function, and neither follows from the water type.
+`veiling_radiance_estimate` gives the usual single-scattering approximation
+for callers with nothing better, but it has to be asked for.
+
+Deliberate limits, all recorded in `DECISIONS.md`:
+
+- **Horizontal paths only.** Observer and target at the same depth.
+- **No forward-scatter blur.** This is the radiance of one point, not the
+  sharpness of an image.
+- **Lambertian targets.**
+
+## What colour is that
+
+```python
+white = scene.downwelling / np.pi          # a perfect diffuser at that depth
+rgb   = jerlov.spectrum_to_srgb(obs.radiance, wl, white=white)
+
+jerlov.spectrum_to_xyz(spectrum, wl)      # unnormalised CIE XYZ
+jerlov.integrate_response(spectrum, wl, sensitivity, sensitivity_wl)
+```
+
+`white` has no default. A radiance spectrum has no colour until something is
+called white, and underwater the useful reference is usually the downwelling
+irradiance at that depth rather than daylight. Both are legitimate and they
+answer different questions:
+
+| white | question answered |
+|---|---|
+| downwelling at depth | what a diver's adapted eye, or a camera white-balanced *there*, sees |
+| daylight at the surface | what a camera set at the surface records |
+
+`integrate_response` takes any spectral sensitivity: three camera channels,
+or a set of photoreceptor absorbances.
+
+Two silent errors are checked rather than assumed:
+
+- **Coverage.** A spectrum spanning 450-650 nm integrated against colour
+  matching functions spanning 360-830 nm quietly drops the ends. Every
+  integration reports how much of the observer it actually covered and warns
+  when it is not essentially all of it.
+- **Gamut.** Underwater colours often fall outside sRGB. Clipping changes
+  them, so `GamutWarning` says so.
+
+## Other entry points
+
+```python
+# Reconstruct a Kd spectrum from one measured value (Austin & Petzold 1986).
+jerlov.kd_spectrum(kd=0.06, wavelength_nm=490, at=[440, 550, 650])
+
+# Estimate b from a transmissometer's c (Smart 2007).
+jerlov.b_from_c(c=0.5, wavelength_nm=555, bw=0.0019, cw=0.0659)
+
+# Use your own measurements; they take exactly the same path.
+jerlov.Water.from_measurements(wavelengths, a=..., b=...)
+```
+
+## Provenance and design
+
+`DATA.md` records, for every shipped table, where it came from, what was
+verified, and what is known to be wrong with it. Eleven defects in the source
+literature are documented there, six of them confirmed.
+
+`DECISIONS.md` records why the package is shaped the way it is, including the
+alternatives that were rejected and why.
+
+## Licence
+
+Apache-2.0. The Williamson & Hollins data are Crown copyright, Dstl, under
+the Open Government Licence v3.0; see `NOTICE`.
+
+## Citation
+
+Cite the concept DOI, which always resolves to the latest version:
+
+> Ishibashi, T. jerlov: inherent optical properties of Jerlov water types,
+> with provenance. Zenodo. https://doi.org/10.5281/zenodo.22321312
+
+Please also cite the sources the coefficients came from; they are listed with
+their DOIs at the top of `DATA.md`. The package is a carrier for other
+people's measurements, and this work does not replace citing them.

jerlov-0.1.1/README.md

@@ -0,0 +1,176 @@
+# jerlov
+
+Inherent optical properties of the Jerlov optical water types, with
+provenance.
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.22321312.svg)](https://doi.org/10.5281/zenodo.22321312)
+
+https://github.com/tishibashi-cpu/jerlov
+
+*Working name; not yet released.*
+
+Every coefficient carries the source it came from. Values that a published
+table got wrong are flagged rather than quietly repaired, and quantities that
+the data do not determine are refused rather than guessed.
+
+```python
+import jerlov
+
+w = jerlov.water("III")          # Williamson & Hollins (2022) by default
+w.a(550), w.b(550), w.c(550)
+```
+
+## Why the source is part of the API
+
+The same Jerlov water type has different coefficients in different papers, and
+the differences are not small. Solonenko & Mobley (2015) obtained a and b by
+inverting Kd; Williamson & Hollins (2022) measured them. At 510 nm their
+scattering coefficients differ by up to a factor of 2.6.
+
+The equations differ too. Both papers use the scattering model of Haltrin
+(1999), but with different constants: Haltrin's Eq. (6) gives a
+small-particle coefficient of 1.151302, and Solonenko & Mobley print and
+compute with 1.513. Reproducing a published table therefore needs that
+paper's own constant, so constants are attached to sources.
+
+## What this package will not do
+
+- **Extrapolate.** Asking for a wavelength outside the data raises.
+- **Fill a gap.** Where a published value is wrong and could not be
+  recovered, the value is NaN and stays NaN through interpolation.
+- **Supply bb.** The backscattering coefficient is not determined by the
+  Jerlov classification. Deriving it from the particle concentrations of the
+  two sources gives answers differing by up to a factor of 31, so
+  `Water.bb` requires an explicit `backscatter_ratio`.
+
+## Provenance warnings
+
+Interpolating across a value that a paper got wrong gives a number that looks
+no different from a sound one. `ProvenanceWarning` is the only thing that
+tells them apart.
+
+```python
+>>> w = jerlov.water("5C", source="solonenko2015")
+>>> w.b(650)
+ProvenanceWarning: b for Jerlov 5C rests on flagged values:
+reconstructed at 650 nm. ...
+```
+
+`Water.caveats()` returns everything known to be doubtful about that water.
+
+## Sources
+
+| key | a, b from | types | range |
+|---|---|---|---|
+| `williamson2022` | measurement | IB-5C | 300-800 nm |
+| `solonenko2015` | inversion of Kd | I-9C | 300-700 nm |
+| `jerlov1976` | Kd only | I-9C | 300-715 nm |
+| `austin1986` | Kd only, replacement values | I-1C | 350-700 nm |
+
+`jerlov.SOURCES` holds the full citation, DOI and caveats for each.
+
+## Looking at something through water
+
+For a horizontal path, the observed radiance splits into the target's light
+that survived and the light the water added along the way:
+
+```python
+import numpy as np, jerlov
+
+wl   = np.arange(450., 651., 50.)
+iops = jerlov.water("III")
+kd   = jerlov.water("III", source="austin1986")
+
+scene = jerlov.Scene.at_depth(iops, 10.0, np.ones_like(wl), wl, kd=kd)
+b_inf = jerlov.veiling_radiance_estimate(
+    iops, scene.downwelling, wl, backscatter_ratio=0.015
+)
+
+obs = scene.observe(np.full_like(wl, 0.8), distance_m=5.0,
+                    veiling_radiance=b_inf)
+obs.direct, obs.veiling, obs.radiance
+obs.veiling_fraction        # how much of what you see is just water
+obs.contrast(background)    # against another target down the same path
+```
+
+`veiling_radiance` has no default. B_inf depends on the backscattering
+coefficient and the phase function, and neither follows from the water type.
+`veiling_radiance_estimate` gives the usual single-scattering approximation
+for callers with nothing better, but it has to be asked for.
+
+Deliberate limits, all recorded in `DECISIONS.md`:
+
+- **Horizontal paths only.** Observer and target at the same depth.
+- **No forward-scatter blur.** This is the radiance of one point, not the
+  sharpness of an image.
+- **Lambertian targets.**
+
+## What colour is that
+
+```python
+white = scene.downwelling / np.pi          # a perfect diffuser at that depth
+rgb   = jerlov.spectrum_to_srgb(obs.radiance, wl, white=white)
+
+jerlov.spectrum_to_xyz(spectrum, wl)      # unnormalised CIE XYZ
+jerlov.integrate_response(spectrum, wl, sensitivity, sensitivity_wl)
+```
+
+`white` has no default. A radiance spectrum has no colour until something is
+called white, and underwater the useful reference is usually the downwelling
+irradiance at that depth rather than daylight. Both are legitimate and they
+answer different questions:
+
+| white | question answered |
+|---|---|
+| downwelling at depth | what a diver's adapted eye, or a camera white-balanced *there*, sees |
+| daylight at the surface | what a camera set at the surface records |
+
+`integrate_response` takes any spectral sensitivity: three camera channels,
+or a set of photoreceptor absorbances.
+
+Two silent errors are checked rather than assumed:
+
+- **Coverage.** A spectrum spanning 450-650 nm integrated against colour
+  matching functions spanning 360-830 nm quietly drops the ends. Every
+  integration reports how much of the observer it actually covered and warns
+  when it is not essentially all of it.
+- **Gamut.** Underwater colours often fall outside sRGB. Clipping changes
+  them, so `GamutWarning` says so.
+
+## Other entry points
+
+```python
+# Reconstruct a Kd spectrum from one measured value (Austin & Petzold 1986).
+jerlov.kd_spectrum(kd=0.06, wavelength_nm=490, at=[440, 550, 650])
+
+# Estimate b from a transmissometer's c (Smart 2007).
+jerlov.b_from_c(c=0.5, wavelength_nm=555, bw=0.0019, cw=0.0659)
+
+# Use your own measurements; they take exactly the same path.
+jerlov.Water.from_measurements(wavelengths, a=..., b=...)
+```
+
+## Provenance and design
+
+`DATA.md` records, for every shipped table, where it came from, what was
+verified, and what is known to be wrong with it. Eleven defects in the source
+literature are documented there, six of them confirmed.
+
+`DECISIONS.md` records why the package is shaped the way it is, including the
+alternatives that were rejected and why.
+
+## Licence
+
+Apache-2.0. The Williamson & Hollins data are Crown copyright, Dstl, under
+the Open Government Licence v3.0; see `NOTICE`.
+
+## Citation
+
+Cite the concept DOI, which always resolves to the latest version:
+
+> Ishibashi, T. jerlov: inherent optical properties of Jerlov water types,
+> with provenance. Zenodo. https://doi.org/10.5281/zenodo.22321312
+
+Please also cite the sources the coefficients came from; they are listed with
+their DOIs at the top of `DATA.md`. The package is a carrier for other
+people's measurements, and this work does not replace citing them.

jerlov-0.1.1/jerlov/__init__.py

@@ -0,0 +1,51 @@
+"""Inherent optical properties of Jerlov water types.
+
+Every coefficient carries its source, and values that a published table got
+wrong are flagged rather than quietly repaired.
+"""
+
+from .colour import (
+    CoverageWarning,
+    GamutWarning,
+    cie_1931_cmf,
+    d65,
+    integrate_response,
+    spectrum_to_srgb,
+    spectrum_to_xyz,
+    xyz_to_srgb,
+)
+from .scene import Observation, Scene, veiling_radiance_estimate
+from .sources import SOURCES, Source, get_source
+from .water import (
+    MissingQuantityError,
+    ProvenanceWarning,
+    Water,
+    b_from_c,
+    kd_spectrum,
+    water,
+)
+
+__all__ = [
+    "SOURCES",
+    "Scene",
+    "Observation",
+    "veiling_radiance_estimate",
+    "spectrum_to_xyz",
+    "spectrum_to_srgb",
+    "xyz_to_srgb",
+    "integrate_response",
+    "cie_1931_cmf",
+    "d65",
+    "GamutWarning",
+    "CoverageWarning",
+    "Source",
+    "get_source",
+    "Water",
+    "water",
+    "kd_spectrum",
+    "b_from_c",
+    "ProvenanceWarning",
+    "MissingQuantityError",
+]
+
+__version__ = "0.1.1"