Add multi-wavelength spectroscopy tutorial by aditya-pandey-dev · Pull Request #203 · JuliaAstro/JuliaAstro.github.io

aditya-pandey-dev · 2026-03-20T13:24:41Z

Closes #202

What's included

A new tutorial at docs/src/tutorials/multi-wavelength-spectroscopy.md covering a realistic end-to-end spectroscopy workflow:

Loading a real SDSS DR14 spectrum from a FITS binary table (FITSIO.jl)
Attaching physical units — Å, erg/s/cm²/Å (Unitful + UnitfulAstro)
Fλ ↔ Fν conversion (Jansky)
Dust extinction with CCM89, OD94, CAL00 laws (DustExtinction.jl)
Spectral axis inspection via spectral_axis / flux_axis (Spectra.jl)
Automatic uncertainty propagation (Measurements.jl)
Synthetic blackbody spectra at 4 temperatures
Spectral arithmetic — sky subtraction, scaling
Cosmological redshift + luminosity distances (Cosmology.jl)

Testing

Includes test/test_tutorial.jl — a standalone verification script:

julia --project=docs/ test/test_tutorial.jl

All 5 dependency tests pass on Julia 1.12.5

Packages exercised

Spectra.jl, FITSIO.jl, DustExtinction.jl, UnitfulAstro.jl, Measurements.jl, Cosmology.jl, Plots.jl

Notes

Code blocks use plain julia fences (not @example) since Spectra.jl
is installed from GitHub and not yet in the General registry
continuum() is referenced as a planned future feature with a link to
Towards SpectraBase.jl [name tbd] Spectra.jl#41
[compat] bounds added for all new registered dependencies

Adds an end-to-end spectroscopy tutorial covering: - Loading real SDSS spectra from FITS files (FITSIO.jl) - Physical units and Fλ↔Fν conversions (Unitful + UnitfulAstro) - Dust extinction with CCM89, OD94, CAL00 laws (DustExtinction.jl) - Spectral axis inspection via spectral_axis/flux_axis (Spectra.jl) - Automatic uncertainty propagation (Measurements.jl) - Synthetic blackbody spectra generation (Spectra.jl) - Spectral arithmetic: sky subtraction and scaling - Cosmological redshift and luminosity distances (Cosmology.jl) Includes test/test_tutorial.jl — standalone verification script. Updates docs/Project.toml with [compat] bounds for all new deps. Closes JuliaAstro#202

DustExtinction='0.6, 1' excluded v0.11.x (current release), creating an unsolvable constraint with FITSIO 0.17 in CI.

@example

Tutorial uses plain julia code blocks (not @example), so docs build environment does not need to install tutorial dependencies. Extra packages were causing CI resolution failures in the JuliaAstroDocs test suite.

The CI test runner picks up all .jl files in test/ and tries to execute them. test_tutorial.jl requires packages not present in the test environment, causing JuliaAstroDocs to error. Users can run the tutorial locally by installing the packages listed in the tutorial's Packages section.

aditya-pandey-dev · 2026-03-21T09:33:36Z

@icweaver can you check the PR. What changes should I do?

cgarling

Interesting example, thanks for the PR. I made some specific comments/suggestions below, here is some high-level feedback:

It would be nice to have this run on CI so the output can be displayed. Could you expand on why you can't use @example here? I thought that if you setup the doc build environment correctly there shouldn't be a problem with importing Spectra.jl even if it isn't in the General registry yet (i.e., using [sources] to set the url in the Project.toml).
Mostly you are dealing with flux density units in this example so we should make the associated plot labels "Flux Density" rather than "Flux" for clarity
I would try to be more consistent with using units when constructing the wavelength / flux density vectors, some places where you are constructing blackbody spectra you are not putting units on the wavelengths/temperatures and I think we want to encourage the use of units
I think that blackbody returns radiance units so you may need to calculate the luminosity density as L_lam(lambda) = 4 \pi^2 R^2 B(lambda,T) where R is the radius of the spherical blackbody (say 1 solar radius) and B(lambda, T) is what blackbody returns. It would be good to check this and amend the blackbody docstring to be more descriptive.
We are mostly using Makie.jl for plotting in our documentation now, idk if anyone has strong feelings on this. I don't mind using Plots.jl but would probably prefer makie

cgarling · 2026-03-29T16:19:10Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+
+### Dereddening the SDSS spectrum
+```julia
+spec_dered = deredden(spec, 0.1)


It would be nice to use DustExtinction.SFD98Map here to get the E(B-V) value for the object here using its coordinates if they are saved in the file (then Av = R_v * E(B-V)) . Depending on the format of the coordinates, you might need to use SkyCoords.jl to convert them.

cgarling · 2026-03-29T16:20:33Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+ws = ustrip.(spectral_axis(spec))
+plot(ws, ustrip.(flux_axis(spec)),       label = "Observed",    lw = 0.5, color = :gray, alpha = 0.6)
+plot!(ws, ustrip.(flux_axis(spec_dered)), label = "Dereddened",  lw = 0.5, color = :steelblue)
+plot!(xlabel = "Wavelength (Å)", ylabel = "Flux  (erg s⁻¹ cm⁻² Å⁻¹)",


Suggested change

plot!(xlabel = "Wavelength (Å)", ylabel = "Flux (erg s⁻¹ cm⁻² Å⁻¹)",

plot!(xlabel = "Wavelength (Å)", ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

cgarling · 2026-03-29T16:20:57Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+
+plot(ustrip.(waves), ustrip.(fluxes),
+    xlabel  = "Wavelength (Å)",
+    ylabel  = "Flux  (erg s⁻¹ cm⁻² Å⁻¹)",


Suggested change

ylabel = "Flux (erg s⁻¹ cm⁻² Å⁻¹)",

ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

cgarling · 2026-03-29T16:21:27Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+plot!(spectral_axis(bb), ustrip.(flux_axis(bb_05)), label = "Av = 0.5", lw = 2)
+plot!(spectral_axis(bb), ustrip.(flux_axis(bb_15)), label = "Av = 1.5", lw = 2)
+plot!(spectral_axis(bb), ustrip.(flux_axis(bb_30)), label = "Av = 3.0", lw = 2)
+plot!(xlabel = "Wavelength (Å)", ylabel = "Flux",


Suggested change

plot!(xlabel = "Wavelength (Å)", ylabel = "Flux",

plot!(xlabel = "Wavelength (Å)", ylabel = "Flux Density",

cgarling · 2026-03-29T16:22:26Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+# Zoom around Hα (6563 Å)
+ha_mask = (ustrip.(waves) .> 6400) .& (ustrip.(waves) .< 6700)
+plot(ustrip.(waves[ha_mask]), ustrip.(fluxes[ha_mask]),
+    xlabel = "Wavelength (Å)", ylabel = "Flux  (erg s⁻¹ cm⁻² Å⁻¹)",


Suggested change

xlabel = "Wavelength (Å)", ylabel = "Flux (erg s⁻¹ cm⁻² Å⁻¹)",

xlabel = "Wavelength (Å)", ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

cgarling · 2026-03-29T16:24:02Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+## Part 5: Spectra with uncertainties
+```julia
+using Measurements
+
+wave_m  = range(4000, 7000, length = 200) * u"angstrom"
+flux_m  = ((5e-17 .± 0.5e-17) .* ones(200)) * u"erg/s/cm^2/angstrom"
+spec_m  = spectrum(wave_m, flux_m)
+
+spec_red = redden(spec_m, 0.5)
+
+println("Original  flux[1] : ", flux_axis(spec_m)[1])
+println("Reddened  flux[1] : ", flux_axis(spec_red)[1])
+```


If this SDSS spectrum contains an error column (which I expect it does) I would show use of Measurements with that data as it's a more practical example.

cgarling · 2026-03-29T16:35:50Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+wave_bb = range(3000, 10000, length = 500)
+bb      = blackbody(wave_bb, 10_000)


I would add units to these

cgarling · 2026-03-29T16:49:17Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+
+for (z, c) in zip([0.0, 0.5, 1.0, 2.0], [:black, :blue, :green, :red])
+    wave_obs = wave_rest .* (1 + z)
+    flux_obs = flux_axis(bb_rest) ./ (1 + z)^2


Should this be (1 + z) / (4 \pi luminosity_dist(cosmo, z)^2)? Also note that I think the blackbody is in radiance units so you may need to calculate the luminosity density as L_lam(lambda) = 4 \pi^2 R^2 B(lambda,T) where R is the radius of the spherical blackbody (say 1 solar radius) and B(lambda, T) is what blackbody returns.

cgarling · 2026-03-29T17:01:44Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+wave_synth = range(1000, 20000, length = 1000)
+
+bb_3k  = blackbody(wave_synth,  3_000)
+bb_6k  = blackbody(wave_synth,  6_000)
+bb_10k = blackbody(wave_synth, 10_000)
+bb_30k = blackbody(wave_synth, 30_000)


I would put units on wave_synth and the temperature for blackbody(w, T)

@example

- @example blocks for CI + Spectra via [sources] in Project.toml - Flux -> Flux Density in all plot ylabels - Units on wave_bb, wave_synth (.* u"angstrom"), temperatures (u"K") - L_lam = 4pi^2 * R^2 * B(lambda,T) correct luminosity formula - SDSS ivar column for real Measurements uncertainties - F_obs = L*(1+z)/(4pi*d_L^2) correct cosmological formula - Plots.jl -> CairoMakie throughout - SFD98Map with ICRSCoords -> GalCoords conversion

…o extra deps

…fixes applied

- Replace synthetic galaxy spectrum with real SDSS plate 1323 data - Use FITS ivar column for real per-pixel σ = 1/√ivar uncertainties - Addresses mentor comment: use Measurements with actual SDSS error column

aditya-pandey-dev · 2026-04-01T15:15:27Z

@cgarling I've added Spectra.jl to docs/Project.toml via
[sources]. However, @example blocks still can't run on CI
because the tutorial makes network calls:

Downloads a real SDSS FITS file (~50 MB)
SFD98Map() downloads dust map tiles (~120 MB)
So i think there are two suitable options : (a) Keep plain julia blocks with a note explaining network
dependency (b) Split into @example (synthetic/offline parts) + plain
julia (network parts)
Which approach would you prefer?

cgarling · 2026-04-08T02:13:38Z

I do Github Actions with network dependencies pretty frequently (e.g., through DataDeps.jl) and can't recall any issues. What exactly is the problem CI is creating, are you hitting a firewall (Github won't let you access external URLs)?

cgarling

Thanks for the update, good progress! More comments below

cgarling · 2026-04-08T02:18:31Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+of 10⁻¹⁷ erg s⁻¹ cm⁻² Å⁻¹ and an `ivar` (inverse-variance) column
+that encodes real per-pixel measurement uncertainties.
+```julia
+using Downloads, FITSIO, Unitful, UnitfulAstro, Measurements


Some of these are duplicated in the ## Setup block above. I would probably just put all the imports in the first code block rather than doing the setup separately but it's a stylistic choice

cgarling · 2026-04-08T02:20:28Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+# Attach units + Measurements.jl uncertainties
+flux_meas = ((flux_raw .± sigma_raw) .* 1e-17) * u"erg/s/cm^2/angstrom"
+
+using Spectra


duplicated above

Suggested change

using Spectra

cgarling · 2026-04-08T02:24:07Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+wv = ustrip.(wave_aa)
+fv = Measurements.value.(ustrip.(flux_meas))
+fe = Measurements.uncertainty.(ustrip.(flux_meas))
+
+fig, ax = lines(wv, fv;
+    axis = (xlabel = "Wavelength (Å)",
+            ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",
+            title  = "SDSS Galaxy — plate 1323, fiber 12"))
+band!(ax, wv, fv .- fe, fv .+ fe; color = (:steelblue, 0.3))
+fig


CairoMakie should be able to take types from Unitful and Measurements directly, you might not have to do all the ustrip shenanigans, I would just try fig, ax = lines(wave_aa, flux_meas; ...).

cgarling · 2026-04-08T02:27:11Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+gal = convert(GalCoords, eq)
+
+dustmap = SFD98Map()
+ebv     = dustmap(rad2deg(gal.l), rad2deg(gal.b))


Suggested change

ebv = dustmap(rad2deg(gal.l), rad2deg(gal.b))

ebv = dustmap(gal.l, gal.b)

dustmap expects inputs in radians

cgarling · 2026-04-08T02:42:02Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+tau   = [ustrip(ext(w * u"angstrom")) * Av for w in wave_raw]
+corr  = 10 .^ (tau ./ 2.5)
+
+fv_raw = Measurements.value.(ustrip.(spec.flux))
+fv_ded = fv_raw .* corr
+
+fig2, ax2 = lines(wv, fv_raw; label = "Raw",
+    axis = (xlabel = "Wavelength (Å)",
+            ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",
+            title  = "CCM89 Dust Dereddening"))
+lines!(ax2, wv, fv_ded; label = "Dereddened", color = :orange)
+axislegend(ax2)
+fig2


Suggested change

tau = [ustrip(ext(w * u"angstrom")) * Av for w in wave_raw]

corr = 10 .^ (tau ./ 2.5)

fv_raw = Measurements.value.(ustrip.(spec.flux))

fv_ded = fv_raw .* corr

fig2, ax2 = lines(wv, fv_raw; label = "Raw",

axis = (xlabel = "Wavelength (Å)",

ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

title = "CCM89 Dust Dereddening"))

lines!(ax2, wv, fv_ded; label = "Dereddened", color = :orange)

axislegend(ax2)

fig2

A_lambda = ext.(wave_raw) .* Av

corr = exp10.(-A_lambda ./ 2.5)

flux_dered = flux_meas ./ corr

fig2, ax2 = lines(wave_aa, flux_meas; label = "Raw",

axis = (title = "CCM89 Dust Dereddening",))

lines!(ax2, wave_aa, flux_dered; label = "Dereddened", color = :orange)

axislegend(ax2)

fig2

CCM89 returns A_\lambda / Av for input wavelength \lambda so you just multiply by Av to get the extinction in magnitudes at the input wavelength. Then corr here will be <1 by definition and you can deredden the spectrum by dividing the observed spectrum by the expected attenuation corr. When you deredden a spectrum you are trying to infer what its intrinsic luminosity is given an observed luminosity, so you must have flux_dered >= flux_raw

cgarling · 2026-04-08T02:51:42Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+# Compare multiple temperatures — wave_synth with units
+wave_synth = collect(range(1000, 20000, length = 1000)) .* u"angstrom"
+temps      = [3_000u"K", 6_000u"K", 10_000u"K", 30_000u"K"]
+labels_bb  = ["3 000 K", "6 000 K", "10 000 K", "30 000 K"]
+colors_bb  = [:red, :orange, :steelblue, :purple]
+
+fig3, ax3 = lines(ustrip.(wave_synth),
+                  ustrip.(blackbody(wave_synth, temps[1]).flux);
+    label = labels_bb[1], color = colors_bb[1],
+    axis  = (xlabel = "Wavelength (Å)",
+             ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹ sr⁻¹)",
+             title  = "Blackbody Spectra"))
+for (T, lab, col) in zip(temps[2:end], labels_bb[2:end], colors_bb[2:end])
+    lines!(ax3, ustrip.(wave_synth),
+           ustrip.(blackbody(wave_synth, T).flux);
+           label = lab, color = col)
+end
+axislegend(ax3, position = :rt)
+fig3


Suggested change

# Compare multiple temperatures — wave_synth with units

wave_synth = collect(range(1000, 20000, length = 1000)) .* u"angstrom"

temps = [3_000u"K", 6_000u"K", 10_000u"K", 30_000u"K"]

labels_bb = ["3 000 K", "6 000 K", "10 000 K", "30 000 K"]

colors_bb = [:red, :orange, :steelblue, :purple]

fig3, ax3 = lines(ustrip.(wave_synth),

ustrip.(blackbody(wave_synth, temps[1]).flux);

label = labels_bb[1], color = colors_bb[1],

axis = (xlabel = "Wavelength (Å)",

ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹ sr⁻¹)",

title = "Blackbody Spectra"))

for (T, lab, col) in zip(temps[2:end], labels_bb[2:end], colors_bb[2:end])

lines!(ax3, ustrip.(wave_synth),

ustrip.(blackbody(wave_synth, T).flux);

label = lab, color = col)

end

axislegend(ax3, position = :rt)

fig3

# Compare multiple temperatures — wave_synth with units

wave_synth = collect(range(1000, 20000, length = 1000)) .* u"angstrom"

temps = [3_000u"K", 6_000u"K", 10_000u"K", 30_000u"K"]

labels_bb = ["3 000 K", "6 000 K", "10 000 K", "30 000 K"]

colors_bb = [:red, :orange, :steelblue, :purple]

fig3, ax3 = lines(wave_synth,

blackbody(wave_synth, temps[1]).flux;

label = labels_bb[1], color = colors_bb[1],

axis = (title = "Blackbody Spectra",

yscale = log10, yticks = LogTicks(LinearTicks(5))))

for (T, lab, col) in zip(temps[2:end], labels_bb[2:end], colors_bb[2:end])

lines!(ax3, wave_synth,

blackbody(wave_synth, T).flux;

label = lab, color = col)

end

axislegend(ax3, position = :rt)

fig3

Here's an example showing how to let Makie.jl handle plotting quantities with units from Unitful.jl. I also made the y-axis a logscale to better distinguish between them.

cgarling · 2026-04-08T03:02:49Z

docs/src/tutorials/multi-wavelength-spectroscopy.md

+fig4, ax4 = lines(ustrip.(wave_rest), ustrip.(bb_rest.flux);
+    label = "z = 0", color = :black,
+    axis  = (xlabel = "Wavelength (Å)",
+             ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",
+             title  = "Cosmological Surface-Brightness Dimming"))
+
+for (z, col) in zip([0.5, 1.0, 2.0], [:blue, :green, :red])
+    d_L   = uconvert(u"cm", luminosity_dist(cosmo, z))
+    w_obs = wave_rest .* (1 + z)
+    F_obs = L_lam .* (1 + z) ./ (4π .* d_L.^2)
+    lines!(ax4, ustrip.(w_obs), ustrip.(F_obs); label = "z = $z", color = col)
+end
+axislegend(ax4, position = :rt)
+fig4


Suggested change

fig4, ax4 = lines(ustrip.(wave_rest), ustrip.(bb_rest.flux);

label = "z = 0", color = :black,

axis = (xlabel = "Wavelength (Å)",

ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

title = "Cosmological Surface-Brightness Dimming"))

for (z, col) in zip([0.5, 1.0, 2.0], [:blue, :green, :red])

d_L = uconvert(u"cm", luminosity_dist(cosmo, z))

w_obs = wave_rest .* (1 + z)

F_obs = L_lam .* (1 + z) ./ (4π .* d_L.^2)

lines!(ax4, ustrip.(w_obs), ustrip.(F_obs); label = "z = $z", color = col)

end

axislegend(ax4, position = :rt)

fig4

fig4, ax4 = lines(ustrip.(wave_rest), ustrip.(bb_rest.flux);

label = "z = 0", color = :black,

axis = (xlabel = "Wavelength (Å)",

ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

yscale = log10, yticks=LogTicks(LinearTicks(5)),

title = "Cosmological Surface-Brightness Dimming"))

for (z, col) in zip([0.1, 0.5, 1.0], [:blue, :green, :red])

d_L = uconvert(u"cm", luminosity_dist(cosmo, z))

w_obs = wave_rest .* (1 + z)

F_obs = L_lam .* (1 + z) ./ (4π .* d_L.^2)

lines!(ax4, ustrip.(w_obs), ustrip.(F_obs); label = "z = $z", color = col)

end

axislegend(ax4, position = :rt)

fig4

Changed to display a little better

aditya-pandey-dev added 7 commits March 20, 2026 18:29

Fix: add newline at end of Project.toml

c20e924

Fix: remove strict compat bounds causing DustExtinction conflict

f15060a

DustExtinction='0.6, 1' excluded v0.11.x (current release), creating an unsolvable constraint with FITSIO 0.17 in CI.

Fix: remove Spectra.jl from docs/Project.toml

699466e

Fix: revert docs/Project.toml to original deps

b7ea6ad

Tutorial uses plain julia code blocks (not @example), so docs build environment does not need to install tutorial dependencies. Extra packages were causing CI resolution failures in the JuliaAstroDocs test suite.

Fix: restore all required deps in docs/Project.toml

6830528

aditya-pandey-dev mentioned this pull request Mar 23, 2026

GSoC 2026 Proposals: Integrate a modern lazy-loading alternative for large-scale spectroscopic database processing (Aditya Kumar Pandey) OpenAstronomy/gsoc-proposals#21

Open

5 tasks

cgarling reviewed Mar 29, 2026

View reviewed changes

aditya-pandey-dev added 7 commits March 31, 2026 14:51

Fix: address all cgarling review comments

cdea606

Fix: use plain julia blocks (Spectra.jl not in General registry yet)

e7c0108

Fix: correct Cosmology.jl UUID in docs/Project.toml

734911c

Fix: revert docs/Project.toml to original - plain julia blocks need n…

ffe896c

…o extra deps

Fix: complete tutorial rewrite - CairoMakie, no Plots.jl, all mentor …

fa112c1

…fixes applied

Fix: use real SDSS DR14 spectrum with ivar-based uncertainties in Part 1

8b26c8e

- Replace synthetic galaxy spectrum with real SDSS plate 1323 data - Use FITS ivar column for real per-pixel σ = 1/√ivar uncertainties - Addresses mentor comment: use Measurements with actual SDSS error column

This was referenced Apr 2, 2026

JuliaAstro: Spectra.jl across the electromagnetic spectrum (Aditya Kumar Pandey) aditya-pandey-dev/gsoc-proposals#1

Closed

JuliaAstro: Spectra.jl across the electromagnetic spectrum (Aditya Kumar Pandey) OpenAstronomy/gsoc-proposals#49

Open

cgarling reviewed Apr 8, 2026

View reviewed changes

	plot!(xlabel = "Wavelength (Å)", ylabel = "Flux (erg s⁻¹ cm⁻² Å⁻¹)",
	plot!(xlabel = "Wavelength (Å)", ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

	ylabel = "Flux (erg s⁻¹ cm⁻² Å⁻¹)",
	ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

	xlabel = "Wavelength (Å)", ylabel = "Flux (erg s⁻¹ cm⁻² Å⁻¹)",
	xlabel = "Wavelength (Å)", ylabel = "Flux Density (erg s⁻¹ cm⁻² Å⁻¹)",

		wave_bb = range(3000, 10000, length = 500)
		bb = blackbody(wave_bb, 10_000)

	ebv = dustmap(rad2deg(gal.l), rad2deg(gal.b))
	ebv = dustmap(gal.l, gal.b)

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aditya-pandey-dev commented Mar 20, 2026 •

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