update docs

ptiede · Jul 25, 2023 · 0f481fb · 0f481fb
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diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -23,6 +23,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install libhdf5-dev
           sudo apt-get install --reinstall libxcb-xinerama0
+          sudo apt-get install qt5-default
       - uses: actions/checkout@v2
       - name: Setup python
         uses: actions/setup-python@v1

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -23,6 +23,7 @@ Pyehtim = "3d61700d-6e5b-419a-8e22-9c066cf00468"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9"
+VLBISkyModels = "d6343c73-7174-4e0f-bb64-562643efbeca"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]

diff --git a/docs/make.jl b/docs/make.jl
@@ -8,6 +8,8 @@ using Pyehtim
 using Zygote
 using Comrade
 using ComradeBase
+using VLBISkyModels
+using InteractiveUtils
 
 using Literate
 using Pkg
@@ -57,7 +59,7 @@ makedocs(;
     modules=[ComradeBase, Comrade,
              ComradeOptimization, ComradeAHMC,
              ComradeNested, ComradeDynesty,
-             ComradeAdaptMCMC, PolarizedTypes],
+             ComradeAdaptMCMC, PolarizedTypes, VLBISkyModels],
     repo="https://github.com/ptiede/Comrade.jl/blob/{commit}{path}#{line}",
     sitename="Comrade.jl",
     pages=Any[

diff --git a/docs/src/api.md b/docs/src/api.md
@@ -65,8 +65,10 @@ VLBISkyModels.NFFTAlg(::Comrade.EHTObservation)
 ### Polarized Models
 
 ```@docs
-ComradeBase.mbreve
-ComradeBase.evpa(pimg::ComradeBase.AbstractPolarizedModel, p)
+PolarizedTypes.mbreve
+PolarizedTypes.m̆
+PolarizedTypes.evpa
+PolarizedTypes.linearpol
 ```
 
 
@@ -145,20 +147,13 @@ Comrade.IsCube
 ## Misc
 
 ```@docs
-Comrade.μas2rad
-Comrade.rad2μas
-Comrade.NonAnalyticTest
 Comrade.station_tuple
-Comrade.center_image
-Comrade.convolve!
-Comrade.convolve
 Comrade.dirty_image
 Comrade.dirty_beam
 ```
 
 ## Internal (Not Public API)
 ```@docs
-VLBISkyModels.ThreadedModel
 Comrade.extract_FRs
 ```
 
diff --git a/docs/src/base_api.md b/docs/src/base_api.md
@@ -105,7 +105,6 @@ PolarizedTypes.CoherencyMatrix
 PolarizedTypes.evpa
 PolarizedTypes.m̆
 PolarizedTypes.linearpol
-PolarizedTypes.SingleStokes
 PolarizedTypes.innerprod
 PolarizedTypes.basis_components
 PolarizedTypes.basis_transform

diff --git a/examples/data.jl b/examples/data.jl
@@ -40,11 +40,12 @@ lcamp  = extract_table(obs, LogClosureAmplitudes(; snrcut=3.0)) # extract minima
 # For polarization we first load the data in the cirular polarization basis
 # Additionally, we load the array table at the same time to load the telescope mounts.
 obseht = Pyehtim.load_uvfits_and_array(
-    joinpath(dirname(pathof(Comrade)), "..", "examples", "SR1_M87_2017_096_lo_hops_netcal_StokesI.uvfits"),
-    joinpath(dirname(pathof(Comrade)), "..", "examples", "PolarizedExamples/polarized_gaussian_all_corruptions.uvfits"),
-    polrep="circ")
+                joinpath(dirname(pathof(Comrade)), "..", "examples", "PolarizedExamples/polarized_gaussian_all_corruptions.uvfits"),
+                joinpath(dirname(pathof(Comrade)), "..", "examples", "PolarizedExamples/array.txt"),
+                polrep="circ"
+                        )
 obs = Pyehtim.scan_average(obseht)
-dcoh = extract_table(obs, Coherencies())
+coh = extract_table(obs, Coherencies())
 
 
 # !!! warning

diff --git a/examples/hybrid_imaging.jl b/examples/hybrid_imaging.jl
@@ -270,7 +270,7 @@ plot(img, title="MAP Image")
 using ComradeAHMC
 using Zygote
 metric = DiagEuclideanMetric(ndim)
-chain, stats = sample(rng, post, AHMC(;metric, autodiff=Val(:Zygote)), 1000; nadapts=500, init_params=xopt)
+chain, stats = sample(rng, post, AHMC(;metric, autodiff=Val(:Zygote)), 700; nadapts=500, init_params=xopt)
 # We then remove the adaptation/warmup phase from our chain
 chain = chain[501:end]
 stats = stats[501:end]
@@ -283,7 +283,7 @@ stats = stats[501:end]
 # so the posterior is not sampling from the correct stationary distribution.
 
 using StatsBase
-msamples = skymodel.(Ref(post), chain[begin:10:end]);
+msamples = skymodel.(Ref(post), chain[begin:2:end]);
 
 # The mean image is then given by
 imgs = intensitymap.(msamples, fovxy, fovxy, 128, 128)

diff --git a/examples/imaging_closures.jl b/examples/imaging_closures.jl
@@ -177,7 +177,7 @@ plot(img, title="MAP Image")
 using ComradeAHMC
 using Zygote
 metric = DiagEuclideanMetric(ndim)
-chain, stats = sample(post, AHMC(;metric, autodiff=Val(:Zygote)), 2_000; nadapts=1_000, init_params=xopt)
+chain, stats = sample(post, AHMC(;metric, autodiff=Val(:Zygote)), 700; nadapts=500, init_params=xopt)
 
 
 # !!! warning

diff --git a/examples/imaging_pol.jl b/examples/imaging_pol.jl
@@ -159,7 +159,7 @@ function instrument(θ, metadata)
     ## Now construct the basis transformation cache
     jT = jonesT(tcache)
 
-    # Gain product parameters
+    ## Gain product parameters
     gPa = exp.(lgp .+ 0im)
     gRa = exp.(lgp .+ lgr .+ 0im)
     Gp = jonesG(gPa, gRa, scancache)

diff --git a/examples/imaging_vis.jl b/examples/imaging_vis.jl
@@ -300,7 +300,7 @@ plot(gt, layout=(3,3), size=(600,500))
 #-
 using ComradeAHMC
 metric = DiagEuclideanMetric(ndim)
-chain, stats = sample(rng, post, AHMC(;metric, autodiff=Val(:Zygote)), 1_000; nadapts=500, init_params=xopt)
+chain, stats = sample(rng, post, AHMC(;metric, autodiff=Val(:Zygote)), 700; nadapts=500, init_params=xopt)
 
 #-
 # !!! note

diff --git a/src/observations/observations.jl b/src/observations/observations.jl
@@ -160,10 +160,45 @@ function extract_table(obs, dataproduct::Coherencies)
 end
 
 # internal methods to extract information from `obs`
+"""
+    extract_cphase(obs; kwargs...)
+
+Extracts the closure phases from an `obs`.
+This is an internal method for dispatch. Only use this if
+interfacing Comrade with a new data type.
+"""
 function extract_cphase    end
+"""
+    extract_lcamp(obs; kwargs...)
+
+Extracts the log-closure amplitudes from an `obs`.
+This is an internal method for dispatch. Only use this if
+interfacing Comrade with a new data type.
+"""
 function extract_lcamp     end
+"""
+    extract_amp(obs; kwargs...)
+
+Extracts the visibility amplitudes from an `obs`.
+This is an internal method for dispatch. Only use this if
+interfacing Comrade with a new data type.
+"""
 function extract_amp       end
+"""
+    extract_vis(obs; kwargs...)
+
+Extracts the stokes I complex visibilities from an obs.
+This is an internal method for dispatch. Only use this if
+interfacing Comrade with a new data type.
+"""
 function extract_vis       end
+"""
+    extract_coherency(obs; kwargs...)
+
+Extracts the full coherency matrix from an observation.
+This is an internal method for dispatch. Only use this if
+interfacing Comrade with a new data type.
+"""
 function extract_coherency end