rename to ResponseCache

docs/src/api.md

@@ -25,7 +25,7 @@ Comrade.caltable(::Comrade.JonesCache, ::AbstractVector)
 Comrade.caltable(::Comrade.EHTObservation, ::AbstractVector)
 Comrade.DesignMatrix
 Comrade.JonesCache
-Comrade.TransformCache
+Comrade.ResponseCache
 Comrade.JonesModel
 Comrade.VLBIModel
 Comrade.CalPrior

examples/imaging_pol.jl

@@ -199,7 +199,7 @@ skymeta = (;K, cache, grid)
 #
 # First, we will define our deterministic transform cache. Note that this dataset has need
 # been pre-corrected for feed rotation, so we need to add those into the `tcache`.
-tcache = TransformCache(dvis; add_fr=true, ehtim_fr_convention=false)
+tcache = ResponseCache(dvis; add_fr=true, ehtim_fr_convention=false)
 #-
 # Next we define our cache that maps quantities e.g., gain products, that change from scan-to-scan.
 scancache = jonescache(dvis, ScanSeg())

ext/ComradeMakieExt.jl

@@ -7,7 +7,4 @@ else
     using ..Makie
 end
 
-
-
-
 end

ext/ComradeVIDAExt.jl

@@ -0,0 +1,14 @@
+module ComradeVIDAExt
+
+using Comrade
+if isdefined(Base, :get_extension)
+    using VIDA
+else
+    using ..VIDA
+end
+
+function Comrade.template_align(div::VIDA.AbstractDivergence, m, lower, upper)
+
+end
+
+end

lib/ComradeAHMC/src/ComradeAHMC.jl

@@ -443,7 +443,13 @@ end
 function load_table(out::String, indices::Union{Base.Colon, UnitRange, StepRange}=Base.Colon(); table="samples")
     @assert isdir(abspath(out)) "$out is not a directory. This isn't where the HMC samples are stored"
     @assert isfile(joinpath(abspath(out), "parameters.jld2")) "parameters.jld2 "
-    return load_table(load(joinpath(abspath(out), "parameters.jld2"), "params"), indices; table)
+    p = load(joinpath(abspath(out), "parameters.jld2"), "params")
+    if p.filename != abspath(out)
+        @warn "filename stored in params does not equal what was passed\n"*
+                 "we will load the path passed\n  $(out)."
+        p = DiskOutput(out, p.nfiles, p.stride, p.nsamples)
+    end
+    return load_table(p, indices; table)
 end
 
 

src/align.jl

@@ -0,0 +1,3 @@
+export template_align
+
+function template_align end

src/calibration/calibration.jl

@@ -13,7 +13,7 @@ end
 
 """
     JonesModel(jones::JonesPairs, refbasis = CirBasis())
-    JonesModel(jones::JonesPairs, tcache::TransformCache)
+    JonesModel(jones::JonesPairs, tcache::ResponseCache)
 
 Constructs the intrument corruption model using pairs of jones matrices `jones` and a
 reference basis

src/calibration/jones.jl

@@ -1,5 +1,5 @@
 export JonesCache, TrackSeg, ScanSeg, FixedSeg, IntegSeg, jonesG, jonesD, jonesT,
-       TransformCache, JonesModel, jonescache, station_tuple, jonesmap
+       ResponseCache, JonesModel, jonescache, station_tuple, jonesmap
 
 """
     $(TYPEDEF)
@@ -879,7 +879,7 @@ on sky reference basis.
 # Fields
 $(FIELDS)
 """
-struct TransformCache{M, B<:PolBasis} <: AbstractJonesCache
+struct ResponseCache{M, B<:PolBasis} <: AbstractJonesCache
     """
     Transform matrices for the first stations
     """
@@ -895,7 +895,7 @@ struct TransformCache{M, B<:PolBasis} <: AbstractJonesCache
 end
 
 """
-    TransformCache(obs::EHTObservation; add_fr=true, ehtim_fr_convention=false, ref::PolBasis=CirBasis())
+    ResponseCache(obs::EHTObservation; add_fr=true, ehtim_fr_convention=false, ref::PolBasis=CirBasis())
 
 Constructs the cache that holds the transformation from the **chosen** on-sky reference basis
 to the basis that the telescope measures the electric fields given an observation `obs`.
@@ -904,36 +904,47 @@ are included in the transformation cache with the `add_fr` toggle. The user can
 using the keyword argument `ref` which is the (R,L) circular basis by default.
 
 # Notes
-We use the following definition for our feed rotations
+We use the following definition for our feed rotations in circular basis
 
 ```
     exp(-iθ)  0
     0         exp(iθ)
 ```
 
+and in the linear feed basis
+
+```
+    cos(θ) sin(θ)
+   -sin(θ) cos(θ)
+```
+
 # Warning
 eht-imaging can sometimes pre-rotate the coherency matrices. As a result the field rotation can sometimes
 be applied twice. To compensate for this we have added a `ehtim_fr_convention` which will fix this.
 """
-function TransformCache(obs::EHTObservation; add_fr=true, ehtim_fr_convention=false, ref::PolBasis=CirBasis())
+function ResponseCache(obs::EHTObservation; add_fr=true, ehtim_fr_convention=false, ref::PolBasis=CirBasis())
     T1 = StructArray(map(x -> basis_transform(ref, x[1]), obs.data.polbasis))
     T2 = StructArray(map(x -> basis_transform(ref, x[2]), obs.data.polbasis))
+    # Our feed rotation matrix from extract_FRs always returns the rotation according to
+    # a circular basis. We then transform to a linear basis before constructing the basis
+    Tcirc1 = StructArray(map(x -> basis_transform(CirBasis(), x[1]), obs.data.polbasis))
+    Tcirc2 = StructArray(map(x -> basis_transform(CirBasis(), x[2]), obs.data.polbasis))
     if add_fr
         field_rotations = extract_FRs(obs; ehtim_fr_convention)
-        T1 .= field_rotations.m1.*T1
-        T2 .= field_rotations.m2.*T2
+        @. T1 .= Tcirc1*field_rotations.m1*adjoint(Tcirc1)*T1
+        @. T2 .= Tcirc2*field_rotations.m2*adjoint(Tcirc2)*T2
     end
-    return TransformCache{typeof(T1), typeof(ref)}(T1, T2, ref)
+    return ResponseCache{typeof(T1), typeof(ref)}(T1, T2, ref)
 end
 
 """
-    jonesT(tcache::TransformCache)
+    jonesT(tcache::ResponseCache)
 
 Returns a `JonesPair` of matrices that transform from the model coherency matrices basis
 to the on-sky coherency basis, this includes the feed rotation and choice of polarization feeds.
 """
-jonesT(tcache::TransformCache) = JonesPairs(tcache.T1, tcache.T2)
-JonesModel(jones::J, tcache::TransformCache) where {J} = JonesModel(jones, tcache.refbasis)
+jonesT(tcache::ResponseCache) = JonesPairs(tcache.T1, tcache.T2)
+JonesModel(jones::J, tcache::ResponseCache) where {J} = JonesModel(jones, tcache.refbasis)
 
 
 """
@@ -1036,6 +1047,7 @@ function extract_FRs(obs::EHTObservation; ehtim_fr_convention=false)
     pars  = tarr.fr_parallactic
     offs  = tarr.fr_offset
 
+
     # get station names
     bls = config.data.baseline
     ant1 = first.(bls)

test/Core/bayes.jl

@@ -97,7 +97,7 @@ end
 
 @testset "RadioLikelihood" begin
     _,vis, amp, lcamp, cphase, coh = load_data()
-    tcache = TransformCache(coh)
+    tcache = ResponseCache(coh)
     lklhd_amp = RadioLikelihood(test_model, amp)
     lklhd_cp = RadioLikelihood(test_model, cphase)
     lklhd_lc = RadioLikelihood(test_model, lcamp)

test/Core/gains.jl

@@ -216,7 +216,7 @@ end
     scancache = jonescache(dcoh, ScanSeg())
     scancache2 = jonescache(dcoh, segs)
 
-    tcache = TransformCache(dcoh; add_fr=true)
+    tcache = ResponseCache(dcoh; add_fr=true)
 
 
 
@@ -282,7 +282,7 @@ end
     scancache = jonescache(dcoh, ScanSeg())
     phasecache= jonescache(dcoh, ScanSeg(); autoref=SingleReference(:AA, 1.0+0.0im))
     trackcache= jonescache(dcoh, TrackSeg())
-    tcache    = TransformCache(dcoh; add_fr=true)
+    tcache    = ResponseCache(dcoh; add_fr=true)
 
     dga = CalPrior(station_tuple(dcoh, LogNormal(0.0, 0.1)), scancache)
     dgp = CalPrior(station_tuple(dcoh, Uniform(0.0, 2π)), phasecache)

test/Core/observation.jl

@@ -89,7 +89,7 @@ using Pyehtim
     plot(m, amp)
     plot(m, lcamp)
     plot(m,cphase)
-    jt = jonesT(TransformCache(dcoh))
+    jt = jonesT(ResponseCache(dcoh))
     mp = Comrade.VLBIModel(JonesModel(jt), PolarizedModel(m, ZeroModel(), ZeroModel(), 0.1*Gaussian()))
     plot(mp, dcoh)
     #residual(m, vis)