# API

## Simulation

`CMBLensing.load_sim`

— Function`load_sim(;kwargs...)`

The starting point for many typical sessions. Creates a `BaseDataSet`

object with some simulated data, returing the DataSet and simulated truths, which can then be passed to other maximization / sampling functions. E.g.:

```
@unpack f,ϕ,ds = load_sim(;
θpix = 2,
Nside = 128,
pol = :P,
T = Float32
)
```

Keyword arguments:

`θpix`

— Angular resolution, in arcmin.`Nside`

— Number of pixels in the map as an`(Ny,Nx)`

tuple, or a single number for square maps.`pol`

— One of`:I`

,`:P`

, or`:IP`

to select intensity, polarization, or both.`T = Float32`

— Precision, either`Float32`

or`Float64`

.`storage = Array`

— Set to`CuArray`

to use GPU.`Nbatch = 1`

— Number of batches of data in this dataset.`μKarcminT = 3`

— Noise level in temperature in μK-arcmin.`ℓknee = 100`

— 1/f noise knee.`αknee = 3`

— 1/f noise slope.`beamFWHM = 0`

— Beam full-width-half-max in arcmin.`pixel_mask_kwargs = (;)`

— NamedTuple of keyword arguments to pass to`make_mask`

to create the pixel mask.`bandpass_mask = LowPass(3000)`

— Operator which performs Fourier-space masking.`fiducial_θ = (;)`

— NamedTuple of keyword arguments passed to`camb()`

for the fiducial model.`seed = nothing`

— Specific seed for the simulation.`L = LenseFlow`

— Lensing operator.

Returns a named tuple of `(;f, f̃, ϕ, n, ds, Cℓ, proj)`

.

`CMBLensing.resimulate`

— Function`resimulate(ds::DataSet; [f, ϕ, n, f̃, rng, seed])`

Make a new DataSet with the data replaced by a simulation. Keyword argument fields will be used instead of new simulations, if they are provided.

Returns a named tuple of `(;ds, f, ϕ, n, f̃)`

.

`CMBLensing.resimulate!`

— Function`resimulate!(ds::DataSet; [f, ϕ, n, f̃, rng, seed])`

Replace the data in this DataSet in-place with a simulation. Keyword argument fields will be used instead of new simulations, if they are provided.

Returns a named tuple of `(;ds, f, ϕ, n, f̃)`

.

## Lensing estimation

`CMBLensing.MAP_joint`

— Function`MAP_joint(ds::DataSet; kwargs...)`

Compute the maximum a posteriori (i.e. "MAP") estimate of the joint posterior, $\mathcal{P}(f,\phi,\theta\,|\,d)$, or compute a quasi-sample.

Keyword arguments:

`nsteps`

— The maximum number of iterations for the maximizer.`ϕstart = 0`

— Starting point of the maximizer.`ϕtol = nothing`

— If given, stop when`ϕ`

updates reach this tolerance.`ϕtol`

is roughly the relative per-pixel standard deviation between changes to`ϕ`

and draws from the`ϕ`

prior. Values in the range $10^{-2}-10^{-4}$ are reasonable.`lbfgs_rank = 5`

— The maximum rank of the LBFGS approximation to the Hessian.`conjgrad_kwargs = (;)`

— Passed to the inner call to`conjugate_gradient`

.`progress = true`

— Whether to show the progress bar.`Nϕ = :qe`

— Noise to use in the initial approximation to the Hessian. Can give`:qe`

to use the quadratic estimate noise.`quasi_sample = false`

—`false`

to compute the MAP,`true`

to iterate quasi-samples, or an integer to compute a fixed-seed quasi-sample.`history_keys`

— What quantities to include in the returned`history`

. Can be any subset of`(:f, :f°, :ϕ, :∇ϕ_lnP, :χ², :lnP)`

.

Returns a tuple `(f, ϕ, history)`

where `f`

is the best-fit (or quasi-sample) field, `ϕ`

is the lensing potential, and `history`

contains the history of steps during the run.

`CMBLensing.MAP_marg`

— Function`MAP_marg(ds; kwargs...)`

Compute the maximum a posteriori (i.e. "MAP") estimate of the marginal posterior, $\mathcal{P}(\phi,\theta\,|\,d)$.

`CMBLensing.sample_joint`

— Function`sample_joint(ds::DataSet; kwargs...)`

Sample the joint posterior, $\mathcal{P}(f,\phi,\theta\,|\,d)$.

Keyword arguments:

`nsamps_per_chain`

— The number of samples per chain.`nchains = 1`

— Number of chains in parallel.`nchunk = 1`

— Number of steps between parallel chain communication.`nsavemaps = 1`

— Number of steps in between saving maps into chain.`nburnin_always_accept = 0`

— Number of steps at the beginning of the chain to always accept HMC steps regardless of integration error.`nburnin_fixθ = 0`

— Number of steps at the beginning of the chain before starting to sample`θ`

.`Nϕ = :qe`

— Noise to use in the initial approximation to the Hessian. Can give`:qe`

to use the quadratic estimate noise.`chains = nothing`

—`nothing`

to start a new chain; the return value from a previous call to`sample_joint`

to resume those chains;`:resume`

to resume chains from a file given by`filename`

`θrange`

— Range and density to grid sample parameters as a NamedTuple, e.g.`(Aϕ=range(0.7,1.3,length=20),)`

.`θstart`

— Starting values of parameters as a NamedTuple, e.g.`(Aϕ=1.2,)`

, or nothing to randomly sample from θrange`ϕstart`

— Starting`ϕ`

, either a`Field`

object,`:quasi_sample`

, or`:best_fit`

`metadata`

— Does nothing, but is saved into the chain file`nhmc = 1`

— Number of HMC passes per`ϕ`

Gibbs step.`symp_kwargs = fill((N=25, ϵ=0.01), nhmc)`

— an array of NamedTupe kwargs to pass to`symplectic_integrate`

. E.g.`[(N=50,ϵ=0.1),(N=25,ϵ=0.01)]`

would do 50 large steps then 25 smaller steps per each Gibbs pass. If specified,`nhmc`

is ignored.`wf_kwargs`

— Keyword arguments to pass to`argmaxf_lnP`

in the Wiener Filter Gibbs step.`MAP_kwargs`

— Keyword arguments to pass to`MAP_joint`

when computing the starting point.

`CMBLensing.argmaxf_lnP`

— Function```
argmaxf_lnP(ϕ, ds::DataSet; kwargs...)
argmaxf_lnP(ϕ, θ, ds::DataSet; kwargs...)
argmaxf_lnP(Lϕ, ds::DataSet; kwargs...)
```

Computes either the Wiener filter at fixed $\phi$, or a sample from this slice along the posterior.

Keyword arguments:

`which`

—`:wf`

,`:sample`

, or`fluctuation`

to compute 1) the Wiener filter, i.e. the best-fit of $\mathcal{P}(f\,|\,\phi,d)$, 2) a sample from $\mathcal{P}(f\,|\,\phi,d)$, or 3) a sample minus the Wiener filter, i.e. the fluctuation on top of the mean.`fstart`

— starting guess for`f`

for the conjugate gradient solver`conjgrad_kwargs`

— Passed to the inner call to`conjugate_gradient`

`CMBLensing.quadratic_estimate`

— Function```
quadratic_estimate(ds::DataSet, which; wiener_filtered=true)
quadratic_estimate((ds₁::DataSet, ds₂::DataSet), which; wiener_filtered=true)
```

Compute the quadratic estimate of `ϕ`

given data.

The `ds`

or `(ds₁,ds₂)`

tuple contain the DataSet object(s) which house the data and covariances used in the estimate. Note that only the Fourier-diagonal approximations for the beam, mask, and noise, i.e. `B̂`

, `M̂`

, and `Cn̂`

, are accounted for. To account full operators (if they are not actually Fourier-diagonal), you should compute the impact using Monte Carlo.

If a tuple is passed in, the result will come from correlating the data from `ds₁`

with that from `ds₂`

.

An optional keyword argument `AL`

can be passed in case the QE normalization was already computed, in which case it won't be recomputed during the calculation.

Returns a named tuple of `(;ϕqe, AL, Nϕ)`

where `ϕqe`

is the (possibly Wiener filtered, depending on `wiener_filtered`

option) quadratic estimate, `AL`

is the normalization (which is already applied to ϕqe, it does not need to be applied again), and `Nϕ`

is the analytic N⁰ noise bias (Nϕ==AL if using unlensed weights, currently only Nϕ==AL is always returned, no matter the weights)

## Field constructors

`CMBLensing.FlatMap`

— Type```
FlatMap(Ix::AbstractArray; [θpix=1])
FlatMap(Ix::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatMap`

object from an `AbstractArray`

. The array dimensions should be `(Ny,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`CMBLensing.FlatFourier`

— Type```
FlatFourier(Il::AbstractArray; Ny, [θpix=1])
FlatFourier(Il::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatFourier`

object from an `AbstractArray`

. The array dimensions should be `(Ny÷2+1,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `Ny`

must be given as keyword argument. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`CMBLensing.FlatQUMap`

— Type```
FlatQUMap(Qx::AbstractArray, Ux::AbstractArray; [θpix=1])
FlatQUMap(Qx::AbstractArray, Ux::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatQUMap`

object from some `AbstractArrays`

. The array dimensions should be `(Ny,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`FlatQUMap(Q::FlatMap, U::FlatMap)`

Construct a `FlatQUMap`

object from other `FlatMap`

objects. Projection/metadata and batch size is required to be the same for the arguments.

`CMBLensing.FlatQUFourier`

— Type```
FlatQUFourier(Ql::AbstractArray, Ul::AbstractArray; Ny, [θpix=1])
FlatQUFourier(Ql::AbstractArray, Ul::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatQUFourier`

object from some `AbstractArrays`

. The array dimensions should be `(Ny÷2+1,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `Ny`

must be given as keyword argument. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`FlatQUFourier(Q::FlatFourier, U::FlatFourier)`

Construct a `FlatQUFourier`

object from other `FlatFourier`

objects. Projection/metadata and batch size is required to be the same for the arguments.

`CMBLensing.FlatEBMap`

— Type```
FlatEBMap(Ex::AbstractArray, Bx::AbstractArray; [θpix=1])
FlatEBMap(Ex::AbstractArray, Bx::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatEBMap`

object from some `AbstractArrays`

. The array dimensions should be `(Ny,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`FlatEBMap(E::FlatMap, B::FlatMap)`

Construct a `FlatEBMap`

object from other `FlatMap`

objects. Projection/metadata and batch size is required to be the same for the arguments.

`CMBLensing.FlatEBFourier`

— Type```
FlatEBFourier(El::AbstractArray, Bl::AbstractArray; Ny, [θpix=1])
FlatEBFourier(El::AbstractArray, Bl::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatEBFourier`

object from some `AbstractArrays`

. The array dimensions should be `(Ny÷2+1,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `Ny`

must be given as keyword argument. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`FlatEBFourier(E::FlatFourier, B::FlatFourier)`

Construct a `FlatEBFourier`

object from other `FlatFourier`

objects. Projection/metadata and batch size is required to be the same for the arguments.

`CMBLensing.FlatIQUMap`

— Type```
FlatIQUMap(Ix::AbstractArray, Qx::AbstractArray, Ux::AbstractArray; [θpix=1])
FlatIQUMap(Ix::AbstractArray, Qx::AbstractArray, Ux::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatIQUMap`

object from some `AbstractArrays`

. The array dimensions should be `(Ny,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`FlatIQUMap(I::FlatMap, Q::FlatMap, U::FlatMap)`

Construct a `FlatIQUMap`

object from other `FlatMap`

objects. Projection/metadata and batch size is required to be the same for the arguments.

`CMBLensing.FlatIQUFourier`

— Type```
FlatIQUFourier(Il::AbstractArray, Ql::AbstractArray, Ul::AbstractArray; Ny, [θpix=1])
FlatIQUFourier(Il::AbstractArray, Ql::AbstractArray, Ul::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatIQUFourier`

object from some `AbstractArrays`

. The array dimensions should be `(Ny÷2+1,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `Ny`

must be given as keyword argument. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`FlatIQUFourier(I::FlatFourier, Q::FlatFourier, U::FlatFourier)`

Construct a `FlatIQUFourier`

object from other `FlatFourier`

objects. Projection/metadata and batch size is required to be the same for the arguments.

`CMBLensing.FlatIEBMap`

— Type```
FlatIEBMap(Ix::AbstractArray, Ex::AbstractArray, Bx::AbstractArray; [θpix=1])
FlatIEBMap(Ix::AbstractArray, Ex::AbstractArray, Bx::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatIEBMap`

object from some `AbstractArrays`

. The array dimensions should be `(Ny,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`FlatIEBMap(I::FlatMap, E::FlatMap, B::FlatMap)`

Construct a `FlatIEBMap`

object from other `FlatMap`

objects. Projection/metadata and batch size is required to be the same for the arguments.

`CMBLensing.FlatIEBFourier`

— Type```
FlatIEBFourier(Il::AbstractArray, El::AbstractArray, Bl::AbstractArray; Ny, [θpix=1])
FlatIEBFourier(Il::AbstractArray, El::AbstractArray, Bl::AbstractArray, proj::FieldMetadata)
```

Construct a `FlatIEBFourier`

object from some `AbstractArrays`

. The array dimensions should be `(Ny÷2+1,Nx[,Nbatch])`

, where `Ny`

and `Nx`

are the number of pixels in the map in the y/x direction, and `Nbatch`

is an optional batch dimension. `Ny`

must be given as keyword argument. `θpix`

is the angular resolution in arcmin (default=1). A second positional argument `proj`

can be used instead of keyword arguments to specify the projection/metadata (currently the only builtin projection is `ProjLambert`

, which is the default if keyword arguments are used).

`FlatIEBFourier(I::FlatFourier, E::FlatFourier, B::FlatFourier)`

Construct a `FlatIEBFourier`

object from other `FlatFourier`

objects. Projection/metadata and batch size is required to be the same for the arguments.

## Lensing operators

`CMBLensing.LenseFlow`

— Type`LenseFlow(ϕ, [n=7])`

`LenseFlow`

is the ODE-based lensing algorithm from Millea, Anderes, & Wandelt, 2019. The number of steps in the ODE solver is controlled by `n`

. The action of the operator, as well as its adjoint, inverse, inverse-adjoint, and gradient of any of these w.r.t. `ϕ`

can all be computed. The log-determinant of the operation is zero independent of `ϕ`

, in the limit of `n`

high enough.

`CMBLensing.BilinearLens`

— Type`BilinearLens(ϕ)`

`BilinearLens`

is a lensing operator that computes lensing with bilinear interpolation. The action of the operator, as well as its adjoint, inverse, inverse-adjoint, and gradient w.r.t. `ϕ`

can all be computed. The log-determinant of the operation is non-zero and can't be computed.

Internally, `BilinearLens`

forms a sparse matrix with the interpolation weights, which can be applied and adjoint-ed extremely fast (e.g. at least an order of magnitude faster than `LenseFlow`

). Inverse and inverse-adjoint lensing is somewhat slower since it requires an iterative solve, here performed with the preconditioned generalized minimal residual algorithm.

`CMBLensing.Taylens`

— Type`Taylens(ϕ, order)`

`Taylens`

is a lensing operator which lenses a map with a nearest-pixel permute step followed by power series expansion in the residual displacement, to any order. This is the algorithm from Næss&Louis 2013.

`CMBLensing.PowerLens`

— Type`PowerLens(ϕ, order)`

`PowerLens`

is a lensing operator which lenses a map with a power series expansion in $\nabla \phi$ to any order.

The action of the operator and its adjoint can be computed.

`CMBLensing.antilensing`

— Function`antilensing(L::PowerLens)`

Create a `PowerLens`

operator that lenses by `-ϕ`

instead.

## Configuration options

`CMBLensing.FFTW_NUM_THREADS`

— ConstantThe number of threads used by FFTW for CPU FFTs (default is the environment variable `FFTW_NUM_THREADS`

, or if that is not specified its `Sys.CPU_THREADS÷2`

). This must be set before creating any `FlatField`

objects.

`CMBLensing.FFTW_TIMELIMIT`

— ConstantTime-limit for FFT planning on CPU (default: 5 seconds). This must be set before creating any `FlatField`

objects.

## Other

`CMBLensing.batch`

— Method```
batch(fs::FlatField...)
batch(fs::Vector{<:FlatField})
```

Concatenate one of more FlatFields along the "batch" dimension (dimension 4 of the underlying array). For the inverse operation, see `unbatch`

.

`CMBLensing.beamCℓs`

— Method`beamCℓs(;beamFWHM, ℓmax=8000)`

Compute the beam power spectrum, often called $W_\ell$. A map should be multiplied by the square root of this.

`CMBLensing.cpu`

— Method`cpu(x)`

Recursively move an object to CPU memory. See also `gpu`

.

`CMBLensing.gradhess`

— Method`gradhess(f)`

Compute the gradient $g^i = \nabla^i f$, and the hessian, $H_j^{\,i} = \nabla_j \nabla^i f$.

`CMBLensing.kde`

— Method```
kde(samples::AbstractVector; [boundary=(min,max), normalize="integral" or "max"])
kde(samples::AbstractMatrix; [boundary=[(min1,max1),(min2,max2)], normalize="integral" or "max", smooth_scale_2D])
```

Return a Kernel Density Estimate for a set of 1D or 2D samples. The return object is a function which can be evaluated anywhere to compute the PDF. If provided, `boundary`

specifies a hard upper/lower bound for the 1 or 2 or parameters, `normalize`

specifies whether to normalize the PDF to unit integral or unit maximum, and `smooth_scale_2D`

specifies how much smoothing to do for the 2D case.

Based on Python GetDist, which must be installed.

`CMBLensing.lnP`

— Method```
lnP(t, fₜ, ϕₜ, ds::DataSet)
lnP(t, fₜ, ϕₜ, θ, ds::DataSet)
```

Compute the log posterior probability in the joint parameterization as a function of the field, $f_t$, the lensing potential, $\phi_t$, and possibly some cosmological parameters, $\theta$. The subscript $t$ can refer to either a "time", e.g. passing `t=0`

corresponds to the unlensed parametrization and `t=1`

to the lensed one, or can be `:mix`

correpsonding to the mixed parametrization. In all cases, the arguments `fₜ`

and `ϕₜ`

should then be $f$ and $\phi$ in that particular parametrization.

If any parameters $\theta$ are provided, we also include the determinant terms for covariances which depend on $\theta$. In the mixed parametrization, we also include any Jacobian determinant terms that depend on $\theta$.

The argument `ds`

should be a `DataSet`

and stores the masks, data, etc... needed to construct the posterior.

`CMBLensing.load_camb_Cℓs`

— Method```
load_camb_Cℓs(;path_prefix, custom_tensor_params=nothing,
unlensed_scalar_postfix, unlensed_tensor_postfix, lensed_scalar_postfix, lenspotential_postfix)
```

Load some Cℓs from CAMB files.

`path_prefix`

specifies the prefix for the files, which are then expected to have the normal CAMB postfixes: `scalCls.dat`

, `tensCls.dat`

, `lensedCls.dat`

, `lenspotentialCls.dat`

, unless otherwise specified via the other keyword arguments. `custom_tensor_params`

can be used to call CAMB directly for the `unlensed_tensors`

, rather than reading them from a file (since alot of times this file doesn't get saved). The value should be a Dict/NamedTuple which will be passed to a call to `camb`

, e.g. `custom_tensor_params=(r=0,)`

for zero tensors.

`CMBLensing.load_chains`

— Method`load_chains(filename; burnin=0, burnin_chunks=0, thin=1, join=false, unbatch=true)`

Load a single chain or multiple parallel chains which were written to a file by `sample_joint`

.

Keyword arguments:

`burnin`

— Remove this many samples from the start of each chain, or if negative, keep only this many samples at the end of each chain.`burnin_chunks`

— Same as burnin, but in terms of chain "chunks" stored in the chain file, rather than in terms of samples.`thin`

— If`thin`

is an integer, thin the chain by this factor. If`thin == :hasmaps`

, return only samples which have maps saved. If thin is a`Function`

, filter the chain by this function (e.g.`thin=haskey(:g)`

on Julia 1.5+)`unbatch`

— If true, unbatch the chains if they are batched.`join`

— If true, concatenate all the chains together.`skip_missing_chunks`

— Skip missing chunks in the chain instead of terminating the chain there.

The object returned by this function is a `Chain`

or `Chains`

object, which simply wraps an `Array`

of `Dicts`

or an `Array`

of `Array`

of `Dicts`

, respectively (each sample is a `Dict`

). The wrapper object has some extra indexing properties for convenience:

- It can be indexed as if it were a single multidimensional object, e.g.
`chains[1,:,:accept]`

would return the`:accept`

key of all samples in the first chain. - Leading colons can be dropped, i.e.
`chains[:,:,:accept]`

is the same as`chains[:accept]`

. - If some samples are missing a particular key,
`missing`

is returned for those samples insted of an error. - The recursion goes arbitrarily deep into the objects it finds. E.g., since sampled parameters are stored in a
`NamedTuple`

like`(Aϕ=1.3,)`

in the`θ`

key of each sample`Dict`

, you can do`chain[:θ,:Aϕ]`

to get all`Aϕ`

samples as a vector.

`CMBLensing.mean_std_and_errors`

— Method`mean_std_and_errors(samples; N_bootstrap=10000)`

Get the mean and standard deviation of a set of correlated `samples`

from a chain where the error on the mean and standard deviation is estimated with bootstrap resampling using the calculated "effective sample size" of the chain.

`CMBLensing.mix`

— Method```
mix(f, ϕ, ds::DataSet)
mix(f, ϕ, θ, ds::DataSet)
```

Compute the mixed `(f°, ϕ°)`

from the unlensed field `f`

and lensing potential `ϕ`

, given the definition of the mixing matrices in `ds`

evaluated at parameters `θ`

(or at fiducial values if no `θ`

provided).

`CMBLensing.noiseCℓs`

— Method`noiseCℓs(;μKarcminT, beamFWHM=0, ℓmax=8000, ℓknee=100, αknee=3)`

Compute the (:TT,:EE,:BB,:TE) noise power spectra given white noise + 1/f. Polarization noise is scaled by $\sqrt{2}$ relative to `μKarcminT`

. `beamFWHM`

is in arcmin.

`CMBLensing.pixwin`

— Method`pixwin(θpix, ℓ)`

Returns the pixel window function for square flat-sky pixels of width `θpix`

(in arcmin) evaluated at some `ℓ`

s. This is the scaling of k-modes, the scaling of the power spectrum will be pixwin^2.

`CMBLensing.simulate`

— Method`simulate(Σ; rng=global_rng_for(Σ), seed=nothing)`

Draw a simulation from the covariance matrix `Σ`

, i.e. draw a random vector $\xi$ such that the covariance $\langle \xi \xi^\dagger \rangle = \Sigma$.

The random number generator `rng`

will be used and advanced in the proccess, and is by default the appropriate one depending on if `Σ`

is backed by `Array`

or `CuArray`

.

The `seed`

argument can also be used to seed the `rng`

.

`CMBLensing.symplectic_integrate`

— Method`symplectic_integrate(x₀, p₀, Λ, U, δUδx, N=50, ϵ=0.1, progress=false)`

Do a symplectic integration of the potential energy `U`

(with gradient `δUδx`

) starting from point `x₀`

with momentum `p₀`

and mass matrix `Λ`

. The number of steps is `N`

and the step size `ϵ`

.

Returns `ΔH, xᵢ, pᵢ`

corresponding to change in Hamiltonian, and final position and momenta. If `history_keys`

is specified a history of requested variables throughout each step is also returned.

`CMBLensing.ud_grade`

— Method`ud_grade(f::Field, θnew, mode=:map, deconv_pixwin=true, anti_aliasing=true)`

Up- or down-grades field `f`

to new resolution `θnew`

(only in integer steps). Two modes are available specified by the `mode`

argument:

`:map`

— Up/downgrade by replicating/averaging pixels in map-space`:fourier`

— Up/downgrade by extending/truncating the Fourier grid

For `:map`

mode, two additional options are possible. If `deconv_pixwin`

is true, deconvolves the pixel window function from the downgraded map so the spectrum of the new and old maps are the same. If `anti_aliasing`

is true, filters out frequencies above Nyquist prior to down-sampling.

`CMBLensing.unbatch`

— Method`unbatch(chains::Chains)`

Expand each chain in this `Chains`

object by unbatching it.

`CMBLensing.unbatch`

— Method`unbatch(chain::Chain)`

Convert a chain of batch-length-`D`

fields to `D`

chains of unbatched fields.

`CMBLensing.unbatch`

— Method`unbatch(f::FlatField)`

Return an Array of FlatFields corresponding to each batch index. For the inverse operation, see `batch`

.

`CMBLensing.unmix`

— Method```
unmix(f°, ϕ°, ds::DataSet)
unmix(f°, ϕ°, θ, ds::DataSet)
```

Compute the unmixed/unlensed `(f, ϕ)`

from the mixed field `f°`

and mixed lensing potential `ϕ°`

, given the definition of the mixing matrices in `ds`

evaluated at parameters `θ`

(or at fiducial values if no `θ`

provided).

`CMBLensing.ParamDependentOp`

— Type`ParamDependentOp(recompute_function::Function)`

Creates an operator which depends on some parameters $\theta$ and can be evaluated at various values of these parameters.

`recompute_function`

should be a function which accepts keyword arguments for $\theta$ and returns the operator. Each keyword must have a default value; the operator will act as if evaluated at these defaults unless it is explicitly evaluated at other parameters.

Example:

```
Cϕ₀ = Diagonal(...) # some fixed Diagonal operator
Cϕ = ParamDependentOp((;Aϕ=1)->Aϕ*Cϕ₀) # create ParamDependentOp
Cϕ(Aϕ=1.1) * ϕ # Cϕ(Aϕ=1.1) is equal to 1.1*Cϕ₀
Cϕ * ϕ # Cϕ alone will act like Cϕ(Aϕ=1) because that was the default above
```

Note: if you are doing parallel work, global variables referred to in the `recompute_function`

need to be distributed to all workers. A more robust solution is to avoid globals entirely and instead ensure all variables are "closed" over (and hence will automatically get distributed). This will happen by default if defining the `ParamDependentOp`

inside any function, or can be forced at the global scope by wrapping everything in a `let`

-block, e.g.:

```
Cϕ = let Cϕ₀=Cϕ₀
ParamDependentOp((;Aϕ=1)->Aϕ*Cϕ₀)
end
```

After executing the code above, `Cϕ`

is now ready to be (auto-)shipped to any workers and will work regardless of what global variables are defined on these workers.

`CMBLensing.RK4Solver`

— Method`RK4Solver(F!::Function, y₀, t₀, t₁, nsteps)`

Solve for $y(t_1)$ with 4th order Runge-Kutta assuming $dy/dt = F(t,y)$ and $y(t_0)$ = $y_0$.

Arguments:

`F!`

— a function`F!(v,t,y)`

`which sets`

v=F(t,y)`

`CMBLensing.@cpu!`

— Macro`@cpu! x y`

Equivalent to `x = cpu(x)`

, `y = cpu(y)`

, etc... for any number of listed variables. See `cpu`

.

`CMBLensing.@ismain`

— Macro`@ismain()`

Return true if the current file is being run as a script.

`CMBLensing.@repeated`

— MacroReturn a tuple with the expression repeated n times

`CMBLensing.@show⌛`

— MacroSee `@⌛`

`CMBLensing.@⌛`

— Macro```
@⌛ [label] code ...
@⌛ [label] function_definition() = ....
```

Label a section of code to be timed. If a label string is not provided, the first form uses the code itselfs as a label, the second uses the function name, and its the body of the function which is timed.

To run the timer and print output, returning the result of the calculation, use

`@show⌛ run_code()`

Timing uses `TimerOutputs.get_defaulttimer()`

.

`CMBLensing.LinearInterpolation`

— Method```
itp = LinearInterpolation(xdat::AbstractVector, ydat::AbstractVector; extrapolation_bc=NaN)
itp(x) # interpolate at x
```

A simple 1D linear interpolation code which is fully Zygote differentiable in either `xdat`

, `ydat`

, or the evaluation point `x`

.

`CMBLensing.QE_leg`

— Method`QE_leg(C::Diagonal, inds...)`

The quadratic estimate and normalization expressions all consist of terms involving products of two "legs", each leg which look like:

`C * l[i] * l̂[j] * l̂[k] * ...`

where C is some field or diagonal covariance, l[i] is the Fourier wave-vector in direction i (for i=1:2), and l̂[i] = l[i]/‖l‖. For example, there's a leg in the EB estimator that looks like:

`(CE * (CẼ+Cn) \ d[:E])) * l[i] * l̂[j] * l̂[k]`

The function `QE_leg`

computes quatities like these, e.g. the above would be given by:

`QE_leg((CE * (CẼ+Cn) \ d[:E])), [i], j, k)`

(where note that specifying whether its the Fourier wave-vector l instead of the unit-vector l̂ is done by putting that index in brackets).

Additionally, all of these terms are symmetric in their indices, i.e. in `(i,j,k)`

in this case. The `QE_leg`

function is smart about this, and is memoized so that each unique set of indices is only computed once. This leads to a pretty drastic speedup for terms with many indices like those that arize in the EE and EB normalizations, and lets us write code which is both clear and fast without having to think too hard about these symmetries.

`CMBLensing.assign_GPU_workers`

— Method`assign_GPU_workers()`

Assign each Julia worker process a unique GPU using `CUDA.device!`

. Workers may be distributed across different hosts, and each host can have multiple GPUs.

`CMBLensing.conjugate_gradient`

— Function```
conjugate_gradient(
M, A, b, x=M\b;
nsteps = length(b),
tol = sqrt(eps()),
progress = false,
callback = nothing,
history_keys = nothing,
history_mod = 1
)
```

Compute `x=A\b`

(where `A`

is positive definite) by conjugate gradient. `M`

is the preconditioner and should be `M≈A`

, and `M\x`

should be fast.

The solver will stop either after `nsteps`

iterations or when `dot(r,r)<tol`

(where `r=A*x-b`

is the residual at that step), whichever occurs first.

Info from the iterations of the solver can be returned if `history_keys`

is specified. `history_keys`

can be one or a tuple of:

`:i`

— current iteration number`:x`

— current solution`:r`

— current residual`r=A*x-b`

`:res`

— the norm of`r`

`:t`

— the time elapsed (in seconds) since the start of the algorithm

`history_mod`

can be used to include every N-th iteration only in `history_keys`

.

`CMBLensing.fftsyms`

— MethodArguments `m`

and `n`

refer to the sizes of an `m`

×`n`

matrix (call it `A`

) that is the output of a real FFT (thus `m=n÷2+1`

)

Returns a tuple of (ireal, iimag, negks) where these are

`ireal`

—`m`

×`n`

mask corrsponding to unique real entries of`A`

`iimag`

—`m`

×`n`

mask corrsponding to unique imaginary entries of`A`

`negks`

—`m`

×`n`

matrix of giving the index into A where the negative k-vector is, s.t.`A[i,j] = A[negks[i,j]]'`

`CMBLensing.fieldvalues`

— MethodReturn the type's fields as a tuple

`CMBLensing.finite_second_derivative`

— Method`finite_second_derivative(x)`

Second derivative of a vector `x`

via finite differences, including at end points.

`CMBLensing.gmres`

— Method`gmres(A, b; maxiter, Pl=I)`

Solve `A \ b`

with `maxiter`

iterations of the generalized minimal residual algorithm. `Pl`

is a left-preconditioner which should approximate `inv(A)`

.

Note: the implemenation is memory inefficient and uses O(n * maxiter) memory, where `n,n=size(A)`

(may not be a big deal for small `maxiter`

), although is totally generic and works with CPU or GPU and dense or sparse matrices, unlike IterativeSolver's `gmres`

.

`CMBLensing.gpu`

— Function`gpu(x)`

Recursively move an object to GPU memory. Note that, unlike `cu(x)`

, this does not change the `eltype`

of any underlying arrays. See also `cpu`

.

`CMBLensing.grid_and_sample`

— Method`grid_and_sample(lnP::Function; range::NamedTuple; progress=false, nsamples=1)`

Interpolate the log pdf `lnP`

with support on `range`

, and return the integrated log pdf as well `nsamples`

samples (drawn via inverse transform sampling)

`lnP`

should either accept a NamedTuple argument and `range`

should be a NamedTuple mapping those same names to `range`

objects specifying where to evaluate `lnP`

, e.g.:

`grid_and_sample(nt->-(nt.x^2+nt.y^2)/2, (x=range(-3,3,length=100),y=range(-3,3,length=100)))`

or `lnP`

should accept a single scalar argument and `range`

should be directly the range for this variable:

`grid_and_sample(x->-x^2/2, range(-3,3,length=100))`

The return value is `(lnP, samples, Px)`

where `lnP`

is an interpolated/smoothed log PDF which can be evaluated anywhere within the original range, `Px`

are sampled points of the original PDF, and `samples`

is a NamedTuple giving the Monte-Carlo samples of each of the parameters.

(Note: only 1D sampling is currently implemented, but 2D like in the example above is planned)

`CMBLensing.lazy_pyimport`

— Method`lazy_pyimport(s)`

Like `pyimport(s)`

, but doesn't actually load anything (not even PyCall) until a property of the returned module is accessed, allowing this to go in `__init__`

and still delay loading PyCall, as well as preventing a Julia module load error if a Python module failed to load.

`CMBLensing.longest_run_of_trues`

— Method`longest_run_of_trues(x)`

The slice corresponding to the longest run of `true`

s in the vector `x`

.

`CMBLensing.paren_errors`

— Method`paren_errors(μ, σ; N_in_paren=2)`

Get a string represntation of `μ ± σ`

in "parenthesis" format, e.g. `1.234 ± 0.012`

becomes `1.234(12)`

.

`CMBLensing.project`

— Method`project(flat_map::FlatField => healpix_proj::ProjHealpix; [rotator])`

Reproject a `flat_map`

back onto the sphere in a Healpix projection specified by `healpix_proj`

. E.g.

```
flat_map = FlatMap(rand(128,128))
f = project(flat_map => ProjHealpix(2048); rotator=pyimport("healpy").Rotator((0,28,23)))
```

The use of `=>`

is to help remember in which order the arguments are specified. Optional keyword argument `rotator`

is a `healpy.Rotator`

object specifying a rotation which rotates the north pole to the center of the desired field.

`CMBLensing.project`

— Method`project(healpix_map::HealpixField => flat_proj::FlatProj; [rotator])`

Project `healpix_map`

to a flat projection specified by `flat_proj`

. E.g.:

```
healpix_map = HealpixMap(rand(12*2048^2))
flat_proj = ProjLambert(Ny=128, Nx=128, θpix=3, T=Float32)
f = project(healpix_map => flat_proj; rotator=pyimport("healpy").Rotator((0,28,23)))
```

The use of `=>`

is to help remember in which order the arguments are specified. Optional keyword argument `rotator`

is a `healpy.Rotator`

object specifying a rotation which rotates the north pole to the center of the desired field. If `healpix_map`

is a `HealpixQU`

, Q/U polarization angles are rotated to be aligned with the local coordinates (sometimes called "polarization flattening").

`CMBLensing.rfft2vec`

— MethodConvert a matrix A which is the output of a real FFT to a real vector, keeping only unqiue real/imaginary entries of A

`CMBLensing.rfft_degeneracy_fac`

— Method`rfft_degeneracy_fac(n)`

Returns an Array which is 2 if the complex conjugate of the corresponding entry in the half-plane real FFT appears in the full-plane FFT, and is 1 othewise. `n`

is the length of the first dimension of the full-plane FFT. The following identity holds:

`sum(abs2.(fft(x)) = sum(rfft_degeneracy_fac(size(x,1)) .* abs2.(rfft(x))`

`CMBLensing.set_distributed_dataset`

— Method```
set_distributed_dataset(ds)
get_distributed_dataset()
```

Sometimes it's more performant to distribute a DataSet object to parallel workers just once, and have them refer to it from the global state, rather than having it get automatically but repeatedly sent as part of closures. This provides that functionality. Use `set_distributed_dataset(ds)`

from the master process to set the global DataSet and `get_distributed_dataset()`

from any process to retrieve it. Repeated calls will not resend `ds`

if it hasn't changed (based on `hash(ds)`

) and if no new workers have been added since the last send.

`CMBLensing.unfold`

— MethodConvert an M×N matrix (with M=N÷2+1) which is the output a real FFT to a full N×N one via symmetries.

`CMBLensing.vec2rfft`

— MethodConvert a vector produced by rfft2vec back into a complex matrix.

`CMBLensing.worker_info`

— Method`worker_info()`

Returns string showing info about assigned workers.

`CMBLensing.Σ`

— Method```
Σ(ϕ::Field, ds; [conjgrad_kwargs])
Σ(Lϕ, ds; [conjgrad_kwargs])
```

An operator for the data covariance, `Cn + M*B*L*Cf*L'*B'*M'`

, which can applied and inverted. `conjgrad_kwargs`

are passed to the underlying call to `conjugate_gradient`

.

`LinearAlgebra.logdet`

— Method`logdet(L::FieldOp, θ)`

If `L`

depends on `θ`

, evaluates `logdet(L(θ))`

offset by its fiducial value at `L()`

. Otherwise, returns 0.

`CMBLensing.BatchedReal`

— Type`BatchedReal(::Vector{<:Real}) <: Real`

Holds a vector of real numbers and broadcasts algebraic operations over them, as well as broadcasting along the batch dimension of `Field`

s, but is itself a `Real`

.

`CMBLensing.@!`

— MacroRewrites `@! x = f(args...)`

to `x = f!(x,args...)`

Special cases for `*`

and `\`

forward to `mul!`

and `ldiv!`

, respectively.

`CMBLensing.@auto_adjoint`

— Macro`@auto_adjoint foo(args...; kwargs...) = body`

is equivalent to

```
_foo(args...; kwargs...) = body
foo(args...; kwargs...) = _foo(args...; kwargs...)
@adjoint foo(args...; kwargs...) = Zygote.pullback(_foo, args...; kwargs...)
```

That is, it defines the function as well as a Zygote adjoint which takes a gradient explicitly through the body of the function, rather than relying on rules which may be defined for `foo`

. Mainly useful in the case that `foo`

is a common function with existing rules, but which you do *not* want to be used.

`CMBLensing.@dict`

— MacroPack some variables in a dictionary

```
> x = 3
> y = 4
> @dict x y z=>5
Dict(:x=>3,:y=>4,:z=>5)
```

`CMBLensing.@ondemand`

— Macro```
@ondemand(Package.function)(args...; kwargs...)
@ondemand(Package.Submodule.function)(args...; kwargs...)
```

Just like calling `Package.function`

or `Package.Submodule.function`

, but `Package`

will be loaded on-demand if it is not already loaded. The call is no longer inferrable.

`CMBLensing.@subst`

— Macro`@subst sum(x*$(y+1) for x=1:2)`

becomes

```
let tmp=(y+1)
sum(x*tmp for x=1:2)
end
```

to aid in writing clear/succinct code that doesn't recompute things unnecessarily.