Update API documentations for LDB. Update API documentation organizat…

…ion.

README.md

@@ -29,34 +29,14 @@ Extension). It contains additional functionalities that complement Wavelets.jl,
 ## Authors
 This package is written and maintained by Zeng Fung Liew and Shozen Dan under the supervision of Professor Naoki Saito at the University of California, Davis.
 
+## What's New (v0.1.13)
+- **Changes in supported types in `denoise` and `denoiseall` functions.** For the `inputtype` positional argument, the initially supported arguments `:acwt` and `:acwpt` are now changed to `:acdwt` and `:acwpd` to match the function name change in `WaveletsExt.ACWT`.
+- **2D Local Discriminant Basis now supported.** 2D version of LDB is now up and running without any changes in the syntax compared to the 1D version.
+
 ## What's New (v0.1.12)
 - **Bug fixes on best basis algorithms** to allow compatibility when partial wavelet decomposition is run.
 - **New function `plot_tfbdry2()` implemented.** Visual representation of leaf nodes for 2D best basis trees now available.
 
-## What's New (v0.1.11)
-- **All types of 2D wavelet transforms up and running.** Discrete wavelet transforms, wavelet packet transforms, and wavelet packet decompositions for standard, autocorrelation, and stationary transforms working well with improved speeds and memory allocations.
-- **2D best basis algorithms up and running.** Best basis algorithms such as standard best basis, joint best basis (JBB), and least statistically dependent basis (LSDB) now support 2D wavelet transforms.
-
-## What's New (v0.1.10)
-- **Direct support for wavelet transform of multiple signals.** Since the current package deals
-  a lot with multiple signals (eg. Joint Best Basis (JBB), group signal denoising, Local
-  Discriminant Basis (LDB)), functions are added to transform all signals at once, allowing
-  for simpler, cleaner and more efficient implementation of transforms for multiple signals.
-- **2D wavelet transforms.** 2D wavelet packet transforms and 2D wavelet packet
-  decompositions are implemented, along with additional functions to navigate through the quadtree.
-- **Improved API documentations.** API documentations contain more explanations for each
-  function argument and more examples of function use cases.
-- **Standardization of function names.** Wavelet transform function names are standardized
-  to:
-    - Discrete wavelet transform (redundant and non-redundant versions) have functions that
-      end with `dwt`, eg. `dwt`, `sdwt`, `acdwt`.
-    - Wavelet packet transform (redundant and non-redundant versions), where only the
-      coefficients of the leaf nodes are kept, have functions that end with `wpt`, eg.
-      `wpt`, `acwpt`, `swpt`.
-    - Wavelet packet decomposition (redundant and non-redundant versions), where all
-      coefficients of each level are recorded, have functions that end with `wpd`, eg.
-      `wpd`, `acwpd`, `swpd`.
-
 ## Installation
 The package is part of the official Julia Registry. It can be install via the Julia REPL.
 ```julia

docs/make.jl

@@ -19,10 +19,10 @@ makedocs(
             "DWT" => "api/dwt.md",
             "ACWT" => "api/acwt.md",
             "SWT" => "api/swt.md",
+            "SIWPD" => "api/siwpd.md",
             "Best Basis" => "api/bestbasis.md",
             "Denoising" => "api/denoising.md",
             "LDB" => "api/ldb.md",
-            "SIWPD" => "api/siwpd.md",
             "Utils" => "api/utils.md",
             "Visualizations" => "api/visualizations.md",
         ]

docs/src/api/acwt.md

@@ -4,8 +4,7 @@
 Modules = [ACWT]
 ```
 
-## Public API
-### Transforms on 1 Signal
+## Transforms on 1 Signal
 ```@docs
 ACWT.acdwt
 ACWT.acdwt!
@@ -21,9 +20,7 @@ ACWT.iacwpd
 ACWT.iacwpd!
 ```
 
-### Transforms on Multiple Signals
-!!! note
-    The following functions currently only support 1D-signals. Transforms on multiple 2D-signals are not yet supported.
+## Transforms on Multiple Signals
 ```@docs
 ACWT.acdwtall
 ACWT.iacdwtall
@@ -33,8 +30,7 @@ ACWT.acwpdall
 ACWT.iacwpdall
 ```
 
-## Private API
-### Utilities
+## Utilities
 ```@docs
 ACWT.autocorr
 ACWT.pfilter
@@ -43,7 +39,7 @@ ACWT.make_acqmfpair
 ACWT.make_acreverseqmfpair
 ```
 
-### Single Step Transforms
+## Single Step Transforms
 ```@docs
 ACWT.acdwt_step
 ACWT.acdwt_step!

docs/src/api/bestbasis.md

@@ -4,8 +4,7 @@
 Modules = [BestBasis]
 ```
 
-## Public API
-### Cost functions and computations
+## Cost functions and computations
 ```@docs
 BestBasis.CostFunction
 BestBasis.LSDBCost
@@ -21,7 +20,14 @@ BestBasis.tree_costs
 BestBasis.tree_costs(::AbstractMatrix{T}, ::AbstractVector{BitVector}, ::SIBB) where T<:Number
 ```
 
-### Best basis computation
+# Best Basis Tree Selection
+```@docs
+BestBasis.bestbasis_treeselection
+BestBasis.bestbasis_treeselection(::AbstractVector{Tc}, ::AbstractVector{Tt}) where {Tc<:AbstractVector{<:Union{Number,Nothing}}, Tt<:BitVector}
+BestBasis.delete_subtree!
+```
+
+## Best basis computation
 ```@docs
 BestBasis.BestBasisType
 BestBasis.LSDB
@@ -32,11 +38,3 @@ Wavelets.Threshold.bestbasistree
 Wavelets.Threshold.bestbasistree(::AbstractMatrix{T}, ::Integer, ::SIBB) where T<:Number
 BestBasis.bestbasistreeall
 ```
-
-# Private API
-```@docs
-BestBasis.bestbasis_treeselection
-BestBasis.bestbasis_treeselection(::AbstractVector{Tc}, ::AbstractVector{Tt}) where {Tc<:AbstractVector{<:Union{Number,Nothing}}, Tt<:BitVector}
-BestBasis.delete_subtree!
-
-```

docs/src/api/denoising.md

@@ -4,7 +4,6 @@
 Modules = [Denoising]
 ```
 
-# Public API
 ## Shrinking Types and Constructors
 ```@docs
 Denoising.RelErrorShrink
@@ -25,7 +24,6 @@ Wavelets.Threshold.denoise
 Denoising.denoiseall
 ```
 
-# Private API
 ## Helper Functions for Threshold Determination and Noise Estimation
 ```@docs
 Denoising.surethreshold

docs/src/api/dwt.md

@@ -4,8 +4,7 @@
 Modules = [DWT]
 ```
 
-## Public API
-### Transforms on 1 Signal
+## Transforms on 1 Signal
 ```@docs
 Wavelets.Transforms.wpt
 Wavelets.Transforms.wpt(::AbstractArray{T,2}, ::OrthoFilter, ::Integer; ::Bool) where T<:Number
@@ -21,7 +20,7 @@ DWT.iwpd
 DWT.iwpd!
 ```
 
-### Transforms on Multiple Signals
+## Transforms on Multiple Signals
 ```@docs
 DWT.dwtall
 DWT.idwtall
@@ -31,8 +30,7 @@ DWT.wpdall
 DWT.iwpdall
 ```
 
-## Private API
-### Single Step Transforms
+## Single Step Transforms
 ```@docs
 DWT.dwt_step
 DWT.dwt_step!

docs/src/api/swt.md

@@ -4,8 +4,7 @@
 Modules = [SWT]
 ```
 
-## Public API
-### Transforms on 1 Signal
+## Transforms on 1 Signal
 ```@docs
 SWT.sdwt
 SWT.sdwt!
@@ -21,7 +20,7 @@ SWT.iswpd
 SWT.iswpd!
 ```
 
-### Transforms on Multiple Signals
+## Transforms on Multiple Signals
 ```@docs
 SWT.sdwtall
 SWT.isdwtall
@@ -31,8 +30,7 @@ SWT.swpdall
 SWT.iswpdall
 ```
 
-## Private API
-### Single Step Transforms
+## Single Step Transforms
 ```@docs
 SWT.sdwt_step
 SWT.sdwt_step!

docs/src/api/utils.md

@@ -4,8 +4,7 @@
 Modules = [Utils]
 ```
 
-## Public API
-### Useful wavelet/signal utilities
+## Useful wavelet/signal utilities
 ```@docs
 Wavelets.Util.maxtransformlevels
 Utils.getbasiscoef
@@ -17,7 +16,7 @@ Utils.coarsestscalingrange
 Utils.finestdetailrange
 ```
 
-### Tree traversing functions
+## Tree traversing functions
 ```@docs
 Wavelets.Util.isvalidtree
 Wavelets.Util.maketree
@@ -28,24 +27,23 @@ Utils.getdepth
 Utils.gettreelength
 ```
 
-### Metrics
+## Metrics
 ```@docs
 Utils.relativenorm
 Utils.psnr
 Utils.snr
 Utils.ssim
 ```
 
-### Dataset generation
+## Dataset generation
 ```@docs
 Utils.ClassData
 Utils.duplicatesignals
 Utils.generatesignals
 Utils.generateclassdata
 ```
 
-## Private API
+## Miscellaneous
 ```@docs
 Utils.main2depthshift
-Utils.packet
 ```

docs/src/manual/transforms.md

@@ -118,7 +118,7 @@ plot(p0, p1, p2, layout=(1,3))
 
 - 2D Example
 ```@example dwt
-using Images, TestImages
+using TestImages
 
 img = testimage("cameraman");
 x = convert(Array{Float64}, img);