Merge pull request #57 from UCD4IDS/dev

Documentation fix, unit test temporary fix

.github/workflows/CI.yml

@@ -8,8 +8,6 @@ on:
     - test/**
     - Project.toml
   pull_request:
-    branches:
-    - master
     paths:
     - src/**
     - test/**

README.md

@@ -31,14 +31,6 @@ 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.
-
 ## Installation
 The package is part of the official Julia Registry. It can be install via the Julia REPL.
 ```julia
@@ -85,5 +77,4 @@ Using the Multiscale Basis Dictionaries*. DOI: [10.1109/TSIPN.2016.2632039](http
 
 
 ## TODO(long term):
-* Inverse Transforms for Shift-Invariant WPT
 * nD wavelet transforms for redundant and non-redundant versions

docs/src/api/siwt.md

@@ -7,7 +7,9 @@ Modules = [SIWT]
 ## Data Structures
 ```@docs
 SIWT.ShiftInvariantWaveletTransformNode
+SIWT.ShiftInvariantWaveletTransformNode(::Array{T},::S,::S,::S,::T) where {T<:AbstractFloat, S<:Integer}
 SIWT.ShiftInvariantWaveletTransformObject
+SIWT.ShiftInvariantWaveletTransformObject(::Array{T}, ::OrthoFilter,::S,::S) where {T<:AbstractFloat, S<:Integer}
 ```
 
 ## Signal Transform and Reconstruction

docs/src/manual/bestbasis.md

@@ -127,14 +127,15 @@ plot(p1, p2, p3, p4, p5, p6, layout=(3,2))
 ## [Best Basis of Shift-Invariant Wavelet Packet Decomposition](@id si_bestbasis)
 One can think of searching for the best basis of the shift-invariant wavelet packet decomposition as a problem of finding ``\min_{b \in B} \sum_{x \in X} M_x(b)``, where ``X`` is all the possible shifted versions of an original signal ``y``. One can compute the best basis tree as follows:
 ```@repl
+using Wavelets, WaveletsExt;
 x = [2,3,-4,5.0];
 wt = wavelet(WT.haar);
 xwObj = siwpd(x, wt, 1, 1);
 xwObj.BestTree          # Original tree (all decomposed nodes)
 
-bestbasistree!(xwObj)   
+bestbasistree!(xwObj);   
 xwObj.BestTree          # Best basis tree
 
-x̂ = isiwpd(xwObj)       # Reconstruction of signal
+x̂ = isiwpd(xwObj);      # Reconstruction of signal
 x̂ == x
 ```

docs/src/manual/transforms.md

@@ -143,6 +143,7 @@ The [Shift-Invariant Wavelet Decomposition (SIWPD)](https://israelcohen.com/wp-c
 
 One can compute the SIWPD of a single signal as follows.
 ```@repl
+using Wavelets, WaveletsExt
 x = [2,3,-4,5.0];
 wt = wavelet(WT.haar);
 xwObj = siwpd(x, wt, 1, 1);

src/mod/Visualizations.jl

@@ -466,11 +466,9 @@ function wiggle!(plt::Plots.Plot,
         # generate the desired plots as of O3/19/2018. Somehow, the relative value of 0,
         # i.e., fillrange=0, works well, which is used temporarily.
         if Orient == :down
-            plot!(plt, inputy, inputx, fillrange=0, fillalpha=0.75, 
-                  fillcolor=FaceColor, linecolor=EdgeColor, orientation=:v)
+            plot!(plt, inputy, inputx, fillrange=0, fillalpha=0.75, fillcolor=FaceColor, linecolor=EdgeColor, orientation=:v)
         else
-            plot!(plt, inputx, inputy, fillrange=0, fillalpha=0.75,
-                  fillcolor=FaceColor, linecolor=EdgeColor)
+            plot!(plt, inputx, inputy, fillrange=0, fillalpha=0.75, fillcolor=FaceColor, linecolor=EdgeColor)
         end
     end
     return plt

test/visualizations.jl

@@ -1,42 +1,48 @@
-tree = BitVector([1,1,1])
-@test Visualizations.treenodes_matrix(tree) == BitArray([1 1; 1 1])
-# plot_tfbdry() test
-p = plot()
-@test isa(plot_tfbdry(tree), Plots.Plot{Plots.GRBackend})
-@test isa(plot_tfbdry(p, tree), Plots.Plot{Plots.GRBackend})
-@test isa(plot_tfbdry!(tree), Plots.Plot{Plots.GRBackend})
-@test isa(plot_tfbdry!(p, tree), Plots.Plot{Plots.GRBackend})
-@test_nowarn plot_tfbdry(tree, start=1)
-@test_throws AssertionError plot_tfbdry(tree, start=2)
-@test_nowarn plot_tfbdry(tree, node_color=:red, background_color=:white, line_color=:black)
-# plot_tfbdry2() test
-tree = maketree(4,4,2,:dwt)
-p = plot()
-@test isa(plot_tfbdry2(tree), Plots.Plot{Plots.GRBackend})
-@test isa(plot_tfbdry2(p, tree), Plots.Plot{Plots.GRBackend})
-@test isa(plot_tfbdry2!(tree), Plots.Plot{Plots.GRBackend})
-@test isa(plot_tfbdry2!(p, tree), Plots.Plot{Plots.GRBackend})
-@test_nowarn plot_tfbdry2(tree)
-@test_nowarn plot_tfbdry2(tree, 4)
-@test_nowarn plot_tfbdry2(tree, 4, 8)
-@test_throws AssertionError plot_tfbdry2(tree, 3, 8)
-@test_throws AssertionError plot_tfbdry2(tree, 4, 3)
-@test_throws AssertionError plot_tfbdry2(tree, 6, 6)
-x = randn(16,5)
-# wiggle() test
-@test typeof(wiggle(x)) == Plots.Plot{Plots.GRBackend}
-p = plot()
-@test typeof(wiggle(p, x)) == Plots.Plot{Plots.GRBackend}
-# wiggle!() test
-@test typeof(wiggle!(x)) == Plots.Plot{Plots.GRBackend}
-@test typeof(wiggle!(p, x)) == Plots.Plot{Plots.GRBackend}
-@test_throws ErrorException("Inconsistent taxis dimension!") wiggle!(p, x, taxis=1:5)
-@test_throws ErrorException("Inconsistent zaxis dimension!") wiggle!(p, x, zaxis=1:4)
-@test_nowarn wiggle!(p, x, sc=0.3)
-@test_nowarn wiggle!(p, x, EdgeColor=:red)
-@test_nowarn wiggle!(p, x, FaceColor=:red)
-@test_nowarn wiggle!(p, x, Overlap=false)
-@test_nowarn wiggle!(p, x, Orient=:down)
-@test_throws AssertionError wiggle!(p, x, Orient=:fail)
-@test_nowarn wiggle!(p, x, ZDir=:reverse)
-@test_throws AssertionError wiggle!(p, x, ZDir=:fail)
+@testset "plot_tfbdry" begin
+    tree = BitVector([1,1,1])
+    @test Visualizations.treenodes_matrix(tree) == BitArray([1 1; 1 1])
+    p = plot()
+    @test isa(plot_tfbdry(tree), Plots.Plot{Plots.GRBackend})
+    @test isa(plot_tfbdry(p, tree), Plots.Plot{Plots.GRBackend})
+    @test isa(plot_tfbdry!(tree), Plots.Plot{Plots.GRBackend})
+    @test isa(plot_tfbdry!(p, tree), Plots.Plot{Plots.GRBackend})
+    @test_nowarn plot_tfbdry(tree, start=1)
+    @test_throws AssertionError plot_tfbdry(tree, start=2)
+    @test_nowarn plot_tfbdry(tree, node_color=:red, background_color=:white, line_color=:black)
+end
+
+@testset "plot_tfbdry2" begin
+    tree = maketree(4,4,2,:dwt)
+    p = plot()
+    @test isa(plot_tfbdry2(tree), Plots.Plot{Plots.GRBackend})
+    @test isa(plot_tfbdry2(p, tree), Plots.Plot{Plots.GRBackend})
+    @test isa(plot_tfbdry2!(tree), Plots.Plot{Plots.GRBackend})
+    @test isa(plot_tfbdry2!(p, tree), Plots.Plot{Plots.GRBackend})
+    @test_nowarn plot_tfbdry2(tree)
+    @test_nowarn plot_tfbdry2(tree, 4)
+    @test_nowarn plot_tfbdry2(tree, 4, 8)
+    @test_throws AssertionError plot_tfbdry2(tree, 3, 8)
+    @test_throws AssertionError plot_tfbdry2(tree, 4, 3)
+    @test_throws AssertionError plot_tfbdry2(tree, 6, 6)
+end
+
+@testset "wiggle" begin
+    x = randn(16,5)
+    # wiggle() test
+    @test typeof(wiggle(x)) == Plots.Plot{Plots.GRBackend}
+    p = plot()
+    @test typeof(wiggle(p, x)) == Plots.Plot{Plots.GRBackend}
+    # wiggle!() test
+    @test typeof(wiggle!(x)) == Plots.Plot{Plots.GRBackend}
+    @test typeof(wiggle!(p, x)) == Plots.Plot{Plots.GRBackend}
+    @test_throws ErrorException("Inconsistent taxis dimension!") wiggle!(p, x, taxis=1:5)
+    @test_throws ErrorException("Inconsistent zaxis dimension!") wiggle!(p, x, zaxis=1:4)
+    @test_nowarn wiggle!(p, x, sc=0.3)
+    @test_nowarn wiggle!(p, x, EdgeColor=:red)
+    @test_nowarn wiggle!(p, x, FaceColor=:red)
+    @test_nowarn wiggle!(p, x, Overlap=false)
+    @test isa(wiggle!(p, x, Orient=:down), Plots.Plot{Plots.GRBackend})     # TODO: Keyword plot(orientation) deprecated. Figure out long term solution to this.
+    @test_throws AssertionError wiggle!(p, x, Orient=:fail)
+    @test_nowarn wiggle!(p, x, ZDir=:reverse)
+    @test_throws AssertionError wiggle!(p, x, ZDir=:fail)
+end