Merge pull request #13 from dsweber2/master

Tests work on remote

.github/workflows/docsBuild.yml

@@ -21,14 +21,17 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt install libxt6 libxrender1 libxext6 libgl1-mesa-glx libqt5widgets5
-      - run: |
+      - name: Instantiate 
+        run: |
           julia --project=docs -e '
             using Pkg
             Pkg.instantiate()
             Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()'
       - name: Build and deploy
-        run: julia --project=docs docs/make.jl
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=docs --code-coverage=user docs/make.jl
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1

LICENSE

@@ -1,21 +1,15 @@
-MIT License
-
-Copyright (c) 2020 dsweber2 <[email protected]> and contributors
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+Copyright 2015-2021 The Regents of the University of California, Davis campus
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+
+Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+
+Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+For further information, please contact [email protected].

Project.toml

@@ -1,7 +1,7 @@
 name = "ContinuousWavelets"
 uuid = "96eb917e-2868-4417-9cb6-27e7ff17528f"
 authors = ["dsweber2 <[email protected]> and contributors"]
-version = "0.3.0"
+version = "0.4.0"
 
 [deps]
 AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"

README.md

@@ -2,6 +2,78 @@
 
 [![Build Status](https://travis-ci.com/dsweber2/ContinuousWavelets.jl.svg?branch=master)](https://travis-ci.com/dsweber2/ContinuousWavelets.jl)
 [![Coverage](https://codecov.io/gh/dsweber2/ContinuousWavelets.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/dsweber2/ContinuousWavelets.jl)
+[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://dsweber2.github.io/ContinuousWavelets.jl/dev/)
 
-This package is an offshoot of Wavelets.jl to contain strictly the continuous
-wavelets. Thanks to github user @fgerick for the initial implementation there.
+This package is an offshoot of [Wavelets.jl](https://github.com/JuliaDSP/Wavelets.jl) for the continuous wavelets.
+Thanks to [Felix Gerick](https://github.com/fgerick) for the initial implementation there, with extension and further adaptation by David Weber and any other contributors listed on the right.
+Currently, it implements 1D continuous wavelet transforms with the following mother wavelets:
+
+![Mothers](/docs/MotherWavelets.svg)
+
+Which covers several standard continuous wavelet families, both real and analytic, as well as continuous versions of the orthogonal wavelet transforms implemented in [Wavelets.jl](https://github.com/JuliaDSP/Wavelets.jl).
+
+Basic Usage
+---------
+Install via the package manager and load with `using`
+
+```julia
+julia> Pkg.add("Wavelets")
+julia> using Wavelets
+```
+
+Basic usage example on a doppler test function. 
+```julia
+using ContinuousWavelets, Plots, Wavelets
+n=2047;
+t = range(0,n/1000,length=n); # 1kHz sampling rate
+f = testfunction(n, "Doppler");
+p1=plot(t, f,legend=false,title="Doppler",xticks=false)
+c = wavelet(Morlet(π), β=2);
+res = cwt(f, c)
+# plotting
+freqs = getMeanFreq(computeWavelets(n, c)[1])
+freqs[1] = 0
+p2=heatmap(t,freqs, abs.(res)', xlabel= "time (s)", ylabel="frequency (Hz)",colorbar=false)
+l=@layout [a{.3h};b{.7h}]
+plot(p1,p2,layout=l)
+```
+![Doppler](/docs/doppler.svg)
+
+As the cwt frame is redundant, there are many choices of dual/inverse frames. There are three available in this package, `NaiveDual()`, `PenroseDual()`, and `DualFrame()`. As a toy example:
+
+``` julia
+f = testfunction(n, "Bumps");
+p1=plot(f,legend=false,title="Bumps",xlims=(0,2000))
+c = wavelet(dog2, β=2);
+res = cwt(f, c)
+# dropping the middle peaks
+res[620:1100,:] .=0
+# and smoothing the remaining peaks
+res[:,10:29] .= 0
+# actually doing the inversion
+dropped = ContinuousWavelets.icwt(res,c,DualFrames())
+
+p1 = plot([dropped f],legend=false, title="Smoothing and dropping bumps")
+p2=heatmap(abs.(res)', xlabel= "time index", ylabel="frequency index",colorbar=false)
+l=@layout [a{.3h};b{.7h}]
+plot(p1,p2,layout=l)
+```
+![Bumps](/docs/bumps.svg)
+
+It can also handle collections of examples at the same time, should you need to do a batch of transforms:
+``` julia
+exs = cat(testfunction(n, "Doppler"),testfunction(n,"Blocks"),testfunction(n,"Bumps"),testfunction(n,"HeaviSine"),dims=2)
+c = wavelet(cDb2, β=2,extraOctaves=-0);
+res = cwt(exs, c)
+```
+![parallel transforms](/docs/multiEx.svg)
+There are also several boundary conditions, depending on the kind of data given; the default `SymBoundary()` symmetrizes the data, while `PerBoundary()` assumes it is periodic, and `ZPBoundary` pads with zeros.
+All wavelets are stored in the Fourier domain, and all transforms consist of performing an fft (possibly an rfft if the data is real) of the input, pointwise multiplication (equivalent to convolution in the time domain), and then returning to the time domain.
+
+Perhaps somewhat unusually, the averaging function, or father wavelet, is included as an option (the bottom row for the figure above). This can be either the paired averaging function or uniform in frequency (the `Dirac` averaging). The frequency coverage of the wavelets can be adjusted both in total frequency range both below by the `averagingLength` or above by the `extraOctaves` (caveat emptor with how well they will be defined in that case). The frequency density can be adjusted both in terms of the quality/scale factor `Q`, as well as how quickly this density falls off as the frequency goes to zero via `β`. Finally, depending on what kind of norm you want to preserve, `p` determines the norm preserved in the frequency domain (so `p=1` maintains the 1-norm in frequency, while `p=Inf` maintains the 1-norm in time).
+
+Possible extensions
+------------
+- Higher dimensional wavelets have yet to be implemented.
+- A DCT implementation of the symmetric boundary to halve the space and computational costs.
+- Various additional wavelet families, such as Morse wavelets.