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mloubout committed Oct 28, 2024
1 parent 2207389 commit d62b8a4
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19 changes: 2 additions & 17 deletions .github/workflows/ci-joli.yaml
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Expand Up @@ -19,7 +19,7 @@ jobs:
fail-fast: false

matrix:
version: ['1.6', '1.7', '1']
version: ['lts', '1.10', '1']
os:
- ubuntu-latest
- macos-latest
Expand All @@ -31,29 +31,14 @@ jobs:
uses: actions/checkout@v2

- name: Setup julia
uses: julia-actions/setup-julia@v1
uses: julia-actions/setup-julia@v2
with:
version: ${{ matrix.version }}
arch: ${{ matrix.arch }}

- name: Set up Python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7

- name: Install wavelets
run: |
python -m pip install --upgrade pip
pip install PyWavelets

- name: Build JOLI
uses: julia-actions/julia-buildpkg@latest

- name: Rebuild PyCall with system python
run: |
export PYTHON=$(which python)
julia --color=yes --check-bounds=yes --project -e 'using Pkg; Pkg.build("PyCall")'
- name: Run tests
uses: julia-actions/julia-runtest@latest

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3 changes: 3 additions & 0 deletions CondaPkg.toml
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@@ -0,0 +1,3 @@
[deps]
python = ""
pywavelets = ""
8 changes: 4 additions & 4 deletions Project.toml
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@@ -1,7 +1,7 @@
name = "JOLI"
uuid = "bb331ad6-a1cf-11e9-23da-9bcb53c69f6f"
authors = ["Henryk Modzelewski <henryk_modzelewski@mac.com>"]
version = "0.8.5"
version = "0.9.0"

[deps]
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
Expand All @@ -16,7 +16,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
NFFT = "efe261a4-0d2b-5849-be55-fc731d526b0d"
Nullables = "4d1e1d77-625e-5b40-9113-a560ec7a8ecd"
Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
SharedArrays = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Expand All @@ -27,12 +27,12 @@ Wavelets = "29a6e085-ba6d-5f35-a997-948ac2efa89a"
ChainRulesCore = "1"
DistributedArrays = "0.5, 0.6"
FFTW = "1"
Flux = "0.12, 0.13"
Flux = "0.12, 0.13, 0.14"
InplaceOps = "0.3.0"
IterativeSolvers = "0.8, 0.9"
NFFT = "0.6 - 0.13"
Nullables = "1"
PyCall = "1.18, 1.90, 1.91, 1.62"
PythonCall = "0.9"
SpecialFunctions = "1.2, 2"
Wavelets = "0.8, 0.9"
julia = "1"
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -53,7 +53,7 @@ JOLI is registered and can be added like any standard julia package with the com

- **CurveLab**: In order to use `joCurvelet2D` or `joCurvelet2DnoFFT` operators, you need to obtain *CurveLab-2.1.2-SLIM*, a SLIM extension to *CurveLab-2.1.2*. The tarball of this extension is available from [curvelet.org](http://www.curvelet.org) under [Software](http://www.curvelet.org/software.html) tab. The installation instructions are included in the tarball of *CurveLab-2.1.2-SLIM*. Note, that CurveLab is free only for academic use and requires registration.

- **PyWavelets**: In order to use `joSWT` that implements 1D stationary/shift invariant wavelet transform, the [PyWavelets](https://github.com/PyWavelets/pywt) package needs to be installed within the python environement used by [PyCall.jl](https://github.com/JuliaPy/PyCall.jl). By default, it will use [Conda.jl](https://github.com/JuliaPy/Conda.jl) and you should follow its directiv to install a package within it. If you have configured `PyCall` with your own python environment you can install `PyWavelets` via `pip install --upgrade PyWavelets`.
- **PyWavelets**: In order to use `joSWT` that implements 1D stationary/shift invariant wavelet transform, the [PyWavelets](https://github.com/PyWavelets/pywt) package needs to be installed within the python environment used by [PythonCall.jl](https://github.com/JuliaPy/PythonCall.jl). By default, it will use [CondaPkg.jl](https://github.com/JuliaPy/CondaPkg.jl) and you should follow its directiv to install a package within it. If you have configured `PythonCall` with your own python environment you can install `PyWavelets` via `pip install --upgrade PyWavelets`.

## Documentation (more to come)

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2 changes: 1 addition & 1 deletion src/JOLI.jl
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Expand Up @@ -51,10 +51,10 @@ using DistributedArrays.SPMD
using LinearAlgebra
using InplaceOps
using IterativeSolvers
using PythonCall
using FFTW
using NFFT
using Wavelets
using PyCall
using SpecialFunctions
using ChainRulesCore

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21 changes: 15 additions & 6 deletions src/joLinearFunctionConstructors/joSWT.jl
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Expand Up @@ -3,25 +3,32 @@
## helper module
module joSWT_etc
using JOLI: jo_convert
using PyCall
using PythonCall

const pywt = PythonCall.pynew()

function __init__()
PythonCall.pycopy!(pywt, pyimport("pywt"))
end

# 1D
function apply_swt(v::Vector{vdt}, wt::String, L::Integer,rdt::DataType,pad::Integer) where vdt<:Union{AbstractFloat,Complex}
pywt = pyimport("pywt")
v = [v;zeros(vdt, pad)]
rv = pywt.swt(v, wt, level=L, start_level=0, norm=true, trim_approx=true)
rv = vcat(rv...)
rv = vcat([PyArray(r) for r in rv]...)
rv = jo_convert(rdt, rv, false)
return rv
end

function apply_iswt(v::Vector{vdt},wt::String,L::Integer,rdt::DataType,pad::Integer) where vdt<:Union{AbstractFloat,Complex}
pywt = pyimport("pywt")
v = reshape(v, :, L+1)
v = [v[:, i] for i=1:L+1]
rv = pywt.iswt(v, wt, norm=true)
rv = PyArray(pywt.iswt(v, wt, norm=true))
# Convert and remove pad
rv = jo_convert(rdt, rv[1:end-pad], false)
return rv
end

end
using .joSWT_etc

Expand Down Expand Up @@ -68,7 +75,7 @@ examples with DDT/RDT
joDWT(m,"sym5"; DDT=Float32,RDT=Float64)
"""
function joSWT(m::Integer,wt::String="db20";
function joSWT(m::Integer, wt::String="db20";
L::Integer=maxtransformlevels(m + m%2),
DDT::DataType=joFloat,RDT::DataType=DDT,
name::String="joSWT")
Expand All @@ -84,3 +91,5 @@ function joSWT(m::Integer,wt::String="db20";
DDT,RDT;
name=name)
end

joSWT(m::Integer, wt::Py; kwargs...) = joSWT(m, string(wt); kwargs...)
2 changes: 1 addition & 1 deletion test/runtests.jl
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Expand Up @@ -5,7 +5,7 @@ using SparseArrays
using InplaceOps
using FFTW
using Wavelets
using PyCall
using PythonCall
using JOLI

jo_type_mismatch_error_set(false)
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4 changes: 2 additions & 2 deletions test/test_joSWT.jl
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,11 @@ try
global swt = pywt.swt
global pywavelet = true
catch
@warn "Skipping joSWTtests - PyCall clouldn't import PyWavelets"
@warn "Skipping joSWTtests - PythonCall clouldn't import PyWavelets"
end

families = ("haar", "db", "sym", "coif")
pywavelet ? wavelets = vcat([pywt.wavelist(name) for name in families]...) : wavelets = []
pywavelet ? wavelets = vcat([pyconvert(Vector{String}, pywt.wavelist(name)) for name in families]...) : wavelets = []

tsname="joSWT"
@testset "$tsname" begin
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