various package status improvement

.github/workflows/UnitTest.yml

@@ -0,0 +1,56 @@
+name: Unit test
+
+on:
+  create:
+    tags:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: ['1.3', '1', 'nightly']
+        os: [ubuntu-latest]
+        arch: [x64]
+        include:
+          - os: windows-latest
+            julia-version: '1'
+            arch: x64
+          - os: macOS-latest
+            julia-version: '1'
+            arch: x64
+          - os: ubuntu-latest
+            julia-version: '1'
+            arch: x86
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: "Set up Julia"
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.arch }}
+
+      - name: Cache artifacts
+        uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts 
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - name: "Unit Test"
+        uses: julia-actions/julia-runtest@master
+
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/docs.yml

@@ -0,0 +1,41 @@
+name: Documentation
+
+on:
+  pull_request:
+  push:
+    branches:
+      - 'master'
+      - 'release-'
+    tags: '*'
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        os: [ubuntu-latest]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Cache artifacts
+        uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts 
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia --project=docs/ docs/make.jl

Project.toml

@@ -4,28 +4,13 @@ authors = ["Peter Kovesi <[email protected]>"]
 version = "0.2.1"
 
 [deps]
-AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
-Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
+ImageMorphology = "787d08f9-d448-5407-9aad-5290dd7ab264"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-TestImages = "5e47fb64-e119-507b-a336-dd2b206d9990"
 
 [compat]
-AbstractFFTs = "0.3, 0.4, 0.5, 1.0"
-Documenter = "0.24, 0.25, 0.26, 0.27"
 FFTW = "1"
-FileIO = "1"
-ImageMagick = "1"
-Images = "0.9, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24"
-TestImages = "1"
+ImageCore = "0.9"
+ImageMorphology = "0.3"
 julia = "1.3"
-
-[extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test"]

docs/Project.toml

@@ -0,0 +1,12 @@
+[deps]
+DemoCards = "311a05b2-6137-4a5a-b473-18580a3d38b5"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+ImageContrastAdjustment = "f332f351-ec65-5f6a-b3d1-319c6670881a"
+ImageIO = "82e4d734-157c-48bb-816b-45c225c6df19"
+ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
+ImagePhaseCongruency = "10e51d30-6ba1-539a-b97e-c69c597142c4"
+Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+
+[compat]
+Documenter = "0.27"
+DemoCards = "0.4"

docs/examples/config.json

@@ -0,0 +1,11 @@
+{
+    "theme": "grid",
+    "order": [
+        "phase_congruency",
+        "test_images",
+        "misc"
+    ],
+    "properties": {
+        "notebook": "false"
+    }
+}

docs/examples/misc/perfft2.jl

@@ -0,0 +1,54 @@
+# ---
+# title: Fourier transform of Moisan periodic image component
+# id: demo_perfft2
+# cover: assets/perfft2.png
+# author: Peter Kovesi
+# date: 2018-10-26
+# ---
+
+# The function `perfft2()` implements Moisan's "Periodic plus Smooth Image
+# Decomposition" which decomposes an image into two components
+#
+#         img = p + s
+#
+# where `s` is the 'smooth' component with mean 0 and `p` is the 'periodic' component
+# which has no sharp discontinuities when one moves cyclically across the image
+# boundaries.
+#
+# This decomposition is very useful when one wants to obtain an FFT of an image
+# with minimal artifacts introduced from the boundary discontinuities. The image
+# `p` gathers most of the image information but avoids periodization artifacts.
+#
+# Reference:
+# L. Moisan, "Periodic plus Smooth Image Decomposition", Journal of
+# Mathematical Imaging and Vision, vol 39:2, pp. 161-179, 2011.
+
+using Images
+using FFTW
+using ImagePhaseCongruency
+using ImageContrastAdjustment
+using TestImages
+
+img = Float64.(Gray.(testimage("lena")))
+
+IMG = fft(img)               # 'Standard' fft
+(P, S, p, s) = perfft2(img)  # 'Periodic' fft
+
+mosaic(
+    adjust_histogram(Gray.(p), LinearStretching()),
+    adjust_histogram(s, LinearStretching()),
+    ## Note the vertical and horizontal cross in
+    ## the spectrum induced by the non-periodic edges.
+    adjust_histogram(log.(abs.(fftshift(IMG)) .+ 1), LinearStretching()),
+    ## Note the clean spectrum because p is periodic.
+    adjust_histogram(log.(abs.(fftshift(P)) .+ 1), LinearStretching());
+    nrow=2, rowmajor=true
+)
+# Top 1) left: periodic component 2) right: smooth component
+#
+# Bottom 3) left: spectrum of standard FFT 4) right: spectrum of periodic component
+
+# save cover image #src
+isdir("assets") || mkdir("assets") #src
+cover = Gray.(adjust_histogram(log.(abs.(fftshift(P)) .+ 1), LinearStretching())) #src
+save(joinpath("assets", "perfft2.png"), cover) #src

docs/examples/phase_congruency/phasecong3.jl

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+# ---
+# title: Log-Gabor filters v3
+# id: demo_phasecong3
+# cover: assets/phasecong3.png
+# author: Peter Kovesi
+# date: 2018-10-26
+# ---
+
+# Use of the function `phasecong3()` allows corner points to be detected as well. These
+# corner points are a subset of the edge image and, unlike other corner detectors, their
+# location is precise and stable over different scales.
+
+using TestImages
+using Images
+using ImagePhaseCongruency
+
+img = restrict(testimage("mandril_gray"))
+(edges, corners) = phasecong3(img)
+
+mosaic(
+    img,
+    adjust_histogram(Gray.(edges), LinearStretching()),
+    adjust_histogram(corners, LinearStretching()),
+    nrow=1
+)
+# Images from top to right: 1) original image 2) edges 3) corners
+
+# save cover image #src
+isdir("assets") || mkdir("assets") #src
+save(joinpath("assets", "phasecong3.png"), adjust_histogram(Gray.(edges), LinearStretching())) #src

docs/examples/phase_congruency/phasecongmono.jl

@@ -0,0 +1,35 @@
+# ---
+# title: Monogenic filters
+# id: demo_phasecongmono
+# cover: assets/phasecongmono.png
+# author: Peter Kovesi
+# date: 2018-10-26
+# ---
+
+# Phase congruency marks all classes of features from steps to lines and is a dimensionless
+# quantity that ranges from 0 to 1. This allows fixed thresholds to be used over wide
+# classes of images.
+
+using TestImages
+using Images
+using ImagePhaseCongruency
+
+img = restrict(testimage("mandril_gray"))
+
+(pc, or, ft, T) = phasecongmono(img)
+nonmax = Images.thin_edges(pc, or)
+
+mosaic(
+    img,
+    adjust_histogram(pc, LinearStretching()),
+    nonmax,
+    hysthresh(nonmax, 0.1, 0.2);
+    nrow=2, rowmajor=true
+)
+
+# Images: 1) top left: original image 2) top right: phase congruency 3) bottom left:
+# non-maximal suppression 4) bottom right: Hystersis thresholded
+
+# save cover image #src
+isdir("assets") || mkdir("assets") #src
+save(joinpath("assets", "phasecongmono.png"), adjust_histogram(Gray.(pc), LinearStretching())) #src

docs/examples/phase_congruency/phasesymmetry.jl

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+# ---
+# title: Symmetric monogenic filters
+# id: demo_phasesymmono
+# cover: assets/phasesymmono.gif
+# author: Peter Kovesi
+# date: 2018-10-26
+# ---
+
+# Phase symmetry responds well to line like features and circular objects.  The number of
+# filter scales will affect the scale of features that are marked. Phase symmetry marks
+# features independently of contrast (a bright circle is not more symmetric than a grey
+# circle) and is a dimensionless quantity between 0 and 1.  However this may not be what one
+# desires in which case the symmetry energy may be of greater interest.
+
+using TestImages
+using Images
+using ImagePhaseCongruency
+
+img = Gray.(testimage("blobs"))
+## Detect regions of bright symmetry (polarity = 1)
+phase_bright, = phasesymmono(img; nscale=5, polarity=1)
+
+## Detect regions of dark symmetry (polarity = -1)
+phase_dark, = phasesymmono(img; nscale=5, polarity=-1)
+
+mosaic(img, phase_bright, phase_dark; nrow=1)
+
+# save cover image #src
+isdir("assets") || mkdir("assets") #src
+save(joinpath("assets", "phasesymmono.gif"), Images.gif([phase_bright, phase_dark]); fps=1) #src

docs/examples/phase_congruency/ppdenoise.jl

@@ -0,0 +1,33 @@
+# ---
+# title: Denoise
+# id: demo_ppdenoise
+# cover: assets/ppdenoise.png
+# author: Peter Kovesi
+# date: 2018-10-26
+# ---
+
+using TestImages
+using Images
+using ImageContrastAdjustment
+using ImagePhaseCongruency
+using Random #hide
+Random.seed!(1234) #hide
+
+## Values in the range 0 to 1
+img = centered(Gray.(restrict(testimage("lighthouse"))))[-127:128, -127:128]
+
+## Add noise with standard deviation of 0.25
+img .+= 0.25 * randn(size(img))
+
+cleanimg = ppdenoise(img; nscale=6, norient=6, mult=2.5, minwavelength=2, sigmaonf=0.55, dthetaonsigma=1.0, k=3, softness=1.0)
+
+mosaic(
+    adjust_histogram(img, LinearStretching()),
+    adjust_histogram(cleanimg, LinearStretching());
+    nrow=1
+)
+
+# save cover image #src
+isdir("assets") || mkdir("assets") #src
+cover = adjust_histogram(Gray.(cleanimg), LinearStretching()) #src
+save(joinpath("assets", "ppdenoise.png"), cover) #src