build based on 82045f2

.github/workflows/CI.yml

@@ -0,0 +1,49 @@
+name: CI
+on:
+  push:
+    paths-ignore:
+      - '*/*.md'
+      - 'docs/**'
+  pull_request:
+    paths-ignore:
+      - '*/*.md'
+      - 'docs/**'
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - 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 }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * 0 # weekly
+  workflow_dispatch:
+
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }} # need ssh
+        run: julia -e 'using CompatHelper; CompatHelper.main()'
+
+# based on:
+# https://github.com/JuliaRegistries/CompatHelper.jl

.github/workflows/Documentation.yml

@@ -0,0 +1,43 @@
+name: Documentation
+
+on:
+  pull_request:
+  push:
+    branches:
+      - 'main'
+      - 'release-'
+    tags: '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.6'
+      - 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 '
+          ENV["JULIA_PKG_SERVER"] = ""
+          using Pkg
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()'
+      - name: BuildAndDeploy
+        env:
+# https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#Authentication:-GITHUB_TOKEN
+#         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=docs/ docs/make.jl

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -0,0 +1,29 @@
+# Files generated by invoking Julia with --code-coverage
+*.jl.cov
+*.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
+
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
+docs/build/
+docs/site/
+
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml
+
+# other
+.DS_Store
+.*.*.swp
+.benchmarkci

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Jeff Fessler
+
+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.

Project.toml

@@ -0,0 +1,20 @@
+name = "SPECTrecon"
+uuid = "ab1be465-a7f0-4423-9048-0ee774b70ed9"
+authors = ["Zongyu Li and Jeff Fessler and group"]
+version = "0.0.1"
+
+[deps]
+AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
+FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
+ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+LinearInterpolators = "2fc109c4-9d77-11e9-32ff-e5c650334c16"
+OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+
+[compat]
+AbstractFFTs = "1.0"
+FFTW = "1.4"
+ImageFiltering = "0.7"
+LinearInterpolators = "0.1"
+OffsetArrays = "1.10"
+julia = "1.6"

README.md

@@ -0,0 +1,42 @@
+# SPECTrecon
+SPECT image reconstruction tools in Julia
+
+https://github.com/JeffFessler/SPECTrecon.jl
+
+[![action status][action-img]][action-url]
+[![pkgeval status][pkgeval-img]][pkgeval-url]
+[![codecov][codecov-img]][codecov-url]
+[![license][license-img]][license-url]
+[![docs-stable][docs-stable-img]][docs-stable-url]
+[![docs-dev][docs-dev-img]][docs-dev-url]
+[![code-style][code-blue-img]][code-blue-url]
+[![ColPrac: Contributor's Guide][colprac-img]][colprac-url]
+
+This repo provides forward and back-projection methods
+for SPECT image reconstruction.
+
+Designed for use with the
+[Michigan Image Reconstruction Toolbox (MIRT)](https://github.com/JeffFessler/MIRT.jl)
+or similar frameworks.
+
+Tested with Julia ≥ 1.6.
+
+<!-- URLs -->
+[action-img]: https://github.com/JeffFessler/SPECTrecon.jl/workflows/CI/badge.svg
+[action-url]: https://github.com/JeffFessler/SPECTrecon.jl/actions
+[build-img]: https://github.com/JeffFessler/SPECTrecon.jl/workflows/CI/badge.svg?branch=main
+[build-url]: https://github.com/JeffFessler/SPECTrecon.jl/actions?query=workflow%3ACI+branch%3Amain
+[pkgeval-img]: https://juliaci.github.io/NanosoldierReports/pkgeval_badges/S/SPECTrecon.svg
+[pkgeval-url]: https://juliaci.github.io/NanosoldierReports/pkgeval_badges/S/SPECTrecon.html
+[code-blue-img]: https://img.shields.io/badge/code%20style-blue-4495d1.svg
+[code-blue-url]: https://github.com/invenia/BlueStyle
+[codecov-img]: https://codecov.io/github/JeffFessler/SPECTrecon.jl/coverage.svg?branch=main
+[codecov-url]: https://codecov.io/github/JeffFessler/SPECTrecon.jl?branch=main
+[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg
+[docs-stable-url]: https://JeffFessler.github.io/SPECTrecon.jl/stable
+[docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
+[docs-dev-url]: https://JeffFessler.github.io/SPECTrecon.jl/dev
+[license-img]: http://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat
+[license-url]: LICENSE
+[colprac-img]: https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet
+[colprac-url]: https://github.com/SciML/ColPrac

accuracy/project.jl

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+# project.jl
+
+using Main.SPECTrecon: SPECTplan, Workarray
+using Main.SPECTrecon: project!
+using MAT
+using LazyAlgebra: vdot
+using LinearAlgebra: norm
+using Plots: plot
+
+function project_error()
+    T = Float32
+    path = "./data/"
+    file = matopen(path*"mumap208.mat")
+    mumap = read(file, "mumap208")
+    close(file)
+
+    file = matopen(path*"psf_208.mat")
+    psfs = read(file, "psf_208")
+    close(file)
+
+    file = matopen(path*"xtrue.mat")
+    xtrue = convert(Array{Float32, 3}, read(file, "xtrue"))
+    close(file)
+
+    file = matopen(path*"proj_jeff_newmumap.mat")
+    proj_jeff = read(file, "proj_jeff")
+    close(file)
+
+    dy = T(4.7952)
+    nview = size(psfs, 4)
+
+    plan1d = SPECTplan(mumap, psfs, dy; interpidx = 1)
+    plan2d = SPECTplan(mumap, psfs, dy; interpidx = 2)
+
+    workarray1d = Vector{Workarray}(undef, plan1d.ncore)
+    workarray2d = Vector{Workarray}(undef, plan2d.ncore)
+
+    for i = 1:plan1d.ncore
+        workarray1d[i] = Workarray(plan1d.T, plan1d.imgsize, plan1d.pad_fft, plan1d.pad_rot) # allocate
+    end
+
+    for i = 1:plan2d.ncore
+        workarray2d[i] = Workarray(plan2d.T, plan2d.imgsize, plan2d.pad_fft, plan2d.pad_rot) # allocate
+    end
+
+
+    (nx, ny, nz) = size(xtrue)
+    nview = size(psfs, 4)
+
+    views1d = zeros(T, nx, nz, nview)
+    views2d = zeros(T, nx, nz, nview)
+
+    project!(views1d, xtrue, plan1d, workarray1d)
+    project!(views2d, xtrue, plan2d, workarray2d)
+
+    nrmse(x, xtrue) = norm(vec(x - xtrue)) / norm(vec(xtrue))
+
+    err1d = zeros(nview)
+    for idx = 1:nview
+        err1d[idx] = nrmse(views1d[:,:,idx], proj_jeff[:,:,idx])
+    end
+
+    err2d = zeros(nview)
+    for idx = 1:nview
+        err2d[idx] = nrmse(views2d[:,:,idx], proj_jeff[:,:,idx])
+    end
+
+    return err1d, err2d
+    # 1d interp: 1e-7 nrmse
+    # 2d interp: 4e-3 nrmse
+end
+
+# shows accuracy
+err1d, err2d = project_error()
+nrmse1d = sum(err1d) / length(err1d)
+nrmse2d = sum(err2d) / length(err2d)
+@show nrmse1d
+@show nrmse2d
+nothing
+# plot(nrmse1d)

accuracy/run_accuracy.jl

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+# run_accuracy.jl
+
+using Main.SPECTrecon
+
+include("project.jl")

dev/.documenter-siteinfo.json

@@ -0,0 +1 @@
+{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-18T01:31:55","documenter_version":"1.4.1"}}

dev/assets/custom.css

@@ -0,0 +1,3 @@
+.docs-sourcelink {
+    opacity:1 !important;
+}