From 65fabb45d2e3808326ff696a2b44065cc3089457 Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Wed, 5 Feb 2020 16:49:22 -0800 Subject: [PATCH 01/11] Docker badge added. --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 149b00e..8a3a3ce 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ experimental sensitivity_ | :------------ | :------------------------------------- | | Documentation | [![][stable-img]][stable-url] [![][dev-img]][dev-url] | | Development | [![][travis-img]][travis-url] [![][appveyor-img]][appveyor-url] [![][codecov-img]][codecov-url] | -| Examples | [![][binder-img]][binder-url] | +| Deployment | [![][docker-img]][docker-url] [![][binder-img]][binder-url] | --- @@ -43,4 +43,7 @@ julia> Pkg.add(PackageSpec(url="https://github.com/MorganAskins/Batman.jl")) [appveyor-img]: https://ci.appveyor.com/api/projects/status/sb0jkbj2thwdu3mr/branch/master?svg=true [appveyor-url]: https://ci.appveyor.com/project/MorganAskins/batman-jl/branch/master +[docker-img]: https://img.shields.io/docker/cloud/build/morganaskins/batman.jl +[docker-url]: https://hub.docker.com/r/morganaskins/batman.jl + [Julia]: http://julialang.org/ From d42ac02b111bf77893869fbfdb4aef94c5a70c76 Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Wed, 5 Feb 2020 17:31:53 -0800 Subject: [PATCH 02/11] All modules autobuild into docs (not clean though) --- README.md | 12 ++++++------ docs/make.jl | 3 ++- docs/src/lib/batman.md | 5 +++++ src/predefined_functions.jl | 4 +++- 4 files changed, 16 insertions(+), 8 deletions(-) create mode 100644 docs/src/lib/batman.md diff --git a/README.md b/README.md index 8a3a3ce..21b36ab 100644 --- a/README.md +++ b/README.md @@ -3,13 +3,13 @@ _A **B**ayesian **A**nalysis **T**oolkit for **M**onitoring **A**nti-**N**eutrinos, written in [Julia], which provides a statistical analysis interface geared towards low-count experiments. BATMAN provides many customizable methods for evaluating confidence intervals and testing -experimental sensitivity_ +experimental sensitivity._ -| | | -| :------------ | :------------------------------------- | -| Documentation | [![][stable-img]][stable-url] [![][dev-img]][dev-url] | -| Development | [![][travis-img]][travis-url] [![][appveyor-img]][appveyor-url] [![][codecov-img]][codecov-url] | -| Deployment | [![][docker-img]][docker-url] [![][binder-img]][binder-url] | +| | | +| :---------------- | :------------------------------------- | +| **Documentation** | [![][stable-img]][stable-url] [![][dev-img]][dev-url] | +| **Development** | [![][travis-img]][travis-url] [![][appveyor-img]][appveyor-url] [![][codecov-img]][codecov-url] | +| **Deployment** | [![][docker-img]][docker-url] [![][binder-img]][binder-url] | --- diff --git a/docs/make.jl b/docs/make.jl index 365ed6d..3ba708f 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -5,7 +5,8 @@ makedocs( sitename="Batman.jl", modules=[Batman], pages = Any[ - "Home" => "index.md" + "Home" => "index.md", + "Library" => map(s -> "lib/$(s)", sort(readdir(joinpath(@__DIR__, "src/lib")))) ] ) diff --git a/docs/src/lib/batman.md b/docs/src/lib/batman.md new file mode 100644 index 0000000..b81cb54 --- /dev/null +++ b/docs/src/lib/batman.md @@ -0,0 +1,5 @@ +# Batman + +```@autodocs +Modules = [Batman] +``` diff --git a/src/predefined_functions.jl b/src/predefined_functions.jl index ba5a038..823615a 100644 --- a/src/predefined_functions.jl +++ b/src/predefined_functions.jl @@ -18,9 +18,11 @@ end """ logpoisson(n, x...) - λ > 0 +```math + λ > 0 \\ λ = sum([x...]) λ - n*log(λ) + n*log(n) - n +```math """ function logpoisson(n, x...) λ = sum([x...]) From 19d3d08146868c5e17c46fc1f2c625f497a5e0cb Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 15:08:20 -0800 Subject: [PATCH 03/11] Updated logo with noise --- docs/src/assets/logo.svg | 17448 ++++++++++++++++++++++++----------- docs/src/index.md | 53 +- 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + diff --git a/docs/src/index.md b/docs/src/index.md index aca802e..c71134b 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -28,23 +28,44 @@ julia> ] Logo for Batman.jl based on ```julia using PyPlot -σ(x) = @. √(1-x^2.0) -e(x) = @. 3σ(x/7.0) -s(x) = @. 4.2 - 0.5x - 2.8σ(0.5x-0.5) -b(x) = @. σ(abs(2-x)-1)-x.^2/11 + 0.5x - 3 -c(x) = [1.7, 1.7, 2.6, 0.9] +p(x, f) = fill_between(x, f.(x), color="black" ) -p(x, f) = fill_between(x, f(abs.(x)), color="black" ) +function bat(x; positive=true) + H(x) = x >= 0 ? 1.0 : 0.0 + σ(x) = @. √(1-x^2.0) + e(x) = @. 3σ(x/7.0) + s(x) = @. 4.2 - 0.5x - 2.8σ(0.5x-0.5) + b(x) = @. σ(abs(2-x)-1)-x.^2/11 + 0.5x - 3 + q(x) = @. 7.5*x*sign(-x) + 8.4 + j(x) = @. -3.0*x*sign(-x) + 0.2 + k(x) = @. 1.7 + c(x) = [1.7, 1.7, 2.6, 0.9] + if positive + if abs(x)>7 + return 0 + elseif abs(x) > 3 + return e.(abs.(x)) + elseif abs(x) > 1 + return s.(abs.(x)) + elseif abs(x) > 0.8 + return q(x) + elseif abs(x) > 0.5 + return j(x) + else + return k(x) + end + else + if abs(x)>7 + return 0 + elseif abs(x) > 4 + return -e.(abs.(x)) + else + return b(abs.(x)) + end + end +end -plt.axis("off") -p(3:0.01:7, e) -p(-7:0.01:-3, e) -p(4:0.01:7, t->-e(t)) -p(-7:0.01:-4, t->-e(t)) -p(1:0.01:3, s) -p(-3:0.01:-1, s) -p(-4:0.01:4, b) -p([0,0.5,0.8,1], c) -p(-[0,0.5,0.8,1], c) +p(-7:0.01:7, a->bat(a; positive=false) ) +p(-7:0.01:7, a->bat(a; positive=true) ) ``` ![](assets/logo.svg) diff --git a/examples/0_Batsignal.ipynb b/examples/0_Batsignal.ipynb index c0c2862..b382368 100644 --- a/examples/0_Batsignal.ipynb +++ b/examples/0_Batsignal.ipynb @@ -23,23 +23,163 @@ "metadata": {}, "outputs": [], "source": [ - "σ(x) = @. √(1-x^2.0)\n", - "e(x) = @. 3σ(x/7.0)\n", - "s(x) = @. 4.2 - 0.5x - 2.8σ(0.5x-0.5)\n", - "b(x) = @. σ(abs(2-x)-1)-x.^2/11 + 0.5x - 3\n", - "c(x) = [1.7, 1.7, 2.6, 0.9]\n", - "\n", - "p(x, f) = fill_between(x, f(abs.(x)), color=\"black\" )\n", - "\n", - "p(3:0.01:7, e)\n", - "p(-7:0.01:-3, e)\n", - "p(4:0.01:7, t->-e(t))\n", - "p(-7:0.01:-4, t->-e(t))\n", - "p(1:0.01:3, s)\n", - "p(-3:0.01:-1, s)\n", - "p(-4:0.01:4, b)\n", - "p([0,0.5,0.8,1], c)\n", - "p(-[0,0.5,0.8,1], c)" + "p(x, f) = fill_between(x, f.(x), color=\"black\" )\n", + "\n", + "function bat(x; positive=true)\n", + " H(x) = x >= 0 ? 1.0 : 0.0\n", + " σ(x) = @. √(1-x^2.0)\n", + " e(x) = @. 3σ(x/7.0)\n", + " s(x) = @. 4.2 - 0.5x - 2.8σ(0.5x-0.5)\n", + " b(x) = @. σ(abs(2-x)-1)-x.^2/11 + 0.5x - 3\n", + " q(x) = @. 7.5*x*sign(-x) + 8.4\n", + " j(x) = @. -3.0*x*sign(-x) + 0.2\n", + " k(x) = @. 1.7\n", + " c(x) = [1.7, 1.7, 2.6, 0.9]\n", + " if positive\n", + " if abs(x)>7\n", + " return 0\n", + " elseif abs(x) > 3\n", + " return e.(abs.(x))\n", + " elseif abs(x) > 1\n", + " return s.(abs.(x))\n", + " elseif abs(x) > 0.8\n", + " return q(x)\n", + " elseif abs(x) > 0.5\n", + " return j(x)\n", + " else\n", + " return k(x)\n", + " end\n", + " else\n", + " if abs(x)>7\n", + " return 0\n", + " elseif abs(x) > 4\n", + " return -e.(abs.(x))\n", + " else\n", + " return b(abs.(x))\n", + " end\n", + " end\n", + "end\n", + "\n", + "p(-7:0.01:7, a->bat(a; positive=false) )\n", + "p(-7:0.01:7, a->bat(a; positive=true) )\n", + "#plt.axis(\"off\")\n", + "#plt.savefig(\"logo.svg\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "## MCBat\n", + "using Random\n", + "using Seaborn\n", + "\n", + "function in_bat(x, y)\n", + " if y >= 0\n", + " if y <= bat(x; positive=true)\n", + " true\n", + " else\n", + " false\n", + " end\n", + " else\n", + " if y >= bat(x; positive=false)\n", + " true\n", + " else\n", + " false\n", + " end\n", + " end\n", + "end\n", + "\n", + "function noise(count)\n", + " rx = rand(Float64, count).*16 .- 8\n", + " ry = rand(Float64, count).*8 .- 4\n", + " a, b = 8, 4\n", + " s = @. ((ry/b)^2 + (rx/a)^2 < 1)\n", + " return rx[s], ry[s]\n", + "end\n", + "\n", + "ev = 5000\n", + "\n", + "tx = rand(Float64, ev).*14 .- 7\n", + "ty = rand(Float64, ev).*6 .- 3\n", + "\n", + "selection = in_bat.(tx, ty)\n", + "\n", + "nx, ny = noise(ev)\n", + "plt.plot(nx, ny, \".\")\n", + "\n", + "plt.plot(tx[selection], ty[selection], \".\", color=\"black\")\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "## MCBat\n", + "using Random\n", + "plt.style.use(\"bat.mplstyle\")\n", + "using Seaborn\n", + "\n", + "Random.seed!(13)\n", + "\n", + "\n", + "function in_bat(x, y)\n", + " if y >= 0\n", + " if y <= bat(x; positive=true)\n", + " true\n", + " else\n", + " false\n", + " end\n", + " else\n", + " if y >= bat(x; positive=false)\n", + " true\n", + " else\n", + " false\n", + " end\n", + " end\n", + "end\n", + "\n", + "function noise(count)\n", + " rx = rand(Float64, count).*16 .- 8\n", + " ry = rand(Float64, count).*8 .- 4\n", + " a, b = 8, 4\n", + " s = @. ((ry/b)^2 + (rx/a)^2 < 1)\n", + " return rx[s], ry[s]\n", + "end\n", + "\n", + "ev = 10000\n", + "\n", + "tx = rand(Float64, ev).*14 .- 7\n", + "ty = rand(Float64, ev).*6 .- 3\n", + "\n", + "selection = in_bat.(tx, ty)\n", + "\n", + "nx, ny = noise(ev)\n", + "bx, by = tx[selection], ty[selection]\n", + "#plt.plot(nx, ny, \".\")\n", + "\n", + "#plt.plot(tx[selection], ty[selection], \".\", color=\"black\")\n", + "\n", + "# g = jointplot(bx, by, kind=\"scatter\", color=(0,0,0,0.2), \n", + "# xlim=(-9,9), ylim=(-5,5), zorder=2)\n", + "#g = kdeplot(bx, by, color=(0,0,0))\n", + "#kdeplot(nx, ny)\n", + "#g.x = nx\n", + "#g.y = ny\n", + "#g.plot_joint(kdeplot, zorder=1, shade=true)\n", + "\n", + "g = jointplot(bx, by, kind=\"scatter\", color=(0,0,0,0.2), \n", + " xlim=(-9,9), ylim=(-5,5), zorder=2)\n", + "g.x = nx\n", + "g.y = ny\n", + "g.plot_joint(kdeplot, zorder=1, shade=true, cmap=\"cividis\")\n", + "\n", + "savefig(\"logo.svg\", transparent=true)" ] } ], From 13f2b2e1ed9e32dff12d0f9f136ea0a8be465c84 Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 15:17:04 -0800 Subject: [PATCH 04/11] Documentation --- src/macros.jl | 1 + src/model.jl | 10 +++++++++- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/src/macros.jl b/src/macros.jl index 339df81..5386d29 100644 --- a/src/macros.jl +++ b/src/macros.jl @@ -7,6 +7,7 @@ current namespace at read-time. # Examples ```julia-repl addfunction lognormalconstraint(x, μ, σ) = (x-μ)^2/2/σ +``` """ macro addfunction(f) :($f) diff --git a/src/model.jl b/src/model.jl index 868b93a..8b30f88 100644 --- a/src/model.jl +++ b/src/model.jl @@ -24,7 +24,15 @@ mutable struct Results upper_bounds::Array{Float64} end -## Generic model functions +""" +optimize_model!(m::Model, nll::NLogLikelihood; + lower_bounds=nothing, upper_bounds=nothing) + +Currently NLopt is used for minimizing the objective function. +optimize_model! produces the objective function from the given +NLogLikelihood which is then passed to NLopt to be minimized. +optimize_model! returns a set of Results. +""" function optimize_model!(m::Model, nll::NLogLikelihood; lower_bounds=nothing, upper_bounds=nothing) function objective(x::Vector, grad::Vector) From 30b01569d86ec253d8f95726d9b3177121a474f7 Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 15:29:07 -0800 Subject: [PATCH 05/11] Unit test for poisson fit --- test/poisson.jl | 17 +++++++++++++++++ test/runtests.jl | 2 +- 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 test/poisson.jl diff --git a/test/poisson.jl b/test/poisson.jl new file mode 100644 index 0000000..e1bd687 --- /dev/null +++ b/test/poisson.jl @@ -0,0 +1,17 @@ +using Batman, Test + +m = CountingExperiment() +add_component!(m, "Signal", 20.0) +add_component!(m, "Bkg 1", 30.0; 0.1) +add_component!(m, "Bkg 2", 30.0; 45.0) +add_component!(m, "Bkg 3", 12.0; 12.0) + +set_counts!(m, 100) + +results = minimize!(m) + +compute_profiled_uncertainties!(results; σ=1) + +signal = getparam(m, "Signal") + +@test signal.fit ≈ 18 rtol=0.5 diff --git a/test/runtests.jl b/test/runtests.jl index 8b574bb..59328fb 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -5,4 +5,4 @@ using Test, Batman # 2. Benchmarking tests; speed of objective functions # 3. Bias / pull for known fits. -@test 1 == 1 +include("poisson.jl") From c682de24da573749e476c8e8ddc249dac773b820 Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 15:56:55 -0800 Subject: [PATCH 06/11] readme index --- docs/src/index.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/src/index.md b/docs/src/index.md index c71134b..0620438 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -9,6 +9,9 @@ type of analysis to be performed including the posterior and prior probability distributions, all while naturally including nuisance parameters (such as systematic uncertainties). +Source code available: +[github.com/MorganAskins/Batman.jl](https://github.com/MorganAskins/Batman.jl) + ## Package features ## Installation From 489a3d5da224df0fc8f15c26304907927487a9a3 Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 16:18:09 -0800 Subject: [PATCH 07/11] Travis do better with codecov --- .travis.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index b94df86..074eace 100644 --- a/.travis.yml +++ b/.travis.yml @@ -14,10 +14,10 @@ env: - PYTHON=python3 after_success: - - julia --project=coverage/ -e 'using Pkg; - Pkg.instantiate(); - using Coverage; - Codecov.submit(Codecov.process_folder());' + - julia -e 'using Pkg; + Pkg.add("Coverage"); + using Coverage; + Codecov.submit(process_folder());' jobs: include: From d63107704b262ffcef5e1dbbdfc5f2a6d6e61fe3 Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 16:34:18 -0800 Subject: [PATCH 08/11] travis please --- .travis.yml | 1 + test/poisson.jl | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 074eace..f371917 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,4 +1,5 @@ language: julia +codecov: true os: - linux diff --git a/test/poisson.jl b/test/poisson.jl index e1bd687..e8c01d5 100644 --- a/test/poisson.jl +++ b/test/poisson.jl @@ -2,9 +2,9 @@ using Batman, Test m = CountingExperiment() add_component!(m, "Signal", 20.0) -add_component!(m, "Bkg 1", 30.0; 0.1) -add_component!(m, "Bkg 2", 30.0; 45.0) -add_component!(m, "Bkg 3", 12.0; 12.0) +add_component!(m, "Bkg 1", 30.0; σ = 0.1) +add_component!(m, "Bkg 2", 30.0; σ = 45.0) +add_component!(m, "Bkg 3", 12.0; σ = 12.0) set_counts!(m, 100) From 6e263ff4fe2c4f7e7cecb84b134e000fcd6d59fc Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 16:49:05 -0800 Subject: [PATCH 09/11] travis!!! --- .travis.yml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index f371917..bdd8c46 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,5 +1,4 @@ language: julia -codecov: true os: - linux @@ -14,12 +13,6 @@ env: matrix: - PYTHON=python3 -after_success: - - julia -e 'using Pkg; - Pkg.add("Coverage"); - using Coverage; - Codecov.submit(process_folder());' - jobs: include: - stage: "Documentation" @@ -28,3 +21,9 @@ jobs: Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate();' - julia --project=docs/ docs/make.jl + +after_success: + - julia -e 'using Pkg; + Pkg.add("Coverage"); + using Coverage; + Codecov.submit(process_folder());' From fbeec2db7a364b2eb685c9090e71df9beaf4a09a Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 17:04:17 -0800 Subject: [PATCH 10/11] Lets go dude --- .travis.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.travis.yml b/.travis.yml index bdd8c46..6307008 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,6 +15,12 @@ env: jobs: include: + - stage: "Testing" + script: + - julia --project=docs/ -e 'using Pkg; + Pkg.develop(PackageSpec(path=pwd())); + Pkg.instantiate();' + - julia -e 'using Pkg; Pkg.test(coverage=true);' - stage: "Documentation" script: - julia --project=docs/ -e 'using Pkg; From 81e448ad3c2c7aecb43823498b6ecd8f1ff856ef Mon Sep 17 00:00:00 2001 From: Morgan Askins Date: Thu, 6 Feb 2020 17:08:54 -0800 Subject: [PATCH 11/11] This is the way to travis really --- .travis.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 6307008..cf1dd65 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,18 +15,13 @@ env: jobs: include: - - stage: "Testing" - script: - - julia --project=docs/ -e 'using Pkg; - Pkg.develop(PackageSpec(path=pwd())); - Pkg.instantiate();' - - julia -e 'using Pkg; Pkg.test(coverage=true);' - stage: "Documentation" script: - julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate();' - julia --project=docs/ docs/make.jl + - julia -e 'using Pkg; Pkg.test(coverage=true);' after_success: - julia -e 'using Pkg;