Fix new emitters (#83)

* initial refactoring 1. rm Emitter2.jl 2. split Emitters.jl into separate submodule files 3. mv Emitters.Visualization -> Vis 4. rm hacky root-level include("Emitters.jl") 5. fix incorrect import statements * docs-oriented namespace fixes * spelling/grammar * remove dodgy exports * remove docstrings from glasscat source files * remove docstrings from CARGILLE * rm SVector * add missing doc spectrumpower * add page for notebook utilities * add autodocs for OpticSim.Geometry * remove redundant struct * fix code style issues * remove random whitespace * remove redundant comments above docstrings * fix docstrings to follow existing conventions * fix many function type signatures * move exports to top of files to provide clear submodule headers * Int -> Integer * added empty docstrings for generate, visual_size and apply these functions clearly need documentation * bug fixes and doc changes warrant a patch number upgrade Co-authored-by: BrianGun <[email protected]>
microsoft · Apr 12, 2021 · 999b8a6 · 999b8a6 · alfredclwong · Apr 13, 2021
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diff --git a/Project.toml b/Project.toml
@@ -2,7 +2,7 @@ name = "OpticSim"
 uuid = "24114763-4efb-45e7-af0e-cde916beb153"
 authors = ["Brian Guenter", "Charlie Hewitt", "Ran Gal", "Alfred Wong"]
 repository = "https://github.com/microsoft/OpticSim.jl"
-version = "0.4.1"
+version = "0.4.2"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

diff --git a/deps/generate.jl b/deps/generate.jl
@@ -198,18 +198,15 @@ function catalog_to_modstring(start_id::Integer, catalogname::AbstractString, ca
     modstrings = [
         "module $catalogname",
         "using ..GlassCat: Glass, GlassID, AGF",
-        # "using StaticArrays: SVector",
         "export $(join(keys(catalog), ", "))",
         ""
     ]
     for (glassname, glassinfo) in catalog
-        # skip docstrings for CI builds to avoid 'missing docstring' warnings in makedocs
-        docstring = isCI ? "" : glassinfo_to_docstring(glassinfo, id, catalogname, glassname)
         argstring = glassinfo_to_argstring(glassinfo, id)
-        append!(modstrings, [docstring, "const $glassname = Glass($argstring)", ""])
+        push!(modstrings, "const $glassname = Glass($argstring)")
         id += 1
     end
-    append!(modstrings, ["end #module", ""]) # last "" is for \n at EOF
+    append!(modstrings, ["end # module", ""]) # last "" is for \n at EOF
 
     return id, join(modstrings, "\n")
 end

diff --git a/docs/make.jl b/docs/make.jl
@@ -21,7 +21,7 @@
 # SOFTWARE
 
 using Documenter
-using OpticSim, OpticSim.Geometry, OpticSim.Emitters
+using OpticSim
 
 makedocs(
     sitename = "OpticSim.jl",
@@ -49,6 +49,7 @@ makedocs(
         "Glass Functions" => "glasscat.md",
         "Optimization" => "optimization.md",
         "Cloud Execution" => "cloud.md",
+        "Notebook utilities" => "notebooksutils.md",
         "Reference" => "ref.md",
         "Roadmap" => "roadmap.md"
     ],

diff --git a/docs/src/basic_types.md b/docs/src/basic_types.md
@@ -11,26 +11,26 @@ using OpticSim, OpticSim.Geometry
 Representing a 3D vector.
 
 ```@docs
-Geometry.Vec3
-Geometry.unitX3
-Geometry.unitY3
-Geometry.unitZ3
-Geometry.zero3
-Geometry.one3
+OpticSim.Geometry.Vec3
+OpticSim.Geometry.unitX3
+OpticSim.Geometry.unitY3
+OpticSim.Geometry.unitZ3
+OpticSim.Geometry.zero3
+OpticSim.Geometry.one3
 ```
 
 ## Vec4
 
 Representing a 4D vector 
 
 ```@docs
-Geometry.Vec4
-Geometry.unitX4
-Geometry.unitY4
-Geometry.unitZ4
-Geometry.unitW4
-Geometry.zero4
-Geometry.one4
+OpticSim.Geometry.Vec4
+OpticSim.Geometry.unitX4
+OpticSim.Geometry.unitY4
+OpticSim.Geometry.unitZ4
+OpticSim.Geometry.unitW4
+OpticSim.Geometry.zero4
+OpticSim.Geometry.one4
 ```
 
 ## Transform
@@ -39,17 +39,16 @@ Representing a general 3D transform (4x4 matrix). Currently only used as a rigid
 Transforms are used to position surfaces within the CSG tree, position emitters in 3D, etc. 
 
 ```@docs
-Geometry.Transform
-Geometry.identitytransform
-Geometry.rotationX
-Geometry.rotationY
-Geometry.rotationZ
-Geometry.rotation
-Geometry.rotationd
-Geometry.rotate
-Geometry.translation
-Geometry.rotmat
-Geometry.rotmatd
-Geometry.rotmatbetween
+OpticSim.Geometry.Transform
+OpticSim.Geometry.identitytransform
+OpticSim.Geometry.rotationX
+OpticSim.Geometry.rotationY
+OpticSim.Geometry.rotationZ
+OpticSim.Geometry.rotation
+OpticSim.Geometry.rotationd
+OpticSim.Geometry.rotate
+OpticSim.Geometry.translation
+OpticSim.Geometry.rotmat
+OpticSim.Geometry.rotmatd
+OpticSim.Geometry.rotmatbetween
 ```
-
diff --git a/docs/src/csg.md b/docs/src/csg.md
@@ -12,7 +12,7 @@ The code for this in our system would look this this:
 ```@example
 using OpticSim # hide
 cyl = Cylinder(0.7)
-cyl_cross = csgunion(csgunion(leaf(cyl), leaf(cyl, rotationd(90, 0, 0))), leaf(cyl, rotationd(0, 90, 0)))
+cyl_cross = csgunion(csgunion(leaf(cyl), leaf(cyl, Geometry.rotationd(90, 0, 0))), leaf(cyl, Geometry.rotationd(0, 90, 0)))
 
 cube = Cuboid(1.0, 1.0, 1.0)
 sph = Sphere(1.3)

diff --git a/docs/src/emitters_new.md b/docs/src/emitters_new.md
@@ -21,7 +21,7 @@ The [`OpticSim`](index.html) package comes with various implementations of each
   * [`Emitters.Origins.Point`](@ref) - a single point
   * [`Emitters.Origins.RectUniform`](@ref) - a uniformly sampled rectangle with user defined number of samples
   * [`Emitters.Origins.RectGrid`](@ref) - a rectangle sampled in a grid fashion
-  * [`Emitters.Origins.Hexapolar`](@ref) - a circle (or an ellipse) sampled in an hexapolar fasion (rings)
+  * [`Emitters.Origins.Hexapolar`](@ref) - a circle (or an ellipse) sampled in an hexapolar fashion (rings)
 - Rays Directions Distribution - the interface **length** returns the number of samples, and **generate** returns the n'th sample.
   * [`Emitters.Directions.Constant`](@ref)
   * [`Emitters.Directions.RectGrid`](@ref)
@@ -30,7 +30,7 @@ The [`OpticSim`](index.html) package comes with various implementations of each
 
 ## [Examples of Basic Emitters](@id basic_emitters)
 
-**Note**: All the examples on this page assumes the followin statement was executed:
+**Note**: All of the examples on this page assume that the following statement was executed:
 
 ```@example
 using OpticSim, OpticSim.Geometry, OpticSim.Emitters
@@ -209,7 +209,7 @@ P = AngularPower.Lambertian()
 O = Origins.RectGrid(1.0, 1.0, 3, 3)
 D = Directions.HexapolarCone(deg2rad(5.0), 3)	
 	
-# construct the srouce. in this example a "pixel" source will contain only one source as we are simulating a "b/w" display. 
+# construct the source. in this example a "pixel" source will contain only one source as we are simulating a "b/w" display. 
 # for RGB displays we can combine 3 sources to simulate "a pixel".
 Tr = Transform(Vec3(0.5, 0.5, 0.0))
 source1 = Sources.Source(Tr, S, O, D, P)
@@ -232,7 +232,7 @@ end
 Tr = Transform(Vec3(0.0, 0.0, 0.0))
 my_display = Sources.CompositeSource(Tr, pixels)
 
-Vis.draw(my_display)                                                # render the display - nothing bu the origins primities
+Vis.draw(my_display)                                                # render the display - nothing but the origins primitives
 rays = AbstractArray{OpticalRay{Float64, 3}}(collect(my_display))   # collect the rays generated by the display
 Vis.draw!(rays)                                                     # render the rays 
 
@@ -261,6 +261,7 @@ A display example using composite sources.
 Emitters.Spectrum.Uniform
 Emitters.Spectrum.DeltaFunction
 Emitters.Spectrum.Measured
+Emitters.Spectrum.spectrumpower
 ```
 
 ## [Angular Power Distribution](@id angular_power_distribution)

diff --git a/docs/src/examples.md b/docs/src/examples.md
@@ -37,51 +37,6 @@ nothing # hide
 
 ![Cooke triplet visualization](assets/cooke.png)
 
-## Zoom Lens
-
-```@example
-using OpticSim
-
-using DataFrames
-function zoom_lens(pos = 1)
-    if pos == 0
-        stop = 2.89
-        zoom = 9.48
-        dist = 4.46970613
-    elseif pos == 1
-        stop = 3.99
-        zoom = 4.48
-        dist = 21.21
-    else
-        stop = 4.90
-        zoom = 2.00
-        dist = 43.81
-    end
-    return AxisymmetricOpticalSystem{Float64}(
-        DataFrame(Surface = [:Object, :Stop, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, :Image],
-                  Radius = [Inf64, Inf64, -1.6202203499676E+01, -4.8875855327468E+01, 1.5666614444619E+01, -4.2955326460481E+01, 1.0869565217391E+02, 2.3623907394283E+01, -1.6059097478722E+01, -4.2553191489362E+02, -3.5435861091425E+01, -1.4146272457208E+01, -2.5125628140704E+02, -2.2502250225023E+01, -1.0583130489999E+01, -4.4444444444444E+01, Inf64],
-                  Aspherics = [missing, missing, missing, missing, missing, [(4, 1.03860000000E-04), (6, 1.42090000000E-07), (8, -8.84950000000E-09), (10, 1.24770000000E-10), (12, -1.03670000000E-12), (14, 3.65560000000E-15)], missing, missing, [(4, 4.27210000000E-05), (6, 1.24840000000E-07), (8, 9.70790000000E-09), (10, -1.84440000000E-10), (12, 1.86440000000E-12), (14, -7.79750000000E-15)], [(4, 1.13390000000E-04), (6, 4.81650000000E-07), (8, 1.87780000000E-08), (10, -5.75710000000E-10), (12, 8.99940000000E-12), (14, -4.67680000000E-14)], missing, missing, missing, missing, missing, missing, missing],
-                  Thickness = [Inf64, 0.0, 5.18, 0.10, 4.40, 0.16, 1.0, 4.96, zoom, 4.04, 1.35, 1.0, 2.80, 3.0, 1.22, dist, missing],
-                  Material = [OpticSim.GlassCat.Air, OpticSim.GlassCat.Air, OpticSim.GlassCat.OHARA.S_LAH66, OpticSim.GlassCat.Air, OpticSim.GlassCat.NIKON.LLF6, OpticSim.GlassCat.Air, OpticSim.GlassCat.OHARA.S_TIH6, OpticSim.GlassCat.OHARA.S_FSL5, OpticSim.GlassCat.Air, OpticSim.GlassCat.OHARA.S_FSL5, OpticSim.GlassCat.Air, OpticSim.GlassCat.OHARA.S_LAL8, OpticSim.GlassCat.OHARA.S_FSL5, OpticSim.GlassCat.Air, OpticSim.GlassCat.OHARA.S_LAH66, OpticSim.GlassCat.Air, missing],
-                  SemiDiameter = [Inf64, stop, 3.85433218451, 3.85433218451, 4.36304692871, 4.36304692871, 4.72505505439, 4.72505505439, 4.72505505439, 4.45240784026, 4.45240784026, 4.50974054117, 4.50974054117, 4.50974054117, 4.76271114409, 4.76271114409, 15.0]))
-end
-@show zoom_lens(0)
-Vis.drawtracerays(zoom_lens(0), test = true, trackallrays = true, numdivisions = 50, resolution = (1200, 600))
-Vis.make2dy() # hide
-Vis.save("assets/zoom0.png") # hide
-Vis.drawtracerays(zoom_lens(1), test = true, trackallrays = true, numdivisions = 50, resolution = (1200, 600))
-Vis.make2dy() # hide
-Vis.save("assets/zoom1.png") # hide
-Vis.drawtracerays(zoom_lens(2), test = true, trackallrays = true, numdivisions = 50, resolution = (1200, 600))
-Vis.make2dy() # hide
-Vis.save("assets/zoom2.png") # hide
-nothing # hide
-```
-
-![Zoom position 1 visualization](assets/zoom0.png)
-![Zoom position 2 visualization](assets/zoom1.png)
-![Zoom position 3 visualization](assets/zoom2.png)
-
 ## Schmidt Cassegrain Telescope
 
 ```@example

diff --git a/docs/src/notebooksutils.md b/docs/src/notebooksutils.md
@@ -0,0 +1,14 @@
+# Notebook utilities
+
+```@meta
+CurrentModule = NotebooksUtils
+```
+
+[TODO]
+
+```@docs
+run_sample
+SetBackend
+run
+InitNotebook
+```
diff --git a/docs/src/ref.md b/docs/src/ref.md
@@ -14,6 +14,11 @@ Pages   = ["ref.md"]
 Modules = [OpticSim]
 ```
 
+## Geometry
+```@autodocs
+Modules = [OpticSim.Geometry]
+```
+
 ## Zernike
 
 ```@autodocs

diff --git a/src/Geometry/Geometry.jl b/src/Geometry/Geometry.jl
@@ -26,6 +26,9 @@ module Geometry
 include("Transform.jl")
 
 end # module Geometry
+export Geometry
+
+
 using .Geometry
 
 include("Ray.jl")

diff --git a/src/GlassCat/data/CARGILLE.jl b/src/GlassCat/data/CARGILLE.jl
@@ -24,49 +24,10 @@
 
 module CARGILLE
 using ..GlassCat: Glass, GlassID, OTHER
-using StaticArrays: SVector
 
-"""    CARGILLE.OG0608
-```
-ID:                      OTHER:1
-RI @ 587nm:              1.457518
-Abbe Number:             57.18978
-ΔPgF:                    0.008
-TCE (÷1e-6):             800.0
-Density:                 0.878g/m³
-Valid wavelengths:       0.32μm to 1.55μm
-Reference Temp:          25°C
-```
-"""
-const OG0608 = Glass(GlassID(OTHER, 1), -2, 1.4451400, 0.0043176, -1.80659e-5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.32, 1.55, -0.0009083144750540808, 0.0, 0.0, 0.0, 0.0, 0.0, 25.0, 0.008, -1.0, -1.0, 800.0, -1.0, 0, -1.0, [SVector(0.32, 0.03, 10.0), SVector(0.365, 0.16, 100.0), SVector(0.4047, 0.40, 100.0), SVector(0.480, 0.71, 100.0), SVector(0.4861, 0.72, 100.0), SVector(0.5461, 0.80, 100.0), SVector(0.5893, 0.90, 100.0), SVector(0.6328, 0.92, 100.0), SVector(0.6439, 0.95, 100.0), SVector(0.6563, 0.96, 100.0), SVector(0.6943, 0.99, 100.0), SVector(0.840, 0.99, 100.0), SVector(0.10648, 0.74, 100.0), SVector(0.1300, 0.39, 100.0), SVector(0.1550, 0.16, 100.0)], 1.457518, -1.0, -1.0, 0, 57.18978, 0, 0.878, -1)
-
-"""    CARGILLE.OG0607
-```
-ID:                      OTHER:2
-RI @ 587nm:              1.457587
-Abbe Number:             57.19833
-ΔPgF:                    0.008
-TCE (÷1e-6):             700.0
-Density:                 0.878g/m³
-Valid wavelengths:       0.32μm to 1.55μm
-Reference Temp:          25°C
-```
-"""
-const OG0607 = Glass(GlassID(OTHER, 2), -2, 1.44503, 0.0044096, -2.85878e-5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.32, 1.55, -0.0009083144750540808, 0.0, 0.0, 0.0, 0.0, 0.0, 25.0, 0.008, -1.0, -1.0, 700.0, -1.0, 0, -1.0, [SVector(0.32, 0.15, 10.0), SVector(0.365, 0.12, 100.0), SVector(0.4047, 0.42, 100.0), SVector(0.480, 0.78, 100.0), SVector(0.4861, 0.79, 100.0), SVector(0.5461, 0.86, 100.0), SVector(0.5893, 0.90, 100.0), SVector(0.6328, 0.92, 100.0), SVector(0.6439, 0.90, 100.0), SVector(0.6563, 0.92, 100.0), SVector(0.6943, 0.98, 100.0), SVector(0.840, 0.99, 100.0), SVector(0.10648, 0.61, 100.0), SVector(0.1300, 0.39, 100.0), SVector(0.1550, 0.11, 100.0)], 1.457587, -1.0, -1.0, 0, 57.19833, 0, 0.878, -1)
-
-"""    CARGILLE.OG081160
-```
-ID:                      OTHER:3
-RI @ 587nm:              1.515549
-Abbe Number:             36.82493
-ΔPgF:                    0.014
-TCE (÷1e-6):             700.0
-Density:                 1.11g/m³
-Valid wavelengths:       0.32μm to 1.55μm
-Reference Temp:          25°C
-```
-"""
-const OG081160 = Glass(GlassID(OTHER, 3), -2, 1.49614, 0.00692199, -8.07052e-5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.32, 1.55, -0.000885983052189022, 0.0, 0.0, 0.0, 0.0, 0.0, 25.0, 0.014, -1.0, -1.0, 700.0, -1.0, 0, -1.0, [SVector(0.32, 0.04, 100.0), SVector(0.365, 0.13, 100.0), SVector(0.4047, 0.26, 100.0), SVector(0.480, 0.48, 100.0), SVector(0.4861, 0.49, 100.0), SVector(0.5461, 0.60, 100.0), SVector(0.5893, 0.68, 100.0), SVector(0.6328, 0.71, 100.0), SVector(0.6439, 0.73, 100.0), SVector(0.6563, 0.74, 100.0), SVector(0.6943, 0.76, 100.0), SVector(0.840, 0.83, 100.0), SVector(0.10648, 0.86, 100.0), SVector(0.1300, 0.89, 100.0), SVector(0.1550, 0.90, 100.0)], 1.515549, -1.0, -1.0, 0, 36.82493, 0, 1.11, -1)
+const OG0608 = Glass(GlassID(OTHER, 1), -2, 1.4451400, 0.0043176, -1.80659e-5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.32, 1.55, -0.0009083144750540808, 0.0, 0.0, 0.0, 0.0, 0.0, 25.0, 0.008, -1.0, -1.0, 800.0, -1.0, 0, -1.0, [(0.32, 0.03, 10.0), (0.365, 0.16, 100.0), (0.4047, 0.40, 100.0), (0.480, 0.71, 100.0), (0.4861, 0.72, 100.0), (0.5461, 0.80, 100.0), (0.5893, 0.90, 100.0), (0.6328, 0.92, 100.0), (0.6439, 0.95, 100.0), (0.6563, 0.96, 100.0), (0.6943, 0.99, 100.0), (0.840, 0.99, 100.0), (0.10648, 0.74, 100.0), (0.1300, 0.39, 100.0), (0.1550, 0.16, 100.0)], 1.457518, -1.0, -1.0, 0, 57.18978, 0, 0.878, -1)
+const OG0607 = Glass(GlassID(OTHER, 2), -2, 1.44503, 0.0044096, -2.85878e-5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.32, 1.55, -0.0009083144750540808, 0.0, 0.0, 0.0, 0.0, 0.0, 25.0, 0.008, -1.0, -1.0, 700.0, -1.0, 0, -1.0, [(0.32, 0.15, 10.0), (0.365, 0.12, 100.0), (0.4047, 0.42, 100.0), (0.480, 0.78, 100.0), (0.4861, 0.79, 100.0), (0.5461, 0.86, 100.0), (0.5893, 0.90, 100.0), (0.6328, 0.92, 100.0), (0.6439, 0.90, 100.0), (0.6563, 0.92, 100.0), (0.6943, 0.98, 100.0), (0.840, 0.99, 100.0), (0.10648, 0.61, 100.0), (0.1300, 0.39, 100.0), (0.1550, 0.11, 100.0)], 1.457587, -1.0, -1.0, 0, 57.19833, 0, 0.878, -1)
+const OG081160 = Glass(GlassID(OTHER, 3), -2, 1.49614, 0.00692199, -8.07052e-5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.32, 1.55, -0.000885983052189022, 0.0, 0.0, 0.0, 0.0, 0.0, 25.0, 0.014, -1.0, -1.0, 700.0, -1.0, 0, -1.0, [(0.32, 0.04, 100.0), (0.365, 0.13, 100.0), (0.4047, 0.26, 100.0), (0.480, 0.48, 100.0), (0.4861, 0.49, 100.0), (0.5461, 0.60, 100.0), (0.5893, 0.68, 100.0), (0.6328, 0.71, 100.0), (0.6439, 0.73, 100.0), (0.6563, 0.74, 100.0), (0.6943, 0.76, 100.0), (0.840, 0.83, 100.0), (0.10648, 0.86, 100.0), (0.1300, 0.89, 100.0), (0.1550, 0.90, 100.0)], 1.515549, -1.0, -1.0, 0, 36.82493, 0, 1.11, -1)
 
 end
 

diff --git a/src/NotebooksUtils/NotebooksUtils.jl b/src/NotebooksUtils/NotebooksUtils.jl
@@ -71,7 +71,7 @@ function run(; port=nothing, path=nothing, sysimage_file=nothing, auto_detect_sy
         local file_path = $path
         local sysimage_file_path = $sysimage_file
 
-        if (file_path==nothing)
+        if (file_path === nothing)
             @info "Launching Pluto"
         else
             file_path = fix_path(file_path)

diff --git a/src/OpticSim.jl b/src/OpticSim.jl
@@ -44,12 +44,7 @@ include("constants.jl")
 include("utilities.jl")
 include("Geometry/Geometry.jl")
 include("Optical/Optical.jl")
-include("Visualization/Visualization.jl")
-
-# TODO: RG: the following include is seperated from the Optical include due to the new approach of putting the visualazation
-# part with the logic. We need to come up with a better approch to how and where visualization code should reside.
-include("Optical/Emitters.jl")      # defines the Emitters module
-
+include("Vis/Vis.jl")
 include("Examples/Examples.jl")
 include("Optimization/Optimization.jl")
 include("Cloud/Cloud.jl")