add(docs): structure and features in docs

Author: kunzaatko

docs/make.jl

@@ -12,14 +12,22 @@ makedocs(;
         prettyurls=get(ENV, "CI", "false") == "true",
         canonical="https://kunzaatko.github.io/TransferFunctions.jl",
         edit_link="trunk",
-        assets=String[],
+        assets=String[]
     ),
     pages=[
         "Home" => "index.md",
-    ],
+        "Theory" => "pages/01_theory.md",
+        "General Interface" => "pages/02_interface.md",
+        "Transfer Functions" => [
+            "Transfer Function Models" => "pages/03_model_tfs.md",
+            "Transfer Functions Measurements" => "pages/04_measured_tfs.md"],
+        "References" => [
+            "API Reference" => "pages/05_apireference.md",
+            "Bibliography References" => "pages/06_references.md"
+        ]]
 )
 
 deploydocs(;
     repo="github.com/kunzaatko/TransferFunctions.jl",
-    devbranch="trunk",
+    devbranch="trunk"
 )

docs/src/index.md

@@ -1,14 +1,19 @@
 ```@meta
 CurrentModule = TransferFunctions
 ```
+# TransferFunctions.jl
 
-# TransferFunctions
+_Transfer functions for optical systems_
 
-Documentation for [TransferFunctions](https://github.com/kunzaatko/TransferFunctions.jl).
+## Package Features
 
-```@index
-```
+!!! note
+    If you want to know more about the model of image formation in optical systems (cameras, microscopes, etc.) see
+    [theory](@ref "Theory Overview") section.
+
+- Generate OTF, PSF, MTF or PTF from a model or measured data
+- Convert between OTF and PSF for models and measurements
+- Models of transfer functions (OTF and PSF)
+- Define a transfer function from its Zernicke coefficients <!-- TODO:  -->
+- Estimate the Zernicke coefficients for a measured transfer function <!-- TODO: -->
 
-```@autodocs
-Modules = [TransferFunctions]
-```

docs/src/pages/01_theory.md

@@ -0,0 +1,6 @@
+## Theory Overview
+
+!!! note
+    All of the models assume *incoherent illumination* sources (i.e. where the radiation from the source has inocoherent frequency light). This is an approximation for most optical setups, but one that is used almost universally (e.g. in fluorescence microscopy).
+
+<!-- TODO: -->

docs/src/pages/02_interface.md

@@ -0,0 +1,7 @@
+```@meta
+CurrentModule = TransferFunctions
+```
+# Models
+- [`IdealOTFwithCurvature`](@ref)
+- [`BornWolf`](@ref)
+- [`GibsonLanni`](@ref)

docs/src/pages/03_model_tfs.md

@@ -0,0 +1,4 @@
+```@autodocs
+Modules = [TransferFunctions]
+Order   = [:function, :type]
+```

docs/src/pages/04_measured_tfs.md

@@ -1,9 +1,3 @@
-@doc raw"""
-This module implements diffraction transfer function models that are widely used in microscopy. The base type for any transfer function is `TransferFunction` and further disambiguates to [`MeasuredTransferFunction`](@ref) and [`ModelTransferFunction`](@ref).
-
-!!! warning
-    All of the models assume *incoherent illumination* sources (i.e. where the radiation from the source is inocoherent). This is an approximation for most optical setups, but one that is used almost universally (e.g. in fluorescence microscopy).
-"""
 module TransferFunctions
 using SimpleTraits
 using Unitful

docs/src/pages/05_apireference.md

@@ -13,14 +13,15 @@ end
 Generate an otf for the given transfer function with the size `wh` (size of `img`) and with a pixel distance of `Δxy`
 
 !!! note
-    The pixel size/distance (`Δxy`) is only required for a [model transfer function](@ref ModelTransferFunction). If it
-    is  not provided for a `MeasuredTransferFunction`, then the pixel distance from the measurement is used.
+    The pixel size/distance (`Δxy`) is required for a [model transfer function](@ref ModelTransferFunction) and optional
+    for a [`MeasuredTransferFunction`](@ref).
 
 # Arguments
 * `tf::TransferFunction`: transfer function model/measure to generate the OTF for
 * `wh::Tuple{Integer, Integer}` or `wh::Integer`: (width, height) of the generated OTF. `wh` ↦ `(wh, wh)` if `wh isa Integer`.
 * `Δxy::Tuple{Length, Length}` or `Δxy::Length`: Separation of pixels in the ``x`` and ``y`` dimensions of the generated
-    OTF image. `Δxy` ↦ `(Δxy, Δxy)` if `Δxy isa Length`.
+    OTF image. `Δxy` ↦ `(Δxy, Δxy)` if `Δxy isa Length`. (default: pixel distance from the measurement for a 
+    [`MeasuredTransferFunction`](@ref))
 * `δ::Tuple = (0,0)`: shift of the OTF in the image plane in pixels. This is useful for some algorithms, e.g. in 
     structured illumination microscopy reconstruction algorithms.
 """