17100492288

Committed 20 Aug 2025 01:52PM UTC coverage: 0.0% (-74.8%) from 74.77%

Build # 17100492288

Build Type

push

github

Committed by

kunzaatko

Commit Message

feat: introduce comprehensive transfer function models

This commit significantly expands the available transfer function models and
refactors the documentation structure to support them.

Changes include:
- **New Models:** Added Airy Disc, Gaussian, Born & Wolf, Gibson & Lanni, and
  Circular Pupil transfer function models.
- **Documentation Overhaul:** Restructured the manual pages, separating linear
  and nonlinear transfer functions, and creating dedicated sections for
  individual model types. Updated `InterLinks` for new dependencies and removed
  old API reference sections.
- **Dependency Updates:**
    - Added `ComponentArrays` and `Rotations` for new functionalities.
    - Removed `ImageFiltering` dependency.
    - Updated `InterfaceFunctions` compatibility.

Run Details

0 of 169 new or added lines in 12 files covered. (0.0%)

364 existing lines in 15 files now uncovered.

0 of 633 relevant lines covered (0.0%)

0.0 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

0.0

/src/psf/point-spread-function.jl

using InterfaceFunctions
using Roots
using Base: Fix
using TransferFunctions.Apodization

"""
    PointSpreadFunction{N} <: LinearShiftInvariantTransferFunction{N}
A point spread function is a description of a transfer functions specifying the intensity transfer of a single point
source in the object plane into a region of the image plane.

# Implementation
To create a new Point spread function (PSF) `A <: PointSpreadFunction`, you must define the __intensity__ at a given
[length](@extref Unitful `Length`) coordinate `intensity(psf::A, x::Length, y::Length)`.
"""
abstract type PointSpreadFunction{N} <: LinearShiftInvariantTransferFunction{N} end
Broadcast.broadcastable(tf::PointSpreadFunction) = Ref(tf)

"""
    PointSpreadFunctionSymmetry
A marker type that indicates the symmetries of a `PointSpreadFunction` which may lead to optimized methods.

Subtypes thus far include [`ZAxisRadialSymmetry`](@ref) and [`NoSymmetry`](@ref).
"""
abstract type PointSpreadFunctionSymmetry end
Broadcast.broadcastable(s::PointSpreadFunctionSymmetry) = Ref(s)

"""
    ZAxisRadialSymmetry <: PointSpreadFunctionSymmetry
``z`` axis radial symmetry of a `PointSpreadFunction` indicates that the PSF is symmetric in the radially around the
z-axis.
"""
struct ZAxisRadialSymmetry <: PointSpreadFunctionSymmetry end

"""
    NoSymmetry <: PointSpreadFunctionSymmetry
`NoSymmetry` marks a `PointSpreadFunction` that is not symmetric in any way. You need to compute every ``x``, ``y``,
``z`` coordinate separately. 
"""
struct NoSymmetry <: PointSpreadFunctionSymmetry end

"""
    symmtery(psf::PointSpreadFunction)
Marks the symmetries of a `PointSpreadFunction`.
"""
@interface symmetry(::PointSpreadFunction) = NoSymmetry()

"""
    intensity(psf::PointSpreadFunction, x::Length, y::Length)
The intensity of a `PSF` at a given location.
"""
@interface response(psf::PointSpreadFunction, args...) = response(symmetry(psf), psf, args...)
@inline response(::ZAxisRadialSymmetry, psf::PointSpreadFunction, x::Length, y::Length) = intensity(psf, hypot(x, y))
@inline response(::ZAxisRadialSymmetry, psf::PointSpreadFunction, x::Length, y::Length, z::Length) = intensity(psf, hypot(x, y), z)
@inline response(::NoSymmetry, psf::PointSpreadFunction, x::Length, y::Length) = intensity(psf, x, y)
@inline response(::NoSymmetry, psf::PointSpreadFunction, x::Length, y::Length, z::Length) = intensity(psf, x, y, z)

"""
    PSFModel <: PointSpreadFunction 
`PointSpreadFunction` subtype for PSF models. A `PSF` model is a `PointSpreadFunction` that has parameters accessible
through [`params`](@ref) and can be fitted to data.
"""
abstract type PSFModel{N} <: PointSpreadFunction{N} end

include("methods.jl")

# Augmentations
include("./rotated-psf.jl")
include("./scaled-psf.jl")

include("./psf-array.jl")

# Models
include("./models/airy-disc.jl")
include("./models/gaussian.jl")

include("./models/gibson-lanni.jl")
include("./models/born-wolf.jl")


include("./estimation.jl")

export response, psf
export BornWolf, GibsonLanni, PSFArray

1	using InterfaceFunctions
2	using Roots
3	using Base: Fix
4	using TransferFunctions.Apodization
5
6	"""
7	PointSpreadFunction{N} <: LinearShiftInvariantTransferFunction{N}
8	A point spread function is a description of a transfer functions specifying the intensity transfer of a single point
9	source in the object plane into a region of the image plane.
10
11	# Implementation
12	To create a new Point spread function (PSF) `A <: PointSpreadFunction`, you must define the __intensity__ at a given
13	[length](@extref Unitful `Length`) coordinate `intensity(psf::A, x::Length, y::Length)`.
14	"""
15	abstract type PointSpreadFunction{N} <: LinearShiftInvariantTransferFunction{N} end
UNCOV 16	Broadcast.broadcastable(tf::PointSpreadFunction) = Ref(tf)	×
17
18	"""
19	PointSpreadFunctionSymmetry
20	A marker type that indicates the symmetries of a `PointSpreadFunction` which may lead to optimized methods.
21
22	Subtypes thus far include [`ZAxisRadialSymmetry`](@ref) and [`NoSymmetry`](@ref).
23	"""
24	abstract type PointSpreadFunctionSymmetry end
NEW 25	Broadcast.broadcastable(s::PointSpreadFunctionSymmetry) = Ref(s)	×
26
27	"""
28	ZAxisRadialSymmetry <: PointSpreadFunctionSymmetry
29	``z`` axis radial symmetry of a `PointSpreadFunction` indicates that the PSF is symmetric in the radially around the
30	z-axis.
31	"""
32	struct ZAxisRadialSymmetry <: PointSpreadFunctionSymmetry end
33
34	"""
35	NoSymmetry <: PointSpreadFunctionSymmetry
36	`NoSymmetry` marks a `PointSpreadFunction` that is not symmetric in any way. You need to compute every ``x``, ``y``,
37	``z`` coordinate separately.
38	"""
39	struct NoSymmetry <: PointSpreadFunctionSymmetry end
40
41	"""
42	symmtery(psf::PointSpreadFunction)
43	Marks the symmetries of a `PointSpreadFunction`.
44	"""
NEW 45	@interface symmetry(::PointSpreadFunction) = NoSymmetry()	×
46
47	"""
48	intensity(psf::PointSpreadFunction, x::Length, y::Length)
49	The intensity of a `PSF` at a given location.
50	"""
NEW 51	@interface response(psf::PointSpreadFunction, args...) = response(symmetry(psf), psf, args...)	×
NEW 52	@inline response(::ZAxisRadialSymmetry, psf::PointSpreadFunction, x::Length, y::Length) = intensity(psf, hypot(x, y))	×
NEW 53	@inline response(::ZAxisRadialSymmetry, psf::PointSpreadFunction, x::Length, y::Length, z::Length) = intensity(psf, hypot(x, y), z)	×
NEW 54	@inline response(::NoSymmetry, psf::PointSpreadFunction, x::Length, y::Length) = intensity(psf, x, y)	×
NEW 55	@inline response(::NoSymmetry, psf::PointSpreadFunction, x::Length, y::Length, z::Length) = intensity(psf, x, y, z)	×
56
57	"""
58	PSFModel <: PointSpreadFunction
59	`PointSpreadFunction` subtype for PSF models. A `PSF` model is a `PointSpreadFunction` that has parameters accessible
60	through [`params`](@ref) and can be fitted to data.
61	"""
62	abstract type PSFModel{N} <: PointSpreadFunction{N} end
63
64	include("methods.jl")
65
66	# Augmentations
67	include("./rotated-psf.jl")
68	include("./scaled-psf.jl")
69
70	include("./psf-array.jl")
71
72	# Models
73	include("./models/airy-disc.jl")
74	include("./models/gaussian.jl")
75
76	include("./models/gibson-lanni.jl")
77	include("./models/born-wolf.jl")
78
79
80	include("./estimation.jl")
81
82	export response, psf
83	export BornWolf, GibsonLanni, PSFArray

kunzaatko / TransferFunctions.jl / 17100492288

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous