Using AffineMap instead of 4x4 array now.

- fixed some typos
- bidsdata.jl now contains what could be the beginnings of a BIDS based
datadeps
- traits contains non BIDS entities properties

Manifest.toml

@@ -44,6 +44,12 @@ git-tree-sha1 = "a2a6a5fea4d6f730ec4c18a76d27ec10e8ec1c50"
 uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 version = "1.0.0"
 
+[[CoordinateTransformations]]
+deps = ["Compat", "Rotations", "StaticArrays"]
+git-tree-sha1 = "47f05d0b7f4999609f92e657147df000818c1f24"
+uuid = "150eb455-5306-5404-9cee-2592286d6298"
+version = "0.5.0"
+
 [[DataAPI]]
 git-tree-sha1 = "674b67f344687a88310213ddfa8a2b3c76cc4252"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
@@ -233,6 +239,12 @@ git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
 version = "0.2.0"
 
+[[Rotations]]
+deps = ["LinearAlgebra", "StaticArrays", "Statistics"]
+git-tree-sha1 = "cb70e13ed3d4b37caf93960676ef415da5979a93"
+uuid = "6038ab10-8711-5258-84ad-4b1120ba62dc"
+version = "0.12.1"
+
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
@@ -268,6 +280,12 @@ git-tree-sha1 = "268052ee908b2c086cc0011f528694f02f3e2408"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
 version = "0.9.0"
 
+[[StaticArrays]]
+deps = ["InteractiveUtils", "LinearAlgebra", "Random", "Statistics", "Test"]
+git-tree-sha1 = "3841b39ed5f047db1162627bf5f80a9cd3e39ae2"
+uuid = "90137ffa-7385-5640-81b9-e52037218182"
+version = "0.10.3"
+
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

Project.toml

@@ -4,8 +4,11 @@ authors = ["Tokazama <zchristensen7@gmail.com>"]
 version = "0.1.0"
 
 [deps]
+CoordinateTransformations = "150eb455-5306-5404-9cee-2592286d6298"
 ImageAxes = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac"
 ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
 ImageMetadata = "bc367c6b-8a6b-528e-b4bd-a4b897500b49"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"

src/NeuroCore.jl

@@ -1,19 +1,29 @@
 module NeuroCore
 
 using ImageCore, ImageAxes, Unitful, ImageMetadata, Markdown
+using StaticArrays, Rotations, CoordinateTransformations
 
 export NeuroMetadata,
        NeuroMetaArray,
        BIDSMetadata,
-       neurohelp
-       #=
+       # methods
        calmax,
-       calmax!,
        calmin,
-       calmin!,
-       magic_bytes,
-       magic_bytes!
-       =#
+       description,
+       freqdim,
+       is_anatomical,
+       is_functional,
+       is_electrophysiology,
+       neurohelp,
+       phasedim,
+       stream_offset,
+       slicedim,
+       slice_end,
+       slice_start,
+       spatial_offset,
+       spatial_units,
+       time_units
+
 
 const OneF64Sec = 1.0u"s"
 const F64Sec = typeof(OneF64Sec)
@@ -29,33 +39,25 @@ const IntDeg = typeof(OneIntDeg)
 
 const CoordinateList = Dict{Symbol,NTuple{3,Float64}}
 
+const NeuroAffine{R} = AffineMap{R,SArray{Tuple{3},Float64,1,3}}
+
 include("enums.jl")
 include("properties.jl")
 include("coordinates.jl")
 include("bids_entities.jl")
-include("modalities.jl")
-include("modality_agnostic.jl")
-include("event_table.jl")
+include("bidsdata.jl")
 include("getproperty.jl")
-include("bidsmetadata.jl")
 include("metadata.jl")
 include("array.jl")
+include("traits.jl")
 
 """
-    neurohelp(func[; extended = false])
-
-For help on a specific function's arguments, type `help_arguments(function_name)`.
+    neurohelp(func[;])
 
-For help on a specific function's attributes, type `help_attributes(plot_Type)`.
-
-Use the optional `extended = true` keyword argument to see more details.
 """
-neurohelp(func; kw_args...) = neurohelp(stdout, func; kw_args...) #defaults to STDOUT
-
-function neurohelp(io::IO, input::Symbol; extended = false)
-    return neurohelp(io, getproperty(NeuroCore, input); extended=extended)
-end
-function neurohelp(io::IO, input; extended = false)
+neurohelp(func) = neurohelp(stdout, func)
+neurohelp(io::IO, input::Symbol) = neurohelp(io, getproperty(NeuroCore, input))
+function neurohelp(io::IO, input)
     buffer = IOBuffer()
     println(buffer, Base.Docs.doc(input))
     Markdown.parse(String(take!(buffer)))

src/array.jl

@@ -7,102 +7,3 @@ NeuroMetaArray(x::AbstractArray, p::AbstractDict) = NeuroMetaArray(x, NeuroMetad
 NeuroMetaArray(x; kwargs...) = NeuroMetaArray(x, NeuroMetadata(; kwargs...))
 
 Base.getproperty(x::NeuroMetaArray, s::Symbol) = getproperty(properties(x), s)
-
-"""
-    spatial_offset(img)
-
-Provides the offset of each dimension (i.e., where each spatial axis starts).
-"""
-spatial_offset(x) = first.(coords_indices(x))
-
-
-"""
-    spatial_units(img)
-
-Returns the units (i.e. Unitful.unit) that each spatial axis is measured in. If not
-available `nothing` is returned for each spatial axis.
-"""
-spatial_units(x) = unit.(eltype.(spatial_indices(x)))
-
-"""
-    freqdim(x) -> Int
-
-Which spatial dimension (1, 2, or 3) corresponds to phase acquisition. If not
-applicable to scan type defaults to `0`.
-"""
-freqdim(x) = getter(x, :freqdim, Int, 0)
-freqdim!(x, val) = setter!(x, :freqdim, Int, val)
-
-"""
-    slicedim(x) -> Int
-
-Which dimension slices where acquired at throughout MRI acquisition.
-"""
-slicedim(x) = getter(x, :slicedim, Int, i -> 0)
-slicedim!(x, val) = setter!(x, :slicedim, Int, val)
-
-"""
-    phasedim(x) -> Int
-
-Which spatial dimension (1, 2, or 3) corresponds to phase acquisition.
-"""
-phasedim(x) = getter(x, :phasedim, Int, i -> 0)
-phasedim!(x, val) = setter!(x, :phasedim, Int, val)
-
-"""
-    slice_start(x) -> Int
-
-Which slice corresponds to the first slice acquired during MRI acquisition
-(i.e. not padded slices). Defaults to `1`.
-"""
-slice_start(x) = getter(x, :slice_start, Int, i -> 1)
-slice_start!(x, val) = setter!(x, :slice_start, Int, val)
-
-"""
-    slice_end(x) -> Int
-
-Which slice corresponds to the last slice acquired during MRI acquisition
-(i.e. not padded slices).
-"""
-slice_end(x) = getter(x, :slice_end, Int, i -> 1)
-slice_end!(x, val) = setter!(x, :slice_end, Int, val)
-
-"""
-    time_units(img)
-
-Returns the units (i.e. Unitful.unit) the time axis is measured in. If not available
-`nothing` is returned.
-"""
-time_units(x) = unit(eltype(timeaxis(x)))
-
-"""
-    start_time(x) -> F64Sec
-
-Returns start time in seconds in relation to the start of acquisition of the first
-data sample in the corresponding neural dataset (negative values are allowed).
-"""
-start_time(x) = first(timeaxis(x))
-
-"""
-    calmax(x)
-
-Specifies maximum element for display puproses. Defaults to the maximum of `x`.
-"""
-calmax(x::Any) = getter(x, :calmax, i -> _caltype(x), i -> _calmax(i))
-calmax!(x::Any, val::Any) = setter!(x, :calmax, val, i -> _caltype(i))
-
-"""
-    calmin(x)
-
-Specifies minimum element for display puproses. Defaults to the minimum of `x`.
-"""
-calmin(x) = getter(x, :calmin, i -> _caltype(i), i -> _calmin(i))
-calmin!(x, val) = setter!(x, :calmin, val, i -> _caltype(i))
-
-###
-_caltype(x::AbstractArray{T}) where {T} = T
-_caltype(x::Any) = Float64
-_calmax(x::AbstractArray) = maximum(x)
-_calmax(x::Any) = one(Float64)
-_calmin(x::AbstractArray) = minimum(x)
-_calmin(x::Any) = one(Float64)

src/bids_entities.jl

@@ -2,7 +2,7 @@
     AcquisitionDuration(x) -> F64Sec
 
 Duration (in seconds) of volume acquisition. This field is REQUIRED for
-sequences that are described with the VolumeTimingfield and that not have the
+sequences that are described with the VolumeTimingfield and that do not have the
 SliceTiming field set to allowed for accurate calculation of "acquisition time".
 This field is mutually exclusive with RepetitionTime.
 """

src/event_table.jl → src/bidsdata.jl

@@ -1,3 +1,37 @@
+"""
+    BIDSMetadata
+
+Metadata for describing a BIDS dataset.
+
+
+* `name::String`: The name of the dataset
+* `bids_version::String`: The version of the BIDS standard that was used.
+* `license::Union{String,Nothing}`: Returns the license that a given dataset is
+  distributed under? The use of license name abbreviations is suggested for
+  specifying a license (e.g., PD, PDDL, CCO).
+* `authors::Union{Vector{String},Nothing}`: list of individuals who contributed
+  to the creation/curation of the dataset.
+* `acknowledgedgements::Union{String,Nothing}`: Returns the text acknowledging
+  contributions of individuals or institutions beyond those listed in Authors or Funding.
+* `how_to_acknowledge::Union{String,Nothing}`: Instructions how researchers using
+  this dataset should acknowledge the original authors. This field can also be used
+  to define a publication that should be cited in publications that use the dataset.
+* `funding::Union{Vector{String},Nothing}`: List of sources of funding (grant numbers)
+* `references::Union{Vector{String},Nothing}`: List of references to publication
+  that contain information on the dataset, or links.
+* `doi::Union{String,Nothing}`: Returns the Document Object Identifier of the dataset (not the corresponding paper)
+"""
+Base.@kwdef struct BIDSMetadata
+    name::String
+    bids_version::String
+    license::Union{String,Nothing}=nothing
+    authors::Union{Vector{String},Nothing}=nothing
+    acknowledgedgements::Union{String,Nothing}=nothing
+    how_to_acknowledge::Union{String,Nothing}=nothing
+    funding::Union{Vector{String},Nothing}=nothing
+    references::Union{Vector{String},Nothing}=nothing
+    doi::Union{String,Nothing}=nothing
+end
 
 # TODO FileIO integration
 # TODO HED format should probably involve its own package