From 33f29ae104a3bae066347fe5c80de7e90112e403 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Tue, 20 Feb 2024 20:08:33 +0000 Subject: [PATCH] build based on 6a52f72 --- .documenter-siteinfo.json | 2 +- function_list/index.html | 2 +- geo/index.html | 20 ++++++++--------- high_level/index.html | 46 +++++++++++++++++++-------------------- index.html | 2 +- low_level/index.html | 30 ++++++++++++------------- plotting/index.html | 6 ++--- 7 files changed, 54 insertions(+), 54 deletions(-) diff --git a/.documenter-siteinfo.json b/.documenter-siteinfo.json index aff6301..c9c95c2 100644 --- a/.documenter-siteinfo.json +++ b/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-02-20T20:03:55","documenter_version":"1.2.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-02-20T20:08:25","documenter_version":"1.2.1"}} \ No newline at end of file diff --git a/function_list/index.html b/function_list/index.html index 2b66f8e..22ead83 100644 --- a/function_list/index.html +++ b/function_list/index.html @@ -1,2 +1,2 @@ -Alphabetical function list · Minc2.jl
GitHub

Index

+Alphabetical function list · Minc2.jl
GitHub

Index

diff --git a/geo/index.html b/geo/index.html index 2910a8a..8c203ce 100644 --- a/geo/index.html +++ b/geo/index.html @@ -1,26 +1,26 @@ -Gemetric transformation functions · Minc2.jl
GitHub

Functions for gemetric transformations

Base.length — Method
Base.length(tr::AnyTransform)

Length of concatenated transform

source
Base.show — Method
Base.show(io::IO, z::GridTransform{T,F,I})

Print summary information about grid transform

source
Base.show — Method
Base.show(io::IO, z::InverseGridTransform{T,F,I})

Print summary information about inverse grid transform

source
Minc2.array — Method
array(grid::GridTransform)

Extract underlying plain array

  • grid - GridTransform
source
Minc2.array — Method
array(grid::InverseGridTransform)

Extract underlying plain array

  • grid - InverseGridTransform
source
Minc2.decompose — Method

decompose(rot, shift)

Decompose affine transform specified as rotation matrix ans shift vector into three components start, step, direction cosines

  • rot - rotation matrix (3x3)
  • shift - shift vector (3)
source
Minc2.decompose — Method
decompose(tfm::Matrix{T})

Decompose affine transform into three components start, step, direction cosines

source
Minc2.decompose — Method
decompose(tfm::AffineTransform{T})

Decompose affine transform into three components start, step, direction cosines

  • tfm - affine transform
source
Minc2.interpolate_field — Method
interpolate_field(
+Gemetric transformation functions · Minc2.jl
GitHub
Functions for gemetric transformations
Base.length — Method
Base.length(tr::AnyTransform)
Length of concatenated transform
source
Base.show — Method
Base.show(io::IO, z::GridTransform{T,F,I})
Print summary information about grid transform
source
Base.show — Method
Base.show(io::IO, z::InverseGridTransform{T,F,I})
Print summary information about inverse grid transform
source
Minc2.array — Method
array(grid::GridTransform)
Extract underlying plain array
  • grid - GridTransform
source
Minc2.array — Method
array(grid::InverseGridTransform)
Extract underlying plain array
  • grid - InverseGridTransform
source
Minc2.decompose — Method
decompose(rot, shift)
Decompose affine transform specified as rotation matrix ans shift vector into three components start, step, direction cosines
  • rot - rotation matrix (3x3)
  • shift - shift vector (3)
source
Minc2.decompose — Method
decompose(tfm::Matrix{T})
Decompose affine transform into three components start, step, direction cosines
source
Minc2.decompose — Method
decompose(tfm::AffineTransform{T})
Decompose affine transform into three components start, step, direction cosines
  • tfm - affine transform
source
Minc2.interpolate_field — Method
interpolate_field(
         v2w::AffineTransform{T},
         itp_vector_field::I, 
-        p::SVector{3,T} )::SVector{3,T}
Internal support function
  • v2w - voxel to world affine transform
  • itp_vector_field - vector field
  • p - point to transform
source
Minc2.inv — Method
inv(::IdentityTransform)::IdentityTransform
Invert IdentityTransform transform, does nothing
source
Minc2.inv — Method
inv(t::AffineTransform{T})::AffineTransform{T}
Invert AffineTransform transform
  • t - AffineTransform
source
Minc2.inv — Method
inv(t::GridTransform{T,F,VF})::InverseGridTransform{T,F,VF}
Invert GridTransform transform
  • t - GridTransform
source
Minc2.inv — Method
inv(t::InverseGridTransform{T,F,VF})::GridTransform{T,F,VF}
Invert InverseGridTransform transform
  • t - InverseGridTransform
source
Minc2.inv — Method
inv(t::Vector{T})::Vector{AnyTransform}
Invert concatenated transform
  • t - concatenated transform
source
Minc2.transform_point — Method
transform_point(
+        p::SVector{3,T} )::SVector{3,T}
Internal support function
  • v2w - voxel to world affine transform
  • itp_vector_field - vector field
  • p - point to transform
source
Minc2.inv — Method
inv(::IdentityTransform)::IdentityTransform
Invert IdentityTransform transform, does nothing
source
Minc2.inv — Method
inv(t::AffineTransform{T})::AffineTransform{T}
Invert AffineTransform transform
  • t - AffineTransform
source
Minc2.inv — Method
inv(t::GridTransform{T,F,VF})::InverseGridTransform{T,F,VF}
Invert GridTransform transform
  • t - GridTransform
source
Minc2.inv — Method
inv(t::InverseGridTransform{T,F,VF})::GridTransform{T,F,VF}
Invert InverseGridTransform transform
  • t - InverseGridTransform
source
Minc2.inv — Method
inv(t::Vector{T})::Vector{AnyTransform}
Invert concatenated transform
  • t - concatenated transform
source
Minc2.transform_point — Method
transform_point(
         tfm::GridTransform{T,F}, p::SVector{3,T};
-        _whatever...)::SVector{3,T} where {T,F}
Apply forward grid transform to a point
  • tfm - grid transform
  • p - point to transform
source
Minc2.transform_point — Method
transform_point(
+        _whatever...)::SVector{3,T} where {T,F}
Apply forward grid transform to a point
  • tfm - grid transform
  • p - point to transform
source
Minc2.transform_point — Method
transform_point(
     tfm::AffineTransform{T}, 
     p::CartesianIndex{3};
-    _whatever...)::SVector{3,T}
Apply inverse grid transform reimplements algorithm from MNIformats/gridtransforms.c:gridinversetransform_point
  • tfm - affine transform
  • p - point to transform
source
Minc2.transform_point — Method
transform_point(
+    _whatever...)::SVector{3,T}
Apply inverse grid transform reimplements algorithm from MNIformats/gridtransforms.c:gridinversetransform_point
  • tfm - affine transform
  • p - point to transform
source
Minc2.transform_point — Method
transform_point(
     tfm::AffineTransform{T}, 
     p::CartesianIndex{3};
-    _whatever...)::SVector{3,T}
Apply affine transform to CartesianIndices
  • tfm - affine transform
  • p - point to transform
source
Minc2.transform_point — Method
transform_point(
+    _whatever...)::SVector{3,T}
Apply affine transform to CartesianIndices
  • tfm - affine transform
  • p - point to transform
source
Minc2.transform_point — Method
transform_point(
         tfm::AffineTransform{T}, 
         p::SVector{3,T};
-        _whatever...)::SVector{3,T}
Apply affine transform to a point
  • tfm - affine transform
  • p - point to transform
source
Minc2.transform_point — Method
transform_point(tfm::IdentityTransform, 
+        _whatever...)::SVector{3,T}
Apply affine transform to a point
  • tfm - affine transform
  • p - point to transform
source
Minc2.transform_point — Method
transform_point(tfm::IdentityTransform, 
     p::SVector{3,T};
-    _whatever...)
  • tfm - IdentityTransform
  • p - point to transform
Apply identity transform to a point (returns same point)
source
Minc2.transform_point — Method
transform_point(
+    _whatever...)
  • tfm - IdentityTransform
  • p - point to transform
Apply identity transform to a point (returns same point)
source
Minc2.transform_point — Method
transform_point(
     tfm::Vector{XFM},
     p::SVector{3,T};
     max_iter::Int=10,
-    ftol::Float64=1.0/80)::SVector{3,T}
Apply concatenated transform to a point
  • tfm - concatenated transform
  • p - point to transform
  • max_iter - maximum number of iterations for inverse transform
  • ftol - tolerance for inverse transform
source
Minc2.voxel_to_world — Method
voxel_to_world(grid::GridTransform)
Extract voxel to world affine transform from a GridTransform
  • grid - GridTransform
source
Minc2.voxel_to_world — Method
voxel_to_world(grid::InverseGridTransform)
Extract voxel to world affine transform from a InverseGridTransform
  • grid - InverseGridTransform
source
Minc2.world_to_voxel — Method
world_to_voxel(grid::GridTransform)
Extract world to voxel affine transform from a GridTransform
  • grid - GridTransform
source
Minc2.world_to_voxel — Method
world_to_voxel(grid::InverseGridTransform)
Extract world to voxel affine transform from a InverseGridTransform
  • grid - InverseGridTransform
source
Minc2.AffineTransform — Method
AffineTransform(rot, shift) Create affine transform from rotation and shift
  • rot - rotation matrix-like (3x3)
  • shift - shift vector-like (3)
source
Minc2.GridTransform — Method
GridTransform(
+    ftol::Float64=1.0/80)::SVector{3,T}
Apply concatenated transform to a point
  • tfm - concatenated transform
  • p - point to transform
  • max_iter - maximum number of iterations for inverse transform
  • ftol - tolerance for inverse transform
source
Minc2.voxel_to_world — Method
voxel_to_world(grid::GridTransform)
Extract voxel to world affine transform from a GridTransform
  • grid - GridTransform
source
Minc2.voxel_to_world — Method
voxel_to_world(grid::InverseGridTransform)
Extract voxel to world affine transform from a InverseGridTransform
  • grid - InverseGridTransform
source
Minc2.world_to_voxel — Method
world_to_voxel(grid::GridTransform)
Extract world to voxel affine transform from a GridTransform
  • grid - GridTransform
source
Minc2.world_to_voxel — Method
world_to_voxel(grid::InverseGridTransform)
Extract world to voxel affine transform from a InverseGridTransform
  • grid - InverseGridTransform
source
Minc2.AffineTransform — Method
AffineTransform(rot, shift) Create affine transform from rotation and shift
  • rot - rotation matrix-like (3x3)
  • shift - shift vector-like (3)
source
Minc2.GridTransform — Method
GridTransform(
     voxel_to_world::AffineTransform{T},
-    vector_field::Array{F, 4})
Construct GridTransform from voxel to world transform and a vector field
  • voxel_to_world - voxel to world affine transform
  • vector_field - vector field
source
Minc2.GridTransform — Method
GridTransform(::Type{T}=Float64,::Type{F}=Float64)
Construct empty GridTransform, which should generate identity transform
source
Minc2.InverseGridTransform — Method
InverseGridTransform(
+    vector_field::Array{F, 4})
Construct GridTransform from voxel to world transform and a vector field
  • voxel_to_world - voxel to world affine transform
  • vector_field - vector field
source
Minc2.GridTransform — Method
GridTransform(::Type{T}=Float64,::Type{F}=Float64)
Construct empty GridTransform, which should generate identity transform
source
Minc2.InverseGridTransform — Method
InverseGridTransform(
     voxel_to_world::AffineTransform{T},
-    vector_field::Array{F, 4})
Construct InverseGridTransform from voxel to world transform     and a vector field
  • voxel_to_world - voxel to world affine transform
  • vector_field - vector field
source

+    vector_field::Array{F, 4})

Construct InverseGridTransform from voxel to world transform and a vector field

  • voxel_to_world - voxel to world affine transform
  • vector_field - vector field
source
diff --git a/high_level/index.html b/high_level/index.html index 9f6dbc6..c3f5341 100644 --- a/high_level/index.html +++ b/high_level/index.html @@ -1,25 +1,25 @@ -High level functions · Minc2.jl
GitHub

High level functions for operations on MRI scans

3D Volume information

Minc2.voxel_to_world — Function
voxel_to_world(grid::GridTransform)

Extract voxel to world affine transform from a GridTransform

  • grid - GridTransform
source
voxel_to_world(grid::InverseGridTransform)

Extract voxel to world affine transform from a InverseGridTransform

  • grid - InverseGridTransform
source
voxel_to_world(hdr::MincHeader)::AffineTransform{Float64}

Give AffineTransform for world to voxel transformation based on header

source
voxel_to_world(h::VolumeHandle,ijk::Vector{Float64})::Vector{Float64}

Convert contignuous 0-based voxel indexes (I,J,K) to world coordinates (X,Y,Z) 0-based

source
voxel_to_world(vol::Volume3D)

Extract voxel to world affine transform from a Volume3D

source
Minc2.world_to_voxel — Function
world_to_voxel(grid::GridTransform)

Extract world to voxel affine transform from a GridTransform

  • grid - GridTransform
source
world_to_voxel(grid::InverseGridTransform)

Extract world to voxel affine transform from a InverseGridTransform

  • grid - InverseGridTransform
source
world_to_voxel(h::VolumeHandle, xyz::Vector{Float64})::Vector{Float64}

Convert world coordinates (X,Y,Z) to contignuous voxel indexes (I,J,K) 0-based

source
world_to_voxel(hdr::MincHeader)::AffineTransform{Float64}

Give AffineTransform for voxel to world transformation

source
world_to_voxel(vol::Volume3D)

Extract world to voxel affine transform from a Volume3D

source
Minc2.array — Function
array(grid::GridTransform)

Extract underlying plain array

  • grid - GridTransform
source
array(grid::InverseGridTransform)

Extract underlying plain array

  • grid - InverseGridTransform
source
array(vol::Volume3D)

Extract underlying plain array

source

File IO functions

Loading 3D volumes

Minc2.read_volume — Function
read_volume(fn::String; store::Type{T}=Float64)::Volume3D{T}

Read Volume3D from minc file

  • fn - filename
  • store - underlying array type
source
Minc2.read_nifti_volume — Function
read_nifti_volume(fn::AbstractString; store::Type{T}=Float64)::Volume3D{T}

Read Volume3D from .nii or .nii.gz file

source

Saving 3D volumes

Minc2.save_volume — Function
save_volume(fn::AbstractString, 
+High level functions · Minc2.jl
GitHub
High level functions for operations on MRI scans
3D Volume information
Minc2.voxel_to_world — Function
voxel_to_world(grid::GridTransform)
Extract voxel to world affine transform from a GridTransform
  • grid - GridTransform
source
voxel_to_world(grid::InverseGridTransform)
Extract voxel to world affine transform from a InverseGridTransform
  • grid - InverseGridTransform
source
voxel_to_world(hdr::MincHeader)::AffineTransform{Float64}
Give AffineTransform for world to voxel transformation based on header
source
voxel_to_world(h::VolumeHandle,ijk::Vector{Float64})::Vector{Float64}
Convert contignuous 0-based voxel indexes (I,J,K) to world coordinates (X,Y,Z) 0-based
source
voxel_to_world(vol::Volume3D)
Extract voxel to world affine transform from a Volume3D
source
Minc2.world_to_voxel — Function
world_to_voxel(grid::GridTransform)
Extract world to voxel affine transform from a GridTransform
  • grid - GridTransform
source
world_to_voxel(grid::InverseGridTransform)
Extract world to voxel affine transform from a InverseGridTransform
  • grid - InverseGridTransform
source
world_to_voxel(h::VolumeHandle, xyz::Vector{Float64})::Vector{Float64}
Convert world coordinates (X,Y,Z) to contignuous voxel indexes (I,J,K) 0-based
source
world_to_voxel(hdr::MincHeader)::AffineTransform{Float64}
Give AffineTransform for voxel to world transformation
source
world_to_voxel(vol::Volume3D)
Extract world to voxel affine transform from a Volume3D
source
Minc2.array — Function
array(grid::GridTransform)
Extract underlying plain array
  • grid - GridTransform
source
array(grid::InverseGridTransform)
Extract underlying plain array
  • grid - InverseGridTransform
source
array(vol::Volume3D)
Extract underlying plain array
source
File IO functions
Loading 3D volumes
Minc2.read_volume — Function
read_volume(fn::String; store::Type{T}=Float64)::Volume3D{T}
Read Volume3D from minc file
  • fn - filename
  • store - underlying array type
source
Minc2.read_nifti_volume — Function
read_nifti_volume(fn::AbstractString; store::Type{T}=Float64)::Volume3D{T}
Read Volume3D from .nii or .nii.gz file
source
Saving 3D volumes
Minc2.save_volume — Function
save_volume(fn::AbstractString, 
     vol::Volume3D{T,N}; 
     store::Type{S}=Float32,
-    history=nothing)
Save Volume3D to minc file
  • fn - filename
  • vol - Volume3D to save
  • store - underlying MINC data type, to be used for storage
source
Minc2.save_nifti_volume — Function
save_nifti_volume(fn::AbstractString, vol::Volume3D{T}; 
-    store::Type{S}=Float32, history=nothing)
Save Volume3D into .nii or .nii.gz file
source
Loading transformations
Minc2.read_itk_nifti_transform — Function
read_itk_nifti_transform(fn::AbstractString;
-    store::Type{T}=Float32)::Minc2.GridTransform{Float64,T}
Read ANTs style warp transform
source
Minc2.read_ants_transform — Function
read_ants_transform(fn::AbstractString; store::Type{T}=Float32)::Minc2.AnyTransform
Read .txt and .nii(.nii.gz) transforms produces by ANTs
source
Saving transformations
Minc2.save_transforms — Function
save_transforms(fname::String, 
+    history=nothing)
Save Volume3D to minc file
  • fn - filename
  • vol - Volume3D to save
  • store - underlying MINC data type, to be used for storage
source
Minc2.save_nifti_volume — Function
save_nifti_volume(fn::AbstractString, vol::Volume3D{T}; 
+    store::Type{S}=Float32, history=nothing)
Save Volume3D into .nii or .nii.gz file
source
Loading transformations
Minc2.read_itk_nifti_transform — Function
read_itk_nifti_transform(fn::AbstractString;
+    store::Type{T}=Float32)::Minc2.GridTransform{Float64,T}
Read ANTs style warp transform
source
Minc2.read_ants_transform — Function
read_ants_transform(fn::AbstractString; store::Type{T}=Float32)::Minc2.AnyTransform
Read .txt and .nii(.nii.gz) transforms produces by ANTs
source
Saving transformations
Minc2.save_transforms — Function
save_transforms(fname::String, 
     xfm::Union{Vector{XFM}, XFM};
-    grid_store::Type{T}=Float32 ) where {T, XFM<:AnyTransform}
Save transformations into .xfm file, 
Arguments
  • fname: output file name
  • xfm: vector of transformations to save, or a single transformation
  • grid_store: type of storage for grid files (default: Float32)
source
Minc2.save_itk_nifti_transform — Function
save_itk_nifti_transform(fn::AbstractString,
-    xfm::Minc2.GridTransform{Float64,T}; store::Type{S}=Float32)
Write ANTs style warp transform
source
3D Volume creation
Minc2.Volume3D — Type
Volume3D{T,N}
An abstract 3D volume, could be vector field or volume with time dimension
source
Minc2.empty_volume_like — Function
empty_volume_like(
+    grid_store::Type{T}=Float32 ) where {T, XFM<:AnyTransform}
Save transformations into .xfm file, 
Arguments
  • fname: output file name
  • xfm: vector of transformations to save, or a single transformation
  • grid_store: type of storage for grid files (default: Float32)
source
Minc2.save_itk_nifti_transform — Function
save_itk_nifti_transform(fn::AbstractString,
+    xfm::Minc2.GridTransform{Float64,T}; store::Type{S}=Float32)
Write ANTs style warp transform
source
3D Volume creation
Minc2.Volume3D — Type
Volume3D{T,N}
An abstract 3D volume, could be vector field or volume with time dimension
source
Minc2.empty_volume_like — Function
empty_volume_like(
         fn::String; 
-        store::Type{T}=Float64, history=nothing)::Volume3D{T}
Create an empty Volume3D
  • fn - filename of a minc file that is used for sampling information
  • store - underlying array type
source
empty_volume_like(
+        store::Type{T}=Float64, history=nothing)::Volume3D{T}
Create an empty Volume3D
  • fn - filename of a minc file that is used for sampling information
  • store - underlying array type
source
empty_volume_like(
     vol::Volume3D{T1,N}; 
     store::Type{T}=Float64, 
-    history=nothing)
Create an empty Volume3D
  • vol - Volume3D that is used for sampling information
  • store - underlying array type
  • history - minc history
source
Minc2.full_volume_like — Function
full_volume_like(
+    history=nothing)
Create an empty Volume3D
  • vol - Volume3D that is used for sampling information
  • store - underlying array type
  • history - minc history
source
Minc2.full_volume_like — Function
full_volume_like(
         fn::String,
         fill::T=zero(T); 
-        store::Type{T}=Float64, history=nothing)::Volume3D{T}
Create an empty Volume3D
  • fn - filename of a minc file that is used for sampling information
  • store - underlying array type
source
full_volume_like(
+        store::Type{T}=Float64, history=nothing)::Volume3D{T}
Create an empty Volume3D
  • fn - filename of a minc file that is used for sampling information
  • store - underlying array type
source
full_volume_like(
     vol::Volume3D{T1,N}; 
     store::Type{T}=Float64, 
-    history=nothing)
Create an empty Volume3D
  • vol - Volume3D that is used for sampling information
  • store - underlying array type
  • history - minc history
source
3D Volume manipulations
Minc2.resample_volume — Function
resample_volume(
+    history=nothing)
Create an empty Volume3D
  • vol - Volume3D that is used for sampling information
  • store - underlying array type
  • history - minc history
source
3D Volume manipulations
Minc2.resample_volume — Function
resample_volume(
     in_vol::Volume3D{T,3};
     like::Union{Volume3D{O,3},Nothing}=nothing,
     tfm::Union{Vector{XFM},XFM,Nothing}=nothing, 
@@ -28,7 +28,7 @@
     fill=0.0,
     order=1,
     ftol=1.0/80,
-    max_iter=10)::Volume3D
Resample Volume3D using transformation 
  • in_vol - input Volume3D
  • like - Volume3D that is used for sampling information
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • tfm  - transformation to apply (i.e from output to input) (instead of itfm)
  • interp - interpolation method
  • fill - fill value
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Equivalent to mincresample minc command
source
Minc2.resample_volume! — Function
resample_volume!(in_vol::AbstractArray{T,3}, 
+    max_iter=10)::Volume3D
Resample Volume3D using transformation 
  • in_vol - input Volume3D
  • like - Volume3D that is used for sampling information
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • tfm  - transformation to apply (i.e from output to input) (instead of itfm)
  • interp - interpolation method
  • fill - fill value
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Equivalent to mincresample minc command
source
Minc2.resample_volume! — Function
resample_volume!(in_vol::AbstractArray{T,3}, 
     out_vol::AbstractArray{T,3}, 
     v2w::AffineTransform{C}, 
     w2v::AffineTransform{C}, 
@@ -36,7 +36,7 @@
     interp::I=BSpline(Quadratic(Line(OnCell()))),
     fill=0.0,
     ftol=1.0/80,
-    max_iter=10)
Resample 3D array using transformation 
  • in_vol - input 3D array
  • out_vol - output 3D array
  • v2w - voxel to world affine transform in the output array
  • w2v - world to voxel affine transform in the input array
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • interp - interpolation method
  • fill - fill value
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
source
resample_volume!(
+    max_iter=10)
Resample 3D array using transformation 
  • in_vol - input 3D array
  • out_vol - output 3D array
  • v2w - voxel to world affine transform in the output array
  • w2v - world to voxel affine transform in the input array
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • interp - interpolation method
  • fill - fill value
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
source
resample_volume!(
     in_vol::Volume3D{T,3}, 
     out_vol::Volume3D{O,3}; 
     tfm::Union{Vector{XFM},XFM,Nothing}=nothing, 
@@ -45,34 +45,34 @@
     fill=0.0, 
     order=nothing,
     ftol=1.0/80,
-    max_iter=10)::Volume3D{O,3}
Resample Volume3D using transformation 
  • in_vol - input Volume3D
  • out_vol - output Volume3D
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • tfm  - transformation to apply (i.e from output to input) (instead of itfm)
  • interp - interpolation method
  • fill - fill value
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Equivalent to mincresample minc command
source
Minc2.resample_grid — Function
resample_grid(
+    max_iter=10)::Volume3D{O,3}
Resample Volume3D using transformation 
  • in_vol - input Volume3D
  • out_vol - output Volume3D
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • tfm  - transformation to apply (i.e from output to input) (instead of itfm)
  • interp - interpolation method
  • fill - fill value
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Equivalent to mincresample minc command
source
Minc2.resample_grid — Function
resample_grid(
     in_grid::Volume3D{T,4}, 
     itfm::Union{Vector{XFM}, XFM}; 
-    like::Union{Nothing,Volume3D{L,4}}=nothing)::Volume3D{T,4}
Resample Volume3D that contain 4D array, using transformation, assume 1st dimension is non spatial
  • in_grid - input Volume3D with 4D array describing vector field
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • like - Volume3D that is used for sampling information
source
Minc2.resample_grid! — Function
resample_grid!(
+    like::Union{Nothing,Volume3D{L,4}}=nothing)::Volume3D{T,4}
Resample Volume3D that contain 4D array, using transformation, assume 1st dimension is non spatial
  • in_grid - input Volume3D with 4D array describing vector field
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • like - Volume3D that is used for sampling information
source
Minc2.resample_grid! — Function
resample_grid!(
     in_grid::Volume3D{T,4},
     out_grid::Volume3D{T,4},
-    itfm::Union{Vector{XFM}, XFM}=nothing)::Volume3D{T,4}
Resample Volume3D that contain 4D array, using transformation, assume 1st dimension is non spatial
  • in_grid - input Volume3D with 4D array describing vector field
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • like - Volume3D that is used for sampling information
source
Minc2.crop_volume — Function
crop_volume(in_vol::Volume3D{T,N},crop;
-    fill_val::T=zero(T))::Volume3D{T,N}
Crop (or pad) a volume
  • in_vol - input Volume3D
  • crop - crop specification for each direction,    e.g. [(10,10),(20,20),(5,10)] , negative values mean padding
source
Minc2.calculate_jacobian — Function
calculate_jacobian(
+    itfm::Union{Vector{XFM}, XFM}=nothing)::Volume3D{T,4}
Resample Volume3D that contain 4D array, using transformation, assume 1st dimension is non spatial
  • in_grid - input Volume3D with 4D array describing vector field
  • itfm - inverse of the  transformation to apply (i.e from output to input)
  • like - Volume3D that is used for sampling information
source
Minc2.crop_volume — Function
crop_volume(in_vol::Volume3D{T,N},crop;
+    fill_val::T=zero(T))::Volume3D{T,N}
Crop (or pad) a volume
  • in_vol - input Volume3D
  • crop - crop specification for each direction,    e.g. [(10,10),(20,20),(5,10)] , negative values mean padding
source
Minc2.calculate_jacobian — Function
calculate_jacobian(
     tfm::Union{Vector{XFM},XFM};
     like::Volume3D{T,3}; 
     interp::I=BSpline(Quadratic(Line(OnCell()))),
     ftol=1.0/80,
-    max_iter=10)::Volume3D{T,3}
Calculate dense jacobian determinant field for an arbitrary transformation
  • tfm  - transformation to use
  • out_vol - output Volume3D
  • interp - interpolation method
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Roughly equivalent to mincblob minc command
source
Minc2.calculate_jacobian! — Function
calculate_jacobian!(
+    max_iter=10)::Volume3D{T,3}
Calculate dense jacobian determinant field for an arbitrary transformation
  • tfm  - transformation to use
  • out_vol - output Volume3D
  • interp - interpolation method
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Roughly equivalent to mincblob minc command
source
Minc2.calculate_jacobian! — Function
calculate_jacobian!(
     tfm::Union{Vector{XFM},XFM},
     out_vol::AbstractArray{T,3},
     out_v2w::AffineTransform{C};
     interp::I=BSpline(Quadratic(Line(OnCell()))),
     ftol=1.0/80,
-    max_iter=10)
Calculate dense jacobian determinant field for an arbitrary transformation
  • tfm  - transformation to use
  • out_vol - output 3D array
  • out_v2w - voxel to world affine transform in the output array
  • interp - interpolation method
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Roughly equivalent to mincblob minc command
source
calculate_jacobian!(
+    max_iter=10)
Calculate dense jacobian determinant field for an arbitrary transformation
  • tfm  - transformation to use
  • out_vol - output 3D array
  • out_v2w - voxel to world affine transform in the output array
  • interp - interpolation method
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Roughly equivalent to mincblob minc command
source
calculate_jacobian!(
     tfm::Union{Vector{XFM},XFM}, 
     out_vol::Volume3D{T,3}; 
     interp::I=BSpline(Quadratic(Line(OnCell()))),
     ftol=1.0/80,
-    max_iter=10)::Volume3D{T,3}
Calculate dense jacobian determinant field for an arbitrary transformation
  • tfm  - transformation to use
  • out_vol - output Volume3D
  • interp - interpolation method
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Roughly equivalent to mincblob minc command
source
Missing docstring.
Missing docstring for Minc2.GridTransform. Check Documenter's build log for details.
Missing docstring.
Missing docstring for Minc2.InverseGridTransform. Check Documenter's build log for details.
Minc2.tfm_to_grid — Function
tfm_to_grid(
+    max_iter=10)::Volume3D{T,3}
Calculate dense jacobian determinant field for an arbitrary transformation
  • tfm  - transformation to use
  • out_vol - output Volume3D
  • interp - interpolation method
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
Roughly equivalent to mincblob minc command
source
Missing docstring.
Missing docstring for Minc2.GridTransform. Check Documenter's build log for details.
Missing docstring.
Missing docstring for Minc2.InverseGridTransform. Check Documenter's build log for details.
Minc2.tfm_to_grid — Function
tfm_to_grid(
     tfm::Union{Vector{XFM}, XFM},
     ref::G;
-    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::Volume3D{T,4}
Convert arbitrary transformation  into Volume3D with 4D array containing vector field
  • tfm - transformation to use
  • v2w - voxel to world affine transform in the output array
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
source
Minc2.normalize_tfm — Function
normalize_tfm(tfm::Union{Vector{XFM}, XFM},
+    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::Volume3D{T,4}
Convert arbitrary transformation  into Volume3D with 4D array containing vector field
  • tfm - transformation to use
  • v2w - voxel to world affine transform in the output array
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
source
Minc2.normalize_tfm — Function
normalize_tfm(tfm::Union{Vector{XFM}, XFM},
     ref::G;
-    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::GridTransform{Float64,T}
Convert arbitrary transformation  into a single GridTransform
  • tfm - transformation to use
  • ref - GridTransform that is used for sampling information
  • store - underlying array type
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
source
normalize_tfm(tfm::Union{Vector{XFM}, XFM},
+    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::GridTransform{Float64,T}
Convert arbitrary transformation  into a single GridTransform
  • tfm - transformation to use
  • ref - GridTransform that is used for sampling information
  • store - underlying array type
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
source
normalize_tfm(tfm::Union{Vector{XFM}, XFM},
     ref::G;
-    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::GridTransform{Float64,T}
Convert arbitrary transformation  into a single GridTransform
  • tfm - transformation to use
  • ref - Volume3D that is used for sampling information
  • store - underlying array type
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
source

+    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::GridTransform{Float64,T}

Convert arbitrary transformation into a single GridTransform

  • tfm - transformation to use
  • ref - Volume3D that is used for sampling information
  • store - underlying array type
  • ftol - tolerance, for inverse transformations
  • max_iter - maximum number of iterations, for inverse transformations
source
diff --git a/index.html b/index.html index aee2f88..8e3ca56 100644 --- a/index.html +++ b/index.html @@ -91,4 +91,4 @@ resize_to_layout!(fig) -save("mni_icbm152_gm.png", fig, px_per_unit = 1)

Will produce MNI-ICBM152

More examples

See examples directory for more examples:

Documentation for MINC

Documentations for underlying libminc and minc tools is available at https://en.wikibooks.org/wiki/MINC

+save("mni_icbm152_gm.png", fig, px_per_unit = 1)

Will produce MNI-ICBM152

More examples

See examples directory for more examples:

Documentation for MINC

Documentations for underlying libminc and minc tools is available at https://en.wikibooks.org/wiki/MINC

diff --git a/low_level/index.html b/low_level/index.html index 160e297..a7c0be4 100644 --- a/low_level/index.html +++ b/low_level/index.html @@ -1,25 +1,25 @@ -Low level functions · Minc2.jl
GitHub

Low level functions for IO on .mnc and .xfm files

Minc2.attributes — Method
attributes(h::VolumeHandle, g::String)

List attributes defined inside given group

source
Minc2.create_header_from_v2w — Method
create_header_from_v2w(
+Low level functions · Minc2.jl
GitHub
Low level functions for IO on .mnc and .xfm files
Minc2.attributes — Method
attributes(h::VolumeHandle, g::String)
List attributes defined inside given group
source
Minc2.create_header_from_v2w — Method
create_header_from_v2w(
     sz, t::AffineTransform{T};
     vector_dim::Bool=false, 
     time_step::Union{Float64,Nothing}=nothing,
-    time_start::Union{Float64,Nothing}=nothing)::MincHeader
Internal: Generate header from the voxel to world transform and volume size
source
Minc2.create_minc_file — Method
create_minc_file(h::VolumeHandle, path::AbstractString)
Create empty minc file on disk, structure need to be defined in advance
source
Minc2.define_minc_file — Method
define_minc_file(hdr::MincHeader,::Type{Store}=Float32,::Type{Repr}=Store)
Define new minc file structure, return handle
source
Minc2.empty_like_minc_volume_raw — Method
empty_like_minc_volume_raw( h::VolumeHandle,
-    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader}
Allocate empty volume using handle return volume, storage header
source
Minc2.empty_like_minc_volume_raw — Method
empty_like_minc_volume_raw(path::String, ::Type{T}=Float32 )::
-        Tuple{Array{T}, Minc2.MincHeader}
Create empty volume similar to existing file return volume, representation header,storage header
source
Minc2.empty_like_minc_volume_std — Method
empty_like_minc_volume_std(h::VolumeHandle, 
-    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader}
Read the actual volume using handle return volume, representation header,storage header
source
Minc2.empty_like_minc_volume_std — Method
empty_like_minc_volume_std(path::String, 
-    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader}
allocate empty volume using path as a reference return volume, representation header,storage header
source
Minc2.get_attribute — Method
get_attribute(h::VolumeHandle,g::String,a::String; default=missing)
Convenience function for reading specific attribute, return default value if not found also convert Array into the first value if it's a one-length array
source
Minc2.ndim — Method
ndim(h::VolumeHandle)::Int
Query number of dimensions in the minc file
source
Minc2.read_attribute — Method
read_attribute(h::VolumeHandle, 
+    time_start::Union{Float64,Nothing}=nothing)::MincHeader
Internal: Generate header from the voxel to world transform and volume size
source
Minc2.create_minc_file — Method
create_minc_file(h::VolumeHandle, path::AbstractString)
Create empty minc file on disk, structure need to be defined in advance
source
Minc2.define_minc_file — Method
define_minc_file(hdr::MincHeader,::Type{Store}=Float32,::Type{Repr}=Store)
Define new minc file structure, return handle
source
Minc2.empty_like_minc_volume_raw — Method
empty_like_minc_volume_raw( h::VolumeHandle,
+    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader}
Allocate empty volume using handle return volume, storage header
source
Minc2.empty_like_minc_volume_raw — Method
empty_like_minc_volume_raw(path::String, ::Type{T}=Float32 )::
+        Tuple{Array{T}, Minc2.MincHeader}
Create empty volume similar to existing file return volume, representation header,storage header
source
Minc2.empty_like_minc_volume_std — Method
empty_like_minc_volume_std(h::VolumeHandle, 
+    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader}
Read the actual volume using handle return volume, representation header,storage header
source
Minc2.empty_like_minc_volume_std — Method
empty_like_minc_volume_std(path::String, 
+    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader}
allocate empty volume using path as a reference return volume, representation header,storage header
source
Minc2.get_attribute — Method
get_attribute(h::VolumeHandle,g::String,a::String; default=missing)
Convenience function for reading specific attribute, return default value if not found also convert Array into the first value if it's a one-length array
source
Minc2.ndim — Method
ndim(h::VolumeHandle)::Int
Query number of dimensions in the minc file
source
Minc2.read_attribute — Method
read_attribute(h::VolumeHandle, 
     group::String,
-    attribute::String)::Union{String, AbstractVector, Nothing}
Read minc2 header attribute :param group: attribute group name :param attribute: attribute name :return:
source
Minc2.read_minc_volume_raw — Method
read_minc_volume_raw(h::VolumeHandle, 
-    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader}
Read the actual volume using handle return volume, storage header
source
Minc2.read_minc_volume_raw — Method
read_minc_volume_raw(path::String, ::Type{T}=Float32 )::
-    Tuple{Array{T}, Minc2.MincHeader}
Read the actual volume using path return volume, representation header,storage header
source
Minc2.read_minc_volume_std — Method
read_minc_volume_std(h::VolumeHandle, 
-    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader}
Read the actual volume using handle return volume, representation header,storage header
source
Minc2.read_minc_volume_std — Method
read_minc_volume_std(path::String, ::Type{T}=Float32 )::
-    Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader}
Read the actual volume using path return volume, representation header,storage header
source
Minc2.read_minc_volume_std_history — Method
read_minc_volume_std_history(path::String, ::Type{T}=Float32 )::
-    Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader, Union{String,Nothing}}
Read the actual volume using path return volume, representation header,storage header
source
Minc2.voxel_to_world — Method
voxel_to_world(hdr::MincHeader)::AffineTransform{Float64}
Give AffineTransform for world to voxel transformation based on header
source
Minc2.voxel_to_world — Method
voxel_to_world(h::VolumeHandle,ijk::Vector{Float64})::Vector{Float64}
Convert contignuous 0-based voxel indexes (I,J,K) to world coordinates (X,Y,Z) 0-based
source
Minc2.world_to_voxel — Method
world_to_voxel(hdr::MincHeader)::AffineTransform{Float64}
Give AffineTransform for voxel to world transformation
source
Minc2.world_to_voxel — Method
world_to_voxel(h::VolumeHandle, xyz::Vector{Float64})::Vector{Float64}
Convert world coordinates (X,Y,Z) to contignuous voxel indexes (I,J,K) 0-based
source
Minc2.write_attribute — Method
write_attribute(h::VolumeHandle, group::String, attribute::String, value::T)
Store attribute into minc2 file :param group:  group name :param attribute:  attribute name :param value:  attribute value :return:
source
Minc2.write_minc_volume_raw — Method
write_minc_volume_raw(path::String, ::Type{Store}, 
+    attribute::String)::Union{String, AbstractVector, Nothing}
Read minc2 header attribute :param group: attribute group name :param attribute: attribute name :return:
source
Minc2.read_minc_volume_raw — Method
read_minc_volume_raw(h::VolumeHandle, 
+    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader}
Read the actual volume using handle return volume, storage header
source
Minc2.read_minc_volume_raw — Method
read_minc_volume_raw(path::String, ::Type{T}=Float32 )::
+    Tuple{Array{T}, Minc2.MincHeader}
Read the actual volume using path return volume, representation header,storage header
source
Minc2.read_minc_volume_std — Method
read_minc_volume_std(h::VolumeHandle, 
+    ::Type{T}=Float32 )::Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader}
Read the actual volume using handle return volume, representation header,storage header
source
Minc2.read_minc_volume_std — Method
read_minc_volume_std(path::String, ::Type{T}=Float32 )::
+    Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader}
Read the actual volume using path return volume, representation header,storage header
source
Minc2.read_minc_volume_std_history — Method
read_minc_volume_std_history(path::String, ::Type{T}=Float32 )::
+    Tuple{Array{T}, Minc2.MincHeader, Minc2.MincHeader, Union{String,Nothing}}
Read the actual volume using path return volume, representation header,storage header
source
Minc2.voxel_to_world — Method
voxel_to_world(hdr::MincHeader)::AffineTransform{Float64}
Give AffineTransform for world to voxel transformation based on header
source
Minc2.voxel_to_world — Method
voxel_to_world(h::VolumeHandle,ijk::Vector{Float64})::Vector{Float64}
Convert contignuous 0-based voxel indexes (I,J,K) to world coordinates (X,Y,Z) 0-based
source
Minc2.world_to_voxel — Method
world_to_voxel(hdr::MincHeader)::AffineTransform{Float64}
Give AffineTransform for voxel to world transformation
source
Minc2.world_to_voxel — Method
world_to_voxel(h::VolumeHandle, xyz::Vector{Float64})::Vector{Float64}
Convert world coordinates (X,Y,Z) to contignuous voxel indexes (I,J,K) 0-based
source
Minc2.write_attribute — Method
write_attribute(h::VolumeHandle, group::String, attribute::String, value::T)
Store attribute into minc2 file :param group:  group name :param attribute:  attribute name :param value:  attribute value :return:
source
Minc2.write_minc_volume_raw — Method
write_minc_volume_raw(path::String, ::Type{Store}, 
     store_hdr::Union{MincHeader, Nothing}, 
     volume::Array{Repr};like::Union{String, Nothing}=nothing, 
-    history::Union{String, Nothing}=nothing )
Write full volume to file, need to provide details of file structure return nothing
source
Minc2.write_minc_volume_raw — Method
write_minc_volume_raw(h::VolumeHandle, volume::Array{T} )
write full volume to file, file should be defined and created return nothing
source
Minc2.write_minc_volume_std — Method
write_minc_volume_std(path::String, ::Type{Store}, 
+    history::Union{String, Nothing}=nothing )
Write full volume to file, need to provide details of file structure return nothing
source
Minc2.write_minc_volume_raw — Method
write_minc_volume_raw(h::VolumeHandle, volume::Array{T} )
write full volume to file, file should be defined and created return nothing
source
Minc2.write_minc_volume_std — Method
write_minc_volume_std(path::String, ::Type{Store}, 
     store_hdr::Union{MincHeader, Nothing}, 
     volume::Array{Repr};like::Union{String, Nothing}=nothing, 
-    history::Union{String, Nothing}=nothing )
Write full volume to file, need to provide details of file structure return nothing
source
Minc2.write_minc_volume_std — Method
write_minc_volume_std(h::VolumeHandle, volume::Array{T} )
write full volume to file, file should be defined and created return nothing
source
Minc2.MincHeader — Type
MincHeader
Structure describing spatial orientation and sampling of the minc file 
source
Minc2.minc2_spatial — Constant
Low Level: Mapping MINC2 spatial dimensions to proper spatial dimension (should be identity for spatial dims)
source
Minc2.append_grid_transform — Method
append_grid_transform(h::TransformHandle, grid_file::String; inv::Bool=false)
Low level: Append grid transform  to an open transformation handle
source
Minc2.append_linear_transform — Method
append_linear_transform(h::TransformHandle, lin::AffineTransform)
Low level: Append affine transform to an open transformation handle
source
Minc2.concat_xfm — Method
concat_xfm(h::TransformHandle, i::TransformHandle)
Low level: concatenate two transfomations
source
Minc2.get_grid_transform — Method
get_grid_transform(h::TransformHandle; n::Int64=0)
Low level: extract reference to a grid file from open handle
source
Minc2.get_linear_transform — Method
get_linear_transform(h::TransformHandle; n::Int64=0)::AffineTransform{Float64}
Low level: extract AffineTransform{Float64} from open handle
source
Minc2.get_linear_transform_param — Method
get_linear_transform_param(h::TransformHandle;n::Int64=0,center::Union{Nothing,Vector{Float64}}=nothing)
Low level: extact transformation parameters from affine transform , returns named tuple with fields center, translations, scales, shears, rotations
source
Minc2.get_n_concat — Method
get_n_concat(h::TransformHandle)::Int64
Low level: Get number of transformations in open handle
source
Minc2.get_n_type — Method
get_n_type(h::TransformHandle; n::Int64=0)::XFM
Low level: Get transform type  for nth transform in open handle
source
Minc2.inverse_transform_point — Method
inverse_transform_point(h::TransformHandle, xyz::Vector{Float64})::Vector{Float64}
Low level: Inverse transform point xyz using minc transform h
source
Minc2.load_transforms — Method
load_transforms(h::TransformHandle)::Vector{AnyTransform}
Low level: Load all transforms from open .XFM handle
source
Minc2.save_transforms — Method
save_transforms(fname::String, 
+    history::Union{String, Nothing}=nothing )
Write full volume to file, need to provide details of file structure return nothing
source
Minc2.write_minc_volume_std — Method
write_minc_volume_std(h::VolumeHandle, volume::Array{T} )
write full volume to file, file should be defined and created return nothing
source
Minc2.MincHeader — Type
MincHeader
Structure describing spatial orientation and sampling of the minc file 
source
Minc2.minc2_spatial — Constant
Low Level: Mapping MINC2 spatial dimensions to proper spatial dimension (should be identity for spatial dims)
source
Minc2.append_grid_transform — Method
append_grid_transform(h::TransformHandle, grid_file::String; inv::Bool=false)
Low level: Append grid transform  to an open transformation handle
source
Minc2.append_linear_transform — Method
append_linear_transform(h::TransformHandle, lin::AffineTransform)
Low level: Append affine transform to an open transformation handle
source
Minc2.concat_xfm — Method
concat_xfm(h::TransformHandle, i::TransformHandle)
Low level: concatenate two transfomations
source
Minc2.get_grid_transform — Method
get_grid_transform(h::TransformHandle; n::Int64=0)
Low level: extract reference to a grid file from open handle
source
Minc2.get_linear_transform — Method
get_linear_transform(h::TransformHandle; n::Int64=0)::AffineTransform{Float64}
Low level: extract AffineTransform{Float64} from open handle
source
Minc2.get_linear_transform_param — Method
get_linear_transform_param(h::TransformHandle;n::Int64=0,center::Union{Nothing,Vector{Float64}}=nothing)
Low level: extact transformation parameters from affine transform , returns named tuple with fields center, translations, scales, shears, rotations
source
Minc2.get_n_concat — Method
get_n_concat(h::TransformHandle)::Int64
Low level: Get number of transformations in open handle
source
Minc2.get_n_type — Method
get_n_type(h::TransformHandle; n::Int64=0)::XFM
Low level: Get transform type  for nth transform in open handle
source
Minc2.inverse_transform_point — Method
inverse_transform_point(h::TransformHandle, xyz::Vector{Float64})::Vector{Float64}
Low level: Inverse transform point xyz using minc transform h
source
Minc2.load_transforms — Method
load_transforms(h::TransformHandle)::Vector{AnyTransform}
Low level: Load all transforms from open .XFM handle
source
Minc2.save_transforms — Method
save_transforms(fname::String, 
     xfm::Union{Vector{XFM}, XFM};
-    grid_store::Type{T}=Float32 ) where {T, XFM<:AnyTransform}
Save transformations into .xfm file, 
Arguments
  • fname: output file name
  • xfm: vector of transformations to save, or a single transformation
  • grid_store: type of storage for grid files (default: Float32)
source
Minc2.save_xfm_file — Method
save_xfm_file(h::TransformHandle, path::String)
Low level: Save information into file from an open handle
source
Minc2.transform_point — Method
transform_point(h::TransformHandle, xyz::Vector{Float64})::Vector{Float64}
Low level: Transform point xyz using minc transform h
source
Minc2.XFM — Type
@enum XFM
Low level: transformation types stored in .xfm file
source

+    grid_store::Type{T}=Float32 ) where {T, XFM<:AnyTransform}

Save transformations into .xfm file,

Arguments

  • fname: output file name
  • xfm: vector of transformations to save, or a single transformation
  • grid_store: type of storage for grid files (default: Float32)
source
Minc2.save_xfm_file — Method
save_xfm_file(h::TransformHandle, path::String)

Low level: Save information into file from an open handle

source
Minc2.transform_point — Method
transform_point(h::TransformHandle, xyz::Vector{Float64})::Vector{Float64}

Low level: Transform point xyz using minc transform h

source
Minc2.XFM — Type

@enum XFM

Low level: transformation types stored in .xfm file

source
diff --git a/plotting/index.html b/plotting/index.html index 1b0e33b..35b4054 100644 --- a/plotting/index.html +++ b/plotting/index.html @@ -25,7 +25,7 @@ cmap = :rainbow, levels = [20,30], show_colorbar = true, - nslices = 4)

Draws a segmentation seg on top of anat in a grid layout layout

source

Show MNI-ICBM152 template contours with GM proability map

using CairoMakie
+    nslices = 4)

Draws a segmentation seg on top of anat in a grid layout layout

source

Show MNI-ICBM152 template contours with GM proability map

using CairoMakie
 using Minc2
 
 # read T1w scan
@@ -50,7 +50,7 @@
     cmap=:rainbow, levels=[20, 40],
     heat_limits=nothing, 
     show_colorbar=true,
-    nslices=4)

Draws a heatmap of heat on top of anat in a grid layout layout.

source

Show two-tailed t-statistics on DBM style analysis

using CairoMakie
+    nslices=4)

Draws a heatmap of heat on top of anat in a grid layout layout.

source

Show two-tailed t-statistics on DBM style analysis

using CairoMakie
 using Minc2
 
 # read T1w scan and crop black area around ROI
@@ -97,4 +97,4 @@
     alpha=0.7,
     colorbar_label="",
     slices_gap=5,
-    colorbar_gap=10)

Draws a two-sided (symmetric positive and negative) heatmap of heat on top of anat in a grid layout layout.

source + colorbar_gap=10)

Draws a two-sided (symmetric positive and negative) heatmap of heat on top of anat in a grid layout layout.

source