save_volume(fn::AbstractString,
+High level functions · Minc2.jl voxel_to_world(grid::GridTransform)Extract voxel to world affine transform from a GridTransform
source voxel_to_world(grid::InverseGridTransform)Extract voxel to world affine transform from a InverseGridTransform
grid - InverseGridTransformsource 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 world_to_voxel(grid::GridTransform)Extract world to voxel affine transform from a GridTransform
source world_to_voxel(grid::InverseGridTransform)Extract world to voxel affine transform from a InverseGridTransform
grid - InverseGridTransformsource 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 array(grid::GridTransform)Extract underlying plain array
source array(grid::InverseGridTransform)Extract underlying plain array
grid - InverseGridTransformsource array(vol::Volume3D)Extract underlying plain array
source history(vol::Volume3D)Extract history metadata
source read_volume(fn::String; store::Type{T}=Float64)::Volume3D{T}Read Volume3D from minc file
fn - filenamestore - underlying array typesource read_nifti_volume(fn::AbstractString; store::Type{T}=Float64)::Volume3D{T}Read Volume3D from .nii or .nii.gz file
source save_volume(fn::AbstractString,
vol::Volume3D{T,N};
store::Type{S}=Float32,
- history=nothing)Save Volume3D to minc file
fn - filenamevol - Volume3D to savestore - underlying MINC data type, to be used for storagesource save_nifti_volume(fn::AbstractString, vol::Volume3D{T};
- store::Type{S}=Float32, history=nothing)Save Volume3D into .nii or .nii.gz file
source read_transforms(fname::String)::Vector{AnyTransform}Read transformations from .xfm file fname
source read_itk_nifti_transform(fn::AbstractString;
- store::Type{T}=Float32)::Minc2.GridTransform{Float64,T}Read ANTs style warp transform
source read_ants_transform(fn::AbstractString; store::Type{T}=Float32)::Minc2.AnyTransformRead .txt and .nii(.nii.gz) transforms produces by ANTs
source save_transforms(fname::String,
+ history=nothing)Save Volume3D to minc file
fn - filenamevol - Volume3D to savestore - underlying MINC data type, to be used for storagesource save_nifti_volume(fn::AbstractString, vol::Volume3D{T};
+ store::Type{S}=Float32, history=nothing)Save Volume3D into .nii or .nii.gz file
source read_transforms(fname::String)::Vector{AnyTransform}Read transformations from .xfm file fname
source read_itk_nifti_transform(fn::AbstractString;
+ store::Type{T}=Float32)::Minc2.GridTransform{Float64,T}Read ANTs style warp transform
source read_ants_transform(fn::AbstractString; store::Type{T}=Float32)::Minc2.AnyTransformRead .txt and .nii(.nii.gz) transforms produces by ANTs
source 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 namexfm: vector of transformations to save, or a single transformationgrid_store: type of storage for grid files (default: Float32)source save_itk_nifti_transform(fn::AbstractString,
- xfm::Minc2.GridTransform{Float64,T}; store::Type{S}=Float32)Write ANTs style warp transform
source save_itk_txt_transform(fn::AbstractString,
- xfm::Minc2.AffineTransform{Float64})Write affine transform in ITK .txt format
source Volume3D{T,N}An abstract 3D volume, could be vector field or volume with time dimension
source empty_volume_like(
+ grid_store::Type{T}=Float32 ) where {T, XFM<:AnyTransform}Save transformations into .xfm file,
Arguments
fname: output file namexfm: vector of transformations to save, or a single transformationgrid_store: type of storage for grid files (default: Float32)source save_itk_nifti_transform(fn::AbstractString,
+ xfm::Minc2.GridTransform{Float64,T}; store::Type{S}=Float32)Write ANTs style warp transform
source save_itk_txt_transform(fn::AbstractString,
+ xfm::Minc2.AffineTransform{Float64})Write affine transform in ITK .txt format
source Volume3D{T,N}An abstract 3D volume, could be vector field or volume with time dimension
source 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 informationstore - underlying array typesource 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 informationstore - underlying array typesource empty_volume_like(
vol::Volume3D{T1,N};
store::Type{T}=Float64,
- history=nothing)Create an empty Volume3D
vol - Volume3D that is used for sampling informationstore - underlying array typehistory - minc historysource full_volume_like(
+ history=nothing)Create an empty Volume3D
vol - Volume3D that is used for sampling informationstore - underlying array typehistory - minc historysource 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 informationstore - underlying array typesource 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 informationstore - underlying array typesource full_volume_like(
vol::Volume3D{T1,N};
store::Type{T}=Float64,
- history=nothing)Create an empty Volume3D
vol - Volume3D that is used for sampling informationstore - underlying array typehistory - minc historysource resample_volume(
+ history=nothing)Create an empty Volume3D
vol - Volume3D that is used for sampling informationstore - underlying array typehistory - minc historysource 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)::Volume3DResample Volume3D using transformation
in_vol - input Volume3Dlike - Volume3D that is used for sampling informationitfm - 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 methodfill - fill valueftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsEquivalent to mincresample minc command
source resample_volume!(in_vol::AbstractArray{T,3},
+ max_iter=10)::Volume3DResample Volume3D using transformation
in_vol - input Volume3Dlike - Volume3D that is used for sampling informationitfm - 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 methodfill - fill valueftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsEquivalent to mincresample minc command
source 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 arrayout_vol - output 3D arrayv2w - voxel to world affine transform in the output arrayw2v - world to voxel affine transform in the input arrayitfm - inverse of the transformation to apply (i.e from output to input)interp - interpolation methodfill - fill valueftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationssource resample_volume!(
+ max_iter=10)Resample 3D array using transformation
in_vol - input 3D arrayout_vol - output 3D arrayv2w - voxel to world affine transform in the output arrayw2v - world to voxel affine transform in the input arrayitfm - inverse of the transformation to apply (i.e from output to input)interp - interpolation methodfill - fill valueftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationssource 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 Volume3Dout_vol - output Volume3Ditfm - 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 methodfill - fill valueftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsEquivalent to mincresample minc command
source resample_grid(
+ max_iter=10)::Volume3D{O,3}Resample Volume3D using transformation
in_vol - input Volume3Dout_vol - output Volume3Ditfm - 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 methodfill - fill valueftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsEquivalent to mincresample minc command
source 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 fielditfm - inverse of the transformation to apply (i.e from output to input)like - Volume3D that is used for sampling informationsource 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 fielditfm - inverse of the transformation to apply (i.e from output to input)like - Volume3D that is used for sampling informationsource 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 fieldout_grid - output Volume3D with 4D array describing vector fielditfm - inverse of the transformation to apply (i.e from output to input)source crop_volume(in_vol::Volume3D{T,N},crop;
- fill_val::T=zero(T))::Volume3D{T,N}Crop (or pad) a volume
in_vol - input Volume3Dcrop - crop specification for each direction, e.g. [(10,10),(20,20),(5,10)] , negative values mean paddingsource 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 fieldout_grid - output Volume3D with 4D array describing vector fielditfm - inverse of the transformation to apply (i.e from output to input)source crop_volume(in_vol::Volume3D{T,N},crop;
+ fill_val::T=zero(T))::Volume3D{T,N}Crop (or pad) a volume
in_vol - input Volume3Dcrop - crop specification for each direction, e.g. [(10,10),(20,20),(5,10)] , negative values mean paddingsource 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 useout_vol - output Volume3Dinterp - interpolation methodftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsRoughly equivalent to mincblob minc command
source calculate_jacobian!(
+ max_iter=10)::Volume3D{T,3}Calculate dense jacobian determinant field for an arbitrary transformation
tfm - transformation to useout_vol - output Volume3Dinterp - interpolation methodftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsRoughly equivalent to mincblob minc command
source 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 useout_vol - output 3D arrayout_v2w - voxel to world affine transform in the output arrayinterp - interpolation methodftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsRoughly equivalent to mincblob minc command
source calculate_jacobian!(
+ max_iter=10)Calculate dense jacobian determinant field for an arbitrary transformation
tfm - transformation to useout_vol - output 3D arrayout_v2w - voxel to world affine transform in the output arrayinterp - interpolation methodftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsRoughly 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 useout_vol - output Volume3Dinterp - interpolation methodftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsRoughly equivalent to mincblob minc command
source Missing docstring for Minc2.GridTransform. Check Documenter's build log for details.
Missing docstring for Minc2.InverseGridTransform. Check Documenter's build log for details.
tfm_to_grid(
+ max_iter=10)::Volume3D{T,3}Calculate dense jacobian determinant field for an arbitrary transformation
tfm - transformation to useout_vol - output Volume3Dinterp - interpolation methodftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationsRoughly equivalent to mincblob minc command
source Missing docstring for Minc2.GridTransform. Check Documenter's build log for details.
Missing docstring for Minc2.InverseGridTransform. Check Documenter's build log for details.
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 usev2w - voxel to world affine transform in the output arrayftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationssource 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 usev2w - voxel to world affine transform in the output arrayftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationssource 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 useref - GridTransform that is used for sampling informationstore - underlying array typeftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationssource 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 useref - GridTransform that is used for sampling informationstore - underlying array typeftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationssource 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 useref - Volume3D that is used for sampling informationstore - underlying array typeftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformationssource
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This document was generated with Documenter.jl version 1.7.0 on Wednesday 11 September 2024 . Using Julia version 1.6.7.
Convert arbitrary transformation into a single GridTransform
tfm - transformation to useref - Volume3D that is used for sampling informationstore - underlying array typeftol - tolerance, for inverse transformationsmax_iter - maximum number of iterations, for inverse transformations