-
Notifications
You must be signed in to change notification settings - Fork 34
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #50 from JuliaNeuroscience/extensions
Update extensions interface
- Loading branch information
Showing
5 changed files
with
194 additions
and
155 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,182 @@ | ||
|
|
||
| @inline function to_ecode(x::Int32) | ||
| if x === Int32(2) | ||
| return :DICOM | ||
| elseif x === Int32(4) | ||
| return :AFNI | ||
| elseif x === Int32(6) | ||
| return :Comment | ||
| elseif x === Int32(8) | ||
| return :XCEDE | ||
| elseif x === Int32(10) | ||
| return :JimDimInfo | ||
| elseif x === Int32(12) | ||
| return :WorkflowFWDS | ||
| elseif x === Int32(14) | ||
| return :Freesurfer | ||
| elseif x === Int32(16) | ||
| return :PyPickly | ||
| elseif x === Int32(18) | ||
| return :MindIdent | ||
| elseif x === Int32(20) | ||
| return :BValue | ||
| elseif x === Int32(22) | ||
| return :SphericalDirection | ||
| elseif x === Int32(24) | ||
| return :DTComponent | ||
| elseif x === Int32(26) | ||
| return :SHCDegreeOrder | ||
| elseif x === Int32(28) | ||
| return :Voxbo | ||
| elseif x === Int32(30) | ||
| return :Caret | ||
| elseif x === Int32(32) | ||
| return :CIfTI | ||
| elseif x === Int32(34) | ||
| return :VariableFrameTiming | ||
| elseif x === Int32(38) | ||
| return :Eval | ||
| elseif x === Int32(40) | ||
| return :Matlab | ||
| else | ||
| return :Ignore | ||
| end | ||
| end | ||
|
|
||
| @inline function ecode_to_int(x::Symbol) | ||
| if x === :DICOM | ||
| return Int32(2) | ||
| elseif x === :AFNI | ||
| return Int32(4) | ||
| elseif x === :Comment | ||
| return Int32(6) | ||
| elseif x === :XCEDE | ||
| return Int32(8) | ||
| elseif x === :JimDimInfo | ||
| return Int32(10) | ||
| elseif x === :WorkflowFWDS | ||
| return Int32(12) | ||
| elseif x === :Freesurfer | ||
| return Int32(14) | ||
| elseif x === :PyPickly | ||
| return Int32(16) | ||
| elseif x === :MindIdent | ||
| return Int32(18) | ||
| elseif x === :BValue | ||
| return Int32(20) | ||
| elseif x === :SphericalDirection | ||
| return Int32(22) | ||
| elseif x === :DTComponent | ||
| return Int32(24) | ||
| elseif x === :SHCDegreeOrder | ||
| return Int32(26) | ||
| elseif x === :Voxbo | ||
| return Int32(28) | ||
| elseif x === :Caret | ||
| return Int32(30) | ||
| elseif x === :CIfTI | ||
| return Int32(32) | ||
| elseif x === :VariableFrameTiming | ||
| return Int32(34) | ||
| elseif x === :Eval | ||
| return Int32(38) | ||
| elseif x === :Matlab | ||
| return Int32(40) | ||
| else | ||
| return Int32(0) | ||
| end | ||
| end | ||
|
|
||
| """ | ||
| NIfTIExtension | ||
| * `ecode::Int32`: extension code that can be interpreted used `ecode(::NIfTIExtension)` | ||
| * `edata::Vector{UInt8}`: raw data with no byte-swapping | ||
| """ | ||
| struct NIfTIExtension | ||
| ecode::Int32 | ||
| edata::Vector{UInt8} | ||
| end | ||
|
|
||
| """ | ||
| NIfTI Extension Codes | ||
| * Ignore | ||
| * DICOM: intended for raw DICOM attributes | ||
| * AFNI: Robert W Cox: [email protected] https://afni.nimh.nih.gov/afni | ||
| * Comment: plain ASCII text only | ||
| * XCEDE: http://www.nbirn.net/Resources/Users/Applications/xcede/index.html | ||
| * JIMDimInfo: Dimensionalinformation for the JIM software (XML format) | ||
| * WorkflowFWDS: | ||
| * Freesurfer: | ||
| * PyPickle: embedded Python objects | ||
| * MiNDIdent: LONI MiND codes: http://www.loni.ucla.edu/twiki/bin/view/Main/MiND | ||
| * BValue | ||
| * SphericalDirection | ||
| * DTComponent | ||
| * SHCDegreeOrder | ||
| * Voxbo: www.voxbo.org | ||
| * Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation | ||
| * CIfTI | ||
| * VariableFrameTiming | ||
| * AgilentProcpar | ||
| * Eval | ||
| * Matlab | ||
| """ | ||
| ecode(x::NIfTIExtension) = to_ecode(x.ecode) | ||
| ecode(x::Vector{NIfTIExtension}) = map(ecode, x) | ||
|
|
||
|
|
||
| # Calculates the size of a NIfTI extension | ||
| """ | ||
| esize(ex::NIfTIExtension) | ||
| NIfTIExtensions should be of a byte size that is a mulitple of 16. This includes | ||
| raw encoding of the the `ecode` (as an Int32) and the esize itself (also as an | ||
| Int32). Therefore, `8 + sizeof(ex.edata)` should be divisible by 16. | ||
| """ | ||
| function esize(ex::NIfTIExtension) | ||
| ret = 8 + length(ex.edata) | ||
| @assert ret%16 != 0 "NIfTIExtension has innapropriate size. See docstrings for more details." | ||
| return ret | ||
| end | ||
|
|
||
| function read_extensions(io, n) | ||
| ret = NIfTIExtension[] | ||
| if eof(io) | ||
| return ret | ||
| else | ||
| b1 = read(io, UInt8) | ||
| # GZIP doesn't skip so we read and throw away | ||
| read(io, UInt8) | ||
| read(io, UInt8) | ||
| read(io, UInt8) | ||
| if b1 === zero(UInt8) | ||
| return ret | ||
| else | ||
| counter = position(io) | ||
| while counter < (n-1) | ||
| esize = read(io, Int32) | ||
| ec = read(io, Int32) | ||
| push!(ret, NIfTIExtension(ec, read!(io, Array{UInt8}(undef, esize-8)))) | ||
| counter += esize | ||
| end | ||
| return ret | ||
| end | ||
| end | ||
| end | ||
|
|
||
| function write(io::IO, x::Vector{NIfTIExtension}) | ||
| if isempty(x) | ||
| write(io, fill(UInt8(0), 4)) | ||
| else | ||
| write(io, UInt8[1, 0, 0, 0]) | ||
| for ex in x | ||
| write(io, Int32(esize(ex))) | ||
| write(io, ex.ecode) | ||
| write(io, ex.edata) | ||
| # write(io, zeros(UInt8, esize(ex) - length(ex.edata))) | ||
| end | ||
| end | ||
| end | ||
|
|
Oops, something went wrong.
a328763There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
@JuliaRegistrator register
a328763There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Registration pull request created: JuliaRegistries/General/29970
After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.
This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via: