Merge pull request #52 from JuliaNeuroscience/5.4

Patch bump for #51 and changed `nidim` to `to_dim_i16` b/c it is slightly faster and preps for
NIfTI-v2 headers

Project.toml

@@ -1,6 +1,6 @@
 name = "NIfTI"
 uuid = "a3a9e032-41b5-5fc4-967a-a6b7a19844d3"
-version = "0.5.3"
+version = "0.5.4"
 
 [deps]
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

src/NIfTI.jl

@@ -107,13 +107,6 @@ function byteswap(hdr::NIfTI1Header)
     hdr
 end
 
-function string_tuple(x::String, n::Int)
-    a = codeunits(x)
-    padding = zeros(UInt8, n-length(a))
-    (a..., padding...)
-end
-string_tuple(x::AbstractString) = string_tuple(bytestring(x))
-
 struct NIVolume{T<:Number,N,R} <: AbstractArray{T,N}
     header::NIfTI1Header
     extensions::Vector{NIfTIExtension}
@@ -131,22 +124,6 @@ NIVolume(header::NIfTI1Header, extensions::Vector{NIfTIExtension}, raw::Abstract
 NIVolume(header::NIfTI1Header, raw::AbstractArray{Bool,N}) where {N} =
     NIVolume{Bool,N,typeof(raw)}(header, NIfTIExtension[], raw)
 
-# Conversion factors to mm/ms
-# http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/xyzt_units.html
-const SPATIAL_UNIT_MULTIPLIERS = [
-    1000,   # 1 => NIfTI_UNITS_METER
-    1,      # 2 => NIfTI_UNITS_MM
-    0.001   # 3 => NIfTI_UNITS_MICRON
-]
-const TIME_UNIT_MULTIPLIERS = [
-    1000,   # NIfTI_UNITS_SEC
-    1,      # NIfTI_UNITS_MSEC
-    0.001,  # NIfTI_UNITS_USEC
-    1,      # NIfTI_UNITS_HZ
-    1,      # NIfTI_UNITS_PPM
-    1       # NIfTI_UNITS_RADS
-]
-
 # Always in mm
 voxel_size(header::NIfTI1Header) =
     [header.pixdim[i] * SPATIAL_UNIT_MULTIPLIERS[header.xyzt_units & Int8(3)] for i = 2:min(header.dim[1], 3)+1]
@@ -179,14 +156,6 @@ function dim_info(header::NIfTI1Header, dim_info::Tuple{T, T, T}) where {T<:Inte
     header.dim_info = to_dim_info(dim_info)
 end
 
-# Gets dim to be used in header
-function nidim(x::AbstractArray)
-    dim = ones(Int16, 8)
-    dim[1] = ndims(x)
-    dim[2:dim[1]+1] = [size(x)...]
-    return (dim...,)
-end
-
 # Gets the size of a type in bits
 nibitpix(t::Type) = Int16(sizeof(t)*8)
 nibitpix(::Type{Bool}) = Int16(1)
@@ -334,7 +303,7 @@ function NIVolume(
     end
 
     NIVolume(NIfTI1Header(SIZEOF_HDR1, string_tuple(data_type, 10), string_tuple(db_name, 18), extents, session_error,
-        regular, to_dim_info(dim_info), nidim(raw), intent_p1, intent_p2,
+        regular, to_dim_info(dim_info), to_dim_i16(size(raw)), intent_p1, intent_p2,
         intent_p3, intent_code, eltype_to_int16(t), nibitpix(t),
         slice_start, (qfac, voxel_size..., time_step, 0, 0, 0), 352,
         scl_slope, scl_inter, slice_end, slice_code,
@@ -348,7 +317,7 @@ end
 # Validates the header of a volume and updates it to match the volume's contents
 function niupdate(vol::NIVolume{T}) where {T}
     vol.header.sizeof_hdr = SIZEOF_HDR1
-    vol.header.dim = nidim(vol.raw)
+    vol.header.dim = to_dim_i16(size(vol.raw))
     vol.header.datatype = eltype_to_int16(T)
     vol.header.bitpix = nibitpix(T)
     vol.header.vox_offset = isempty(vol.extensions) ? Int32(352) :

src/parsers.jl

@@ -193,7 +193,41 @@ function hdr_to_img(file::AbstractString)
     end
 end
 
+function string_tuple(x::String, n::Int)
+    a = codeunits(x)
+    padding = zeros(UInt8, n-length(a))
+    (a..., padding...)
+end
+string_tuple(x::AbstractString) = string_tuple(bytestring(x))
+
+# Conversion factors to mm/ms
+# http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/xyzt_units.html
+const SPATIAL_UNIT_MULTIPLIERS = [
+    1000,   # 1 => NIfTI_UNITS_METER
+    1,      # 2 => NIfTI_UNITS_MM
+    0.001   # 3 => NIfTI_UNITS_MICRON
+]
+const TIME_UNIT_MULTIPLIERS = [
+    1000,   # NIfTI_UNITS_SEC
+    1,      # NIfTI_UNITS_MSEC
+    0.001,  # NIfTI_UNITS_USEC
+    1,      # NIfTI_UNITS_HZ
+    1,      # NIfTI_UNITS_PPM
+    1       # NIfTI_UNITS_RADS
+]
 
+# Gets dim to be used in header
+function to_dim_i16(x::NTuple{N}) where {N}
+    return ntuple(Val(8)) do i
+        if i === 1
+            Int16(N)
+        elseif i > (N + 1)
+            zero(Int16)
+        else
+            @inbounds(getfield(x, i - 1))
+        end
+    end
+end
 
 #=
 to_spatial_units(x::Int8) = _to_spatial_units(x & 0x07)