c_nifti 0.0.1

data/lib/c_nifti/header_element/datatype/unsigned_char.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class UnsignedChar < Base
+        def self.to_i; 2; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/unsigned_int.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class UnsignedInt < Base
+        def self.to_i; 768; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/unsigned_long_long.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class UnsignedLongLong < Base
+        def self.to_i; 1280; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/unsigned_short.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class UnsignedShort < Base
+        def self.to_i; 512; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/dimensions.rb

@@ -0,0 +1,53 @@
+module CNifti
+  module HeaderElement
+    module Dimensions
+      def ndim
+        @nifti_image.ndim
+      end
+
+      def nvox
+        @nifti_image.nvox
+      end
+
+      def nx
+        @nifti_image.nx
+      end
+
+      def ny
+        @nifti_image.ny
+      end
+
+      def nz
+        @nifti_image.nz
+      end
+
+      def nt
+        @nifti_image.nt
+      end
+
+      def nu
+        @nifti_image.nu
+      end
+
+      def nv
+        @nifti_image.nv
+      end
+
+      def nw
+        @nifti_image.nw
+      end
+
+      def dim
+        @nifti_image.dim
+      end
+
+      def nbyper
+        @nifti_image.nbyper
+      end
+
+      def datatype
+        CNifti::HeaderElement::Datatype.to_datatype(@nifti_image.datatype)
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/intents.rb

@@ -0,0 +1,25 @@
+module CNifti
+  module HeaderElement
+    module Intents
+      def intent_code
+        @nifti_image.intent_code
+      end
+
+      def intent_p1
+        @nifti_image.intent_p1
+      end
+
+      def intent_p2
+        @nifti_image.intent_p2
+      end
+
+      def intent_p3
+        @nifti_image.intent_p3
+      end
+
+      def intent_name
+        @nifti_image.intent_name
+      end      
+    end
+  end
+end

data/lib/c_nifti/header_element/metadata.rb

@@ -0,0 +1,49 @@
+module CNifti
+  module HeaderElement
+    module Metadata
+      def description
+        @nifti_image.descrip
+      end
+
+      def description=(value)
+        @nifti_image.descrip = value
+      end
+
+      def aux_file
+        @nifti_image.aux_file
+      end
+
+      def aux_file=(value)
+        @nifti_image.aux_file = value
+      end
+
+      def file_name
+        @nifti_image.fname
+      end
+
+      def file_name=(value)
+        @nifti_image.filenames = value # This actually sets iname and iname_offset as well
+      end
+
+      def image_name
+        @nifti_image.iname
+      end
+
+      def image_name_offset
+        @nifti_image.iname_offset
+      end
+
+      def swapsize
+        @nifti_image.swapsize
+      end
+
+      def byteorder
+        @nifti_image.byteorder
+      end
+
+      def analyze75_orient
+        @nifti_image.analyze75_orient
+      end      
+    end
+  end
+end

data/lib/c_nifti/header_element/miscellaneous.rb

@@ -0,0 +1,25 @@
+module CNifti
+  module HeaderElement
+    module Miscellaneous
+      def scl_slope
+        @nifti_image.scl_slope
+      end
+
+      def scl_inter
+        @nifti_image.scl_inter
+      end
+
+      def cal_min
+        @nifti_image.cal_min
+      end
+
+      def cal_max
+        @nifti_image.cal_max
+      end
+
+      def type
+        @nifti_image.nifti_type
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/quaternions.rb

@@ -0,0 +1,33 @@
+module CNifti
+  module HeaderElement
+    module Quaternions
+      def quatern_b
+        @nifti_image.quatern_b
+      end
+
+      def quatern_c
+        @nifti_image.quatern_c
+      end
+
+      def quatern_d
+        @nifti_image.quatern_d
+      end
+
+      def qoffset_x
+        @nifti_image.qoffset_x
+      end
+
+      def qoffset_y
+        @nifti_image.qoffset_y
+      end
+
+      def qoffset_z
+        @nifti_image.qoffset_z
+      end
+
+      def qfac
+        @nifti_image.qfac
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/spacings.rb

@@ -0,0 +1,45 @@
+module CNifti
+  module HeaderElement
+    module Spacings
+      def dx
+        @nifti_image.dx
+      end
+
+      def dy
+        @nifti_image.dy
+      end
+
+      def dz
+        @nifti_image.dz
+      end
+
+      def dt
+        @nifti_image.dt
+      end
+
+      def du
+        @nifti_image.du
+      end
+
+      def dv
+        @nifti_image.dv
+      end
+
+      def dw
+        @nifti_image.dw
+      end
+
+      def pixel_dimensions
+        @nifti_image.pixdim
+      end
+
+      def qform_code
+        @nifti_image.qform_code
+      end
+
+      def sform_code
+        @nifti_image.sform_code
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/timings.rb

@@ -0,0 +1,37 @@
+module CNifti
+  module HeaderElement
+    module Timings
+      def freq_dim
+        @nifti_image.freq_dim
+      end
+
+      def phase_dim
+        @nifti_image.phase_dim
+      end
+
+      def slice_dim
+        @nifti_image.slice_dim
+      end
+
+      def slice_code
+        @nifti_image.slice_code
+      end
+
+      def slice_start
+        @nifti_image.slice_start
+      end
+
+      def slice_end
+        @nifti_image.slice_end
+      end
+
+      def slice_duration
+        @nifti_image.slice_duration
+      end
+
+      def toffset
+        @nifti_image.toffset
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/transforms.rb

@@ -0,0 +1,21 @@
+module CNifti
+  module HeaderElement
+    module Transforms
+      def qto_xyz
+        @nifti_image.qto_xyz
+      end
+
+      def qto_ijk
+        @nifti_image.qto_ijk
+      end
+
+      def sto_xyz
+        @nifti_image.sto_xyz
+      end
+
+      def sto_ijk
+        @nifti_image.sto_ijk
+      end
+    end
+  end
+end

data/lib/c_nifti/image.rb

@@ -0,0 +1,31 @@
+require 'nifticlib'
+
+module CNifti
+  class Image
+    attr_reader :header, :data
+
+    def initialize(attributes={dimensions: [1, 1], datatype: HeaderElement::Datatype::SignedInt})
+      @nifti_image = NIfTICLib::NIfTIImage.new(([attributes[:dimensions].count] + attributes[:dimensions]), # The first element is the dimensions count which is concatenated to the actual dimensions
+                                              attributes[:datatype].to_i,                                  # Integer datatype
+                                              1)                                                           # Always initialize the data
+
+      @header = Header.new(@nifti_image)
+      @data = Data.new(@nifti_image)
+    end
+
+    def open(path)
+      @nifti_image = NIfTICLib.read(path)
+
+      @header = Header.new(@nifti_image)
+      @data = Data.new(@nifti_image)
+
+      self
+    end
+
+    def save_as(path)
+      NIfTICLib.write(@nifti_image, path)
+
+      return true
+    end
+  end
+end

data/lib/c_nifti/version.rb

@@ -0,0 +1,3 @@
+module CNifti
+  VERSION = "0.0.1"
+end

data/lib/nifticlib.rb

@@ -0,0 +1 @@
+require 'nifticlib/nifticlib'

data/spec/data_spec.rb

@@ -0,0 +1,112 @@
+require 'spec_helper'
+
+describe CNifti::Data do
+  let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
+  subject { CNifti::Data.new(nifti_image) }
+
+  describe 'raw' do
+    it 'is expected call the data method from NIfTICLib::NIfTIImage' do
+      nifti_image.expects(:data).returns([4])
+
+      expect(subject.raw).to eq([4])
+    end
+  end
+
+  describe 'get_raw' do
+    it 'is expected call the get_data method from NIfTICLib::NIfTIImage' do
+      nifti_image.expects(:get_data).with(0).returns(4)
+
+      expect(subject.get_raw(0)).to eq(4)
+    end
+  end
+
+  describe 'set_raw' do
+    it 'is expected call the set_data method from NIfTICLib::NIfTIImage' do
+      nifti_image.expects(:set_data).with(0, 4).returns(4)
+
+      expect(subject.set_raw(0,4)).to eq(4)
+    end
+  end
+
+  describe 'shape' do
+    let!(:dim) { [2, 3, 3] }
+
+    before :each do
+      nifti_image.stubs(:dim).returns(dim)
+    end
+
+    it 'is expected call the set_data method from NIfTICLib::NIfTIImage' do
+      expect(subject.shape).to eq(dim[1..-1])
+    end
+  end
+
+  describe '[]' do
+    let!(:shape) { [3, 3] }
+
+    before :each do
+      nifti_image.stubs(:shape).returns(shape)
+    end
+
+    context 'with an index over bounds' do
+      let(:index) {3}
+
+      it 'is expected to raise a IndexError' do
+        expect{ subject[index] }.to raise_error(IndexError)
+      end
+    end
+
+    context 'with valid index' do
+      context 'with the last dimension' do
+        context 'with a Range' do
+          let(:index) { 0..1 }
+
+          it 'is expected to return a array' do
+            expect(subject[0][index]).to be_a(Array)
+          end
+        end
+
+        context 'with a Fixnum' do
+          let(:index) {2}
+
+          it 'is expected to return a Value' do
+            expect(subject[0][index]).to eq(0)
+          end
+        end
+      end
+
+      context 'with a intermediary dimension' do
+        let(:index) {2}
+
+        it 'is expected to return a Data instance' do
+          expect(subject[index]).to be_a(CNifti::Data)
+        end
+      end
+    end
+  end
+
+  describe '[]=' do
+    let!(:shape) { [3, 3] }
+
+    before :each do
+      nifti_image.stubs(:shape).returns(shape)
+    end
+
+    context 'with the last dimension' do
+      context 'with a Fixnum' do
+        let(:index) {2}
+
+        it 'is expected to return a Value' do
+          expect(subject[0][index] = 2).to eq(2)
+        end
+      end
+    end
+
+    context 'with a intermediary dimension' do
+      let(:index) {2}
+
+      it 'is expected to raise a IndexError' do
+        expect{ subject[index] = 2 }.to raise_error(IndexError)
+      end
+    end
+  end
+end