c_nifti 0.0.1

data/spec/header_element/miscellaneous_spec.rb

@@ -0,0 +1,48 @@
+require 'spec_helper'
+
+describe CNifti::Header do
+  let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
+  subject { CNifti::Header.new(nifti_image) }
+
+  describe 'miscellaneous' do
+    describe 'scl_slope' do
+      it 'is expected call the scl_slope method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:scl_slope).returns(1.4)
+
+        expect(subject.scl_slope).to eq(1.4)
+      end
+    end
+
+    describe 'scl_inter' do
+      it 'is expected call the scl_inter method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:scl_inter).returns(1.4)
+
+        expect(subject.scl_inter).to eq(1.4)
+      end
+    end
+
+    describe 'cal_min' do
+      it 'is expected call the cal_min method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:cal_min).returns(1.4)
+
+        expect(subject.cal_min).to eq(1.4)
+      end
+    end
+
+    describe 'cal_max' do
+      it 'is expected call the cal_max method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:cal_max).returns(1.4)
+
+        expect(subject.cal_max).to eq(1.4)
+      end
+    end
+
+    describe 'type' do
+      it 'is expected call the nifti_type method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:nifti_type).returns(1)
+
+        expect(subject.type).to eq(1)
+      end
+    end
+  end
+end

data/spec/header_element/quaternions_spec.rb

@@ -0,0 +1,64 @@
+require 'spec_helper'
+
+describe CNifti::Header do
+  let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
+  subject { CNifti::Header.new(nifti_image) }
+
+  describe 'quaternions' do
+    describe 'quatern_b' do
+      it 'is expected call the quatern_b method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:quatern_b).returns(1.4)
+
+        expect(subject.quatern_b).to eq(1.4)
+      end
+    end
+
+    describe 'quatern_c' do
+      it 'is expected call the quatern_c method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:quatern_c).returns(1.4)
+
+        expect(subject.quatern_c).to eq(1.4)
+      end
+    end
+
+    describe 'quatern_d' do
+      it 'is expected call the quatern_d method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:quatern_d).returns(1.4)
+
+        expect(subject.quatern_d).to eq(1.4)
+      end
+    end
+
+    describe 'qoffset_x' do
+      it 'is expected call the qoffset_x method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:qoffset_x).returns(1.4)
+
+        expect(subject.qoffset_x).to eq(1.4)
+      end
+    end
+
+    describe 'qoffset_y' do
+      it 'is expected call the qoffset_y method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:qoffset_y).returns(1.4)
+
+        expect(subject.qoffset_y).to eq(1.4)
+      end
+    end
+
+    describe 'qoffset_z' do
+      it 'is expected call the qoffset_z method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:qoffset_z).returns(1.4)
+
+        expect(subject.qoffset_z).to eq(1.4)
+      end
+    end
+
+    describe 'qfac' do
+      it 'is expected call the qfac method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:qfac).returns(1.4)
+
+        expect(subject.qfac).to eq(1.4)
+      end
+    end
+  end
+end

data/spec/header_element/spacings_spec.rb

@@ -0,0 +1,88 @@
+require 'spec_helper'
+
+describe CNifti::Header do
+  let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
+  subject { CNifti::Header.new(nifti_image) }
+
+  describe 'spacings' do
+    describe 'dx' do
+      it 'is expected call the dx method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:dx).returns(1.4)
+
+        expect(subject.dx).to eq(1.4)
+      end
+    end
+
+    describe 'dy' do
+      it 'is expected call the dy method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:dy).returns(1.4)
+
+        expect(subject.dy).to eq(1.4)
+      end
+    end
+
+    describe 'dz' do
+      it 'is expected call the dz method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:dz).returns(1.4)
+
+        expect(subject.dz).to eq(1.4)
+      end
+    end
+
+    describe 'dt' do
+      it 'is expected call the dt method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:dt).returns(1.4)
+
+        expect(subject.dt).to eq(1.4)
+      end
+    end
+
+    describe 'du' do
+      it 'is expected call the du method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:du).returns(1.4)
+
+        expect(subject.du).to eq(1.4)
+      end
+    end
+
+    describe 'dv' do
+      it 'is expected call the dv method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:dv).returns(1.4)
+
+        expect(subject.dv).to eq(1.4)
+      end
+    end
+
+    describe 'dw' do
+      it 'is expected call the dw method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:dw).returns(1.4)
+
+        expect(subject.dw).to eq(1.4)
+      end
+    end
+
+    describe 'pixel_dimensions' do
+      it 'is expected call the pixdim method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:pixdim).returns([1.4])
+
+        expect(subject.pixel_dimensions).to eq([1.4])
+      end
+    end
+
+    describe 'qform_code' do
+      it 'is expected call the qform_code method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:qform_code).returns(1.4)
+
+        expect(subject.qform_code).to eq(1.4)
+      end
+    end
+
+    describe 'sform_code' do
+      it 'is expected call the sform_code method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:sform_code).returns(1.4)
+
+        expect(subject.sform_code).to eq(1.4)
+      end
+    end
+  end
+end

data/spec/header_element/timings_spec.rb

@@ -0,0 +1,72 @@
+require 'spec_helper'
+
+describe CNifti::Header do
+  let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
+  subject { CNifti::Header.new(nifti_image) }
+
+  describe 'timings' do
+    describe 'freq_dim' do
+      it 'is expected call the freq_dim method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:freq_dim).returns(4)
+
+        expect(subject.freq_dim).to eq(4)
+      end
+    end
+
+    describe 'phase_dim' do
+      it 'is expected call the phase_dim method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:phase_dim).returns(4)
+
+        expect(subject.phase_dim).to eq(4)
+      end
+    end
+
+    describe 'slice_dim' do
+      it 'is expected call the slice_dim method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:slice_dim).returns(4)
+
+        expect(subject.slice_dim).to eq(4)
+      end
+    end
+
+    describe 'slice_code' do
+      it 'is expected call the slice_code method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:slice_code).returns(4)
+
+        expect(subject.slice_code).to eq(4)
+      end
+    end
+
+    describe 'slice_start' do
+      it 'is expected call the slice_start method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:slice_start).returns(4)
+
+        expect(subject.slice_start).to eq(4)
+      end
+    end
+
+    describe 'slice_end' do
+      it 'is expected call the slice_end method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:slice_end).returns(4)
+
+        expect(subject.slice_end).to eq(4)
+      end
+    end
+
+    describe 'slice_duration' do
+      it 'is expected call the slice_duration method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:slice_duration).returns(1.4)
+
+        expect(subject.slice_duration).to eq(1.4)
+      end
+    end
+
+    describe 'toffset' do
+      it 'is expected call the toffset method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:toffset).returns(1.4)
+
+        expect(subject.toffset).to eq(1.4)
+      end
+    end
+  end
+end

data/spec/header_element/transforms_spec.rb

@@ -0,0 +1,64 @@
+require 'spec_helper'
+
+describe CNifti::Header do
+  let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
+  subject { CNifti::Header.new(nifti_image) }
+
+  describe 'transforms' do
+    describe 'qto_xyz' do
+      it 'is expected call the qto_xyz method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:qto_xyz).returns([[1,0,0,0],
+                                              [0,1,0,0],
+                                              [0,0,1,0],
+                                              [0,0,0,1]])
+
+        expect(subject.qto_xyz).to eq([[1,0,0,0],
+                                       [0,1,0,0],
+                                       [0,0,1,0],
+                                       [0,0,0,1]])
+      end
+    end
+
+    describe 'qto_ijk' do
+      it 'is expected call the qto_ijk method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:qto_ijk).returns([[1,0,0,0],
+                                              [0,1,0,0],
+                                              [0,0,1,0],
+                                              [0,0,0,1]])
+
+        expect(subject.qto_ijk).to eq([[1,0,0,0],
+                                       [0,1,0,0],
+                                       [0,0,1,0],
+                                       [0,0,0,1]])
+      end
+    end
+
+    describe 'sto_xyz' do
+      it 'is expected call the sto_xyz method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:sto_xyz).returns([[1,0,0,0],
+                                              [0,1,0,0],
+                                              [0,0,1,0],
+                                              [0,0,0,1]])
+
+        expect(subject.sto_xyz).to eq([[1,0,0,0],
+                                       [0,1,0,0],
+                                       [0,0,1,0],
+                                       [0,0,0,1]])
+      end
+    end
+
+    describe 'sto_ijk' do
+      it 'is expected call the sto_ijk method from NIfTICLib::NIfTIImage' do
+        nifti_image.expects(:sto_ijk).returns([[1,0,0,0],
+                                              [0,1,0,0],
+                                              [0,0,1,0],
+                                              [0,0,0,1]])
+
+        expect(subject.sto_ijk).to eq([[1,0,0,0],
+                                       [0,1,0,0],
+                                       [0,0,1,0],
+                                       [0,0,0,1]])
+      end
+    end
+  end
+end

data/spec/image_spec.rb

@@ -0,0 +1,39 @@
+require 'spec_helper'
+
+describe CNifti::Image do
+  describe 'new' do
+    let(:dims) { [3,3,3] }
+
+    before :each do
+      CNifti::HeaderElement::Datatype::Base.expects(:to_i).returns(0)
+    end
+
+    it 'is expected call the new method from NIfTICLib::NIfTIImage' do
+      NIfTICLib::NIfTIImage.expects(:new).with(([3] + dims), 0, 1)
+
+      CNifti::Image.new(dimensions: dims, datatype: CNifti::HeaderElement::Datatype::Base)
+    end
+  end
+
+  describe 'open' do
+    let(:path) { 'test/test.nii.gz' }
+    let(:nifti_image) { FactoryGirl.build(:nifti_image) }
+
+    it 'is expected to read from path and set the header and data' do
+      NIfTICLib.expects(:read).with(path).returns(nifti_image)
+
+      expect(subject.open(path)).to be_a(CNifti::Image)
+    end
+  end
+
+  describe 'save_as' do
+    let(:path) { 'test/test.nii.gz' }
+    let(:nifti_image) { FactoryGirl.build(:nifti_image) }
+
+    it 'is expected to read from path and set the header and data' do
+      NIfTICLib.expects(:write).returns(nifti_image)
+
+      expect(subject.save_as(path)).to be_truthy
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,85 @@
+require 'mocha/api'
+
+# Test coverage report
+require 'simplecov'
+
+SimpleCov.start do
+  add_filter "/spec/"
+  add_filter "/features/"
+
+  coverage_dir 'coverage/rspec'
+end
+
+require 'c_nifti'
+
+require 'factory_girl'
+FactoryGirl.find_definitions
+
+# This file was generated by the `rails generate rspec:install` command. Conventionally, all
+# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
+# The generated `.rspec` file contains `--require rails_helper` which will cause this
+# file to always be loaded, without a need to explicitly require it in any files.
+#
+# Given that it is always loaded, you are encouraged to keep this file as
+# light-weight as possible. Requiring heavyweight dependencies from this file
+# will add to the boot time of your test suite on EVERY test run, even for an
+# individual file that may not need all of that loaded. Instead, make a
+# separate helper file that requires this one and then use it only in the specs
+# that actually need it.
+#
+# The `.rspec` file also contains a few flags that are not defaults but that
+# users commonly want.
+#
+# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
+RSpec.configure do |config|
+# The settings below are suggested to provide a good initial experience
+# with RSpec, but feel free to customize to your heart's content.
+
+  # These two settings work together to allow you to limit a spec run
+  # to individual examples or groups you care about by tagging them with
+  # `:focus` metadata. When nothing is tagged with `:focus`, all examples
+  # get run.
+  config.filter_run :focus
+  config.run_all_when_everything_filtered = true
+
+  # Many RSpec users commonly either run the entire suite or an individual
+  # file, and it's useful to allow more verbose output when running an
+  # individual spec file.
+  if config.files_to_run.one?
+    # Use the documentation formatter for detailed output,
+    # unless a formatter has already been configured
+    # (e.g. via a command-line flag).
+    config.default_formatter = 'doc'
+  end
+
+  # Print the 10 slowest examples and example groups at the
+  # end of the spec run, to help surface which specs are running
+  # particularly slow.
+  config.profile_examples = 10
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  config.order = :random
+
+  # Seed global randomization in this process using the `--seed` CLI option.
+  # Setting this allows you to use `--seed` to deterministically reproduce
+  # test failures related to randomization by passing the same `--seed` value
+  # as the one that triggered the failure.
+  Kernel.srand config.seed
+
+  # rspec-expectations config goes here. You can use an alternate
+  # assertion/expectation library such as wrong or the stdlib/minitest
+  # assertions if you prefer.
+  config.expect_with :rspec do |expectations|
+    # Enable only the newer, non-monkey-patching expect syntax.
+    # For more details, see:
+    #   - http://myronmars.to/n/dev-blog/2012/06/rspecs-new-expectation-syntax
+    expectations.syntax = :expect
+  end
+
+  # rspec-mocks config goes here. You can use an alternate test double
+  # library (such as bogus or mocha) by changing the `mock_with` option here.
+  config.mock_with :mocha
+end