c_nifti 0.0.1
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- checksums.yaml +7 -0
- data/.gitignore +37 -0
- data/.rspec +2 -0
- data/.ruby-gemset +1 -0
- data/.ruby-version +1 -0
- data/COPYING +621 -0
- data/COPYING.lesser +166 -0
- data/Gemfile +4 -0
- data/README.md +117 -0
- data/Rakefile +6 -0
- data/c_nifti.gemspec +31 -0
- data/ext/nifticlib/extconf.rb +30 -0
- data/ext/nifticlib/include/nifti_image.h +2 -0
- data/ext/nifticlib/include/nifti_image_converters.h +3 -0
- data/ext/nifticlib/include/nifti_image_dimensions.h +1 -0
- data/ext/nifticlib/include/nifti_image_intents.h +1 -0
- data/ext/nifticlib/include/nifti_image_metadata.h +1 -0
- data/ext/nifticlib/include/nifti_image_quaternions.h +1 -0
- data/ext/nifticlib/include/nifti_image_spacings.h +1 -0
- data/ext/nifticlib/include/nifti_image_timings.h +1 -0
- data/ext/nifticlib/include/nifti_image_transforms.h +1 -0
- data/ext/nifticlib/nifti_image.c +169 -0
- data/ext/nifticlib/nifti_image_converters.c +65 -0
- data/ext/nifticlib/nifti_image_dimensions.c +113 -0
- data/ext/nifticlib/nifti_image_intents.c +45 -0
- data/ext/nifticlib/nifti_image_metadata.c +133 -0
- data/ext/nifticlib/nifti_image_quaternions.c +59 -0
- data/ext/nifticlib/nifti_image_spacings.c +87 -0
- data/ext/nifticlib/nifti_image_timings.c +66 -0
- data/ext/nifticlib/nifti_image_transforms.c +38 -0
- data/ext/nifticlib/nifticlib-2.0.0/CMakeLists.txt +140 -0
- data/ext/nifticlib/nifticlib-2.0.0/CTestConfig.cmake +13 -0
- data/ext/nifticlib/nifticlib-2.0.0/LICENSE +9 -0
- data/ext/nifticlib/nifticlib-2.0.0/Makefile +265 -0
- data/ext/nifticlib/nifticlib-2.0.0/Makefile.cross_mingw32 +94 -0
- data/ext/nifticlib/nifticlib-2.0.0/README +79 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/CMakeLists.txt +7 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz +0 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/Makefile +21 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/README_regress +50 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/@show.diffs +33 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/@test +80 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/CMakeLists.txt +47 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/bricks_test.sh +32 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/comment_test.sh +65 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dci_test.sh +46 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dsets_test.sh +61 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dts_test.sh +75 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/fetch_data_test.sh +45 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/mod_header_test.sh +60 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/newfiles_test.sh +36 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c01.versions +10 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c02.nt.help +5 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c03.hist +5 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c04.disp.anat0.info +7 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c05.mod.hdr +9 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c06.add.ext +22 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c07.cbl.4bricks +8 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c08.dts.19.36.11 +4 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c09.dts4.compare +9 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c10.dci.ts4 +15 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c10a.dci.run.210 +16 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c11.add.comment +8 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c12.check.comments +7 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c13.check.hdrs +5 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c14.make.dsets +21 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c15.new.files +21 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c16.rand.swap +35 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c17.file.case +34 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/niftilib/CMakeLists.txt +15 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/niftilib/nifti_test.c +690 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/niftilib/nifti_test2.c +32 -0
- data/ext/nifticlib/nifticlib-2.0.0/Updates.txt +110 -0
- data/ext/nifticlib/nifticlib-2.0.0/bin/.gitkeep +0 -0
- data/ext/nifticlib/nifticlib-2.0.0/docs/Doxy_nifti.txt +123 -0
- data/ext/nifticlib/nifticlib-2.0.0/docs/Doxyfile.ORIG +746 -0
- data/ext/nifticlib/nifticlib-2.0.0/examples/CMakeLists.txt +15 -0
- data/ext/nifticlib/nifticlib-2.0.0/examples/Makefile +48 -0
- data/ext/nifticlib/nifticlib-2.0.0/examples/clib_01_read_write.c +94 -0
- data/ext/nifticlib/nifticlib-2.0.0/examples/fsl_api_driver.c +142 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/CMakeLists.txt +32 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/Makefile +29 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/fslio.c +2426 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/fslio.tcl +83 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imcp +65 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imglob +59 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imln +37 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/immv +64 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imrm +29 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imtest +53 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/remove_ext +33 -0
- data/ext/nifticlib/nifticlib-2.0.0/include/.gitkeep +0 -0
- data/ext/nifticlib/nifticlib-2.0.0/nifticdf/CMakeLists.txt +28 -0
- data/ext/nifticlib/nifticlib-2.0.0/nifticdf/Makefile +28 -0
- data/ext/nifticlib/nifticlib-2.0.0/nifticdf/nifticdf.c +11107 -0
- data/ext/nifticlib/nifticlib-2.0.0/niftilib/CMakeLists.txt +33 -0
- data/ext/nifticlib/nifticlib-2.0.0/niftilib/Makefile +31 -0
- data/ext/nifticlib/nifticlib-2.0.0/niftilib/nifti1_io.c +7509 -0
- data/ext/nifticlib/nifticlib-2.0.0/packaging/DevPackage.template +18 -0
- data/ext/nifticlib/nifticlib-2.0.0/packaging/nifticlib.spec +62 -0
- data/ext/nifticlib/nifticlib-2.0.0/real_easy/nifti1_read_write.c +361 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/CMakeLists.txt +73 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/Makefile +55 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/nifti1_test.c +95 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/nifti_stats.c +95 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/nifti_tool.c +4193 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/nifti_tool.h +163 -0
- data/ext/nifticlib/nifticlib-2.0.0/znzlib/CMakeLists.txt +31 -0
- data/ext/nifticlib/nifticlib-2.0.0/znzlib/Makefile +33 -0
- data/ext/nifticlib/nifticlib-2.0.0/znzlib/znzlib.c +322 -0
- data/ext/nifticlib/nifticlib.c +107 -0
- data/ext/nifticlib/patches/nifticlib_fpic.patch +13 -0
- data/features/read_modify_write.feature +11 -0
- data/features/step_definitions/nifti_image_steps.rb +16 -0
- data/features/support/env.rb +14 -0
- data/features/support/fixtures/sample.nii.gz +0 -0
- data/lib/c_nifti.rb +9 -0
- data/lib/c_nifti/data.rb +70 -0
- data/lib/c_nifti/header.rb +16 -0
- data/lib/c_nifti/header_element.rb +13 -0
- data/lib/c_nifti/header_element/datatype.rb +49 -0
- data/lib/c_nifti/header_element/datatype/base.rb +9 -0
- data/lib/c_nifti/header_element/datatype/binary.rb +11 -0
- data/lib/c_nifti/header_element/datatype/double.rb +11 -0
- data/lib/c_nifti/header_element/datatype/float.rb +11 -0
- data/lib/c_nifti/header_element/datatype/long_double.rb +11 -0
- data/lib/c_nifti/header_element/datatype/long_long.rb +11 -0
- data/lib/c_nifti/header_element/datatype/signed_char.rb +11 -0
- data/lib/c_nifti/header_element/datatype/signed_int.rb +11 -0
- data/lib/c_nifti/header_element/datatype/signed_short.rb +11 -0
- data/lib/c_nifti/header_element/datatype/unsigned_char.rb +11 -0
- data/lib/c_nifti/header_element/datatype/unsigned_int.rb +11 -0
- data/lib/c_nifti/header_element/datatype/unsigned_long_long.rb +11 -0
- data/lib/c_nifti/header_element/datatype/unsigned_short.rb +11 -0
- data/lib/c_nifti/header_element/dimensions.rb +53 -0
- data/lib/c_nifti/header_element/intents.rb +25 -0
- data/lib/c_nifti/header_element/metadata.rb +49 -0
- data/lib/c_nifti/header_element/miscellaneous.rb +25 -0
- data/lib/c_nifti/header_element/quaternions.rb +33 -0
- data/lib/c_nifti/header_element/spacings.rb +45 -0
- data/lib/c_nifti/header_element/timings.rb +37 -0
- data/lib/c_nifti/header_element/transforms.rb +21 -0
- data/lib/c_nifti/image.rb +31 -0
- data/lib/c_nifti/version.rb +3 -0
- data/lib/nifticlib.rb +1 -0
- data/spec/data_spec.rb +112 -0
- data/spec/factories/nifti_images.rb +9 -0
- data/spec/header_element/datatype/base_spec.rb +9 -0
- data/spec/header_element/datatype/binary_spec.rb +9 -0
- data/spec/header_element/datatype/double_spec.rb +9 -0
- data/spec/header_element/datatype/float_spec.rb +9 -0
- data/spec/header_element/datatype/long_double_spec.rb +9 -0
- data/spec/header_element/datatype/long_long_spec.rb +9 -0
- data/spec/header_element/datatype/signed_char_spec.rb +9 -0
- data/spec/header_element/datatype/signed_int_spec.rb +9 -0
- data/spec/header_element/datatype/signed_short_spec.rb +9 -0
- data/spec/header_element/datatype/unsigned_char_spec.rb +9 -0
- data/spec/header_element/datatype/unsigned_int_spec.rb +9 -0
- data/spec/header_element/datatype/unsigned_long_long.rb +9 -0
- data/spec/header_element/datatype/unsigned_short_spec.rb +9 -0
- data/spec/header_element/datatype_spec.rb +109 -0
- data/spec/header_element/dimensions_spec.rb +105 -0
- data/spec/header_element/intents_spec.rb +48 -0
- data/spec/header_element/metadata_spec.rb +96 -0
- data/spec/header_element/miscellaneous_spec.rb +48 -0
- data/spec/header_element/quaternions_spec.rb +64 -0
- data/spec/header_element/spacings_spec.rb +88 -0
- data/spec/header_element/timings_spec.rb +72 -0
- data/spec/header_element/transforms_spec.rb +64 -0
- data/spec/image_spec.rb +39 -0
- data/spec/spec_helper.rb +85 -0
- metadata +363 -0
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require 'spec_helper'
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describe CNifti::Header do
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let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
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subject { CNifti::Header.new(nifti_image) }
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describe 'miscellaneous' do
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describe 'scl_slope' do
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it 'is expected call the scl_slope method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:scl_slope).returns(1.4)
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expect(subject.scl_slope).to eq(1.4)
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end
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end
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describe 'scl_inter' do
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it 'is expected call the scl_inter method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:scl_inter).returns(1.4)
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expect(subject.scl_inter).to eq(1.4)
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end
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end
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describe 'cal_min' do
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it 'is expected call the cal_min method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:cal_min).returns(1.4)
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expect(subject.cal_min).to eq(1.4)
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end
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end
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describe 'cal_max' do
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it 'is expected call the cal_max method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:cal_max).returns(1.4)
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expect(subject.cal_max).to eq(1.4)
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end
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end
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describe 'type' do
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it 'is expected call the nifti_type method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:nifti_type).returns(1)
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expect(subject.type).to eq(1)
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end
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end
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end
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end
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require 'spec_helper'
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describe CNifti::Header do
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let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
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subject { CNifti::Header.new(nifti_image) }
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describe 'quaternions' do
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describe 'quatern_b' do
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it 'is expected call the quatern_b method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:quatern_b).returns(1.4)
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expect(subject.quatern_b).to eq(1.4)
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end
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end
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describe 'quatern_c' do
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it 'is expected call the quatern_c method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:quatern_c).returns(1.4)
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expect(subject.quatern_c).to eq(1.4)
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end
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end
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describe 'quatern_d' do
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it 'is expected call the quatern_d method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:quatern_d).returns(1.4)
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expect(subject.quatern_d).to eq(1.4)
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end
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end
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describe 'qoffset_x' do
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it 'is expected call the qoffset_x method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:qoffset_x).returns(1.4)
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expect(subject.qoffset_x).to eq(1.4)
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end
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end
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describe 'qoffset_y' do
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it 'is expected call the qoffset_y method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:qoffset_y).returns(1.4)
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expect(subject.qoffset_y).to eq(1.4)
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end
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end
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describe 'qoffset_z' do
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it 'is expected call the qoffset_z method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:qoffset_z).returns(1.4)
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expect(subject.qoffset_z).to eq(1.4)
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end
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end
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describe 'qfac' do
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it 'is expected call the qfac method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:qfac).returns(1.4)
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expect(subject.qfac).to eq(1.4)
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end
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end
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end
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end
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require 'spec_helper'
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describe CNifti::Header do
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let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
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subject { CNifti::Header.new(nifti_image) }
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describe 'spacings' do
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describe 'dx' do
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it 'is expected call the dx method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:dx).returns(1.4)
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expect(subject.dx).to eq(1.4)
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end
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end
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describe 'dy' do
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it 'is expected call the dy method from NIfTICLib::NIfTIImage' do
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nifti_image.expects(:dy).returns(1.4)
|
19
|
+
|
20
|
+
expect(subject.dy).to eq(1.4)
|
21
|
+
end
|
22
|
+
end
|
23
|
+
|
24
|
+
describe 'dz' do
|
25
|
+
it 'is expected call the dz method from NIfTICLib::NIfTIImage' do
|
26
|
+
nifti_image.expects(:dz).returns(1.4)
|
27
|
+
|
28
|
+
expect(subject.dz).to eq(1.4)
|
29
|
+
end
|
30
|
+
end
|
31
|
+
|
32
|
+
describe 'dt' do
|
33
|
+
it 'is expected call the dt method from NIfTICLib::NIfTIImage' do
|
34
|
+
nifti_image.expects(:dt).returns(1.4)
|
35
|
+
|
36
|
+
expect(subject.dt).to eq(1.4)
|
37
|
+
end
|
38
|
+
end
|
39
|
+
|
40
|
+
describe 'du' do
|
41
|
+
it 'is expected call the du method from NIfTICLib::NIfTIImage' do
|
42
|
+
nifti_image.expects(:du).returns(1.4)
|
43
|
+
|
44
|
+
expect(subject.du).to eq(1.4)
|
45
|
+
end
|
46
|
+
end
|
47
|
+
|
48
|
+
describe 'dv' do
|
49
|
+
it 'is expected call the dv method from NIfTICLib::NIfTIImage' do
|
50
|
+
nifti_image.expects(:dv).returns(1.4)
|
51
|
+
|
52
|
+
expect(subject.dv).to eq(1.4)
|
53
|
+
end
|
54
|
+
end
|
55
|
+
|
56
|
+
describe 'dw' do
|
57
|
+
it 'is expected call the dw method from NIfTICLib::NIfTIImage' do
|
58
|
+
nifti_image.expects(:dw).returns(1.4)
|
59
|
+
|
60
|
+
expect(subject.dw).to eq(1.4)
|
61
|
+
end
|
62
|
+
end
|
63
|
+
|
64
|
+
describe 'pixel_dimensions' do
|
65
|
+
it 'is expected call the pixdim method from NIfTICLib::NIfTIImage' do
|
66
|
+
nifti_image.expects(:pixdim).returns([1.4])
|
67
|
+
|
68
|
+
expect(subject.pixel_dimensions).to eq([1.4])
|
69
|
+
end
|
70
|
+
end
|
71
|
+
|
72
|
+
describe 'qform_code' do
|
73
|
+
it 'is expected call the qform_code method from NIfTICLib::NIfTIImage' do
|
74
|
+
nifti_image.expects(:qform_code).returns(1.4)
|
75
|
+
|
76
|
+
expect(subject.qform_code).to eq(1.4)
|
77
|
+
end
|
78
|
+
end
|
79
|
+
|
80
|
+
describe 'sform_code' do
|
81
|
+
it 'is expected call the sform_code method from NIfTICLib::NIfTIImage' do
|
82
|
+
nifti_image.expects(:sform_code).returns(1.4)
|
83
|
+
|
84
|
+
expect(subject.sform_code).to eq(1.4)
|
85
|
+
end
|
86
|
+
end
|
87
|
+
end
|
88
|
+
end
|
@@ -0,0 +1,72 @@
|
|
1
|
+
require 'spec_helper'
|
2
|
+
|
3
|
+
describe CNifti::Header do
|
4
|
+
let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
|
5
|
+
subject { CNifti::Header.new(nifti_image) }
|
6
|
+
|
7
|
+
describe 'timings' do
|
8
|
+
describe 'freq_dim' do
|
9
|
+
it 'is expected call the freq_dim method from NIfTICLib::NIfTIImage' do
|
10
|
+
nifti_image.expects(:freq_dim).returns(4)
|
11
|
+
|
12
|
+
expect(subject.freq_dim).to eq(4)
|
13
|
+
end
|
14
|
+
end
|
15
|
+
|
16
|
+
describe 'phase_dim' do
|
17
|
+
it 'is expected call the phase_dim method from NIfTICLib::NIfTIImage' do
|
18
|
+
nifti_image.expects(:phase_dim).returns(4)
|
19
|
+
|
20
|
+
expect(subject.phase_dim).to eq(4)
|
21
|
+
end
|
22
|
+
end
|
23
|
+
|
24
|
+
describe 'slice_dim' do
|
25
|
+
it 'is expected call the slice_dim method from NIfTICLib::NIfTIImage' do
|
26
|
+
nifti_image.expects(:slice_dim).returns(4)
|
27
|
+
|
28
|
+
expect(subject.slice_dim).to eq(4)
|
29
|
+
end
|
30
|
+
end
|
31
|
+
|
32
|
+
describe 'slice_code' do
|
33
|
+
it 'is expected call the slice_code method from NIfTICLib::NIfTIImage' do
|
34
|
+
nifti_image.expects(:slice_code).returns(4)
|
35
|
+
|
36
|
+
expect(subject.slice_code).to eq(4)
|
37
|
+
end
|
38
|
+
end
|
39
|
+
|
40
|
+
describe 'slice_start' do
|
41
|
+
it 'is expected call the slice_start method from NIfTICLib::NIfTIImage' do
|
42
|
+
nifti_image.expects(:slice_start).returns(4)
|
43
|
+
|
44
|
+
expect(subject.slice_start).to eq(4)
|
45
|
+
end
|
46
|
+
end
|
47
|
+
|
48
|
+
describe 'slice_end' do
|
49
|
+
it 'is expected call the slice_end method from NIfTICLib::NIfTIImage' do
|
50
|
+
nifti_image.expects(:slice_end).returns(4)
|
51
|
+
|
52
|
+
expect(subject.slice_end).to eq(4)
|
53
|
+
end
|
54
|
+
end
|
55
|
+
|
56
|
+
describe 'slice_duration' do
|
57
|
+
it 'is expected call the slice_duration method from NIfTICLib::NIfTIImage' do
|
58
|
+
nifti_image.expects(:slice_duration).returns(1.4)
|
59
|
+
|
60
|
+
expect(subject.slice_duration).to eq(1.4)
|
61
|
+
end
|
62
|
+
end
|
63
|
+
|
64
|
+
describe 'toffset' do
|
65
|
+
it 'is expected call the toffset method from NIfTICLib::NIfTIImage' do
|
66
|
+
nifti_image.expects(:toffset).returns(1.4)
|
67
|
+
|
68
|
+
expect(subject.toffset).to eq(1.4)
|
69
|
+
end
|
70
|
+
end
|
71
|
+
end
|
72
|
+
end
|
@@ -0,0 +1,64 @@
|
|
1
|
+
require 'spec_helper'
|
2
|
+
|
3
|
+
describe CNifti::Header do
|
4
|
+
let!(:nifti_image) { FactoryGirl.build(:nifti_image) }
|
5
|
+
subject { CNifti::Header.new(nifti_image) }
|
6
|
+
|
7
|
+
describe 'transforms' do
|
8
|
+
describe 'qto_xyz' do
|
9
|
+
it 'is expected call the qto_xyz method from NIfTICLib::NIfTIImage' do
|
10
|
+
nifti_image.expects(:qto_xyz).returns([[1,0,0,0],
|
11
|
+
[0,1,0,0],
|
12
|
+
[0,0,1,0],
|
13
|
+
[0,0,0,1]])
|
14
|
+
|
15
|
+
expect(subject.qto_xyz).to eq([[1,0,0,0],
|
16
|
+
[0,1,0,0],
|
17
|
+
[0,0,1,0],
|
18
|
+
[0,0,0,1]])
|
19
|
+
end
|
20
|
+
end
|
21
|
+
|
22
|
+
describe 'qto_ijk' do
|
23
|
+
it 'is expected call the qto_ijk method from NIfTICLib::NIfTIImage' do
|
24
|
+
nifti_image.expects(:qto_ijk).returns([[1,0,0,0],
|
25
|
+
[0,1,0,0],
|
26
|
+
[0,0,1,0],
|
27
|
+
[0,0,0,1]])
|
28
|
+
|
29
|
+
expect(subject.qto_ijk).to eq([[1,0,0,0],
|
30
|
+
[0,1,0,0],
|
31
|
+
[0,0,1,0],
|
32
|
+
[0,0,0,1]])
|
33
|
+
end
|
34
|
+
end
|
35
|
+
|
36
|
+
describe 'sto_xyz' do
|
37
|
+
it 'is expected call the sto_xyz method from NIfTICLib::NIfTIImage' do
|
38
|
+
nifti_image.expects(:sto_xyz).returns([[1,0,0,0],
|
39
|
+
[0,1,0,0],
|
40
|
+
[0,0,1,0],
|
41
|
+
[0,0,0,1]])
|
42
|
+
|
43
|
+
expect(subject.sto_xyz).to eq([[1,0,0,0],
|
44
|
+
[0,1,0,0],
|
45
|
+
[0,0,1,0],
|
46
|
+
[0,0,0,1]])
|
47
|
+
end
|
48
|
+
end
|
49
|
+
|
50
|
+
describe 'sto_ijk' do
|
51
|
+
it 'is expected call the sto_ijk method from NIfTICLib::NIfTIImage' do
|
52
|
+
nifti_image.expects(:sto_ijk).returns([[1,0,0,0],
|
53
|
+
[0,1,0,0],
|
54
|
+
[0,0,1,0],
|
55
|
+
[0,0,0,1]])
|
56
|
+
|
57
|
+
expect(subject.sto_ijk).to eq([[1,0,0,0],
|
58
|
+
[0,1,0,0],
|
59
|
+
[0,0,1,0],
|
60
|
+
[0,0,0,1]])
|
61
|
+
end
|
62
|
+
end
|
63
|
+
end
|
64
|
+
end
|
data/spec/image_spec.rb
ADDED
@@ -0,0 +1,39 @@
|
|
1
|
+
require 'spec_helper'
|
2
|
+
|
3
|
+
describe CNifti::Image do
|
4
|
+
describe 'new' do
|
5
|
+
let(:dims) { [3,3,3] }
|
6
|
+
|
7
|
+
before :each do
|
8
|
+
CNifti::HeaderElement::Datatype::Base.expects(:to_i).returns(0)
|
9
|
+
end
|
10
|
+
|
11
|
+
it 'is expected call the new method from NIfTICLib::NIfTIImage' do
|
12
|
+
NIfTICLib::NIfTIImage.expects(:new).with(([3] + dims), 0, 1)
|
13
|
+
|
14
|
+
CNifti::Image.new(dimensions: dims, datatype: CNifti::HeaderElement::Datatype::Base)
|
15
|
+
end
|
16
|
+
end
|
17
|
+
|
18
|
+
describe 'open' do
|
19
|
+
let(:path) { 'test/test.nii.gz' }
|
20
|
+
let(:nifti_image) { FactoryGirl.build(:nifti_image) }
|
21
|
+
|
22
|
+
it 'is expected to read from path and set the header and data' do
|
23
|
+
NIfTICLib.expects(:read).with(path).returns(nifti_image)
|
24
|
+
|
25
|
+
expect(subject.open(path)).to be_a(CNifti::Image)
|
26
|
+
end
|
27
|
+
end
|
28
|
+
|
29
|
+
describe 'save_as' do
|
30
|
+
let(:path) { 'test/test.nii.gz' }
|
31
|
+
let(:nifti_image) { FactoryGirl.build(:nifti_image) }
|
32
|
+
|
33
|
+
it 'is expected to read from path and set the header and data' do
|
34
|
+
NIfTICLib.expects(:write).returns(nifti_image)
|
35
|
+
|
36
|
+
expect(subject.save_as(path)).to be_truthy
|
37
|
+
end
|
38
|
+
end
|
39
|
+
end
|
data/spec/spec_helper.rb
ADDED
@@ -0,0 +1,85 @@
|
|
1
|
+
require 'mocha/api'
|
2
|
+
|
3
|
+
# Test coverage report
|
4
|
+
require 'simplecov'
|
5
|
+
|
6
|
+
SimpleCov.start do
|
7
|
+
add_filter "/spec/"
|
8
|
+
add_filter "/features/"
|
9
|
+
|
10
|
+
coverage_dir 'coverage/rspec'
|
11
|
+
end
|
12
|
+
|
13
|
+
require 'c_nifti'
|
14
|
+
|
15
|
+
require 'factory_girl'
|
16
|
+
FactoryGirl.find_definitions
|
17
|
+
|
18
|
+
# This file was generated by the `rails generate rspec:install` command. Conventionally, all
|
19
|
+
# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
|
20
|
+
# The generated `.rspec` file contains `--require rails_helper` which will cause this
|
21
|
+
# file to always be loaded, without a need to explicitly require it in any files.
|
22
|
+
#
|
23
|
+
# Given that it is always loaded, you are encouraged to keep this file as
|
24
|
+
# light-weight as possible. Requiring heavyweight dependencies from this file
|
25
|
+
# will add to the boot time of your test suite on EVERY test run, even for an
|
26
|
+
# individual file that may not need all of that loaded. Instead, make a
|
27
|
+
# separate helper file that requires this one and then use it only in the specs
|
28
|
+
# that actually need it.
|
29
|
+
#
|
30
|
+
# The `.rspec` file also contains a few flags that are not defaults but that
|
31
|
+
# users commonly want.
|
32
|
+
#
|
33
|
+
# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
|
34
|
+
RSpec.configure do |config|
|
35
|
+
# The settings below are suggested to provide a good initial experience
|
36
|
+
# with RSpec, but feel free to customize to your heart's content.
|
37
|
+
|
38
|
+
# These two settings work together to allow you to limit a spec run
|
39
|
+
# to individual examples or groups you care about by tagging them with
|
40
|
+
# `:focus` metadata. When nothing is tagged with `:focus`, all examples
|
41
|
+
# get run.
|
42
|
+
config.filter_run :focus
|
43
|
+
config.run_all_when_everything_filtered = true
|
44
|
+
|
45
|
+
# Many RSpec users commonly either run the entire suite or an individual
|
46
|
+
# file, and it's useful to allow more verbose output when running an
|
47
|
+
# individual spec file.
|
48
|
+
if config.files_to_run.one?
|
49
|
+
# Use the documentation formatter for detailed output,
|
50
|
+
# unless a formatter has already been configured
|
51
|
+
# (e.g. via a command-line flag).
|
52
|
+
config.default_formatter = 'doc'
|
53
|
+
end
|
54
|
+
|
55
|
+
# Print the 10 slowest examples and example groups at the
|
56
|
+
# end of the spec run, to help surface which specs are running
|
57
|
+
# particularly slow.
|
58
|
+
config.profile_examples = 10
|
59
|
+
|
60
|
+
# Run specs in random order to surface order dependencies. If you find an
|
61
|
+
# order dependency and want to debug it, you can fix the order by providing
|
62
|
+
# the seed, which is printed after each run.
|
63
|
+
# --seed 1234
|
64
|
+
config.order = :random
|
65
|
+
|
66
|
+
# Seed global randomization in this process using the `--seed` CLI option.
|
67
|
+
# Setting this allows you to use `--seed` to deterministically reproduce
|
68
|
+
# test failures related to randomization by passing the same `--seed` value
|
69
|
+
# as the one that triggered the failure.
|
70
|
+
Kernel.srand config.seed
|
71
|
+
|
72
|
+
# rspec-expectations config goes here. You can use an alternate
|
73
|
+
# assertion/expectation library such as wrong or the stdlib/minitest
|
74
|
+
# assertions if you prefer.
|
75
|
+
config.expect_with :rspec do |expectations|
|
76
|
+
# Enable only the newer, non-monkey-patching expect syntax.
|
77
|
+
# For more details, see:
|
78
|
+
# - http://myronmars.to/n/dev-blog/2012/06/rspecs-new-expectation-syntax
|
79
|
+
expectations.syntax = :expect
|
80
|
+
end
|
81
|
+
|
82
|
+
# rspec-mocks config goes here. You can use an alternate test double
|
83
|
+
# library (such as bogus or mocha) by changing the `mock_with` option here.
|
84
|
+
config.mock_with :mocha
|
85
|
+
end
|