metamri 0.1.23 → 0.2.0

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@@ -1,23 +1,24 @@
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  # To change this template, choose Tools | Templates
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  # and open the template in the editor.
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- $:.unshift File.join(File.dirname(__FILE__),'..','lib')
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+ require 'test_helper'
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  require 'test/unit'
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  require 'metamri/raw_image_file'
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  class RawImageFileTest < Test::Unit::TestCase
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  def setup
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- # @GE_IFile = 'fixtures/I.001'
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- # @Dicom = 'fixtures/S4_EFGRE3D.0001'
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- # @EarlyGEPfile = 'fixtures/P59392.7'
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- # @LateGEPfile = 'fixtures/P27648.7'
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- # @notafile = 'fixtures/XXX.XXX'
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- # @ged = RawImageFile.new(@GE_IFile)
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- # @did = RawImageFile.new(@Dicom)
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- # @egep = RawImageFile.new(@EarlyGEPfile)
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- # @lgep = RawImageFile.new(@LateGEPfile)
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- @RubyDicom = 'fixtures/s03_bravo.0156'
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+ @GE_IFile = File.join($MRI_DATA), 'test_fixtures/I.001'
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+ @Dicom = File.join($MRI_DATA), 'test_fixtures/S4_EFGRE3D.0001'
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+ @EarlyGEPfile = File.join($MRI_DATA), 'test_fixtures/P59392.7'
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+ @LateGEPfile = File.join($MRI_DATA), 'test_fixtures/P27648.7'
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+ @GEX750Dicom = File.join($MRI_DATA), 'test_fixtures/s03_bravo.0156'
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+ @notafile = File.join($MRI_DATA), 'test_fixtures/XXX.XXX'
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+ @ged = RawImageFile.new(@GE_IFile)
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+ @did = RawImageFile.new(@Dicom)
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+ @egep = RawImageFile.new(@EarlyGEPfile)
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+ @lgep = RawImageFile.new(@LateGEPfile)
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+
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  end
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  def test_gehdr_dicom_init
@@ -32,7 +33,7 @@ class RawImageFileTest < Test::Unit::TestCase
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  end
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  def test_rubydicom_dicom_init
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  assert_nothing_raised do
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- RawImageFile.new(@RubyDicom)
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+ RawImageFile.new(@GEX750Dicom)
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  end
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  end
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  def test_early_gehdr_pfile_init
@@ -0,0 +1,2 @@
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ $MRI_DATA = ENV['MRI_DATA'] || '/Data/vtrak1/raw/test/fixtures/metamri'
metadata CHANGED
@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
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  prerelease: false
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  segments:
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  - 0
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- - 1
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- - 23
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- version: 0.1.23
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+ - 2
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+ - 0
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+ version: 0.2.0
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  platform: ruby
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  authors:
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  - Kristopher J. Kosmatka
@@ -14,7 +14,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2010-11-16 00:00:00 -06:00
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+ date: 2010-11-19 00:00:00 -06:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency
@@ -56,17 +56,16 @@ dependencies:
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  description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
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  email: kk4@medicine.wisc.edu
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  executables:
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- - import_study.rb
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+ - convert_visit.rb
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  - import_visit.rb
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  - import_respiratory_files.rb
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+ - import_study.rb
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  - list_visit
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- - convert_visit.rb
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  extensions: []
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  extra_rdoc_files:
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  - README.rdoc
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  files:
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- - .gitignore
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  - Manifest
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  - README.rdoc
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  - Rakefile
@@ -78,6 +77,7 @@ files:
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  - bin/list_visit
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  - lib/metamri.rb
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  - lib/metamri/core_additions.rb
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+ - lib/metamri/image_dataset_quality_check_resource.rb
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  - lib/metamri/mysql_tools.rb
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  - lib/metamri/nifti_builder.rb
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  - lib/metamri/raw_image_dataset.rb
@@ -88,15 +88,19 @@ files:
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  - lib/metamri/visit_raw_data_directory.rb
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  - lib/metamri/visit_raw_data_directory_resource.rb
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  - metamri.gemspec
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+ - spec/helper_spec.rb
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+ - spec/unit/nifti_builder_spec.rb
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+ - spec/unit/raw_image_dataset_spec.rb
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+ - spec/unit/raw_image_dataset_thumbnail_spec.rb
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+ - spec/unit/raw_image_file_spec.rb
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  - test/fixtures/respiratory_fixtures.yaml
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  - test/fixtures/s03_bravo.0156
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+ - test/fixtures/s03_bravo.0156.yml
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  - test/fixtures/thumbnail.png
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  - test/fixtures/thumbnail_slicer.png
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- - test/helper_spec.rb
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- - test/nifti_builder_spec.rb
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  - test/raw_image_dataset_test.rb
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- - test/raw_image_dataset_thumbnail_spec.rb
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  - test/raw_image_file_test.rb
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+ - test/test_helper.rb
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  - test/visit_duplication_test.rb
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  - test/visit_test.rb
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  has_rdoc: true
@@ -104,8 +108,8 @@ homepage: http://github.com/brainmap/metamri
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  licenses: []
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  post_install_message:
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- rdoc_options:
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- - --charset=UTF-8
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+ rdoc_options: []
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+
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  require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
@@ -130,10 +134,13 @@ signing_key:
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  specification_version: 3
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  summary: MRI metadata
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  test_files:
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- - test/nifti_builder_spec.rb
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+ - spec/helper_spec.rb
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+ - spec/unit/nifti_builder_spec.rb
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+ - spec/unit/raw_image_dataset_spec.rb
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+ - spec/unit/raw_image_dataset_thumbnail_spec.rb
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+ - spec/unit/raw_image_file_spec.rb
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  - test/raw_image_dataset_test.rb
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  - test/raw_image_file_test.rb
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+ - test/test_helper.rb
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  - test/visit_duplication_test.rb
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  - test/visit_test.rb
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- - test/raw_image_dataset_thumbnail_spec.rb
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- - test/helper_spec.rb
data/.gitignore DELETED
@@ -1,7 +0,0 @@
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- *.log
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- *.gem
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- ._*
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- .idea
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- *~
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- test/fixtures/visit_raw_data_directory
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- doc/*