dcm2nii-ruby 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in dcm2nii-ruby.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2012 Simon Rascovsky
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Dcm2nii::Ruby
+
+A Ruby wrapper for the dcm2nii DICOM to NIFTI file conversion utility
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'dcm2nii-ruby'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install dcm2nii-ruby
+
+## Usage
+
+dn = Dcm2nii::Runner.new(input_directory,{options hash})
+
+eg:
+
+dn = Dcm2nii::Runner.new('/Users/simonmd/code/rubycamppus/input/samples/dicom',{reorient_crop:false, reorient:false}) # creates an instance of the DCM2NII runner
+
+dn.command # runs the utility
+
+resulting_file = dn.get_nii # Returns the generated nifti file
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/dcm2nii-ruby.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'dcm2nii-ruby/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "dcm2nii-ruby"
+  gem.version       = Dcm2nii::Runner::VERSION
+  gem.authors       = ["Simon Rascovsky"]
+  gem.email         = ["investigacion@iatm.com.co"]
+  gem.description   = %q{dcm2nii wrapper}
+  gem.summary       = %q{Ruby wrapper for the dcm2nii dicom to nifti conversion utility}
+  gem.homepage      = ""
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+end

data/lib/dcm2nii-ruby.rb

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+require "dcm2nii-ruby/version"
+
+module Dcm2nii
+
+	class Runner
+		@@command_path = '/Applications/mricro/dcm2nii'
+		@@options_map = { anonymize: '-a',
+							settings_file: '-b',
+							collapse_folders: '-c',
+							date_in_filename: '-d',
+							events_in_filename: '-e',
+							source_filename: '-f',
+							gzip: '-g',
+							id_in_filename: '-i',
+							nifti: '-n',
+							output_dir: '-o',
+							protocol_in_filename: 'p',
+							reorient: '-r',
+							spm2_analyze: '-s',
+							convert_images: '-v',
+							reorient_crop: '-x'
+						}
+
+		def self.command_path=(path)
+			@@command_path = path
+		end
+
+		def self.command_path
+			@@command_path
+		end
+
+		def self.options_map
+			@@options_map
+		end
+
+		def initialize(input_dir, opt = {})
+			@input_dir = input_dir
+			@opt = opt
+		end
+
+		def map_vals(val)
+			if val == true || val == false
+				val ? 'Y' : 'N'
+			else
+				val
+			end
+		end
+
+		def map_options(opt ={})
+			opt.inject({}) { |h, (k, v)| h[k] = (self.class.options_map[k] + ' ' + map_vals(v)); h }
+		end
+
+		def argument_list
+			map_options(@opt).collect {|k,v| v}.join(' ')
+		end
+
+		def command
+			command_str = "#{self.class.command_path} #{argument_list} #{@input_dir}"
+			puts "Running DCM2NII with command #{command_str}"
+			result = `#{command_str}`
+			exit_code = $?
+			case exit_code
+				when 0
+					puts "Done running DCM2NII."
+					return result
+				else
+					puts "An error ocurred while running DCM2NII"
+			        #   exit_error = Dcm2nii::Runner::UnexpectedExitError.new
+			        #   exit_error.exit_code = exit_code
+			        #   raise exit_error
+			        # end
+			end
+		end
+
+		def get_nii
+			if @opt[:output_dir]
+				lookup_dir = @opt[:output_dir]
+			else
+				lookup_dir = @input_dir
+			end
+			return `find #{lookup_dir} -name *.nii*`.chomp
+		end
+	end
+end

data/lib/dcm2nii-ruby/version.rb

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+module Dcm2nii
+  class Runner
+    VERSION = "0.0.1"
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: dcm2nii-ruby
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Simon Rascovsky
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-11-21 00:00:00.000000000 Z
+dependencies: []
+description: dcm2nii wrapper
+email:
+- investigacion@iatm.com.co
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- dcm2nii-ruby.gemspec
+- lib/dcm2nii-ruby.rb
+- lib/dcm2nii-ruby/version.rb
+homepage: ''
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Ruby wrapper for the dcm2nii dicom to nifti conversion utility
+test_files: []