dicom_study_factory 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 99412659bf95a3e89d5c891c5bd916e98c5b3d2108dd1f2f8da9d879b28635f6
+  data.tar.gz: d93c8f7e3216c6151dbf413b3db083d4d1c4f485f125a887cbf0509883b7c269
+SHA512:
+  metadata.gz: 63621fc9cec644a17a10e4f4aed3d1e1750c45a3098167afe57da91ef2905275811413b8534ff3ee9f5a2f65ac482d898898cda21d7bdb59bafb7916116d666c
+  data.tar.gz: dfbcec02d054454f5e59075a628762266a1905ed0b53cf73c788502eca23e90c67239b89428cb57841c52ae7dc3ec566c5c917c987126a63b98632faa864dff8

data/.gitignore

@@ -0,0 +1,14 @@
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status
+
+# vim temporay files
+*.sw*

data/.rspec

@@ -0,0 +1,3 @@
+--format documentation
+--color
+--require spec_helper

data/.ruby-version

@@ -0,0 +1 @@
+2.6.1

data/.travis.yml

@@ -0,0 +1,7 @@
+---
+sudo: false
+language: ruby
+cache: bundler
+rvm:
+  - 2.6.1
+before_install: gem install bundler -v 2.0.2

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at diego@myorb.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in dicom_study_factory.gemspec
+gemspec

data/Gemfile.lock

@@ -0,0 +1,97 @@
+PATH
+  remote: .
+  specs:
+    dicom_study_factory (0.1.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    ast (2.4.1)
+    byebug (11.1.3)
+    coderay (1.1.3)
+    diff-lcs (1.4.4)
+    ffi (1.13.1)
+    formatador (0.2.5)
+    guard (2.16.2)
+      formatador (>= 0.2.4)
+      listen (>= 2.7, < 4.0)
+      lumberjack (>= 1.0.12, < 2.0)
+      nenv (~> 0.1)
+      notiffany (~> 0.0)
+      pry (>= 0.9.12)
+      shellany (~> 0.0)
+      thor (>= 0.18.1)
+    guard-compat (1.2.1)
+    guard-rspec (4.7.3)
+      guard (~> 2.1)
+      guard-compat (~> 1.1)
+      rspec (>= 2.99.0, < 4.0)
+    guard-rubocop (1.3.0)
+      guard (~> 2.0)
+      rubocop (~> 0.20)
+    listen (3.2.1)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    lumberjack (1.2.7)
+    method_source (1.0.0)
+    nenv (0.3.0)
+    notiffany (0.1.3)
+      nenv (~> 0.1)
+      shellany (~> 0.0)
+    parallel (1.19.2)
+    parser (2.7.1.4)
+      ast (~> 2.4.1)
+    pry (0.13.1)
+      coderay (~> 1.1)
+      method_source (~> 1.0)
+    rainbow (3.0.0)
+    rake (10.5.0)
+    rb-fsevent (0.10.4)
+    rb-inotify (0.10.1)
+      ffi (~> 1.0)
+    regexp_parser (1.7.1)
+    rexml (3.2.4)
+    rspec (3.9.0)
+      rspec-core (~> 3.9.0)
+      rspec-expectations (~> 3.9.0)
+      rspec-mocks (~> 3.9.0)
+    rspec-core (3.9.2)
+      rspec-support (~> 3.9.3)
+    rspec-expectations (3.9.2)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.9.0)
+    rspec-mocks (3.9.1)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.9.0)
+    rspec-support (3.9.3)
+    rubocop (0.89.1)
+      parallel (~> 1.10)
+      parser (>= 2.7.1.1)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.7)
+      rexml
+      rubocop-ast (>= 0.3.0, < 1.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 1.4.0, < 2.0)
+    rubocop-ast (0.3.0)
+      parser (>= 2.7.1.4)
+    ruby-progressbar (1.10.1)
+    shellany (0.0.1)
+    thor (1.0.1)
+    unicode-display_width (1.7.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 2.0)
+  byebug (~> 11.1)
+  dicom_study_factory!
+  guard-rspec (~> 4.7)
+  guard-rubocop (~> 1.3)
+  rake (~> 10.0)
+  rspec (~> 3.0)
+  rubocop (~> 0.89)
+
+BUNDLED WITH
+   2.0.2

data/Guardfile

@@ -0,0 +1,48 @@
+# frozen_string_literal: true
+
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+## Uncomment and set this to only include directories you want to watch
+# directories %w(app lib config test spec features) \
+#  .select{|d| Dir.exist?(d) ? d : UI.warning("Directory #{d} does not exist")}
+
+## Note: if you are using the `directories` clause above and you are not
+## watching the project directory ('.'), then you will want to move
+## the Guardfile to a watched dir and symlink it back, e.g.
+#
+#  $ mkdir config
+#  $ mv Guardfile config/
+#  $ ln -s config/Guardfile .
+#
+# and, you'll have to watch "config/Guardfile" instead of "Guardfile"
+
+# Note: The cmd option is now required due to the increasing number of ways
+#       rspec may be run, below are examples of the most common uses.
+#  * bundler: 'bundle exec rspec'
+#  * bundler binstubs: 'bin/rspec'
+#  * spring: 'bin/rspec' (This will use spring if running and you have
+#                          installed the spring binstubs per the docs)
+#  * zeus: 'zeus rspec' (requires the server to be started separately)
+#  * 'just' rspec: 'rspec'
+
+guard :rspec, cmd: 'bundle exec rspec' do
+  require 'guard/rspec/dsl'
+  dsl = Guard::RSpec::Dsl.new(self)
+
+  # RSpec files
+  rspec = dsl.rspec
+  watch(rspec.spec_helper) { rspec.spec_dir }
+  watch(rspec.spec_support) { rspec.spec_dir }
+  watch(rspec.spec_files)
+
+  # Ruby files
+  ruby = dsl.ruby
+  dsl.watch_spec_files_for(ruby.lib_files)
+  watch(%r{^lib/dicom_study_factory/(.+)\.rb$}) { |m| "spec/lib/#{m[1]}_spec.rb" }
+end
+
+guard :rubocop do
+  watch(%r{/.+\.rb$})
+  watch(%r{(?:.+/)?\.rubocop(?:_todo)?\.yml$}) { |m| File.dirname(m[0]) }
+end

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2020 Diego Lagos
+
+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

@@ -0,0 +1,43 @@
+# DicomStudyFactory
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/dicom_study_factory`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'dicom_study_factory'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install dicom_study_factory
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/dicom_study_factory. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+## Code of Conduct
+
+Everyone interacting in the DicomStudyFactory project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/dicom_study_factory/blob/master/CODE_OF_CONDUCT.md).

data/Rakefile

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+require 'bundler/gem_tasks'
+require 'rspec/core/rake_task'
+
+RSpec::Core::RakeTask.new(:spec)
+
+task default: :spec

data/bin/console

@@ -0,0 +1,16 @@
+#!/usr/bin/env ruby
+
+# frozen_string_literal: true
+
+require 'bundler/setup'
+require 'dicom_study_factory'
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require 'irb'
+IRB.start(__FILE__)

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/dicom_study_factory.gemspec

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+lib = File.expand_path('lib', __dir__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'dicom_study_factory/version'
+
+Gem::Specification.new do |spec|
+  spec.required_ruby_version = '>= 2.6.1'
+  spec.name          = 'dicom_study_factory'
+  spec.version       = DicomStudyFactory::VERSION
+  spec.authors       = ['Diego Lagos']
+  spec.email         = ['diego.piccinini@gmail.com']
+
+  spec.summary       = 'Create a dicom files samples filling tags with a factory library'
+  spec.description   = 'We need dicom files populated with the right tags to test and use it for DEMOs.
+  Unfortunately the anonymize process delete all the main tags required to test.
+  For this reason this gem is relevant to create a sample collection.'
+  spec.homepage      = 'https://github.com/diegopiccinini/dicom_study_factory/README.md'
+  spec.license       = 'MIT'
+
+  spec.metadata['allowed_push_host'] = 'https://rubygems.org'
+
+  spec.metadata['homepage_uri'] = spec.homepage
+  spec.metadata['source_code_uri'] = 'https://github.com/diegopiccinini/dicom_study_factory'
+  spec.metadata['changelog_uri'] = 'https://github.com/diegopiccinini/dicom_study_factory/CHANGELOG.md'
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files = Dir.chdir(File.expand_path(__dir__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  end
+  spec.bindir        = 'exe'
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib']
+
+  spec.add_development_dependency 'bundler', '~> 2.0'
+  spec.add_development_dependency 'byebug', '~> 11.1'
+  spec.add_development_dependency 'guard-rspec', '~> 4.7'
+  spec.add_development_dependency 'guard-rubocop', '~> 1.3'
+  spec.add_development_dependency 'rake', '~> 10.0'
+  spec.add_development_dependency 'rspec', '~> 3.0'
+  spec.add_development_dependency 'rubocop', '~> 0.89'
+end

data/lib/dicom_study_factory.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+require 'dicom_study_factory/version'
+require 'dicom_study_factory/transformer'
+
+module DicomStudyFactory
+  class Error < StandardError; end
+  # Your code goes here...
+end

data/lib/dicom_study_factory/transformer.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+require 'fileutils'
+module DicomStudyFactory
+  # Transforme gets all the .dcm files in one directory
+  # and apply a factory data to populate the dicom
+  # with tags
+  class Transformer
+    SOURCE_DIR = 'tmp/source'
+    OUTPUT_DIR = 'tmp/output'
+    def initialize
+      FileUtils.mkdir_p(SOURCE_DIR) unless Dir.exist? SOURCE_DIR
+      FileUtils.mkdir_p(OUTPUT_DIR) unless Dir.exist? OUTPUT_DIR
+    end
+
+    def files
+      Dir.glob(File.join(SOURCE_DIR, '**/*.dcm'))
+    end
+
+    def output_files
+      Dir.glob(File.join(OUTPUT_DIR, '**/*.dcm'))
+    end
+  end
+end

data/lib/dicom_study_factory/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module DicomStudyFactory
+  VERSION = '0.1.0'
+end

metadata

@@ -0,0 +1,166 @@
+--- !ruby/object:Gem::Specification
+name: dicom_study_factory
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Diego Lagos
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2020-08-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '11.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '11.1'
+- !ruby/object:Gem::Dependency
+  name: guard-rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.7'
+- !ruby/object:Gem::Dependency
+  name: guard-rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.89'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.89'
+description: |-
+  We need dicom files populated with the right tags to test and use it for DEMOs.
+    Unfortunately the anonymize process delete all the main tags required to test.
+    For this reason this gem is relevant to create a sample collection.
+email:
+- diego.piccinini@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".ruby-version"
+- ".travis.yml"
+- CHANGELOG.md
+- CODE_OF_CONDUCT.md
+- Gemfile
+- Gemfile.lock
+- Guardfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- dicom_study_factory.gemspec
+- lib/dicom_study_factory.rb
+- lib/dicom_study_factory/transformer.rb
+- lib/dicom_study_factory/version.rb
+homepage: https://github.com/diegopiccinini/dicom_study_factory/README.md
+licenses:
+- MIT
+metadata:
+  allowed_push_host: https://rubygems.org
+  homepage_uri: https://github.com/diegopiccinini/dicom_study_factory/README.md
+  source_code_uri: https://github.com/diegopiccinini/dicom_study_factory
+  changelog_uri: https://github.com/diegopiccinini/dicom_study_factory/CHANGELOG.md
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.6.1
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.0.1
+signing_key: 
+specification_version: 4
+summary: Create a dicom files samples filling tags with a factory library
+test_files: []