metamri 0.2.19 → 0.2.20
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- checksums.yaml +8 -8
- data/.gitignore +0 -0
- data/.rspec +0 -0
- data/Gemfile +0 -0
- data/Manifest +0 -0
- data/README.rdoc +0 -0
- data/Rakefile +0 -0
- data/VERSION +0 -0
- data/bin/convert_visit.rb +1 -1
- data/lib/metamri/core_additions.rb +0 -0
- data/lib/metamri/dicom_additions.rb +0 -0
- data/lib/metamri/image_dataset_quality_check_resource.rb +0 -0
- data/lib/metamri/mysql_tools.rb +0 -0
- data/lib/metamri/nifti_builder.rb +0 -0
- data/lib/metamri/raw_image_dataset.rb +0 -0
- data/lib/metamri/raw_image_dataset_resource.rb +0 -0
- data/lib/metamri/raw_image_dataset_thumbnail.rb +0 -0
- data/lib/metamri/raw_image_file.rb +1 -1
- data/lib/metamri/series_description_parameters.rb +0 -0
- data/lib/metamri/version.rb +1 -1
- data/lib/metamri/visit_raw_data_directory.rb +11 -1
- data/lib/metamri/visit_raw_data_directory_resource.rb +0 -0
- data/lib/metamri.rb +0 -0
- data/metamri.gemspec +0 -0
- data/spec/helper_spec.rb +0 -0
- data/spec/unit/dicom_additions_spec.rb +0 -0
- data/spec/unit/nifti_builder_spec.rb +0 -0
- data/spec/unit/raw_image_dataset_spec.rb +0 -0
- data/spec/unit/raw_image_dataset_thumbnail_spec.rb +0 -0
- data/spec/unit/raw_image_file_spec.rb +0 -0
- data/test/fixtures/respiratory_fixtures.yaml +0 -0
- data/test/fixtures/s03_bravo.0156 +0 -0
- data/test/fixtures/s03_bravo.0156.yml +0 -0
- data/test/fixtures/thumbnail.png +0 -0
- data/test/fixtures/thumbnail_slicer.png +0 -0
- data/test/raw_image_dataset_test.rb +0 -0
- data/test/raw_image_file_test.rb +0 -0
- data/test/test_helper.rb +0 -0
- data/test/visit_duplication_test.rb +0 -0
- data/test/visit_test.rb +0 -0
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,15 +1,15 @@
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1
1
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---
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2
2
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!binary "U0hBMQ==":
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3
3
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metadata.gz: !binary |-
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4
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-
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4
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+
OGU4N2IwMGY5MThkODRlYTQ5NzExNjg0NTk3ZmY3MzJiZGJhNzFlYQ==
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5
5
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data.tar.gz: !binary |-
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6
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-
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6
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+
ZWI3ODNlZjhjYjRlMTQxZDYxMTAxMzY4Y2NmYTNmN2Y0ZDZiNGM3Mg==
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7
7
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SHA512:
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8
8
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metadata.gz: !binary |-
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9
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-
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10
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-
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11
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-
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9
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+
NDUwOWJhOGVhODIyYjE3MmVhOTRhNDI4Y2ViMWFiOWIzYzM5YzFjZTc3M2Vk
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10
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+
NGIxY2FiZjM5NmMwMjE3NDQwY2U4Mzc2ZWMzOWZiNTk1ZDBhOTE3MGQ2YWNi
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11
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+
NmJiN2I2Mzc0OGQxMTQ2YmJlOTk5YzA0MTUwMjRkYWQ0ZTEyNzc=
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12
12
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data.tar.gz: !binary |-
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13
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-
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14
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-
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15
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-
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13
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+
NWU4NTljYmE0MDE4MDQzNGM1ZGQ0MmE1YjM2YTBiY2Q4N2ZhZmI4ODIwOGE3
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14
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+
MjRkZWZjNGVjYjRjNzRiNGZlODkwYjBkNTI0ZjRlMmNhNDM2N2MxZWVlMzdl
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15
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+
YTMyM2I0MTczYWM1MTE1MWM1NjNmMzgwNWRhMTg3NzZkODFhZTY=
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data/.gitignore
CHANGED
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File without changes
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data/.rspec
CHANGED
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File without changes
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data/Gemfile
CHANGED
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File without changes
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data/Manifest
CHANGED
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File without changes
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data/README.rdoc
CHANGED
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File without changes
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data/Rakefile
CHANGED
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File without changes
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data/VERSION
CHANGED
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File without changes
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data/bin/convert_visit.rb
CHANGED
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@@ -42,7 +42,7 @@ def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil
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42
42
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output_directory = output_directory ||= v.default_preprocess_directory
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43
43
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44
44
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begin
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45
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-
default_options = {:ignore_patterns => [/vipr/,/$Processed-Images$/,/900$/,/901$/,/999$/]} # seems to like number , not like string
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45
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+
default_options = {:ignore_patterns => [/vipr/,/pfiles/,/raw/,/$Processed-Images$/,/900$/,/901$/,/999$/]} # seems to like number , not like string
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46
46
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#options = default_options.merge(options)
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47
47
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v.scan(default_options)
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48
48
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v.to_nifti!(output_directory)
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File without changes
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File without changes
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File without changes
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data/lib/metamri/mysql_tools.rb
CHANGED
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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@@ -119,7 +119,7 @@ class RawImageFile
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119
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# puts e.backtrace
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raise e, "Could not find required DICOM Header Meta Element: #{e}"
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121
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rescue StandardError => e
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122
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-
raise e, "Header import failed for file #{@filename}. #{e}"
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122
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+
raise e, "Header import failed for file #{@filename}. #{e} . Has the scanner software version changed? A new version of the p-file reading software (printraw or rdgehdr) might be needed. "
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123
123
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end
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124
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125
125
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# deallocate the header data to save memory space.
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File without changes
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data/lib/metamri/version.rb
CHANGED
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@@ -188,7 +188,17 @@ Returns an array of the created nifti files.
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188
188
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189
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@datasets.each do |dataset|
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190
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nifti_output_path = output_directory
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191
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-
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191
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+
v_basename =File.basename(dataset.directory).gsub(/-/,"").gsub(/_/,"").gsub(/\:/,"").gsub(/\//,"")
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192
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+
v_series_description = "."+dataset.series_description.gsub(/ /,"").gsub(/-/,"").gsub(/_/,"").gsub(/\:/,"").gsub(/\//,"")
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193
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+
if v_basename.include? v_series_description
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194
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+
# want the scan series number - e.g. 00001 at the end
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195
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+
v_tmp_filename = v_basename.gsub(v_series_description,"")
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196
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+
nifti_filename = "#{scanid}_#{dataset.series_description.escape_filename}_#{v_tmp_filename}.nii"
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197
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+
else
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198
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+
nifti_filename = "#{scanid}_#{dataset.series_description.escape_filename}_#{File.basename(dataset.directory).escape_filename}.nii"
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199
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+
end
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200
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+
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201
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+
#nifti_filename = "#{scanid}_#{dataset.series_description.escape_filename}_#{File.basename(dataset.directory).escape_filename}.nii"
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192
202
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193
203
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Pathname.new(dataset.directory).all_dicoms do |dicom_files|
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194
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nifti_input_path = File.dirname(dicom_files.first)
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File without changes
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data/lib/metamri.rb
CHANGED
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File without changes
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data/metamri.gemspec
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data/spec/helper_spec.rb
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data/test/fixtures/thumbnail.png
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File without changes
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File without changes
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data/test/raw_image_file_test.rb
CHANGED
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File without changes
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data/test/test_helper.rb
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File without changes
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File without changes
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data/test/visit_test.rb
CHANGED
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File without changes
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: metamri
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.2.
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4
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+
version: 0.2.20
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Kristopher J. Kosmatka
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@@ -9,7 +9,7 @@ authors:
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9
9
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autorequire:
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10
10
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bindir: bin
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11
11
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cert_chain: []
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12
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-
date:
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12
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+
date: 2014-04-02 00:00:00.000000000 Z
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13
13
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dependencies:
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14
14
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- !ruby/object:Gem::Dependency
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15
15
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name: dicom
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