metamri 0.1.4 → 0.1.5
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- data/.gitignore +1 -0
- data/VERSION +1 -1
- data/bin/convert_visit.rb +75 -0
- data/lib/nifti_builder.rb +0 -1
- data/lib/raw_image_dataset.rb +21 -5
- data/lib/raw_image_file.rb +1 -1
- data/metamri.gemspec +4 -3
- data/test/nifti_builder_spec.rb +11 -8
- metadata +4 -4
data/.gitignore
CHANGED
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.5
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@@ -0,0 +1,75 @@
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1
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+
#!/usr/bin/env ruby
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#
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# == Synopsis
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# A simple utility for converting all the dicom datasets in a directory into niftis. Defaults to the current
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# default preprocessed repository.
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#
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# == Examples
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# convert_visit.rb /Data/vtrak1/raw/ries.aware.visit1/awr001_7854_02102009 ries.aware.visit1
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#
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# == Usage
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# convert_visit.rb <raw_data_directory> <scan_procedure_codename>
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#
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# For help use: import_visit.rb -h
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#
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# == Options
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# -h, --help Displays help message
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# -v, --visit Visit raw data directory, absolute path
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# -p, --scan_procedure scan_procedure codename, e.g. johnson.alz.visit1
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#
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# == Author
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#
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#
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# == Copyright
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# Copyright (c) 2009 WADRC Imaging Core.
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#
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$:.unshift File.join(File.dirname(__FILE__),'..','lib')
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require 'metamri'
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require 'pathname'
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require 'rdoc/usage'
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require 'logger'
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# == Function
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#
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#
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# == Usage
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#
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#
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# == Example
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#
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#
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def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil)
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log = Logger.new(File.basename(raw_directory))
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v = VisitRawDataDirectory.new(raw_directory, scan_procedure_codename)
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puts "+++ Converting #{v.visit_directory} as part of #{v.scan_procedure_name} +++"
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output_directory = output_directory ||= v.default_preprocess_directory
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begin
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v.scan
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v.to_nifti!(output_directory)
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rescue Exception => e
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puts "There was a problem scanning a dataset in #{v.visit_directory}... skipping."
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puts "Exception message: #{e.message}"
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log.error "There was a problem scanning a dataset in #{v.visit_directory}... skipping."
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log.error "Exception message: #{e.message}"
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ensure
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v = nil
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end
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end
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if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
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RDoc::usage() if (ARGV[0] == '-h')
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raw_directory = ARGV[0]
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+
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# This is required for now, will be inferred from path in the future.
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scan_procedure_codename = ARGV[1]
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output_directory = ARGV[2] ? ARGV[2] : nil
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convert_visit(raw_directory, scan_procedure_codename, output_directory)
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end
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data/lib/nifti_builder.rb
CHANGED
@@ -15,7 +15,6 @@ module UnknownImageDataset
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else input_files = "#{Dir.tmpdir}/'#{glob}'"
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end
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-
nifti_output_directory = File.join(nifti_output_directory, 'unknown') if input_options[:append_modality_directory]
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nifti_output_file = File.join(nifti_output_directory, nifti_filename)
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File.makedirs(nifti_output_directory) unless File.directory?(nifti_output_directory)
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data/lib/raw_image_dataset.rb
CHANGED
@@ -27,7 +27,7 @@ class RawImageDataset
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# the file scanned
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attr_reader :scanned_file
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# the scanner source
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-
attr_reader :scanner_source
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attr_reader :scanner_source
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=begin rdoc
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* dir: The directory containing the files.
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@@ -122,7 +122,14 @@ The to3d code is applied as a mixed-in module.
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Returns the to3d command that creates the specified options.
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=end
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def to_nifti(nifti_output_directory, nifti_filename, input_options = {} )
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-
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+
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# Handle the business logic for choosing the right Nifti Builder here.
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# Currently just extend the default unknown builder, since that's the only one that exists.
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if true
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nifti_output_directory = File.join(nifti_output_directory, 'unknown') if input_options[:append_modality_directory]
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extend(UnknownImageDataset)
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end
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nifti_conversion_command, nifti_output_file = self.dataset_to_nifti(nifti_output_directory, nifti_filename, input_options)
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return nifti_conversion_command, nifti_output_file
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end
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@@ -171,10 +178,10 @@ have more component files than shell commands can handle.
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end
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=begin rdoc
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-
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Does same basic string replacements to ensure valid filenames.
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=end
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def escape_filename(filename)
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filename.
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filename.mgsub([[/[\s\:\)\(]+/, "-"], [/\*/, "star"]])
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end
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private
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@@ -186,4 +193,13 @@ private
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end
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-
#### END OF CLASS ####
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#### END OF CLASS ####
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class String
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def mgsub(key_value_pairs=[].freeze)
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regexp_fragments = key_value_pairs.collect { |k,v| k }
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gsub(Regexp.union(*regexp_fragments)) do |match|
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key_value_pairs.detect { |k,v| k =~ match}[1]
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end
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end
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end
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data/lib/raw_image_file.rb
CHANGED
@@ -71,7 +71,7 @@ temporary file.
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def initialize(pathtofile)
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# raise an error if the file doesn't exist
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absfilepath = File.expand_path(pathtofile)
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raise(IOError, "File not found.") if not File.exists?(absfilepath)
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raise(IOError, "File not found at #{absfilepath}.") if not File.exists?(absfilepath)
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@filename = File.basename(absfilepath)
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# try to read the header, raise an IOError if unsuccessful
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data/metamri.gemspec
CHANGED
@@ -5,14 +5,14 @@
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5
5
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Gem::Specification.new do |s|
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s.name = %q{metamri}
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s.version = "0.1.
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s.version = "0.1.5"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Kristopher J. Kosmatka"]
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s.date = %q{2009-12-
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+
s.date = %q{2009-12-18}
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s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
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s.email = %q{kk4@medicine.wisc.edu}
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s.executables = ["import_study.rb", "import_visit.rb", "
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+
s.executables = ["import_study.rb", "import_visit.rb", "convert_visit.rb"]
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s.extra_rdoc_files = [
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"README.rdoc"
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]
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@@ -22,6 +22,7 @@ Gem::Specification.new do |s|
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"README.rdoc",
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"Rakefile",
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"VERSION",
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"bin/convert_visit.rb",
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"bin/import_study.rb",
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"bin/import_visit.rb",
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"lib/metamri.rb",
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data/test/nifti_builder_spec.rb
CHANGED
@@ -9,16 +9,19 @@ require 'raw_image_file'
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describe "Convert Unknown Dicoms to Nifti Files" do
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before(:each) do
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-
@visit = VisitRawDataDirectory.new('/
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@dataset = RawImageDataset.new(
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@visit = VisitRawDataDirectory.new(File.join(File.dirname(__FILE__), 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009'), 'johnson.tbi-va.visit1')
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@dataset = RawImageDataset.new(
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File.join(File.dirname(__FILE__), 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009/001'),
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[RawImageFile.new(File.join(File.dirname(__FILE__), 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009/001/I0001.dcm'))]
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)
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@test_niftis = Array.new
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@output_directories = Array.new
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end
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it "should Convert an anatomical from dicom to nifti using original, unzipped files." do
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@dataset.to_nifti('/tmp/', 'filename.nii', :input_directory =>
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nifti_conversion_command, nifti_output_file = @dataset.to_nifti!('/tmp/', 'filename.nii', :input_directory =>
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nifti_conversion_command.should == "to3d -session /tmp/ -prefix filename.nii
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@dataset.to_nifti('/tmp/', 'filename.nii', :input_directory => @dataset.directory)[0].should == "to3d -session /tmp/ -prefix filename.nii #{@dataset.directory}/'*.dcm'"
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nifti_conversion_command, nifti_output_file = @dataset.to_nifti!('/tmp/', 'filename.nii', :input_directory => @dataset.directory)
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nifti_conversion_command.should == "to3d -session /tmp/ -prefix filename.nii #{@dataset.directory}/'*.dcm'"
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@test_niftis << nifti_output_file
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@output_directories << '/tmp'
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end
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@@ -29,7 +32,7 @@ describe "Convert Unknown Dicoms to Nifti Files" do
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@visit.datasets.each do |ds|
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begin
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nifti_filename = "#{@visit.scanid}_#{ds.escape_filename(ds.series_description)}_#{File.basename(ds.directory)}.nii"
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nifti_conversion_commmand, nifti_output_file = ds.to_nifti!(File.join(Dir.tmpdir, @visit.default_preprocess_directory), nifti_filename, :input_directory =>
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nifti_conversion_commmand, nifti_output_file = ds.to_nifti!(File.join(Dir.tmpdir, @visit.default_preprocess_directory), nifti_filename, :input_directory => ds.directory, :append_modality_directory => true )
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@test_niftis << nifti_output_file
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rescue IOError => e
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puts "-- Error: #{e.message}"
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@@ -40,7 +43,7 @@ describe "Convert Unknown Dicoms to Nifti Files" do
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end
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it "should convert all anatomicals in a visit raw directory using local copy." do
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-
@test_niftis << @visit.to_nifti!
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@test_niftis << @visit.to_nifti!
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end
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it "should create a good to3d command with input directory or dicom files." do
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@@ -75,7 +78,7 @@ describe "Convert Unknown Dicoms to Nifti Files" do
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v.scanid.should == 'adrc00001'
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end
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78
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-
after do
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after(:each) do
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@test_niftis.flatten.each { |nifti| File.delete(nifti) } unless @test_niftis.empty?
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[@output_directories, Dir.tmpdir, '/tmp'].flatten.each do |temp_dir|
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Dir.foreach(temp_dir) {|f| File.delete(File.join(temp_dir, f)) if File.extname(f) == '.nii'}
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: metamri
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version: !ruby/object:Gem::Version
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4
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-
version: 0.1.
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+
version: 0.1.5
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platform: ruby
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authors:
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7
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- Kristopher J. Kosmatka
|
@@ -9,7 +9,7 @@ autorequire:
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bindir: bin
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10
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cert_chain: []
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12
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-
date: 2009-12-
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+
date: 2009-12-18 00:00:00 -06:00
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default_executable:
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14
14
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dependencies: []
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15
15
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@@ -18,8 +18,7 @@ email: kk4@medicine.wisc.edu
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executables:
|
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19
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- import_study.rb
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20
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- import_visit.rb
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-
-
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22
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-
- wrap140.scan.log
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21
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+
- convert_visit.rb
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extensions: []
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24
23
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|
25
24
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extra_rdoc_files:
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@@ -30,6 +29,7 @@ files:
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30
29
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- README.rdoc
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31
30
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- Rakefile
|
32
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- VERSION
|
32
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+
- bin/convert_visit.rb
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33
33
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- bin/import_study.rb
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34
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- bin/import_visit.rb
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35
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- lib/metamri.rb
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