metamri 0.1.0

data/test/raw_image_dataset_test.rb

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+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'test/unit'
+require 'raw_image_dataset'
+require 'raw_image_file'
+
+class RawImageDatasetTest < Test::Unit::TestCase
+  DBFILE = 'fixtures/development.sqlite3'
+  
+  def setup
+    @aa = RawImageFile.new('fixtures/I.001')
+    @bb = RawImageFile.new('fixtures/P27648.7')
+    @cc = RawImageFile.new('fixtures/P59392.7')
+    @dd = RawImageFile.new('fixtures/S4_EFGRE3D.0001')
+    @dset = RawImageDataset.new('/Data/home/kris/NetBeansProjects/ImageData/test/fixtures', [@aa,@bb,@cc,@dd])
+  end
+
+  def test_raw_image_files
+    assert_equal 4, @dset.raw_image_files.length
+    assert_equal '"I.*"', @dset.glob
+    assert_equal "SAG T2 W FSE 1.7 skip 0.3", @dset.series_description
+    assert_equal "ALZMRI002", @dset.rmr_number
+    assert_equal "2003-01-31T04:39:04+00:00", @dset.timestamp.to_s
+    assert_equal "ALZMRI002::2003-01-31T04:39:04+00:00", @dset.dataset_key
+    assert_equal "DELETE FROM image_datasets WHERE dataset_key = 'ALZMRI002::2003-01-31T04:39:04+00:00'", @dset.db_remove
+  end
+  
+  def test_db_insertion
+    assert_raise IndexError do
+      @dset.db_insert!(DBFILE)
+      @dset.db_insert!(DBFILE)
+    end
+  end
+  
+  def test_raw_image_insertion
+    @dset.db_insert_raw_images!(DBFILE)
+  end
+
+  def teardown
+    @dset.db_remove_raw_images!(DBFILE)
+    @dset.db_remove!(DBFILE)
+  end
+end

data/test/raw_image_file_test.rb

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+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'test/unit'
+require 'raw_image_file'
+
+class RawImageFileTest < Test::Unit::TestCase
+  def setup
+    @GEDicom = 'fixtures/I.001'
+    @DiDicom = 'fixtures/S4_EFGRE3D.0001'
+    @EarlyGEPfile = 'fixtures/P59392.7'
+    @LateGEPfile = 'fixtures/P27648.7'
+    @notafile = 'fixtures/XXX.XXX'
+    @ged = RawImageFile.new(@GEDicom)
+    @did = RawImageFile.new(@DiDicom)
+    @egep = RawImageFile.new(@EarlyGEPfile)
+    @lgep = RawImageFile.new(@LateGEPfile)
+  end
+
+  def test_gehdr_dicom_init
+    assert_nothing_raised do
+      RawImageFile.new(@GEDicom)
+    end
+  end
+  def test_dicomhdr_dicom_init
+    assert_nothing_raised do
+      RawImageFile.new(@DiDicom)
+    end
+  end
+  def test_early_gehdr_pfile_init
+    assert_nothing_raised do
+      RawImageFile.new(@EarlyGEPfile)
+    end
+  end
+  def test_late_gehdr_pfile_init
+    assert_nothing_raised do
+      RawImageFile.new(@LateGEPfile)
+    end
+  end
+  def test_nonfile_init
+    assert_raise IOError do
+      RawImageFile.new(@notafile)
+    end
+  end
+  def test_pfile?
+    assert !@ged.pfile?
+    assert !@did.pfile?
+    assert @egep.pfile?
+    assert @lgep.pfile?
+  end
+  def test_dicom?
+    assert @ged.dicom?
+    assert @did.dicom?
+    assert !@egep.dicom?
+    assert !@lgep.dicom?
+  end
+  def test_gehdr_dicom_values
+    assert_equal "I.001", @ged.filename
+    assert_equal "rdgehdr", @ged.hdr_reader
+    assert_equal "dicom", @ged.file_type
+    assert_equal "2003-01-31T05:02:54+00:00", @ged.timestamp.to_s
+    assert_equal "Andys3T", @ged.source
+    assert_equal "ALZMRI002", @ged.rmr_number
+    assert_equal 1.7, @ged.slice_thickness
+    assert_equal 0.3, @ged.slice_spacing
+    assert_equal 240.0, @ged.reconstruction_diameter
+    assert_equal 256, @ged.acquisition_matrix_x
+    assert_equal 256, @ged.acquisition_matrix_y
+    assert_equal 9.0, @ged.rep_time
+    assert_equal 2, @ged.bold_reps
+  end
+  def test_dicomhdr_dicom_values
+    assert_equal "S4_EFGRE3D.0001", @did.filename
+    assert_equal "dicom_hdr", @did.hdr_reader
+    assert_equal "dicom", @did.file_type
+    assert_equal "2006-11-16T10:59:23+00:00", @did.timestamp.to_s
+    assert_equal "Andys3T", @did.source
+    assert_equal "RMRRF2267", @did.rmr_number
+    assert_equal 1.2, @did.slice_thickness
+    assert_equal 1.2, @did.slice_spacing
+    assert_equal 240.0, @did.reconstruction_diameter
+    assert_equal 256, @did.acquisition_matrix_x
+    assert_equal 256, @did.acquisition_matrix_y
+    assert_equal 8.364, @did.rep_time
+    assert_equal 0, @did.bold_reps
+  end
+  def test_early_pfile_values
+    assert_equal "P59392.7", @egep.filename
+    assert_equal "rdgehdr", @egep.hdr_reader
+    assert_equal "pfile", @egep.file_type
+    assert_equal "2003-01-31T04:39:04+00:00", @egep.timestamp.to_s
+    assert_equal "Andys3T", @egep.source
+    assert_equal "ALZMRI002", @egep.rmr_number
+    assert_equal 4.0, @egep.slice_thickness
+    assert_equal 1.0, @egep.slice_spacing
+    assert_equal 240.0, @egep.reconstruction_diameter
+    assert_equal 64, @egep.acquisition_matrix_x
+    assert_equal 64, @egep.acquisition_matrix_y
+    assert_equal 1.999996, @egep.rep_time
+    assert_equal 124, @egep.bold_reps
+  end
+  def test_late_pfile_values
+    assert_equal "P27648.7", @lgep.filename
+    assert_equal "rdgehdr", @lgep.hdr_reader
+    assert_equal "pfile", @lgep.file_type
+    assert_equal "2006-11-16T04:35:02+00:00", @lgep.timestamp.to_s
+    assert_equal "Andys3T", @lgep.source
+    assert_equal "RMRRF2267", @lgep.rmr_number
+    assert_equal 4.0, @lgep.slice_thickness
+    assert_equal 1.0, @lgep.slice_spacing
+    assert_equal 240.0, @lgep.reconstruction_diameter
+    assert_equal 64, @lgep.acquisition_matrix_x
+    assert_equal 64, @lgep.acquisition_matrix_y
+    assert_equal 2.000010, @lgep.rep_time
+    assert_equal 124, @lgep.bold_reps
+  end
+  
+  def test_db_insert
+    @ged.db_insert!('fixtures/development.sqlite3')
+    @did.db_insert!('fixtures/development.sqlite3')
+    @egep.db_insert!('fixtures/development.sqlite3')
+    @lgep.db_insert!('fixtures/development.sqlite3')
+  end
+
+
+
+  def teardown
+    @ged.db_remove!('fixtures/development.sqlite3')
+    @did.db_remove!('fixtures/development.sqlite3')
+    @egep.db_remove!('fixtures/development.sqlite3')
+    @lgep.db_remove!('fixtures/development.sqlite3')
+  end
+end

data/test/visit_duplication_test.rb

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+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'test/unit'
+require 'visit'
+require 'pathname'
+
+
+class RawImageFileTest < Test::Unit::TestCase
+  DBFILE = '/Data/home/kris/TextMateProjects/TransferScans/db/development.sqlite3'
+  
+  def setup
+    # DO NOTHING
+  end
+  
+  def test_scan_and_insert
+    @v = Visit.new( '/Data/vtrak1/raw/alz_2000/alz093', 'ALZ' )
+    @v.scan
+    @v.init_db(DBFILE)
+    @v.db_insert!
+  end
+end

data/test/visit_test.rb

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+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'test/unit'
+require 'visit_raw_data_directory'
+require 'pathname'
+require 'logger'
+
+class RawImageFileTest < Test::Unit::TestCase
+  DBFILE = '/Users/kris/projects/TransferScans/db/development.sqlite3'
+  LOG = Logger.new('visit_test.log', shift_age = 7, shift_size = 1048576)
+  STUDIES = [
+    # Pathname.new('/Data/vtrak1/raw/alz_2000'),
+    # Pathname.new('/Data/vtrak1/raw/alz_2000'),
+    # Pathname.new('/Data/vtrak1/raw/pib_pilot_mri'),
+    # Pathname.new('/Data/vtrak1/raw/johnson.tbi-va.visit1'),
+    # Pathname.new('/Data/vtrak1/raw/wrap140'),
+    Pathname.new('/Data/vtrak1/raw/cms/uwmr'),
+    Pathname.new('/Data/vtrak1/raw/cms/wais'),
+    Pathname.new('/Data/vtrak1/raw/esprit/9month'),
+    Pathname.new('/Data/vtrak1/raw/esprit/baseline')
+    # Pathname.new('/Data/vtrak1/raw/gallagher_pd'),
+    #    Pathname.new('/Data/vtrak1/raw/pc_4000'),
+    #    Pathname.new('/Data/vtrak1/raw/ries.aware.visit1'),
+    #    Pathname.new('/Data/vtrak1/raw/tbi_1000'),
+    #    Pathname.new('/Data/vtrak1/raw/tbi_aware')
+  ]
+  FILTERS = [
+    # /^alz...$/,
+    # /^alz..._[2AB]$/,
+    # /^3..._/,
+    # /^tbi/,
+    # /^25/,
+    /^cms_...$/,
+    /^pc...$/,
+    /^3.._/,
+    /^3.._/
+    # /^pd..._/,
+    #     /^pc...$/,
+    #     /^awr.*\d$/,
+    #     /^tbi...$|^tbi..._2$/,
+    #     /^tbi..._3$/
+  ]
+  PROTOCOLS = ['ALZ_visit1','ALZ_visit2','PIB_PILOT','TBI_VA','WRAP140','CMS_UWMR','CMS_WAIS','ESPRIT_9month',
+    'ESPRIT_baseline','gallagher_pd','pc_4000','ries.aware.visit1','tbi_1000','tbi_aware']
+  
+  def setup
+    # DO NOTHING
+  end
+  
+  def test_scan_and_insert
+    STUDIES.each_with_index do |study, i|
+      filter = FILTERS[i]
+      protocol = PROTOCOLS[i]
+      study.entries.each do |visit|
+        next if visit.to_s =~ /^\./
+        next unless visit.to_s =~ filter
+        visitdir = study + visit
+        v = VisitRawDataDirectory.new( visitdir.to_s )
+        begin
+          v.scan
+          v.db_insert!(DBFILE)
+        rescue Exception => e
+          puts "There was a problem scanning a dataset in #{visitdir}... skipping."
+          puts "Exception message: #{e.message}"
+          LOG.error "There was a problem scanning a dataset in #{visitdir}... skipping."
+          LOG.error "Exception message: #{e.message}"
+        ensure
+          v = nil
+        end
+      end
+    end
+  end
+  
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: metamri
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Kristopher J. Kosmatka
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-12-08 00:00:00 -06:00
+default_executable: 
+dependencies: []
+
+description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
+email: kk4@medicine.wisc.edu
+executables: 
+- import_study.rb
+- import_visit.rb
+extensions: []
+
+extra_rdoc_files: 
+- README.rdoc
+files: 
+- .gitignore
+- Manifest
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/import_study.rb
+- bin/import_visit.rb
+- lib/metamri.rb
+- lib/mysql_tools.rb
+- lib/raw_image_dataset.rb
+- lib/raw_image_file.rb
+- lib/series_description_parameters.rb
+- lib/visit_raw_data_directory.rb
+- metamri.gemspec
+- test/raw_image_dataset_test.rb
+- test/raw_image_file_test.rb
+- test/visit_duplication_test.rb
+- test/visit_test.rb
+has_rdoc: true
+homepage: http://github.com/brainmap/metamri
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 3
+summary: MRI metadata
+test_files: 
+- test/raw_image_dataset_test.rb
+- test/raw_image_file_test.rb
+- test/visit_duplication_test.rb
+- test/visit_test.rb