brainmap-ImageData 0.1.0

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: brainmap-ImageData
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Kristopher J. Kosmatka
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-08-06 00:00:00 -07:00
+default_executable: 
+dependencies: []
+
+description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
+email: kk4@medicine.wisc.edu
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- lib/CLUs/import_study.rb
+- lib/CLUs/import_visit.rb
+- lib/mysql_tools.rb
+- lib/raw_image_dataset.rb
+- lib/raw_image_file.rb
+- lib/series_description.rb
+- lib/visit_raw_data_directory.rb
+- LICENSE
+- README.rdoc
+files: 
+- lib/CLUs/import_study.rb
+- lib/CLUs/import_visit.rb
+- lib/mysql_tools.rb
+- lib/raw_image_dataset.rb
+- lib/raw_image_file.rb
+- lib/series_description.rb
+- lib/visit_raw_data_directory.rb
+- LICENSE
+- Manifest
+- Rakefile
+- README.rdoc
+- test/raw_image_dataset_test.rb
+- test/raw_image_file_test.rb
+- test/visit_duplication_test.rb
+- test/visit_test.rb
+- ImageData.gemspec
+has_rdoc: true
+homepage: http://github.com/brainmap/ImageData
+licenses: 
+post_install_message: 
+rdoc_options: 
+- --line-numbers
+- --inline-source
+- --title
+- ImageData
+- --main
+- README.rdoc
+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: "1.2"
+  version: 
+requirements: []
+
+rubyforge_project: imagedata
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 2
+summary: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
+test_files: 
+- test/raw_image_dataset_test.rb
+- test/raw_image_file_test.rb
+- test/visit_duplication_test.rb
+- test/visit_test.rb