metamri 0.2.2 → 0.2.3

data/.rspec

@@ -0,0 +1 @@
+--color

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.2.3

data/lib/metamri/core_additions.rb

@@ -74,8 +74,7 @@ class Pathname
   def all_dicoms
     local_copies = []
     Dir.mktmpdir do |tempdir|
-      begin
-      
+      # begin
         entries.each do |leaf|
           branch = self + leaf
           if leaf.to_s =~ /^I\.(\.bz2)?$|\.dcm(\.bz2)?$|\.[0-9]+(\.bz2)?$/
@@ -85,9 +84,10 @@ class Pathname
 
         yield local_copies
 
-      ensure
-        local_copies.each { |lc| lc.delete }
-      end
+      # ensure
+        # No ensure needed since Dir.mktmpdir will implode after a block.
+        # local_copies.each { |lc| lc.delete if lc.exist? }
+      # end
     end
     
     return
@@ -147,6 +147,62 @@ class Pathname
   
 end
 
+# Find hash differences.
+class Hash
+  def diff(other)
+    self.keys.inject({}) do |memo, key|
+      unless self[key] == other[key]
+        memo[key] = [self[key], other[key]] 
+      end
+      memo
+    end
+  end
+  
+  def similar(other)
+    self.keys.inject({}) do |memo, key|
+      if self[key] == other[key]
+        memo[key] = self[key]
+      end
+      memo
+    end
+  end
+end
+
+# Method from ftools - requiring fileutils instead for Ruby 1.9 compatibility
+# and explicitly adding this single method.
+class File
+  BUFSIZE = 8 * 1024
+  def self.compare(from, to, verbose = false)
+    $stderr.print from, " <=> ", to, "\n" if verbose
+
+    return false if stat(from).size != stat(to).size
+
+    from = open(from, "rb")
+    to = open(to, "rb")
+
+    ret = false
+    fr = tr = ''
+
+    begin
+      while fr == tr
+        fr = from.read(BUFSIZE)
+        if fr
+          tr = to.read(fr.size)
+        else
+          ret = to.read(BUFSIZE)
+          ret = !ret || ret.length == 0
+          break
+        end
+      end
+    rescue
+      ret = false
+    ensure
+      to.close
+      from.close
+    end
+    ret
+  end
+end
 # =begin rdoc
 # Monkey-patch Float to avoid rounding errors.
 # For more in-depth discussion, see: http://www.ruby-forum.com/topic/179361

data/lib/metamri/dicom_additions.rb

@@ -0,0 +1,63 @@
+# Dicom Additions is a test extension of DICOM to allow for gathering common tags
+class DicomGroup
+  # Array of DObjects to aggregate
+  attr_accessor :dobjects
+  # Hash of tags shared by all DICOMs in Directory
+  attr_reader :tags
+  # DICOM::DObject containing all common tags of the group
+  attr_reader :common
+  
+  # Initialize with an array of strings or DICOM::DObjects to aggregate
+  def initialize(dicomgroup)
+    if dicomgroup.select {|dcm| dcm.is_a? DICOM::DObject }.empty?
+      @dobjects = dicomgroup.collect {|dcm| DICOM::DObject.new(dcm)}
+    else 
+      @dobjects = dicomgroup
+    end
+  end
+  
+  # Return a hash of tags and values of elements common to all DICOMs in the group.
+  def find_common_tags
+    @dobjects.inject(@dobjects.first.to_hash) do |memo, dobj|
+      memo = memo.similar(dobj.to_hash)
+    end
+  end
+  
+  # Return a new DICOM::DObject containing elements common (identical tags and values) to all DICOMs in the group. 
+  def find_common_elements
+    @dobjects.inject do |memo, dobj|
+      memo.remove_elements_that_differ_from dobj
+      memo
+    end
+  end
+  
+end
+
+# Reopen DObject to make tag hash
+class DICOM::DObject
+  # Return hash of {tags => values}
+  def to_hash
+    taghash = {}
+    @tags.each_key {|k| taghash[k] = value(k) }
+    return taghash
+  end
+  
+  # Remove elements from a dobj that aren't identical to self's tags.
+  def remove_elements_that_differ_from(other_dobj)
+    @tags.each_key do |k|
+      unless @tags[k].eql? other_dobj[k]
+        # pp k, [@tags[k].value, other_dobj[k].value]
+        remove k
+      end
+    end
+  end
+
+end
+
+# Reopen DataElement to compare
+class DICOM::DataElement
+  # Compare data elements on their tag and value
+  def eql?(other)
+    @tag == other.instance_eval("@tag") && @value == other.value && @bin == other.instance_eval("@bin")
+  end
+end

data/lib/metamri/raw_image_dataset.rb

@@ -1,6 +1,6 @@
 require 'rubygems'
 require 'sqlite3'
-require 'ftools'
+require 'fileutils'
 require 'metamri/nifti_builder'
 
 
@@ -42,8 +42,11 @@ class RawImageDataset
   attr_reader :dicom_series_uid
   # DICOM Study UID
   attr_reader :dicom_study_uid
+  # Tag Hash of DICOM Keys
+  attr_reader :dicom_taghash
   # Array of Read Error Strings
   attr_reader :read_errors
+
   
   # * dir: The directory containing the files.
   # * files: An array of #RawImageFile objects that compose the complete data set.
@@ -102,7 +105,10 @@ class RawImageDataset
     validates_metainfo_for :dicom_series_uid if dicom?
     
     @dicom_study_uid = @raw_image_files.first.dicom_study_uid
-    validates_metainfo_for :dicom_study_uid if dicom?        
+    validates_metainfo_for :dicom_study_uid if dicom?
+    
+    @dicom_taghash = @raw_image_files.first.dicom_taghash
+    validates_metainfo_for :dicom_taghash if dicom?
         
     $LOG ||= Logger.new(STDOUT)
   end
@@ -154,15 +160,14 @@ class RawImageDataset
      AND timestamp LIKE '#{@timestamp.to_s.split(/\+|Z/).first}%'"
   end
 
-=begin rdoc
-Returns a hash of attributes used for insertion into active record.
-Options:  :thumb => FileHandle to thumbnail includes a thumbnail.
-=end  
+
+  # Returns a hash of attributes used for insertion into active record.
+  # Options:  :thumb => FileHandle to thumbnail includes a thumbnail.
   def attributes_for_active_record(options = {})
     thumbnail = options.has_key?(:thumb) ? options[:thumb] : nil
     
     unless (thumbnail.class == File || thumbnail == nil)
-      raise(IOError, "Thumbnail #{options[:thumb]} must be a #File.")
+      raise(IOError, "Thumbnail #{options[:thumb]} must be a #File instead of #{thumbnail.class}.")
     end
     { :rmr => @rmr_number,
       :series_description => @series_description,
@@ -173,7 +178,9 @@ Options:  :thumb => FileHandle to thumbnail includes a thumbnail.
       :bold_reps => @raw_image_files.first.bold_reps,
       :slices_per_volume => @raw_image_files.first.num_slices,
       :scanned_file => @scanned_file,
-      :thumbnail => thumbnail
+      :thumbnail => thumbnail,
+      :dicom_series_uid => @dicom_series_uid,
+      :dicom_taghash => @dicom_taghash
     }
   end
   
@@ -338,11 +345,29 @@ private
   end
 
   # Ensure that metadata is present in instance variables.
-  # validates_metainfo_for :study_description, :msg => "No study description found" 
+  #
+  # Raises an IndexError if supplied instance variable is nil unless :optional,
+  # and adds a message to the @read_errors array.
+  #
+  # === Parameters
+  #
+  # * <tt>info_variable</tt> -- A string (not including the @ sign) to check to ensure not blank and not empty.
+  #
+  # === Options
+  #
+  # * <tt>:msg</tt> -- An optional message to be added to @read_errors (defaults to "Couldn't find <info_variable>")
+  # * <tt>:optional</tt> -- A boolean to allow adding the error to the array as a warning but not breaking with an error.
+  #  
+  # === Examples
+  #
+  # validates_metainfo_for :study_description, :msg => "No study description found", :optional => true
+  # 
   def validates_metainfo_for(info_variable, options = {})
     raise StandardError, "#{info_variable} must be a symbol" unless info_variable.kind_of? Symbol
-    if self.instance_variable_get("@" + info_variable.to_s).nil?
-      @read_errors << options[:msg] ||= "Couldn't find #{info_variable.to_s}"
+    data = self.instance_variable_get("@" + info_variable.to_s)
+    if data.nil? || data.empty?
+      message = options[:msg] || "Couldn't find #{info_variable.to_s}"
+      @read_errors << message
       raise IndexError, message unless options[:optional]
     end
   end

data/lib/metamri/raw_image_dataset_resource.rb

@@ -132,7 +132,7 @@ class RawImageDatasetResource < ActiveResource::Base
       :headers => { :relative_dataset_path => 'Dataset', :series_description => 'Series Details', :file_count => "File Count", :image_dataset_quality_checks_tablerow => "Quality Checks"}, 
       :fields => [:relative_dataset_path, :series_description, :file_count, :image_dataset_quality_checks_tablerow],
       :description => false, # Turn off rendering row count description at bottom.
-      :resize => false
+      :resize => true
     )
   rescue NameError => e
     raise e

data/lib/metamri/visit_raw_data_directory.rb

@@ -56,6 +56,8 @@ class VisitRawDataDirectory
   attr_accessor :scanid
   # The id of the visit to be used when doing reverse-lookup in data panda.
   attr_accessor :database_id
+  # DICOM Study UID (Visit/Study Unique Identifier)
+  attr_reader :dicom_study_uid
   
   PREPROCESS_REPOSITORY_DIRECTORY = '/Data/vtrak1/preprocessed/visits'
   # DATAPANDA_SERVER = 'http://localhost:3000'
@@ -88,7 +90,9 @@ class VisitRawDataDirectory
     flash "Scanning visit raw data directory #{@visit_directory}" if $LOG.level <= Logger::INFO
     default_options = {:ignore_patterns => []}
     options = default_options.merge(options)
-    puts "Ignoring directories matching: #{options[:ignore_patterns].join(", ")}" unless options[:ignore_patterns].empty?
+    unless options[:ignore_patterns].empty?
+      puts "Ignoring directories matching: #{options[:ignore_patterns].join(", ")}" if $LOG.level <= Logger::INFO
+    end
     
     d = Pathname.new(@visit_directory)
     d.each_subdirectory do |dd|
@@ -107,6 +111,7 @@ class VisitRawDataDirectory
       @rmr_number = get_rmr_number
       @scanner_source = get_scanner_source
       @study_id = get_study_id
+      @dicom_study_uid = get_dicom_study_uid
       flash "Completed scanning #{@visit_directory}" if $LOG.level <= Logger::DEBUG
     else
       raise(IndexError, "No datasets could be scanned for directory #{@visit_directory}")
@@ -120,7 +125,8 @@ class VisitRawDataDirectory
       :rmr => @rmr_number, 
       :path => @visit_directory, 
       :scanner_source => @scanner_source ||= get_scanner_source,
-      :scan_number => @study_id
+      :scan_number => @study_id,
+      :dicom_study_uid => @dicom_study_uid
     }
   end
   
@@ -393,6 +399,14 @@ Returns an array of the created nifti files.
     # raise(IOError, "No valid study id / exam number found.")
   end
   
+  # retrieves exam number / scan id from first #RawImageDataset
+  def get_dicom_study_uid
+    @datasets.each do |ds|
+      return ds.dicom_study_uid unless ds.dicom_study_uid.nil?
+    end
+    raise(IOError, "No valid study uid found from DICOMS.")
+  end
+  
   def get_scan_procedure_based_on_raw_directory
     case @visit_directory
     when /alz_2000.*_2$/

data/lib/metamri.rb

@@ -1,10 +1,10 @@
 $: << File.dirname(__FILE__)
 
-begin
-  require 'rubygems'
-  gem 'activeresource', '<= 2.3.8'
+# begin
+#   require 'rubygems'
+#   gem 'activeresource', '<= 2.3.8'
   require 'active_resource'
-end
+# end
 
 
 require 'metamri/core_additions'
@@ -14,6 +14,7 @@ require 'metamri/visit_raw_data_directory'
 require 'metamri/raw_image_dataset_resource'
 require 'metamri/visit_raw_data_directory_resource'
 require 'metamri/image_dataset_quality_check_resource'
+require 'metamri/dicom_additions'
 
 # require 'metamri/raw_image_dataset_thumbnail'
 # TODO Move raw_image_dataset_thumbnail out of metamri.  
@@ -24,5 +25,4 @@ rescue LoadError
   puts "Hirb must be installed for pretty output. Use 'sudo gem install hirb'"
 end
 
-module Metamri
-end
+# module Metamri; end

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.2.2"
+  s.version = "0.2.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2011-01-18}
+  s.date = %q{2011-02-25}
   s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
   s.email = %q{kk4@medicine.wisc.edu}
   s.executables = ["convert_visit.rb", "import_visit.rb", "import_respiratory_files.rb", "import_study.rb", "list_visit"]
@@ -17,6 +17,7 @@ Gem::Specification.new do |s|
     "README.rdoc"
   ]
   s.files = [
+    ".rspec",
     "Manifest",
     "README.rdoc",
     "Rakefile",
@@ -28,6 +29,7 @@ Gem::Specification.new do |s|
     "bin/list_visit",
     "lib/metamri.rb",
     "lib/metamri/core_additions.rb",
+    "lib/metamri/dicom_additions.rb",
     "lib/metamri/image_dataset_quality_check_resource.rb",
     "lib/metamri/mysql_tools.rb",
     "lib/metamri/nifti_builder.rb",
@@ -40,6 +42,7 @@ Gem::Specification.new do |s|
     "lib/metamri/visit_raw_data_directory_resource.rb",
     "metamri.gemspec",
     "spec/helper_spec.rb",
+    "spec/unit/dicom_additions_spec.rb",
     "spec/unit/nifti_builder_spec.rb",
     "spec/unit/raw_image_dataset_spec.rb",
     "spec/unit/raw_image_dataset_thumbnail_spec.rb",
@@ -57,10 +60,11 @@ Gem::Specification.new do |s|
   ]
   s.homepage = %q{http://github.com/brainmap/metamri}
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.4.1}
+  s.rubygems_version = %q{1.4.2}
   s.summary = %q{MRI metadata}
   s.test_files = [
     "spec/helper_spec.rb",
+    "spec/unit/dicom_additions_spec.rb",
     "spec/unit/nifti_builder_spec.rb",
     "spec/unit/raw_image_dataset_spec.rb",
     "spec/unit/raw_image_dataset_thumbnail_spec.rb",

data/spec/helper_spec.rb

@@ -1,10 +1,10 @@
-begin
-  require 'spec'
-rescue LoadError
-  require 'rubygems' unless ENV['NO_RUBYGEMS']
-  gem 'rspec'
-  require 'spec'
-end
+# begin
+  # require 'spec'
+# rescue LoadError
+  # require 'rubygems' unless ENV['NO_RUBYGEMS']
+  # gem 'rspec'
+  # require 'spec'
+# end
 
 require 'tmpdir'
 require 'fileutils'

data/spec/unit/dicom_additions_spec.rb

@@ -0,0 +1,68 @@
+require 'helper_spec'
+require 'metamri'
+
+describe 'DicomGroup' do
+  before(:each) do
+    @group_array = Dir.glob('/tmp/s01_assetcal/s01_assetcal.0*')[0..1]
+    @group = DicomGroup.new(@group_array)
+    @common = DicomGroup.new(@group_array).find_common_elements
+    @test_output_file = File.join(Dir.tmpdir, 'test.dcm')
+  end
+  it 'should initialize a DicomGroup' do
+    grp = DicomGroup.new(@group_array)
+    grp.should be_an_instance_of DicomGroup
+    grp.dobjects.length.should == 2
+  end
+  
+  it 'should convert files in array to DICOM::DObjects' do
+    @group.dobjects.first.should be_an_instance_of DICOM::DObject
+  end
+  
+  it 'should generate a hash of tags with common values' do
+    tags = @group.find_common_tags
+    tags.length.should == 310
+    tags.should be_a_kind_of Hash
+    tags.should_not be_empty
+  end
+  
+  it 'should remove differing tags' do
+    object_lengths = @group.dobjects.map{|dobj| dobj.to_hash.length}
+    common_dobj = @group.find_common_elements
+    common_dobj.to_hash.length.should be < @group.dobjects.map { |dobj| dobj.to_hash.length }.max
+    # @group.dobjects.map {|dobj| dobj.to_hash.length }.should == object_lengths
+  end
+  
+  it 'should set the DICOM string of common tags' do
+    # Create a dicom object to test to make sure that we can read the string.
+    # segments = @common.encode_segments(4*1024)
+    # @common.send(:insert_missing_meta)
+    # File.open('/tmp/dcmstring', 'wb') {|f| f.puts segments}
+    # puts dcm = DICOM::DObject.new(segments, :bin => true)
+    # puts dcm.errors
+    # dcm.read_success.should be_true
+    # dcm.print_all
+    
+    @common.write(@test_output_file)
+    @common.write_success.should be_true
+    File.exist?(@test_output_file).should be_true
+    d = DICOM::DObject.new(@test_output_file)
+    d.stream.string.should == 'a'
+  end
+  
+  # after(:each) do
+  #   File.delete(@test_output_file) if File.exist?(@test_output_file)
+  # end
+  
+end
+
+describe 'DICOM::DObject' do
+  before(:all) do
+    @group_array = Dir.glob('/tmp/s01_assetcal/s01_assetcal.0*')[0..1]
+  end
+  
+  it "should respond to to_hash" do
+    tags = DICOM::DObject.new(@group_array.first).to_hash
+    tags.should be_a_kind_of Hash
+    tags.should have_key '0019,1081'
+  end
+end

data/spec/unit/nifti_builder_spec.rb

@@ -1,9 +1,8 @@
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
+require 'helper_spec'
+
 require 'rubygems'
-require 'spec'
-require 'fileutils'
-require 'tmpdir'
 require 'metamri'
 
 VISIT_FIXTURE_SRC = '/Data/vtrak1/raw/johnson.tbi-va.visit1/tbiva034_10019_04212010'
@@ -48,8 +47,8 @@ describe "Convert Unknown Dicoms to Nifti Files" do
     @dataset_unzipped.to_nifti('/tmp/', 'filename.nii', :input_directory => @dataset_unzipped.directory)[0].should == "to3d -session /tmp/ -prefix filename.nii #{@dataset_unzipped.directory}/'*.dcm'"
     nifti_conversion_command, nifti_output_file = @dataset_unzipped.to_nifti!('/tmp/', 'filename.nii', :input_directory => @dataset_unzipped.directory)
     nifti_conversion_command.should == "to3d -session /tmp/ -prefix filename.nii #{@dataset_unzipped.directory}/'*.dcm'"
+    File.exist?(nifti_output_file).should be_true
     @test_niftis << nifti_output_file
-    @output_directories << '/tmp'
   end
   
   it "should convert all anatomicals in a visit raw directory using original, unzipped files." do
@@ -106,7 +105,7 @@ describe "Convert Unknown Dicoms to Nifti Files" do
   end
   
   after(:each) do
-    @test_niftis.flatten.each { |nifti| File.delete(nifti) } unless @test_niftis.empty?
+    @test_niftis.flatten.each { |nifti| File.delete(nifti) if File.exist?(nifti) } unless @test_niftis.empty?
     [@output_directories, Dir.tmpdir, '/tmp'].flatten.each do |temp_dir|
       Dir.foreach(temp_dir) {|f| File.delete(File.join(temp_dir, f)) if File.extname(f) == '.nii'}
     end

data/spec/unit/raw_image_dataset_spec.rb

@@ -20,7 +20,7 @@ describe RawImageDataset, "for a single valid DICOM file" do
     ds.raw_image_files.first.should == @valid_raw_image_file
     ds.rmr_number.should == "ID"
     ds.scanned_file.should == @valid_dicom_basename
-    ds.scanner_source.should == "Station"
+    ds.scanner_source.should == "Institution"
     ds.series_description.should == "Ax FSPGR BRAVO T1"
     ds.study_id.should == "1405"
     ds.timestamp.should == DateTime.parse("Wed, 10 Nov 2010 00:00:00 +0000")

data/spec/unit/raw_image_dataset_thumbnail_spec.rb

@@ -1,7 +1,7 @@
 $:.unshift File.join(File.dirname(__FILE__),'..','..','lib')
 $:.unshift File.join(File.dirname(__FILE__))
 
-require 'spec'
+
 require 'escoffier'
 require 'metamri/core_additions'
 require 'metamri/raw_image_dataset'

data/spec/unit/raw_image_file_spec.rb

@@ -35,7 +35,7 @@ describe RawImageFile, "reads a dicom header and extracts metadata" do
       image.series_description.should == "Ax FSPGR BRAVO T1"
       image.slice_spacing.should == "1"
       image.slice_thickness.should == "1"
-      image.source.should == "Station"
+      image.source.should == "Institution"
       # Don't compare floats due to rounding errors, but compare all the other tags in dicom_taghash
       image.dicom_taghash.reject{|k,v| v[:value].kind_of? Float }.should == valid_dicom_taghash.reject{|k,v| v[:value].kind_of? Float }
       image.dicom_study_uid.should == "1.2.840.113619.6.260.4.1294724594.737.1289407877.724"

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  hash: 19
+  hash: 17
   prerelease: 
   segments: 
   - 0
   - 2
-  - 2
-  version: 0.2.2
+  - 3
+  version: 0.2.3
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-01-18 00:00:00 -06:00
+date: 2011-02-25 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -73,6 +73,7 @@ extensions: []
 extra_rdoc_files: 
 - README.rdoc
 files: 
+- .rspec
 - Manifest
 - README.rdoc
 - Rakefile
@@ -84,6 +85,7 @@ files:
 - bin/list_visit
 - lib/metamri.rb
 - lib/metamri/core_additions.rb
+- lib/metamri/dicom_additions.rb
 - lib/metamri/image_dataset_quality_check_resource.rb
 - lib/metamri/mysql_tools.rb
 - lib/metamri/nifti_builder.rb
@@ -96,6 +98,7 @@ files:
 - lib/metamri/visit_raw_data_directory_resource.rb
 - metamri.gemspec
 - spec/helper_spec.rb
+- spec/unit/dicom_additions_spec.rb
 - spec/unit/nifti_builder_spec.rb
 - spec/unit/raw_image_dataset_spec.rb
 - spec/unit/raw_image_dataset_thumbnail_spec.rb
@@ -140,12 +143,13 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.4.1
+rubygems_version: 1.4.2
 signing_key: 
 specification_version: 3
 summary: MRI metadata
 test_files: 
 - spec/helper_spec.rb
+- spec/unit/dicom_additions_spec.rb
 - spec/unit/nifti_builder_spec.rb
 - spec/unit/raw_image_dataset_spec.rb
 - spec/unit/raw_image_dataset_thumbnail_spec.rb