metamri 0.1.17 → 0.1.18

data/Rakefile

@@ -28,6 +28,8 @@ begin
     gemspec.homepage = "http://github.com/brainmap/metamri"
     gemspec.authors = ["Kristopher J. Kosmatka"]
     gemspec.add_dependency('sqlite3-ruby')
+    gemspec.add_dependency('dicom')
+    # gemspec.add_dependency('rmagick')
     gemspec.add_development_dependency('rspec')
   end
   Jeweler::GemcutterTasks.new

data/VERSION

@@ -1 +1 @@
-0.1.17
+0.1.18

data/bin/import_study.rb

@@ -28,11 +28,10 @@
 #
 
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-require 'visit_raw_data_directory'
 require 'pathname'
 require 'rdoc/usage'
 require 'logger'
+require 'metamri'
 
 #:stopdoc:
 STUDIES = {

data/bin/import_visit.rb

@@ -32,11 +32,10 @@
 #
 
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-require 'visit_raw_data_directory'
 require 'pathname'
 require 'rdoc/usage'
 require 'logger'
+require 'metamri'
 
 # == Function
 #   Imports imaging data collected during a single visit into the WADRC Data Tools web application database.

data/lib/metamri/core_additions.rb

@@ -56,7 +56,7 @@ class Pathname
   def first_dicom
     entries.each do |leaf|
       branch = self + leaf
-      if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.0[0-9]+(\.bz2)?$/
+      if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.[0-9]+(\.bz2)?$/
         lc = branch.local_copy
         begin
           yield lc
@@ -77,7 +77,7 @@ class Pathname
       
         entries.each do |leaf|
           branch = self + leaf
-          if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.0[0-9]+(\.bz2)?$/
+          if leaf.to_s =~ /^I\.(\.bz2)?$|\.dcm(\.bz2)?$|\.[0-9]+(\.bz2)?$/
             local_copies << branch.local_copy(tempdir)
           end
         end

data/lib/metamri/nifti_builder.rb

@@ -18,7 +18,7 @@ module UnknownImageDataset
     else input_files = "#{Dir.tmpdir}/'#{glob}'"
     end
     
-    if @raw_image_files.first.rep_time && @raw_image_files.first.bold_reps && @raw_image_files.first.num_slices
+    if @raw_image_files.first.rep_time && @raw_image_files.first.bold_reps && @raw_image_files.first.num_slices && !input_options[:no_timing_options]
       slice_order = "altplus"
       functional_args = "-time:zt #{@raw_image_files.first.num_slices} #{@raw_image_files.first.bold_reps} #{@raw_image_files.first.rep_time} #{slice_order}"
     end
@@ -29,7 +29,7 @@ module UnknownImageDataset
     File.makedirs(nifti_output_directory) unless File.directory?(nifti_output_directory)
     raise(IOError, "Cannot write to #{nifti_output_directory}") unless File.writable?(nifti_output_directory)
         
-    nifti_conversion_command = "to3d -session #{nifti_output_directory} -prefix #{nifti_filename} #{functional_args} #{input_files}"
+    nifti_conversion_command = "to3d -session #{nifti_output_directory} -prefix #{[nifti_filename, functional_args, input_files].compact.join(' ')}"
 
     return nifti_conversion_command, nifti_output_file
   end

data/lib/metamri/raw_image_dataset.rb

@@ -21,6 +21,8 @@ class RawImageDataset
   attr_reader :rmr_number
   # From the first raw image file in the dataset
   attr_reader :timestamp
+  # From the first raw image file in the dataset
+  attr_reader :study_id
   # A key string unique to a dataset composed of the rmr number and the timestamp.
   attr_reader :dataset_key
   # the file scanned
@@ -51,17 +53,26 @@ class RawImageDataset
       raise(IndexError, im.to_s + " is not a RawImageFile") if im.class.to_s != "RawImageFile"
     end
     @raw_image_files = raw_image_files
+    
     @series_description = @raw_image_files.first.series_description
     raise(IndexError, "No series description found") if @series_description.nil?
+    
     @rmr_number = @raw_image_files.first.rmr_number
     raise(IndexError, "No rmr found") if @rmr_number.nil?
+    
     @timestamp = get_earliest_timestamp
     raise(IndexError, "No timestamp found") if @timestamp.nil?
+    
     @dataset_key = @rmr_number + "::" + @timestamp.to_s
+
     @scanned_file = @raw_image_files.first.filename
     raise(IndexError, "No scanned file found") if @scanned_file.nil?
+    
     @scanner_source = @raw_image_files.first.source
     raise(IndexError, "No scanner source found") if @scanner_source.nil?
+        
+    @study_id = @raw_image_files.first.study_id.nil? ? nil : @raw_image_files.first.study_id
+    # raise(IndexError, "No study id / exam number found") if @study_id.nil?
     
     $LOG ||= Logger.new(STDOUT)
   end
@@ -165,7 +176,14 @@ Returns a path to the created dataset as a string if successful.
     begin 
       nifti_conversion_command, nifti_output_file = to_nifti(nifti_output_directory, nifti_filename, input_options)
       puts nifti_conversion_command
-      system "#{nifti_conversion_command}"
+      begin
+        system "#{nifti_conversion_command}"
+        raise ScriptError, "#{nifti_output_file} does not exist." unless File.exist?(nifti_output_file)
+      rescue ScriptError => e
+        input_options[:no_timing_options] = true
+        nifti_conversion_command, nifti_output_file = to_nifti(nifti_output_directory, nifti_filename, input_options)
+        system "#{nifti_conversion_command}"
+      end
       raise(IOError, "Could not convert image dataset: #{@directory} to #{nifti_output_file}") unless $? == 0
     rescue IOError => e
       $LOG.warn "-- Warning: #{e.message}"

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -1,5 +1,5 @@
 require 'dicom'
-require 'rmagick'
+require 'RMagick'
 require 'tmpdir'
 
 # This class is a ruby object encapsulating a .png 2D Thumbnail of a Dataset

data/lib/metamri/raw_image_file.rb

@@ -36,6 +36,8 @@ class RawImageFile
   attr_reader :source
   # An identifier unique to a 'visit', these are assigned by the scanner techs at scan time.
   attr_reader :rmr_number
+  # An identifier unique to a Study Session - AKA Exam Number
+  attr_reader :study_id
   # A short string describing the acquisition sequence. These come from the scanner.
   # code and are used to initialise SeriesDescription objects to find related attributes.
   attr_reader :series_description
@@ -300,79 +302,84 @@ Extracts a collection of metadata from @hdr_data retrieved using the dicom_hdr
 utility.  
 =end
   def dicom_hdr_import
-    meta_matchers = {}
-    meta_matchers[:rmr_number] = { 
+    dicom_tag_templates = {}
+    dicom_tag_templates[:rmr_number] = { 
       :type => :string, 
       :pat => /[ID Accession Number|ID Study Description]\/\/(RMR.*)\n/i, 
       :required => true 
     }
-    meta_matchers[:slice_thickness] = { 
+    dicom_tag_templates[:study_id] = {
+      :type => :string,
+      :pat => /STUDY ID\/\/([0-9]+)/i,
+      :required => true 
+    }
+    dicom_tag_templates[:slice_thickness] = { 
       :type => :float, 
       :pat => /ACQ SLICE THICKNESS\/\/(.*)\n/i,
       :required => false
     }
-    meta_matchers[:slice_spacing] = {
+    dicom_tag_templates[:slice_spacing] = {
       :type => :float,
       :pat => /ACQ SPACING BETWEEN SLICES\/\/(.*)\n/i,
       :required => false
     }
-    meta_matchers[:source] = {
+    dicom_tag_templates[:source] = {
       :type => :string,
       :pat => /ID INSTITUTION NAME\/\/(.*)\n/i,
       :required => true
     } 
-    meta_matchers[:series_description] = {
+    dicom_tag_templates[:series_description] = {
       :type => :string,
       :pat => /ID SERIES DESCRIPTION\/\/(.*)\n/i,
       :required => true 
     }
-    meta_matchers[:gender] = {
+    dicom_tag_templates[:gender] = {
       :type => :string,
       :pat => /PAT PATIENT SEX\/\/(.)/i,
       :required => false
     }
-    meta_matchers[:reconstruction_diameter] = {
+    dicom_tag_templates[:reconstruction_diameter] = {
       :type => :int,
       :pat => /ACQ RECONSTRUCTION DIAMETER\/\/([0-9]+)/i,
       :required => false
     }
-    meta_matchers[:acquisition_matrix_x] = {
+    dicom_tag_templates[:acquisition_matrix_x] = {
       :type => :int,
       :pat => /IMG Rows\/\/ ([0-9]+)/i,
       :required => false
     }
-    meta_matchers[:acquisition_matrix_y] = {
+    dicom_tag_templates[:acquisition_matrix_y] = {
       :type => :int,
       :pat => /IMG Columns\/\/ ([0-9]+)/i,
       :required => false
     }
-    meta_matchers[:num_slices] = {
+    dicom_tag_templates[:num_slices] = {
       :type => :int,
       :pat => /REL Images in Acquisition\/\/([0-9]+)/i,
       :required => false
     }
-    meta_matchers[:bold_reps] = {
+    dicom_tag_templates[:bold_reps] = {
       :type => :int,
       :pat => /REL Number of Temporal Positions\/\/([0-9]+)/i,
       :required => false
     }
-    meta_matchers[:rep_time] = {
+    dicom_tag_templates[:rep_time] = {
       :type => :float,
       :pat => /ACQ Repetition Time\/\/(.*)\n/i,
       :required => false
     }
-    meta_matchers[:date] = {
+    dicom_tag_templates[:date] = {
       :type => :datetime,
       :pat => /ID STUDY DATE\/\/(.*)\n/i #,
       # :required => false
   }
-    meta_matchers[:time] = {
+    dicom_tag_templates[:time] = {
       :type => :datetime,
       :pat => /ID Series Time\/\/(.*)\n/i #,
       # :required => false
     }
     
-    meta_matchers.each_pair do |name, tag_hash|
+    dicom_tag_templates.each_pair do |name, tag_hash|
       begin
         next if tag_hash[:type] == :datetime
         tag_hash[:pat] =~ @hdr_data
@@ -393,9 +400,9 @@ utility.
     end
 
     # Set Timestamp separately because it requires both Date and Time to be extracted.
-    meta_matchers[:date][:pat] =~ @hdr_data
+    dicom_tag_templates[:date][:pat] =~ @hdr_data
     date = $1
-    meta_matchers[:time][:pat] =~ @hdr_data
+    dicom_tag_templates[:time][:pat] =~ @hdr_data
     time = $1
     @timestamp = DateTime.parse(date + time)
     

data/lib/metamri/visit_raw_data_directory.rb

@@ -48,6 +48,8 @@ class VisitRawDataDirectory
   attr_reader :scan_procedure_name
   # scanner source
   attr_accessor :scanner_source
+  # scanner-defined study id / exam number
+  attr_accessor :study_id
   #
   attr_accessor :db
   # Scan ID is the short name for the scan (tbiva018, tbiva018b)
@@ -71,6 +73,7 @@ class VisitRawDataDirectory
     @rmr_number = nil
     @scan_procedure_name = scan_procedure_name.nil? ? get_scan_procedure_based_on_raw_directory : scan_procedure_name
     @db = nil
+    @study_id = nil
     initialize_log
   end
   
@@ -94,6 +97,7 @@ class VisitRawDataDirectory
       @timestamp = get_visit_timestamp
       @rmr_number = get_rmr_number
       @scanner_source = get_scanner_source
+      @study_id = get_study_id
       flash "Completed scanning #{@visit_directory}" if $LOG.level <= Logger::DEBUG
     else
       raise(IndexError, "No datasets could be scanned for directory #{@visit_directory}")
@@ -106,7 +110,8 @@ class VisitRawDataDirectory
       :date => @timestamp.to_s, 
       :rmr => @rmr_number, 
       :path => @visit_directory, 
-      :scanner_source => get_scanner_source
+      :scanner_source => @scanner_source ||= get_scanner_source,
+      :scan_number => @study_id
     }
   end
   
@@ -183,7 +188,7 @@ Returns an array of the created nifti files.
   def to_s
     puts; @visit_directory.length.times { print "-" }; puts
     puts "#{@visit_directory}"
-    puts "#{@rmr_number} - #{@timestamp.strftime('%F')} - #{@scanner_source}"
+    puts "#{@rmr_number} - #{@timestamp.strftime('%F')} - #{@scanner_source} - #{@study_id unless @study_id.nil?}"
     puts
     puts RawImageDataset.to_table(@datasets)
     return
@@ -363,6 +368,14 @@ generates an sql insert statement to insert this visit with a given participant
     raise(IOError, "No valid scanner source found for this visit")
   end
   
+  # retrieves exam number / scan id from first #RawImageDataset
+  def get_study_id
+    @datasets.each do |ds|
+      return ds.study_id unless ds.study_id.nil?
+    end
+    # raise(IOError, "No valid study id / exam number found.")
+  end
+  
   def get_scan_procedure_based_on_raw_directory
     case @visit_directory
     when /alz_2000.*_2$/

data/lib/metamri.rb

@@ -4,10 +4,12 @@ require 'metamri/core_additions'
 require 'metamri/raw_image_file'
 require 'metamri/raw_image_dataset'
 require 'metamri/visit_raw_data_directory'
-require 'metamri/raw_image_dataset_thumbnail'
 require 'metamri/raw_image_dataset_resource'
 require 'metamri/visit_raw_data_directory_resource'
 
+# require 'metamri/raw_image_dataset_thumbnail'
+# TODO Move raw_image_dataset_thumbnail out of metamri.  
+
 begin
   require 'hirb'
 rescue LoadError

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.17"
+  s.version = "0.1.18"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-05-07}
+  s.date = %q{2010-06-04}
   s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
   s.email = %q{kk4@medicine.wisc.edu}
   s.executables = ["import_study.rb", "import_visit.rb", "import_respiratory_files.rb", "list_visit", "convert_visit.rb"]
@@ -67,13 +67,16 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<sqlite3-ruby>, [">= 0"])
+      s.add_runtime_dependency(%q<dicom>, [">= 0"])
       s.add_development_dependency(%q<rspec>, [">= 0"])
     else
       s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
+      s.add_dependency(%q<dicom>, [">= 0"])
       s.add_dependency(%q<rspec>, [">= 0"])
     end
   else
     s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
+    s.add_dependency(%q<dicom>, [">= 0"])
     s.add_dependency(%q<rspec>, [">= 0"])
   end
 end

data/test/nifti_builder_spec.rb

@@ -4,14 +4,11 @@ require 'rubygems'
 require 'spec'
 require 'fileutils'
 require 'tmpdir'
-require 'metamri/core_additions'
-require 'visit_raw_data_directory'
-require 'raw_image_dataset'
-require 'raw_image_file'
+require 'metamri'
 
-VISIT_FIXTURE_SRC = '/Data/vtrak1/raw/johnson.tbi-va.visit1/tbiva018b_9336_12022009'
-VISIT_FIXTURE = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009')
-VISIT_FIXTURE_UNZIPPED = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009_unzipped')
+VISIT_FIXTURE_SRC = '/Data/vtrak1/raw/johnson.tbi-va.visit1/tbiva034_10019_04212010'
+VISIT_FIXTURE = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_directory/tbiva034_10019_04212010')
+VISIT_FIXTURE_UNZIPPED = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_directory/tbiva034_10019_04212010_unzipped')
 
 
 
@@ -102,7 +99,7 @@ describe "Convert Unknown Dicoms to Nifti Files" do
   end
   
   it "should guess scan id" do
-    @visit.scanid.should == 'tbiva018b'
+    @visit.scanid.should == 'tbiva034'
     
     v = VisitRawDataDirectory.new('/Data/vtrak1/preprocessed/visits/asthana.adrc-clinical-core.visit1/adrc00001', 'asthana.adrc-clinical-core.visit1')
     v.scanid.should == 'adrc00001'

data/test/raw_image_dataset_test.rb

@@ -4,8 +4,8 @@
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'test/unit'
-require 'raw_image_dataset'
-require 'raw_image_file'
+require 'metamri/raw_image_dataset'
+require 'metamri/raw_image_file'
 
 class RawImageDatasetTest < Test::Unit::TestCase
   DBFILE = 'fixtures/development.sqlite3'

data/test/raw_image_dataset_thumbnail_spec.rb

@@ -3,9 +3,10 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 require 'spec'
 require 'escoffier'
 require 'tmpdir'
-require 'raw_image_dataset'
-require 'raw_image_file'
-require 'metamri'
+# require 'metamri'
+require 'metamri/core_additions'
+require 'metamri/raw_image_dataset'
+require 'metamri/raw_image_file'
 require 'metamri/raw_image_dataset_thumbnail'
 
 describe "Create a thumbnail png for display." do  

data/test/raw_image_file_test.rb

@@ -4,29 +4,29 @@
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'test/unit'
-require 'raw_image_file'
+require 'metamri/raw_image_file'
 
 class RawImageFileTest < Test::Unit::TestCase
   def setup
-    @GEDicom = 'fixtures/I.001'
-    @DiDicom = 'fixtures/S4_EFGRE3D.0001'
+    @GE_IFile = 'fixtures/I.001'
+    @Dicom = 'fixtures/S4_EFGRE3D.0001'
     @EarlyGEPfile = 'fixtures/P59392.7'
     @LateGEPfile = 'fixtures/P27648.7'
     @notafile = 'fixtures/XXX.XXX'
-    @ged = RawImageFile.new(@GEDicom)
-    @did = RawImageFile.new(@DiDicom)
+    @ged = RawImageFile.new(@GE_IFile)
+    @did = RawImageFile.new(@Dicom)
     @egep = RawImageFile.new(@EarlyGEPfile)
     @lgep = RawImageFile.new(@LateGEPfile)
   end
 
   def test_gehdr_dicom_init
     assert_nothing_raised do
-      RawImageFile.new(@GEDicom)
+      RawImageFile.new(@GE_IFile)
     end
   end
   def test_dicomhdr_dicom_init
     assert_nothing_raised do
-      RawImageFile.new(@DiDicom)
+      RawImageFile.new(@Dicom)
     end
   end
   def test_early_gehdr_pfile_init

data/test/visit_duplication_test.rb

@@ -4,8 +4,8 @@
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'test/unit'
-require 'visit'
 require 'pathname'
+require 'metamri'
 
 
 class RawImageFileTest < Test::Unit::TestCase
@@ -16,7 +16,7 @@ class RawImageFileTest < Test::Unit::TestCase
   end
   
   def test_scan_and_insert
-    @v = Visit.new( '/Data/vtrak1/raw/alz_2000/alz093', 'ALZ' )
+    @v = VisitRawDataDirectory.new( '/Data/vtrak1/raw/alz_2000/alz093', 'ALZ' )
     @v.scan
     @v.init_db(DBFILE)
     @v.db_insert!

data/test/visit_test.rb

@@ -9,7 +9,7 @@ require 'logger'
 require 'metamri'
 
 class RawImageFileTest < Test::Unit::TestCase
-  DBFILE = '/Users/kris/projects/TransferScans/db/development.sqlite3'
+  DBFILE = '~/code/WADRC-Data-Tools/db/development.sqlite3'
   $LOG = Logger.new('visit_test.log', shift_age = 7, shift_size = 1048576)
   STUDIES = [
     # Pathname.new('/Data/vtrak1/raw/alz_2000'),

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 17
-  version: 0.1.17
+  - 18
+  version: 0.1.18
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-05-07 00:00:00 -05:00
+date: 2010-06-04 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -30,7 +30,7 @@ dependencies:
   type: :runtime
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: rspec
+  name: dicom
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
     requirements: 
@@ -39,8 +39,20 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  type: :development
+  type: :runtime
   version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id003
 description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
 email: kk4@medicine.wisc.edu
 executables: