metamri 0.1.23 → 0.2.0

data/lib/metamri/visit_raw_data_directory.rb

@@ -25,17 +25,16 @@ end
 
 
 
-=begin rdoc
-Encapsulates a directory of data acquired during one participant visit.  These
-are the raw data directories that are transfered directly from the scanners and
-archived in the raw data section of the vtrak filesystem.  After initializing, the
-visit can be scanned to extract metadata for all of the images acquired during the
-visit.  The scanning is done in a fairly naive manner: the visit directory is recursively
-walked and in each subdirectory any and all pfiles will be imported in addition to one single
-dicom if any exist.  Thus, only a single dicom file among many in a scan session is used to 
-retrieve information.  checking the individual files for data integrity must be handled
-elsewhere if at all.
-=end
+# Encapsulates a directory of data acquired during one participant visit. These
+# are the raw data directories that are transfered directly from the scanners
+# and archived in the raw data section of the vtrak filesystem. After
+# initializing, the visit can be scanned to extract metadata for all of the
+# images acquired during the visit. The scanning is done in a fairly naive
+# manner: the visit directory is recursively walked and in each subdirectory any
+# and all pfiles will be imported in addition to one single dicom if any exist.
+# Thus, only a single dicom file among many in a scan session is used to
+# retrieve information. checking the individual files for data integrity must be
+# handled elsewhere if at all.
 class VisitRawDataDirectory
   # The absolute path of the visit directory, as a string.
   attr_reader :visit_directory
@@ -96,10 +95,10 @@ class VisitRawDataDirectory
       begin
         matches = options[:ignore_patterns].collect {|pat| dd.to_s =~ pat ? dd : nil }.compact
         next unless matches.empty?
-        dd.each_pfile { |pf| @datasets << import_dataset(pf, dd) }
-        dd.first_dicom { |fd| @datasets << import_dataset(fd, dd) }
-      rescue Exception => e
-        raise(IndexError, "There was an error scaning dataset #{dd}: #{e}")
+        dd.each_pfile { |pf| @datasets << import_dataset(pf, dd);  (print "."; STDOUT.flush) if $LOG.level == Logger::INFO }
+        dd.first_dicom { |fd| @datasets << import_dataset(fd, dd); (print "."; STDOUT.flush) if $LOG.level == Logger::INFO }
+      rescue StandardError => e
+        raise(e, "There was an error scaning dataset #{dd}: #{e}")
       end
     end
     
@@ -220,7 +219,7 @@ Returns an array of the created nifti files.
     end
     
     # Reminder Line
-    puts "(This would be much prettier if you installed hirb.)"
+    puts "(This would be much prettier if you hirb was installed (just type: gem install hirb)."
     
     return
   end
@@ -313,9 +312,8 @@ Returns an array of the created nifti files.
     "SELECT * FROM image_datasets WHERE rmr = '#{ds.rmr_number}' AND path = '#{ds.directory}' AND timestamp = '#{ds.timestamp}'"
   end
   
-=begin rdoc
-generates an sql insert statement to insert this visit with a given participant id
-=end
+
+  # generates an sql insert statement to insert this visit with a given participant id
   def sql_insert_visit(scan_procedure_id=0)
     "INSERT INTO visits 
     (date, scan_procedure_id, scan_number, initials, rmr, radiology_outcome, notes, transfer_mri, transfer_pet,
@@ -324,19 +322,28 @@ generates an sql insert statement to insert this visit with a given participant
     ('#{@timestamp.to_s}', '#{scan_procedure_id.to_s}', '', '', '#{@rmr_number}', 'no', '', 'no', 'no', 
     'no', 'no', 'no', NULL, '#{@visit_directory}', '#{@scanner_source}', '#{DateTime.now}', '#{DateTime.now}')"
   end
-  
+
+  # Build a new RawImageDataset from a path to the rawfile and parent directory.
+  # == Args
+  #  * rawfile: String.  Path to the raw image file to scan.  This should be an unzipped PFile or DICOM, ideally on a local disk for speed.
+  #  * original_parent_directory: String or Pathname. Path of the original parent directory where the RawImageFile resides.
+  # 
+  # Raises an IOError with description if the RawImageFile could not be initialized.
+  # 
+  # Returns a RawImageDataset built from the directory and single rawfile.
   def import_dataset(rawfile, original_parent_directory)
     puts "Importing scan session: #{original_parent_directory.to_s} using raw data file: #{rawfile.basename}" if $LOG.level <= Logger::DEBUG
     
     begin
       rawimagefile = RawImageFile.new(rawfile.to_s)
-    rescue Exception => e
-      raise(IOError, "+++ Trouble reading raw image file #{rawfile}. #{e}")
+    # rescue Exception => e
+    #   raise(e, "+++ Trouble reading raw image file #{rawfile}. #{e}")
     end
     
     return RawImageDataset.new(original_parent_directory.to_s, [rawimagefile])
   end
   
+  
   def convert_dataset(rawfiles, original_parent_directory, nifti_output_directory)
     puts "Converting scan session: #{original_parent_directory.to_s} using raw data file: #{rawfiles.first.basename}"
     rawimagefiles = []

data/metamri.gemspec

@@ -1,69 +1,75 @@
 # Generated by jeweler
 # DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.23"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-11-16}
+  s.date = %q{2010-11-19}
   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"]
+  s.executables = ["convert_visit.rb", "import_visit.rb", "import_respiratory_files.rb", "import_study.rb", "list_visit"]
   s.extra_rdoc_files = [
     "README.rdoc"
   ]
   s.files = [
-    ".gitignore",
-     "Manifest",
-     "README.rdoc",
-     "Rakefile",
-     "VERSION",
-     "bin/convert_visit.rb",
-     "bin/import_respiratory_files.rb",
-     "bin/import_study.rb",
-     "bin/import_visit.rb",
-     "bin/list_visit",
-     "lib/metamri.rb",
-     "lib/metamri/core_additions.rb",
-     "lib/metamri/mysql_tools.rb",
-     "lib/metamri/nifti_builder.rb",
-     "lib/metamri/raw_image_dataset.rb",
-     "lib/metamri/raw_image_dataset_resource.rb",
-     "lib/metamri/raw_image_dataset_thumbnail.rb",
-     "lib/metamri/raw_image_file.rb",
-     "lib/metamri/series_description_parameters.rb",
-     "lib/metamri/visit_raw_data_directory.rb",
-     "lib/metamri/visit_raw_data_directory_resource.rb",
-     "metamri.gemspec",
-     "test/fixtures/respiratory_fixtures.yaml",
-     "test/fixtures/s03_bravo.0156",
-     "test/fixtures/thumbnail.png",
-     "test/fixtures/thumbnail_slicer.png",
-     "test/helper_spec.rb",
-     "test/nifti_builder_spec.rb",
-     "test/raw_image_dataset_test.rb",
-     "test/raw_image_dataset_thumbnail_spec.rb",
-     "test/raw_image_file_test.rb",
-     "test/visit_duplication_test.rb",
-     "test/visit_test.rb"
+    "Manifest",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/convert_visit.rb",
+    "bin/import_respiratory_files.rb",
+    "bin/import_study.rb",
+    "bin/import_visit.rb",
+    "bin/list_visit",
+    "lib/metamri.rb",
+    "lib/metamri/core_additions.rb",
+    "lib/metamri/image_dataset_quality_check_resource.rb",
+    "lib/metamri/mysql_tools.rb",
+    "lib/metamri/nifti_builder.rb",
+    "lib/metamri/raw_image_dataset.rb",
+    "lib/metamri/raw_image_dataset_resource.rb",
+    "lib/metamri/raw_image_dataset_thumbnail.rb",
+    "lib/metamri/raw_image_file.rb",
+    "lib/metamri/series_description_parameters.rb",
+    "lib/metamri/visit_raw_data_directory.rb",
+    "lib/metamri/visit_raw_data_directory_resource.rb",
+    "metamri.gemspec",
+    "spec/helper_spec.rb",
+    "spec/unit/nifti_builder_spec.rb",
+    "spec/unit/raw_image_dataset_spec.rb",
+    "spec/unit/raw_image_dataset_thumbnail_spec.rb",
+    "spec/unit/raw_image_file_spec.rb",
+    "test/fixtures/respiratory_fixtures.yaml",
+    "test/fixtures/s03_bravo.0156",
+    "test/fixtures/s03_bravo.0156.yml",
+    "test/fixtures/thumbnail.png",
+    "test/fixtures/thumbnail_slicer.png",
+    "test/raw_image_dataset_test.rb",
+    "test/raw_image_file_test.rb",
+    "test/test_helper.rb",
+    "test/visit_duplication_test.rb",
+    "test/visit_test.rb"
   ]
   s.homepage = %q{http://github.com/brainmap/metamri}
-  s.rdoc_options = ["--charset=UTF-8"]
   s.require_paths = ["lib"]
   s.rubygems_version = %q{1.3.6}
   s.summary = %q{MRI metadata}
   s.test_files = [
-    "test/nifti_builder_spec.rb",
-     "test/raw_image_dataset_test.rb",
-     "test/raw_image_file_test.rb",
-     "test/visit_duplication_test.rb",
-     "test/visit_test.rb",
-     "test/raw_image_dataset_thumbnail_spec.rb",
-     "test/helper_spec.rb"
+    "spec/helper_spec.rb",
+    "spec/unit/nifti_builder_spec.rb",
+    "spec/unit/raw_image_dataset_spec.rb",
+    "spec/unit/raw_image_dataset_thumbnail_spec.rb",
+    "spec/unit/raw_image_file_spec.rb",
+    "test/raw_image_dataset_test.rb",
+    "test/raw_image_file_test.rb",
+    "test/test_helper.rb",
+    "test/visit_duplication_test.rb",
+    "test/visit_test.rb"
   ]
 
   if s.respond_to? :specification_version then

data/{test → spec}/helper_spec.rb

@@ -10,9 +10,7 @@ require 'tmpdir'
 require 'fileutils'
 require 'yaml'
 require 'pp'
-require 'rubygems'
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 
 $MRI_DATA = ENV['MRI_DATA'] || '/Data/vtrak1/raw/test/fixtures/metamri'
-

data/spec/unit/raw_image_dataset_spec.rb

@@ -0,0 +1,35 @@
+require 'helper_spec'
+require 'logger'
+require 'metamri/raw_image_dataset'
+require 'metamri/raw_image_file'
+
+describe RawImageDataset, "for a single valid DICOM file" do
+  before(:each) do
+    # Since a single, anonymized dicom is sufficiently small, provide it in fixtures for testing.
+    @valid_dicom_basename = 's03_bravo.0156'
+    @valid_dicom = File.join(File.dirname(__FILE__), '..', 'fixtures', @valid_dicom_basename)
+    @valid_raw_image_file = RawImageFile.new(@valid_dicom)
+  end
+  
+  it "should have scan series metadata" do
+    dataset_dir = File.expand_path File.dirname(@valid_dicom)
+    ds = RawImageDataset.new(dataset_dir, @valid_raw_image_file)
+    
+    ds.dataset_key.should == "ID::2010-11-10T00:00:00+00:00"
+    ds.directory.should == dataset_dir
+    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.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")
+    ds.study_description.should == "RMRMABRAVOTEST"
+    ds.dicom?.should be true
+    ds.protocol_name.should == "MERIT220 + TAMI/METS 101"
+    ds.operator_name.should == "Operator"
+    ds.patient_name.should == "Patient"
+    ds.dicom_series_uid.should == "1.2.840.113619.2.260.6945.1176948.30017.1288984188.384"
+    ds.dicom_study_uid.should == "1.2.840.113619.6.260.4.1294724594.737.1289407877.724"
+  end
+end

data/{test → spec/unit}/raw_image_dataset_thumbnail_spec.rb

@@ -1,13 +1,15 @@
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+$:.unshift File.join(File.dirname(__FILE__),'..','..','lib')
+$:.unshift File.join(File.dirname(__FILE__))
 
 require 'spec'
-require 'helper_spec'
 require 'escoffier'
 require 'metamri/core_additions'
 require 'metamri/raw_image_dataset'
 require 'metamri/raw_image_file'
 require 'metamri/raw_image_dataset_thumbnail'
 
+require 'helper_spec'
+
 describe "Create a thumbnail png for display." do  
   before(:all) do
     # # Initialize a local scratch directory to hold fixtures for testing if it doesn't already exist.
@@ -20,15 +22,16 @@ describe "Create a thumbnail png for display." do
     #   `find #{VISIT_FIXTURE_UNZIPPED} -name '*.bz2' -exec bunzip2 {} \\;`
     # end
     @fixture_path = File.join($MRI_DATA, 'mrt00000_000_010101', 'dicoms', 's10_cubet2')
-  end
-  
-  before(:each) do
     @tmpdir = Dir.mktmpdir
     Pathname.new(@fixture_path).prep_mise_to(@tmpdir)
     @dataset_wd = File.join(@tmpdir, File.basename(@fixture_path))
-    @ds = RawImageDataset.new(@dataset_wd, RawImageFile.new(File.join(@dataset_wd, 's10_cubet2.0001')))
-    @valid_thumbnail = File.join('fixtures', 'thumbnail.png')
-    @valid_thumbnail_slicer = File.join('fixtures', 'thumbnail_slicer.png')
+    @dataset_dicom = Dir.glob(File.join(@dataset_wd, '*')).first
+    @ds = RawImageDataset.new(@dataset_wd, RawImageFile.new(@dataset_dicom))
+    @valid_thumbnail = File.join(File.dirname(__FILE__), '..', 'fixtures', 'thumbnail.png')
+    @valid_thumbnail_slicer = File.join(File.dirname(__FILE__), '..', 'fixtures', 'thumbnail_slicer.png')
+  end
+  
+  before(:each) do
     @test_niftis = []
   end
   
@@ -85,6 +88,12 @@ describe "Create a thumbnail png for display." do
     lambda { t.create_thumbnail }.should raise_error(ScriptError, /Error creating thumbnail/ )
   end
   
+  it "should raise an ArgumentError if an invalid processor is given." do
+    t = RawImageDatasetThumbnail.new(@ds)
+    
+    lambda { t.create_thumbnail(nil, :processor => :invalid_processor ) }.should raise_error(ArgumentError, /Invalid :processor option/ )
+  end
+  
   it "should create a thumbnail in a tmpdir without a specified path using FSL Slicer." do
     t = RawImageDatasetThumbnail.new(@ds)
     t.create_thumbnail(nil, {:processor => :slicer})
@@ -95,10 +104,7 @@ describe "Create a thumbnail png for display." do
   end
   
   after(:each) do
-    # @test_niftis.flatten.each { |nifti| File.delete(nifti) } unless @test_niftis.empty?
-    # [@output_directories, @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
+    File.delete('test.png') if File.exist? 'test.png'
   end
   
 end

data/spec/unit/raw_image_file_spec.rb

@@ -0,0 +1,45 @@
+require 'helper_spec'
+require 'metamri/core_additions'
+require 'metamri/raw_image_file'
+
+
+describe RawImageFile, "reads a dicom header and extracts metadata" do
+  before(:each) do
+    # Since a single, anonymized dicom is sufficiently small, provide it in fixtures for testing.
+    @valid_dicom = File.join(File.dirname(__FILE__), '..', 'fixtures', 's03_bravo.0156')
+    @valid_serial_dicom_taghash = File.join(File.dirname(__FILE__), '..', 'fixtures', 's03_bravo.0156.yml')
+  end
+  context "using RubyDicom" do
+    it "should successfully set filename" do
+      image = RawImageFile.new(@valid_dicom)
+      image.filename.should == File.basename(@valid_dicom)
+    end
+    
+    it "should raise an error if the file cannot be found" do
+      lambda { RawImageFile.new('bad_path_to.dcm') }.should raise_error(IOError, /File not found/ )
+    end
+    
+    it "should set valid instance variables" do
+      valid_dicom_taghash = YAML.load_file(@valid_serial_dicom_taghash)
+      
+      image = RawImageFile.new(@valid_dicom)
+      image.file_type.should == "dicom"
+      image.gender.should == "N"
+      [RawImageFile::DICOM_HDR, RawImageFile::RDGEHDR, RawImageFile::RUBYDICOM_HDR].include?(image.hdr_reader).should be true
+      image.acquisition_matrix_x.should == 256
+      image.acquisition_matrix_y.should == 256
+      image.num_slices.should == "156"
+      image.reconstruction_diameter.should == "256"
+      image.rep_time.should == "8.132"
+      image.rmr_number.should == "ID"
+      image.series_description.should == "Ax FSPGR BRAVO T1"
+      image.slice_spacing.should == "1"
+      image.slice_thickness.should == "1"
+      image.source.should == "Station"
+      # 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"
+      image.dicom_series_uid.should == "1.2.840.113619.2.260.6945.1176948.30017.1288984188.384"
+    end
+  end
+end

data/test/fixtures/s03_bravo.0156.yml

@@ -0,0 +1,937 @@
+--- 
+0043,102E: 
+  :value: 
+  :name: Private
+"0043,1010": 
+  :value: 0
+  :name: Private
+0020,000E: 
+  :value: 1.2.840.113619.2.260.6945.1176948.30017.1288984188.384
+  :name: Series Instance UID
+0018,1315: 
+  :value: N
+  :name: Variable Flip Angle Flag
+0018,0094: 
+  :value: "100"
+  :name: Percent Phase Field of View
+0019,1084: 
+  :value: "0.433979"
+  :name: Private
+0018,1316: 
+  :value: "0.21699"
+  :name: SAR
+0009,1027: 
+  :value: 1289386829
+  :name: Private
+0043,102F: 
+  :value: 0
+  :name: Private
+0028,1050: 
+  :value: "2446"
+  :name: Window Center
+0018,0095: 
+  :value: "244.141"
+  :name: Pixel Bandwidth
+0008,1030: 
+  :value: RMRMABRAVOTEST
+  :name: Study Description
+0028,1051: 
+  :value: "4893"
+  :name: Window Width
+0043,108A: 
+  :value: COL
+  :name: Private
+0019,1087: 
+  :value: "0.000000"
+  :name: Private
+0009,10E9: 
+  :value: 1289386828
+  :name: Private
+0008,1140: 
+  :value: 
+  :name: Referenced Image Sequence
+0019,1088: 
+  :value: 0
+  :name: Private
+0019,10BA: 
+  :value: "0.000000"
+  :name: Private
+0019,10BB: 
+  :value: "0.000000"
+  :name: Private
+0019,10BC: 
+  :value: "0.000000"
+  :name: Private
+0021,104F: 
+  :value: 156
+  :name: Private
+7FE0,0010: 
+  :value: 
+  :name: Pixel Data
+0029,1026: 
+  :value: 2
+  :name: Private
+"0020,0052": 
+  :value: 1.2.840.113619.2.260.6945.1176948.30017.1288984188.382
+  :name: Frame of Reference UID
+0019,10A0: 
+  :value: 0
+  :name: Private
+0019,10BD: 
+  :value: "0.000000"
+  :name: Private
+0008,1090: 
+  :value: DISCOVERY MR750
+  :name: Manufacturer's Model Name
+0019,10A1: 
+  :value: 0
+  :name: Private
+0019,10BE: 
+  :value: "0.000000"
+  :name: Private
+0018,0020: 
+  :value: GR
+  :name: Scanning Sequence
+0019,10A2: 
+  :value: 5789
+  :name: Private
+0018,1000: 
+  :value: 0000000608WAISMR
+  :name: Device Serial Number
+"0010,0010": 
+  :value: Patient
+  :name: Patient's Name
+0018,0021: 
+  :value: SS\SK
+  :name: Sequence Variant
+0019,105A: 
+  :value: 246280416.0
+  :name: Private
+0019,10A3: 
+  :value: 0
+  :name: Private
+"0002,0000": 
+  :value: 208
+  :name: File Meta Information Group Length
+"0021,1035": 
+  :value: 1
+  :name: Private
+0018,0022: 
+  :value: FAST_GEMS\EDR_GEMS\ACC_GEMS
+  :name: Scan Options
+0019,1011: 
+  :value: 0
+  :name: Private
+0019,10A4: 
+  :value: 0
+  :name: Private
+"0002,0001": 
+  :value: 
+  :name: File Meta Information Version
+"0021,1036": 
+  :value: 5
+  :name: Private
+0018,0023: 
+  :value: 3D
+  :name: MR Acquisition Type
+0019,1012: 
+  :value: 74
+  :name: Private
+"0040,0242": 
+  :value: MR01OC1
+  :name: Performed Station Name
+"0002,0002": 
+  :value: 1.2.840.10008.5.1.4.1.1.4
+  :name: Media Storage SOP Class UID
+"0021,1037": 
+  :value: 16
+  :name: Private
+0018,0050: 
+  :value: "1"
+  :name: Slice Thickness
+"0040,0243": 
+  :value: MR01
+  :name: Performed Location
+"0002,0003": 
+  :value: 1.2.840.113619.2.260.6945.1176948.29385.1288985252.77
+  :name: Media Storage SOP Instance UID
+0019,10D2: 
+  :value: 0
+  :name: Private
+0008,0030: 
+  :value: "000000.00"
+  :name: Study Time
+0018,1030: 
+  :value: MERIT220 + TAMI/METS 101
+  :name: Protocol Name
+"0010,1010": 
+  :value: 028Y
+  :name: Patient's Age
+"0010,0040": 
+  :value: N
+  :name: Patient's Sex
+0018,0025: 
+  :value: N
+  :name: Angio Flag
+"0020,1040": 
+  :value: 
+  :name: Position Reference Indicator
+0019,108A: 
+  :value: 10
+  :name: Private
+0028,0002: 
+  :value: 1
+  :name: Samples per Pixel
+0019,10D3: 
+  :value: 
+  :name: Private
+0008,0005: 
+  :value: ISO_IR 100
+  :name: Specific Character Set
+0008,0031: 
+  :value: "110028"
+  :name: Series Time
+"0020,1041": 
+  :value: "94.84349823"
+  :name: Slice Location
+0019,108B: 
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