metamri 0.1.22 → 0.1.23

data/VERSION

@@ -1 +1 @@
-0.1.22
+0.1.23

data/bin/list_visit

@@ -40,11 +40,17 @@ require 'metamri'
 def run!
   options = parse_options
   
-  # Default to scanning the current directory if no argument was given.
-  raw_directory = ARGV[0] ||= Dir.pwd
-  raw_directory = File.expand_path(raw_directory)
+  # Default to scanning the current directory if no argument was given,
+  # otherwise go through each list.
+  unless ARGV.length == 1
+    input_directories = ARGV
+  else
+    input_directories = ARGV[0]
+  end
   
-  list_visit raw_directory, options
+  input_directories.each do |raw_directory|
+    list_visit raw_directory, options
+  end
   
 end
 

data/lib/metamri/core_additions.rb

@@ -5,6 +5,12 @@ class String
     mgsub([[/[\s\:\)\(\/\?\,]+/, "-"], [/\*/, "star"], [/\./,""]])
   end
   
+  # Does some basic string replacements to ensure valid directory names.
+  def escape_dirname
+    mgsub( [ [/[\s\:\)\(\?\,]+/, "-"], [/\*/, "star"] ] )
+  end
+  
+  
   # gsub multiple pairs of regexp's
   def mgsub(key_value_pairs=[].freeze)
     regexp_fragments = key_value_pairs.collect { |k,v| k }

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -1,11 +1,24 @@
-require 'dicom'
-require 'RMagick'
 require 'tmpdir'
+begin
+  %W{dicom RMagick}.each do |lib|
+    require lib
+  end
+rescue LoadError => e
+  raise LoadError, "Could not load #{e}.  Thumbnailing will use slicer instead of ruby-dicom."
+end
+  
 
 # This class is a ruby object encapsulating a .png 2D Thumbnail of a Dataset
+# Initialize it with an #RawImageDataset
 class RawImageDatasetThumbnail
+  VALID_PROCESSORS = [:rubydicom, :slicer]
 
-  attr_reader :dataset, :path
+  # The parent #RawImageDataset
+  attr_reader :dataset
+  # The path to the thumbnail image if it's already been created
+  attr_reader :path
+  # The processor for creating the thumbnail (:rubydicom or :slicer)
+  attr_reader :processor
 
   def initialize(dataset)
     if dataset.class == RawImageDataset
@@ -19,41 +32,67 @@ class RawImageDatasetThumbnail
     @path ||= create_thumbnail
   end
   
-  # Returns the path of png and sets the instance variable 'path' after successfull creation.
+  # Creates a thumbnail image (.png or .jpg) and returns the full file path of the thumbnail.
   # Raises a ScriptError if the thumbnail could not be created.
   # Raises a StandardError if the format is incorrect (i.e. P-file instead of DICOM)
-  def create_thumbnail(output = nil)
+  # 
+  # Be sure your filename is a valid unix filename - no spaces.
+  # Sets the @path instance variable and returns the full filename to the thumbnail.
+  #
+  # Pass in either a absolute or relative path or filename for the output image,
+  # and an options hash to manually specify the processor (Ruby Dicom or FSL Slicer).
+  #   {:processor => :rubydicom or :slicer}
+  # 
+  def create_thumbnail(output = nil, options = {:processor => :rubydicom})
     raise StandardError, "Thumbnail available only for DICOM format." unless dataset.raw_image_files.first.dicom?
     if output
       if File.directory?(output)
-        output_directory = output.escape_filename
+        # output is a directory.  Set the output directory but leave filepath nil.
+        output_directory = output.escape_dirname
       else
-        output_directory = File.dirname(output).escape_filename
-        png_filename = File.basename(output).escape_filename
+        # output is a path.  Set the output_directory and specify that the full filepath is already complete.
+        output_directory = File.dirname(output).escape_dirname
+        filepath = output
       end
     else
+      # If no output was given, default to a new temp directory.
       output_directory = Dir.mktmpdir
     end
-    name = @dataset.series_description.escape_filename
-    png_filename ||= File.join(output_directory, name + '.png')
-    nifti_filename ||=  File.join(output_directory, name + '.nii')
+    
+    @processor = options[:processor]
+        
+    # Set a default filepath unless one was explicitly passed in.
+    default_name = @dataset.series_description.escape_filename
+    filepath ||= File.join(output_directory, default_name + '.png')
     
     begin
-      @path = create_thumbnail_with_rubydicom(png_filename)
+      case @processor
+      when :rubydicom
+        @path = create_thumbnail_with_rubydicom(filepath)
+      when :slicer
+        @path = create_thumbnail_with_fsl_slicer(filepath)
+      end
     rescue RangeError, ScriptError => e
-      puts "Could not create thumbnail with rubydicom.  Trying FSL slicer."
-      @path = create_thumbnail_with_fsl_slicer(output_directory, nifti_filename, png_filename)
+      unless @processor == :slicer 
+        puts "Could not create thumbnail with rubydicom.  Trying FSL slicer."
+        @processor = :slicer
+        retry
+      else 
+        raise e
+      end
     end
     
+    raise ScriptError, "Could not create thumbnail from #{@dataset.series_description} - #{File.join(@dataset.directory, @dataset.scanned_file)}" unless @path && File.readable?(@path) 
     return @path
   end
   
   private
   
-  def create_thumbnail_with_rubydicom(output_file = nil)
-    unless output_file && File.writable?(File.dirname(output_file))
-      output_file = File.join(Dir.mktmpdir, dataset.series_description.escape_filename + '.jpg')
-    end
+  # Creates a thumbnail using RubyDicom
+  # Pass in an absolute or relative filepath, including filename and extension.
+  # Returns an absolute path to the created thumbnail image.
+  def create_thumbnail_with_rubydicom(output_file)
+    output_file = File.expand_path(output_file)
 
     dicom_files = Dir.glob(File.join(dataset.directory, dataset.glob))
     if dicom_files.empty?  # Try the glob again with a zipped extension.
@@ -67,29 +106,30 @@ class RawImageDatasetThumbnail
       dcm = DICOM::DObject.new(lc.to_s)
       raise ScriptError, "Could not read dicom #{dicom_file.to_s}" unless dcm.read_success
       image = dcm.get_image_magick(:rescale => true)
-      raise ScriptError, "RubyDicom did not return an image array (this is probably a color image)." unless image
-      image[0].write(output_file)
+      raise ScriptError, "RubyDicom did not return an image array (this is probably a color image)." unless image.kind_of? Magick::Image
+      image.write(output_file)
     end
 
+    raise(ScriptError, "Error creating thumbnail #{output_file}") unless File.exist?(output_file)
+
     return output_file
   end
   
-  def create_thumbnail_with_fsl_slicer(output_directory, nifti_filename, png_filename)
-    nii_path = File.join(output_directory, nifti_filename)
-    @path = File.join(output_directory, png_filename)
+  # Creates a thumbnail using FSL's Slicer bash utility.
+  # Pass in an output filepath.
+  def create_thumbnail_with_fsl_slicer(output_file)
+    nii_tmpdir = Dir.mktmpdir
+    nifti_output_file = File.basename(output_file, File.extname(output_file)) + '.nii'
     Pathname.new(dataset.directory).all_dicoms do |dicom_files| 
       # First Create a Nifti File to read 
-      @dataset.to_nifti!(output_directory, nifti_filename, {:input_directory => File.dirname(dicom_files.first)} )
+      @dataset.to_nifti!(nii_tmpdir, nifti_output_file, {:input_directory => File.dirname(dicom_files.first)} )
     end
-    
-    
-    
     # Then create the .png
-    `slicer #{nii_path} -a #{@path}`
+    `slicer #{File.join(nii_tmpdir, nifti_output_file)} -a #{output_file}`
     
-    raise(ScriptError, "Error creating thumbnail #{@path}") unless File.exist?(@path)
+    raise(ScriptError, "Error creating thumbnail #{output_file}") unless File.exist?(output_file)
     
-    return @path
+    return output_file
   end
   
 end

data/lib/metamri/raw_image_file.rb

@@ -1,7 +1,8 @@
-
+require 'pp'
 require 'rubygems';
 require 'yaml';
 require 'sqlite3';
+require 'dicom'
 
 =begin rdoc
 Implements a collection of metadata associated with a raw image file.  In
@@ -17,6 +18,7 @@ class RawImageFile
   MIN_HDR_LENGTH = 400
   DICOM_HDR = "dicom_hdr"
   RDGEHDR = "rdgehdr"
+  RUBYDICOM_HDR = "rubydicom"
   MONTHS = {
     :jan => "01", :feb => "02", :mar => "03", :apr => "04", :may => "05", 
     :jun => "06", :jul => "07", :aug => "08", :sep => "09", :oct => "10", 
@@ -61,6 +63,14 @@ class RawImageFile
   attr_reader :bold_reps
   # Import Warnings - Fields that could not be read.
   attr_reader :warnings
+  # Serialized RubyDicomHeader Object (for DICOMs only)
+  attr_reader :dicom_header
+  # DICOM Sequence UID
+  attr_reader :dicom_sequence_uid
+  # DICOM Series UID
+  attr_reader :dicom_series_uid
+  # DICOM Study UID
+  attr_reader :dicom_study_uid
 
 =begin rdoc
 Creates a new instance of the class given a path to a valid image file.
@@ -82,7 +92,6 @@ temporary file.
     # try to read the header, raise an IOError if unsuccessful
     begin
       @hdr_data, @hdr_reader = read_header(absfilepath)
-      #puts "@hdr_data: #{@hdr_data}; @hdr_reader: #{@hdr_reader}"
     rescue Exception => e
       raise(IOError, "Header not readable for file #{@filename}. #{e}")
     end
@@ -250,12 +259,15 @@ private
 
 =begin rdoc
 Reads the file header using one of the available header reading utilities. 
-Returns both the header data as a one big string, and the name of the utility 
+Returns both the header data as either a RubyDicom object or one big string, and the name of the utility 
 used to read it.
 
 Note: The rdgehdr is a binary file; the correct version for your architecture must be installed in the path.
 =end
   def read_header(absfilepath)
+    # header = DICOM::DObject.new(absfilepath)
+    # return [header, RUBYDICOM_HDR] if defined? header.read_success && header.read_success
+    
     header = `#{DICOM_HDR} '#{absfilepath}' 2> /dev/null`
     #header = `#{DICOM_HDR} #{absfilepath}`
     if ( header.index("ERROR") == nil and 
@@ -292,11 +304,21 @@ Parses the header data and extracts a collection of instance variables.  If
 =end
   def import_hdr
     raise(IndexError, "No Header Data Available.") if @hdr_data == nil
-    dicom_hdr_import if (@hdr_reader == "dicom_hdr")
-    rdgehdr_import if (@hdr_reader == "rdgehdr")
+    case @hdr_reader
+      when "rubydicom" then rubydicom_hdr_import
+      when "dicom_hdr" then dicom_hdr_import
+      when "rdgehdr" then rdgehdr_import
+    end
   end
 
 
+=begin rdoc
+Extract a collection of metadata from @hdr_data retrieved using RubyDicom
+=end
+def rubydicom_hdr_import
+  
+end
+
 =begin rdoc
 Extracts a collection of metadata from @hdr_data retrieved using the dicom_hdr
 utility.  

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.22"
+  s.version = "0.1.23"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-10-05}
+  s.date = %q{2010-11-16}
   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"]
@@ -40,6 +40,10 @@ Gem::Specification.new do |s|
      "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",
@@ -58,7 +62,8 @@ Gem::Specification.new do |s|
      "test/raw_image_file_test.rb",
      "test/visit_duplication_test.rb",
      "test/visit_test.rb",
-     "test/raw_image_dataset_thumbnail_spec.rb"
+     "test/raw_image_dataset_thumbnail_spec.rb",
+     "test/helper_spec.rb"
   ]
 
   if s.respond_to? :specification_version then

data/test/helper_spec.rb

@@ -0,0 +1,18 @@
+begin
+  require 'spec'
+rescue LoadError
+  require 'rubygems' unless ENV['NO_RUBYGEMS']
+  gem 'rspec'
+  require 'spec'
+end
+
+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/test/raw_image_dataset_thumbnail_spec.rb

@@ -1,9 +1,8 @@
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'spec'
+require 'helper_spec'
 require 'escoffier'
-require 'tmpdir'
-# require 'metamri'
 require 'metamri/core_additions'
 require 'metamri/raw_image_dataset'
 require 'metamri/raw_image_file'
@@ -20,14 +19,17 @@ describe "Create a thumbnail png for display." do
     #   FileUtils.cp_r(VISIT_FIXTURE, VISIT_FIXTURE_UNZIPPED)
     #   `find #{VISIT_FIXTURE_UNZIPPED} -name '*.bz2' -exec bunzip2 {} \\;`
     # end
-    @fixture_path = '/Data/vtrak1/raw/johnson.merit220.visit1/mrt00033_830_04232010/dicoms/s10_cubet2'
+    @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))
+    @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')
+    @test_niftis = []
   end
   
   it "should create a thumbnail in a tmpdir without a specified path." do
@@ -36,6 +38,7 @@ describe "Create a thumbnail png for display." do
     
     File.basename(t.path).should == 'Sag-CUBE-T2.png'
     File.exist?(t.path).should be_true
+    File.compare(@valid_thumbnail, t.path).should be true
   end
   
   it "should create a thumbnail with a specified path." do
@@ -47,10 +50,11 @@ describe "Create a thumbnail png for display." do
     
     t.path.should == output_filename
     File.exist?(t.path).should be_true
+    File.compare(@valid_thumbnail, t.path).should be true
     
   end
   
-  it "should create a thumbnail with a specified path and filename." do
+  it "should create a thumbnail with an absolute path to file." do
     output_filename = "/tmp/test.png"
     File.delete(output_filename) if File.exist?(output_filename)
     
@@ -59,18 +63,40 @@ describe "Create a thumbnail png for display." do
     
     t.path.should == '/tmp/test.png'
     File.exist?(t.path).should be_true
+    File.compare(@valid_thumbnail, t.path).should be true
   end
   
+  it "should create a thumbnail with a relative path to file." do
+    output_filename = "test.png"
+    File.delete(output_filename) if File.exist?(output_filename)
+    
+    t = RawImageDatasetThumbnail.new(@ds)
+    t.create_thumbnail(output_filename)
+    
+    File.exist?(t.path).should be_true
+    File.compare(@valid_thumbnail, t.path).should be true
+  end
+  
+  
   it "should raise a ScriptError if the file could not be created." do
     t = RawImageDatasetThumbnail.new(@ds)
     
     File.stub!(:exist?).and_return(false)
-    lambda { t.create_thumbnail }.should raise_error(ScriptError, /Error creating thumbnail/ )    
+    lambda { t.create_thumbnail }.should raise_error(ScriptError, /Error creating thumbnail/ )
+  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})
+    
+    File.basename(t.path).should == 'Sag-CUBE-T2.png'
+    File.exist?(t.path).should be_true
+    File.compare(@valid_thumbnail_slicer, t.path).should be true
   end
   
   after(:each) do
     # @test_niftis.flatten.each { |nifti| File.delete(nifti) } unless @test_niftis.empty?
-    # [@output_directories, Dir.tmpdir, '/tmp'].flatten.each do |temp_dir|
+    # [@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
   end

data/test/raw_image_file_test.rb

@@ -8,15 +8,16 @@ require 'metamri/raw_image_file'
 
 class RawImageFileTest < Test::Unit::TestCase
   def setup
-    @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(@GE_IFile)
-    @did = RawImageFile.new(@Dicom)
-    @egep = RawImageFile.new(@EarlyGEPfile)
-    @lgep = RawImageFile.new(@LateGEPfile)
+    # @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(@GE_IFile)
+    # @did = RawImageFile.new(@Dicom)
+    # @egep = RawImageFile.new(@EarlyGEPfile)
+    # @lgep = RawImageFile.new(@LateGEPfile)
+    @RubyDicom = 'fixtures/s03_bravo.0156'
   end
 
   def test_gehdr_dicom_init
@@ -29,6 +30,11 @@ class RawImageFileTest < Test::Unit::TestCase
       RawImageFile.new(@Dicom)
     end
   end
+  def test_rubydicom_dicom_init
+    assert_nothing_raised do
+      RawImageFile.new(@RubyDicom)
+    end
+  end
   def test_early_gehdr_pfile_init
     assert_nothing_raised do
       RawImageFile.new(@EarlyGEPfile)

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 22
-  version: 0.1.22
+  - 23
+  version: 0.1.23
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-10-05 00:00:00 -05:00
+date: 2010-11-16 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -89,6 +89,10 @@ files:
 - 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
@@ -132,3 +136,4 @@ test_files:
 - test/visit_duplication_test.rb
 - test/visit_test.rb
 - test/raw_image_dataset_thumbnail_spec.rb
+- test/helper_spec.rb