metamri 0.1.16 → 0.1.17

data/VERSION

@@ -1 +1 @@
-0.1.16
+0.1.17

data/bin/convert_visit.rb

@@ -6,17 +6,19 @@
 #
 # == Examples
 #   convert_visit.rb /Data/vtrak1/raw/ries.aware.visit1/awr001_7854_02102009 ries.aware.visit1 
-
+#   convert_visit.rb /Data/vtrak1/raw/ries.aware.visit1/awr001_7854_02102009 ries.aware.visit1 /Data/scratch/temp_analysis/awr001
 #
 # == Usage 
 #   convert_visit.rb <raw_data_directory> <scan_procedure_codename> 
 #
 #   For help use: import_visit.rb -h
 #
+#	  Currently, the script will create an "unknown" directory in the output 
+#   directory, and will place files named after the series description in the 
+#   dicom header in that directory.  
+#
 # == Options
-#   -h, --help          Displays help message
-#   -v, --visit         Visit raw data directory, absolute path
-#   -p, --scan_procedure      scan_procedure codename, e.g. johnson.alz.visit1
+#   There is currently no option parser in this script.  To be implemented.
 #
 # == Author
 #   
@@ -32,16 +34,7 @@ require 'pathname'
 require 'rdoc/usage'
 require 'logger'
 
-# == Function
-#   
-# 
-# == Usage
-#
-#   convert_visit.rb /Data/vtrak1/raw/ries.aware.visit1/awr001_9999_010110/ ries.aware.visit1 /tmp/awr001
-#
-# == Example
-#   
-#
+
 def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil)
   $LOG = Logger.new(File.join(Dir.tmpdir, File.basename(raw_directory)))  
   v = VisitRawDataDirectory.new(raw_directory, scan_procedure_codename)

data/lib/metamri/core_additions.rb

@@ -1,10 +1,11 @@
+require 'tmpdir'
 class String
 
 =begin rdoc
 Does same basic string replacements to ensure valid filenames.
 =end
   def escape_filename
-    mgsub([[/[\s\:\)\(\/\?]+/, "-"], [/\*/, "star"]])
+    mgsub([[/[\s\:\)\(\/\?\,]+/, "-"], [/\*/, "star"], [/\./,""]])
   end
   
   def mgsub(key_value_pairs=[].freeze)
@@ -98,10 +99,13 @@ class Pathname
   and ensure the local copy is deleted.
 =end
 
-  def local_copy(tempdir = Dir.tmpdir, &block)
+  def local_copy(tempdir = Dir.mktmpdir, &block)
     tfbase = self.to_s =~ /\.bz2$/ ? self.basename.to_s.chomp(".bz2") : self.basename.to_s
     tfbase.escape_filename
     tmpfile = File.join(tempdir, tfbase)
+    # puts tmpfile
+    # puts File.exist?(tmpfile)
+    File.delete(tmpfile) if File.exist?(tmpfile)
     if self.to_s =~ /\.bz2$/
       `bunzip2 -k -c '#{self.to_s}' >> '#{tmpfile}'`
     else

data/lib/{nifti_builder.rb → metamri/nifti_builder.rb}

@@ -4,7 +4,6 @@
 Builds Nifti files from Dicoms.
 =end
 
-TO3D_CMD = 'to3d'
 
 module UnknownImageDataset
   # Always set AFNI GE DICOM Fix to "No" before conversion with to3d.
@@ -19,12 +18,18 @@ 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
+      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
+    
+    
     nifti_output_file = File.join(nifti_output_directory, nifti_filename)
     
     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_CMD} -session #{nifti_output_directory} -prefix #{nifti_filename} #{input_files}"
+    nifti_conversion_command = "to3d -session #{nifti_output_directory} -prefix #{nifti_filename} #{functional_args} #{input_files}"
 
     return nifti_conversion_command, nifti_output_file
   end

data/lib/{raw_image_dataset.rb → metamri/raw_image_dataset.rb}

@@ -1,8 +1,7 @@
-
 require 'rubygems'
 require 'sqlite3'
-require 'nifti_builder'
 require 'ftools'
+require 'metamri/nifti_builder'
 
 =begin rdoc
 A #Dataset defines a single 3D or 4D image, i.e. either a volume or a time series
@@ -28,6 +27,8 @@ class RawImageDataset
   attr_reader :scanned_file
   # the scanner source
   attr_reader :scanner_source
+  # A #RawImageDatasetThumbnail object that composes the thumbnail for the dataset.
+  attr_reader :thumbnail
 
 =begin rdoc
   * dir: The directory containing the files.
@@ -61,6 +62,8 @@ class RawImageDataset
     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?
+    
+    $LOG ||= Logger.new(STDOUT)
   end
 
 =begin rdoc
@@ -102,8 +105,14 @@ at the visit level, or even higher when doing a whole file system scan.
 
 =begin rdoc
 Returns a hash of attributes used for insertion into active record.
+Options:  :thumb => FileHandle to thumbnail includes a thumbnail.
 =end  
-  def attributes_for_active_record
+  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.")
+    end
     { :rmr => @rmr_number,
       :series_description => @series_description,
       :path => @directory,
@@ -112,7 +121,20 @@ Returns a hash of attributes used for insertion into active record.
       :rep_time => @raw_image_files.first.rep_time,
       :bold_reps => @raw_image_files.first.bold_reps,
       :slices_per_volume => @raw_image_files.first.num_slices,
-      :scanned_file => @scanned_file }
+      :scanned_file => @scanned_file,
+      :thumbnail => thumbnail
+    }
+  end
+  
+  def create_thumbnail
+    @thumbnail = RawImageDatasetThumbnail.new(self)
+    @thumbnail.create_thumbnail
+  end
+
+  def thumbnail_for_active_record
+    # Ensure a thumbnail has been created.
+    create_thumbnail unless @thumbnail
+    return File.open(@thumbnail.path)
   end
 
 =begin rdoc
@@ -170,11 +192,16 @@ have more component files than shell commands can handle.
       return 'I.*'
     when /^I/
       return 'I*.dcm'
+    when /.*\.\d{3,4}/
+      return '*.[0-9]*'
     when /\.0/
       return '*.0*'
     else
       return nil
     end
+    # Note - To exclude just yaml files we could also just use the bash glob
+    # '!(*.yaml), but we would have to list all exclusions.  This may turn
+    # out easier in the long run.
   end
   
   

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -0,0 +1,95 @@
+require 'dicom'
+require 'rmagick'
+require 'tmpdir'
+
+# This class is a ruby object encapsulating a .png 2D Thumbnail of a Dataset
+class RawImageDatasetThumbnail
+
+  attr_reader :dataset, :path
+
+  def initialize(dataset)
+    if dataset.class == RawImageDataset
+      @dataset = dataset
+    else
+      raise StandardError, "Dataset #{dataset} class must be RawImageDataset."
+    end
+  end
+  
+  def thumbnail
+    @path ||= create_thumbnail
+  end
+  
+  # Returns the path of png and sets the instance variable 'path' after successfull creation.
+  # 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)
+    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
+      else
+        output_directory = File.dirname(output).escape_filename
+        png_filename = File.basename(output).escape_filename
+      end
+    else
+      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')
+    
+    begin
+      @path = create_thumbnail_with_rubydicom(png_filename)
+    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)
+    end
+    
+    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
+
+    dicom_files = Dir.glob(File.join(dataset.directory, dataset.glob))
+    if dicom_files.empty?  # Try the glob again with a zipped extension.
+      dicom_files = Dir.glob(File.join(dataset.directory, dataset.glob) + '*.bz2')
+    end
+    if dicom_files.empty? # If still empty...
+      raise StandardError, "Could not find dicom files using #{dataset.glob} in #{dataset.directory}"
+    end
+    dicom_file = Pathname(dicom_files[dicom_files.size/2])
+    dicom_file.local_copy do |lc|
+      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)
+    end
+
+    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)
+    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)} )
+    end
+    
+    
+    
+    # Then create the .png
+    `slicer #{nii_path} -a #{@path}`
+    
+    raise(ScriptError, "Error creating thumbnail #{@path}") unless File.exist?(@path)
+    
+    return @path
+  end
+  
+end

data/lib/{raw_image_file.rb → metamri/raw_image_file.rb}

@@ -57,6 +57,8 @@ class RawImageFile
   attr_reader :rep_time
   # Number of bold reps in the complete functional task run.
   attr_reader :bold_reps
+  # Import Warnings - Fields that could not be read.
+  attr_reader :warnings
 
 =begin rdoc
 Creates a new instance of the class given a path to a valid image file.
@@ -73,6 +75,7 @@ temporary file.
     absfilepath = File.expand_path(pathtofile)
     raise(IOError, "File not found at #{absfilepath}.") if not File.exists?(absfilepath)
     @filename = File.basename(absfilepath)
+    @warnings = []
     
     # try to read the header, raise an IOError if unsuccessful
     begin
@@ -384,7 +387,7 @@ utility.
         if tag_hash[:required]
           raise ScriptError, "#{name}"
         else
-          puts "+++ Warning: #{name} could not be found."
+          @warnings << "Tag #{name} could not be found."
         end
       end
     end

data/lib/{visit_raw_data_directory.rb → metamri/visit_raw_data_directory.rb}

@@ -4,11 +4,10 @@ require 'tempfile'
 require 'yaml'
 require 'tmpdir'
 require 'fileutils'
-require 'raw_image_file'
-require 'raw_image_dataset'
 require 'sqlite3'
 require 'logger'
-
+require 'metamri/raw_image_file'
+require 'metamri/raw_image_dataset'
 
 # A shared function that displays a message and the date/time to standard output.
 def flash(msg)
@@ -171,7 +170,7 @@ Returns an array of the created nifti files.
         nifti_input_path = File.dirname(dicom_files.first)
         nifti_conversion_command, nifti_output_file = dataset.to_nifti!(nifti_output_path, nifti_filename, :input_directory => nifti_input_path, :append_modality_directory => true)
         nifti_output_files << nifti_output_file
-      end 
+      end
     end
     
     return nifti_output_files

data/lib/metamri.rb

@@ -1,9 +1,10 @@
 $: << File.dirname(__FILE__)
 
-require 'raw_image_file'
-require 'raw_image_dataset'
-require 'visit_raw_data_directory'
 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'
 

data/metamri.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.16"
+  s.version = "0.1.17"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-04-23}
+  s.date = %q{2010-05-07}
   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", "convert_visit.rb", "import_respiratory_files.rb", "import_visit.rb", "list_visit"]
+  s.executables = ["import_study.rb", "import_visit.rb", "import_respiratory_files.rb", "list_visit", "convert_visit.rb"]
   s.extra_rdoc_files = [
     "README.rdoc"
   ]
@@ -29,18 +29,20 @@ Gem::Specification.new do |s|
      "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",
-     "lib/mysql_tools.rb",
-     "lib/nifti_builder.rb",
-     "lib/raw_image_dataset.rb",
-     "lib/raw_image_file.rb",
-     "lib/series_description_parameters.rb",
-     "lib/visit_raw_data_directory.rb",
      "metamri.gemspec",
      "test/fixtures/respiratory_fixtures.yaml",
      "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"
@@ -51,11 +53,12 @@ Gem::Specification.new do |s|
   s.rubygems_version = %q{1.3.6}
   s.summary = %q{MRI metadata}
   s.test_files = [
-    "test/raw_image_dataset_test.rb",
+    "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/nifti_builder_spec.rb"
+     "test/raw_image_dataset_thumbnail_spec.rb"
   ]
 
   if s.respond_to? :specification_version then

data/test/raw_image_dataset_thumbnail_spec.rb

@@ -0,0 +1,77 @@
+$:.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/raw_image_dataset_thumbnail'
+
+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.
+    # unless File.directory?(VISIT_FIXTURE)
+    #   FileUtils.mkdir_p(File.dirname(VISIT_FIXTURE))
+    #   FileUtils.cp_r(VISIT_FIXTURE_SRC, VISIT_FIXTURE)
+    # end
+    # unless File.directory?(VISIT_FIXTURE_UNZIPPED)
+    #   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'
+  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')))
+  end
+  
+  it "should create a thumbnail in a tmpdir without a specified path." do
+    t = RawImageDatasetThumbnail.new(@ds)
+    t.create_thumbnail
+    
+    File.basename(t.path).should == 'Sag-CUBE-T2.png'
+    File.exist?(t.path).should be_true
+  end
+  
+  it "should create a thumbnail with a specified path." do
+    output_filename = "/tmp/#{@ds.series_description.escape_filename}.png"
+    File.delete(output_filename) if File.exist?(output_filename)
+    
+    t = RawImageDatasetThumbnail.new(@ds)
+    t.create_thumbnail('/tmp/')
+    
+    t.path.should == output_filename
+    File.exist?(t.path).should be_true
+    
+  end
+  
+  it "should create a thumbnail with a specified path and filename." do
+    output_filename = "/tmp/test.png"
+    File.delete(output_filename) if File.exist?(output_filename)
+    
+    t = RawImageDatasetThumbnail.new(@ds)
+    t.create_thumbnail(output_filename)
+    
+    t.path.should == '/tmp/test.png'
+    File.exist?(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/ )    
+  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|
+    #   Dir.foreach(temp_dir) {|f| File.delete(File.join(temp_dir, f)) if File.extname(f) == '.nii'}
+    # end
+  end
+  
+end

data/test/visit_test.rb

@@ -4,9 +4,9 @@
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'test/unit'
-require 'visit_raw_data_directory'
 require 'pathname'
 require 'logger'
+require 'metamri'
 
 class RawImageFileTest < Test::Unit::TestCase
   DBFILE = '/Users/kris/projects/TransferScans/db/development.sqlite3'

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 16
-  version: 0.1.16
+  - 17
+  version: 0.1.17
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-04-23 00:00:00 -05:00
+date: 2010-05-07 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -45,10 +45,10 @@ description: Extraction of MRI metadata and insertion into compatible sqlite3 da
 email: kk4@medicine.wisc.edu
 executables: 
 - import_study.rb
-- convert_visit.rb
-- import_respiratory_files.rb
 - import_visit.rb
+- import_respiratory_files.rb
 - list_visit
+- convert_visit.rb
 extensions: []
 
 extra_rdoc_files: 
@@ -66,18 +66,20 @@ files:
 - 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
-- lib/mysql_tools.rb
-- lib/nifti_builder.rb
-- lib/raw_image_dataset.rb
-- lib/raw_image_file.rb
-- lib/series_description_parameters.rb
-- lib/visit_raw_data_directory.rb
 - metamri.gemspec
 - test/fixtures/respiratory_fixtures.yaml
 - 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
@@ -112,8 +114,9 @@ signing_key:
 specification_version: 3
 summary: MRI metadata
 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/nifti_builder_spec.rb
+- test/raw_image_dataset_thumbnail_spec.rb