metamri 0.1.4 → 0.1.5

data/.gitignore

@@ -3,4 +3,5 @@
 ._*
 .idea
 *~
+test/fixtures/visit_raw_data_directory
 

data/VERSION

@@ -1 +1 @@
-0.1.4
+0.1.5

data/bin/convert_visit.rb

@@ -0,0 +1,75 @@
+#!/usr/bin/env ruby
+#
+# == Synopsis 
+#   A simple utility for converting all the dicom datasets in a directory into niftis.  Defaults to the current
+#   default preprocessed repository.
+#
+# == Examples
+#   convert_visit.rb /Data/vtrak1/raw/ries.aware.visit1/awr001_7854_02102009 ries.aware.visit1 
+
+#
+# == Usage 
+#   convert_visit.rb <raw_data_directory> <scan_procedure_codename> 
+#
+#   For help use: import_visit.rb -h
+#
+# == 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
+#
+# == Author
+#   
+#
+# == Copyright
+#   Copyright (c) 2009 WADRC Imaging Core.
+#
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'metamri'
+require 'pathname'
+require 'rdoc/usage'
+require 'logger'
+
+# == Function
+#   
+# 
+# == Usage
+#   
+#
+# == Example
+#   
+#
+def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil)
+  log = Logger.new(File.basename(raw_directory))  
+  v = VisitRawDataDirectory.new(raw_directory, scan_procedure_codename)
+  puts "+++ Converting #{v.visit_directory} as part of #{v.scan_procedure_name} +++"
+  output_directory = output_directory ||= v.default_preprocess_directory
+
+  begin
+    v.scan
+    v.to_nifti!(output_directory)
+  rescue Exception => e
+    puts "There was a problem scanning a dataset in #{v.visit_directory}... skipping."
+    puts "Exception message: #{e.message}"
+    log.error "There was a problem scanning a dataset in #{v.visit_directory}... skipping."
+    log.error "Exception message: #{e.message}"
+  ensure
+    v = nil
+  end
+end
+
+
+
+if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
+  RDoc::usage() if (ARGV[0] == '-h')
+  raw_directory = ARGV[0]
+
+  # This is required for now, will be inferred from path in the future.
+  scan_procedure_codename = ARGV[1] 
+  
+  output_directory = ARGV[2] ? ARGV[2] : nil
+
+  convert_visit(raw_directory, scan_procedure_codename, output_directory)
+end

data/lib/nifti_builder.rb

@@ -15,7 +15,6 @@ module UnknownImageDataset
     else input_files = "#{Dir.tmpdir}/'#{glob}'"
     end
     
-    nifti_output_directory = File.join(nifti_output_directory, 'unknown') if input_options[:append_modality_directory]
     nifti_output_file = File.join(nifti_output_directory, nifti_filename)
     
     File.makedirs(nifti_output_directory) unless File.directory?(nifti_output_directory)

data/lib/raw_image_dataset.rb

@@ -27,7 +27,7 @@ class RawImageDataset
   # the file scanned
   attr_reader :scanned_file
   # the scanner source
-  attr_reader :scanner_source  
+  attr_reader :scanner_source
 
 =begin rdoc
   * dir: The directory containing the files.
@@ -122,7 +122,14 @@ The to3d code is applied as a mixed-in module.
 Returns the to3d command that creates the specified options.
 =end
   def to_nifti(nifti_output_directory, nifti_filename, input_options = {} )
-    extend(UnknownImageDataset)
+    
+    # Handle the business logic for choosing the right Nifti Builder here.
+    # Currently just extend the default unknown builder, since that's the only one that exists.
+    if true
+      nifti_output_directory = File.join(nifti_output_directory, 'unknown') if input_options[:append_modality_directory]
+      extend(UnknownImageDataset)
+    end
+    
     nifti_conversion_command, nifti_output_file = self.dataset_to_nifti(nifti_output_directory, nifti_filename, input_options)
     return nifti_conversion_command, nifti_output_file
   end
@@ -171,10 +178,10 @@ have more component files than shell commands can handle.
   end
   
 =begin rdoc
-
+Does same basic string replacements to ensure valid filenames.
 =end
   def escape_filename(filename)
-    filename.gsub(/\s|:/,"-" )
+    filename.mgsub([[/[\s\:\)\(]+/, "-"], [/\*/, "star"]])
   end
   
 private
@@ -186,4 +193,13 @@ private
 
 
 end
-#### END OF CLASS ####
+#### END OF CLASS ####
+
+class String
+  def mgsub(key_value_pairs=[].freeze)
+    regexp_fragments = key_value_pairs.collect { |k,v| k }
+    gsub(Regexp.union(*regexp_fragments)) do |match|
+      key_value_pairs.detect { |k,v| k =~ match}[1]
+    end
+  end
+end

data/lib/raw_image_file.rb

@@ -71,7 +71,7 @@ temporary file.
   def initialize(pathtofile)
     # raise an error if the file doesn't exist
     absfilepath = File.expand_path(pathtofile)
-    raise(IOError, "File not found.") if not File.exists?(absfilepath)
+    raise(IOError, "File not found at #{absfilepath}.") if not File.exists?(absfilepath)
     @filename = File.basename(absfilepath)
     
     # try to read the header, raise an IOError if unsuccessful

data/metamri.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.4"
+  s.version = "0.1.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2009-12-11}
+  s.date = %q{2009-12-18}
   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", "alz.visit1.scan.log", "wrap140.scan.log"]
+  s.executables = ["import_study.rb", "import_visit.rb", "convert_visit.rb"]
   s.extra_rdoc_files = [
     "README.rdoc"
   ]
@@ -22,6 +22,7 @@ Gem::Specification.new do |s|
      "README.rdoc",
      "Rakefile",
      "VERSION",
+     "bin/convert_visit.rb",
      "bin/import_study.rb",
      "bin/import_visit.rb",
      "lib/metamri.rb",

data/test/nifti_builder_spec.rb

@@ -9,16 +9,19 @@ require 'raw_image_file'
 describe "Convert Unknown Dicoms to Nifti Files" do
   
   before(:each) do
-    @visit = VisitRawDataDirectory.new('/Data/vtrak1/raw/johnson.tbi-va.visit1/tbiva018b_9336_12022009', 'johnson.tbi-va.visit1')
-    @dataset = RawImageDataset.new('/Data/vtrak1/raw/johnson.tbi-va.visit1/tbiva018b_9336_12022009/001', [RawImageFile.new('/Data/vtrak1/raw/johnson.tbi-va.visit1/tbiva018b_9336_12022009/001/I0001.dcm')])
+    @visit = VisitRawDataDirectory.new(File.join(File.dirname(__FILE__), 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009'), 'johnson.tbi-va.visit1')
+    @dataset = RawImageDataset.new(
+      File.join(File.dirname(__FILE__), 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009/001'), 
+      [RawImageFile.new(File.join(File.dirname(__FILE__), 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009/001/I0001.dcm'))]
+    )
     @test_niftis = Array.new
     @output_directories = Array.new
   end
 
   it "should Convert an anatomical from dicom to nifti using original, unzipped files." do
-    @dataset.to_nifti('/tmp/', 'filename.nii', :input_directory => '/Data/vtrak1/raw/asthana.adrc-clinical-core.visit1/adrc00001_294_12022009/001')[0].should == "to3d -session /tmp/ -prefix filename.nii /Data/vtrak1/raw/asthana.adrc-clinical-core.visit1/adrc00001_294_12022009/001/'*.dcm'"
-    nifti_conversion_command, nifti_output_file = @dataset.to_nifti!('/tmp/', 'filename.nii', :input_directory => '/Data/vtrak1/raw/asthana.adrc-clinical-core.visit1/adrc00001_294_12022009/001')
-    nifti_conversion_command.should == "to3d -session /tmp/ -prefix filename.nii /Data/vtrak1/raw/asthana.adrc-clinical-core.visit1/adrc00001_294_12022009/001/'*.dcm'"
+    @dataset.to_nifti('/tmp/', 'filename.nii', :input_directory => @dataset.directory)[0].should == "to3d -session /tmp/ -prefix filename.nii #{@dataset.directory}/'*.dcm'"
+    nifti_conversion_command, nifti_output_file = @dataset.to_nifti!('/tmp/', 'filename.nii', :input_directory => @dataset.directory)
+    nifti_conversion_command.should == "to3d -session /tmp/ -prefix filename.nii #{@dataset.directory}/'*.dcm'"
     @test_niftis << nifti_output_file
     @output_directories << '/tmp'
   end
@@ -29,7 +32,7 @@ describe "Convert Unknown Dicoms to Nifti Files" do
     @visit.datasets.each do |ds|
       begin 
         nifti_filename = "#{@visit.scanid}_#{ds.escape_filename(ds.series_description)}_#{File.basename(ds.directory)}.nii"
-        nifti_conversion_commmand, nifti_output_file = ds.to_nifti!(File.join(Dir.tmpdir, @visit.default_preprocess_directory), nifti_filename, :input_directory => @dataset.directory, :append_modality_directory => true )
+        nifti_conversion_commmand, nifti_output_file = ds.to_nifti!(File.join(Dir.tmpdir, @visit.default_preprocess_directory), nifti_filename, :input_directory => ds.directory, :append_modality_directory => true )
         @test_niftis << nifti_output_file
       rescue IOError => e
         puts "-- Error: #{e.message}"
@@ -40,7 +43,7 @@ describe "Convert Unknown Dicoms to Nifti Files" do
   end
   
   it "should convert all anatomicals in a visit raw directory using local copy." do
-    @test_niftis << @visit.to_nifti!('/tmp')
+    @test_niftis << @visit.to_nifti!
   end
   
   it "should create a good to3d command with input directory or dicom files." do 
@@ -75,7 +78,7 @@ describe "Convert Unknown Dicoms to Nifti Files" do
     v.scanid.should == 'adrc00001'
   end
   
-  after do
+  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'}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  version: 0.1.4
+  version: 0.1.5
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-12-11 00:00:00 -06:00
+date: 2009-12-18 00:00:00 -06:00
 default_executable: 
 dependencies: []
 
@@ -18,8 +18,7 @@ email: kk4@medicine.wisc.edu
 executables: 
 - import_study.rb
 - import_visit.rb
-- alz.visit1.scan.log
-- wrap140.scan.log
+- convert_visit.rb
 extensions: []
 
 extra_rdoc_files: 
@@ -30,6 +29,7 @@ files:
 - README.rdoc
 - Rakefile
 - VERSION
+- bin/convert_visit.rb
 - bin/import_study.rb
 - bin/import_visit.rb
 - lib/metamri.rb