metamri 0.1.9 → 0.1.10

data/VERSION

@@ -1 +1 @@
-0.1.9
+0.1.10

data/lib/metamri/core_additions.rb

@@ -0,0 +1,17 @@
+class String
+
+=begin rdoc
+Does same basic string replacements to ensure valid filenames.
+=end
+  def escape_filename
+    mgsub([[/[\s\:\)\(\/\?]+/, "-"], [/\*/, "star"]])
+  end
+  
+  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/metamri.rb

@@ -1,6 +1,9 @@
+$: << File.dirname(__FILE__)
+
 require 'raw_image_file'
 require 'raw_image_dataset'
 require 'visit_raw_data_directory'
+require 'metamri/core_additions'
 
 module Metamri
 end

data/lib/raw_image_dataset.rb

@@ -177,12 +177,7 @@ have more component files than shell commands can handle.
     end
   end
   
-=begin rdoc
-Does same basic string replacements to ensure valid filenames.
-=end
-  def escape_filename(filename)
-    filename.mgsub([[/[\s\:\)\(\/]+/, "-"], [/\*/, "star"]])
-  end
+
   
 private
 
@@ -191,15 +186,5 @@ private
     @timestamp = (@raw_image_files.sort_by { |i| i.timestamp }).first.timestamp
   end
 
-
 end
 #### 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

@@ -79,7 +79,7 @@ temporary file.
       @hdr_data, @hdr_reader = read_header(absfilepath)
       #puts "@hdr_data: #{@hdr_data}; @hdr_reader: #{@hdr_reader}"
     rescue Exception => e
-      raise(IOError, "Header not readable. #{e}")
+      raise(IOError, "Header not readable for file #{@filename}. #{e}")
     end
     
     # file type is based on file name but only if the header was read successfully
@@ -90,7 +90,7 @@ temporary file.
     begin
       import_hdr
     rescue Exception => e
-      raise(IOError, "Header import failed. #{e}")
+      raise(IOError, "Header import failed for file #{@filename}. #{e}")
     end
     
     # deallocate the header data to save memory space.

data/lib/visit_raw_data_directory.rb

@@ -157,7 +157,7 @@ Returns an array of the created nifti files.
         
     @datasets.each do |dataset|
       nifti_output_path = output_directory
-      nifti_filename = "#{scanid}_#{dataset.escape_filename(dataset.series_description)}_#{File.basename(dataset.directory)}.nii"
+      nifti_filename = "#{scanid}_#{dataset.series_description.escape_filename}_#{File.basename(dataset.directory).escape_filename}.nii"
 
       Pathname.new(dataset.directory).all_dicoms do |dicom_files| 
         nifti_input_path = File.dirname(dicom_files.first)
@@ -470,6 +470,7 @@ class Pathname
   
   def local_copy(tempdir = Dir.tmpdir)
     tfbase = self.to_s =~ /\.bz2$/ ? self.basename.to_s.chomp(".bz2") : self.basename.to_s
+    tfbase.escape_filename
     tmpfile = File.join(tempdir, tfbase)
     if self.to_s =~ /\.bz2$/
       `bunzip2 -k -c '#{self.to_s}' >> '#{tmpfile}'`

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.9"
+  s.version = "0.1.10"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-01-22}
+  s.date = %q{2010-01-25}
   s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
   s.email = %q{kk4@medicine.wisc.edu}
   s.executables = ["convert_visit.rb", "import_study.rb", "import_visit.rb", "import_respiratory_files.rb"]
@@ -27,6 +27,7 @@ Gem::Specification.new do |s|
      "bin/import_study.rb",
      "bin/import_visit.rb",
      "lib/metamri.rb",
+     "lib/metamri/core_additions.rb",
      "lib/mysql_tools.rb",
      "lib/nifti_builder.rb",
      "lib/raw_image_dataset.rb",

data/test/nifti_builder_spec.rb

@@ -3,54 +3,67 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 require 'rubygems'
 require 'spec'
 require 'fileutils'
+require 'tmpdir'
 require 'visit_raw_data_directory'
 require 'raw_image_dataset'
 require 'raw_image_file'
 
-VISIT_FIXTURE = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009')
 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')
+
+
 
 describe "Convert Unknown Dicoms to Nifti Files" 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)
+      #FileUtils.mkdir_p(File.dirname(VISIT_FIXTURE))
+      #FileUtils.cp_r(VISIT_FIXTURE_SRC, VISIT_FIXTURE)
+      #FileUtils.cp_r(VISIT_FIXTURE, VISIT_FIXTURE_UNZIPPED)
+      `find #{VISIT_FIXTURE_UNZIPPED} -name '*.bz2' -exec bunzip2 {} \\;`
+    #end
   end
   
   before(:each) do
     @visit = VisitRawDataDirectory.new(VISIT_FIXTURE, 'johnson.tbi-va.visit1')
     @dataset = RawImageDataset.new(
       File.join(VISIT_FIXTURE, '001'), 
-      [RawImageFile.new(File.join(VISIT_FIXTURE, '001/I0001.dcm'))]
+      [RawImageFile.new(File.join(VISIT_FIXTURE, '001/I0001.dcm.bz2'))]
+    )
+    
+    @visit_unzipped = VisitRawDataDirectory.new(VISIT_FIXTURE_UNZIPPED, 'johnson.tbi-va.visit1')
+    @dataset_unzipped = RawImageDataset.new(
+      File.join(VISIT_FIXTURE_UNZIPPED, '001'), 
+      [RawImageFile.new(File.join(VISIT_FIXTURE_UNZIPPED, '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 => @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'"
+    @dataset_unzipped.to_nifti('/tmp/', 'filename.nii', :input_directory => @dataset_unzipped.directory)[0].should == "to3d -session /tmp/ -prefix filename.nii #{@dataset_unzipped.directory}/'*.dcm'"
+    nifti_conversion_command, nifti_output_file = @dataset_unzipped.to_nifti!('/tmp/', 'filename.nii', :input_directory => @dataset_unzipped.directory)
+    nifti_conversion_command.should == "to3d -session /tmp/ -prefix filename.nii #{@dataset_unzipped.directory}/'*.dcm'"
     @test_niftis << nifti_output_file
     @output_directories << '/tmp'
   end
   
   it "should convert all anatomicals in a visit raw directory using original, unzipped files." do
-    @visit.scan
+    @visit_unzipped.scan
     
-    @visit.datasets.each do |ds|
+    @visit_unzipped.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 => ds.directory, :append_modality_directory => true )
+        nifti_filename = "#{@visit_unzipped.scanid}_#{ds.series_description.escape_filename}_#{File.basename(ds.directory)}.nii"
+        nifti_conversion_commmand, nifti_output_file = ds.to_nifti!(File.join(Dir.tmpdir, @visit_unzipped.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}"
       end
     end
     
-    @output_directories = File.join(@visit.default_preprocess_directory, 'unknown')
+    @output_directories = File.join(@visit_unzipped.default_preprocess_directory, 'unknown')
   end
   
   it "should convert all anatomicals in a visit raw directory using local copy." do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  version: 0.1.9
+  version: 0.1.10
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-01-22 00:00:00 -06:00
+date: 2010-01-25 00:00:00 -06:00
 default_executable: 
 dependencies: []
 
@@ -35,6 +35,7 @@ files:
 - bin/import_study.rb
 - bin/import_visit.rb
 - lib/metamri.rb
+- lib/metamri/core_additions.rb
 - lib/mysql_tools.rb
 - lib/nifti_builder.rb
 - lib/raw_image_dataset.rb