metamri 0.1.8 → 0.1.9

data/VERSION

@@ -1 +1 @@
-0.1.8
+0.1.9

data/lib/raw_image_dataset.rb

@@ -146,7 +146,7 @@ Returns a path to the created dataset as a string if successful.
       system "#{nifti_conversion_command}"
       raise(IOError, "Could not convert image dataset: #{@directory} to #{nifti_output_file}") unless $? == 0
     rescue IOError => e
-      raise "-- Warning: #{e.message}"
+      $LOG.warn "-- Warning: #{e.message}"
     end
     return nifti_conversion_command, nifti_output_file
   end

data/lib/raw_image_file.rb

@@ -249,14 +249,14 @@ 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_HDR} #{absfilepath} 2> /dev/null`
+    header = `#{DICOM_HDR} '#{absfilepath}' 2> /dev/null`
     #header = `#{DICOM_HDR} #{absfilepath}`
     if ( header.index("ERROR") == nil and 
          header.chomp != "" and 
          header.length > MIN_HDR_LENGTH )
       return [ header, DICOM_HDR ]
     end
-    header = `#{RDGEHDR} #{absfilepath} 2> /dev/null`
+    header = `#{RDGEHDR} '#{absfilepath}' 2> /dev/null`
     #header = `#{RDGEHDR} #{absfilepath}`
     if ( header.chomp != "" and
          header.length > MIN_HDR_LENGTH )

data/lib/visit_raw_data_directory.rb

@@ -472,7 +472,7 @@ class Pathname
     tfbase = self.to_s =~ /\.bz2$/ ? self.basename.to_s.chomp(".bz2") : self.basename.to_s
     tmpfile = File.join(tempdir, tfbase)
     if self.to_s =~ /\.bz2$/
-      `bunzip2 -k -c #{self.to_s} >> #{tmpfile}`
+      `bunzip2 -k -c '#{self.to_s}' >> '#{tmpfile}'`
     else
       FileUtils.cp(self.to_s, tmpfile)
     end

data/metamri.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.8"
+  s.version = "0.1.9"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-01-20}
+  s.date = %q{2010-01-22}
   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", "convert_visit.rb", "import_respiratory_files.rb"]
+  s.executables = ["convert_visit.rb", "import_study.rb", "import_visit.rb", "import_respiratory_files.rb"]
   s.extra_rdoc_files = [
     "README.rdoc"
   ]

data/test/nifti_builder_spec.rb

@@ -2,17 +2,28 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'rubygems'
 require 'spec'
+require 'fileutils'
 require 'visit_raw_data_directory'
 require 'raw_image_dataset'
 require 'raw_image_file'
 
-describe "Convert Unknown Dicoms to Nifti Files" do
+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'
+
+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
+  end
   
   before(:each) do
-    @visit = VisitRawDataDirectory.new(File.join(File.dirname(__FILE__), 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009'), 'johnson.tbi-va.visit1')
+    @visit = VisitRawDataDirectory.new(VISIT_FIXTURE, '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'))]
+      File.join(VISIT_FIXTURE, '001'), 
+      [RawImageFile.new(File.join(VISIT_FIXTURE, '001/I0001.dcm'))]
     )
     @test_niftis = Array.new
     @output_directories = Array.new

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  version: 0.1.8
+  version: 0.1.9
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -9,16 +9,16 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-01-20 00:00:00 -06:00
+date: 2010-01-22 00:00:00 -06:00
 default_executable: 
 dependencies: []
 
 description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
 email: kk4@medicine.wisc.edu
 executables: 
+- convert_visit.rb
 - import_study.rb
 - import_visit.rb
-- convert_visit.rb
 - import_respiratory_files.rb
 extensions: []