metamri 0.1.5 → 0.1.6

data/VERSION

@@ -1 +1 @@
-0.1.5
+0.1.6

data/bin/convert_visit.rb

@@ -42,7 +42,7 @@ require 'logger'
 #   
 #
 def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil)
-  log = Logger.new(File.basename(raw_directory))  
+  $LOG = Logger.new(File.join(Dir.tmpdir, 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
@@ -53,8 +53,8 @@ def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil
   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}"
+    $LOG.error "There was a problem scanning a dataset in #{v.visit_directory}... skipping."
+    $LOG.error "Exception message: #{e.message}"
   ensure
     v = nil
   end

data/bin/import_respiratory_files.rb

@@ -0,0 +1,87 @@
+#!/usr/bin/env ruby
+#
+# == Synopsis 
+#
+# == Examples
+#
+# == Usage
+#
+# == Options
+#
+# == Author
+#   
+# == Copyright
+#   Copyright (c) 2010 WADRC Imaging Core.
+#
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'metamri'
+require 'pathname'
+require 'rdoc/usage'
+require 'logger'
+
+# Assumptions: Respiratory files are large and in order.
+def match_respiratory_files(path)
+  #File.join(Dir.tmpdir, File.basename(path), DateTime.now.to_s)
+  $LOG = Logger.new($stdout)  
+  $LOG.level = Logger::INFO
+  path = File.expand_path(path)
+  
+  raw_directory = '/tmp/awr001_7854_02102009'
+  visit = VisitRawDataDirectory.new(raw_directory)
+  visit.scan
+  visit_epi_files = Array.new
+  visit.datasets.each do |dataset|
+    $LOG.debug dataset.series_description
+    visit_epi_files << dataset.directory if dataset.series_description =~ /fMRI/i
+  end
+  $LOG.debug visit_epi_files
+  
+  large_files = Array.new
+  
+  Dir.open(path) do |dir|
+    dir.each do |file|
+      next if File.directory?(file)
+      if file =~ /^ECGData.*/
+        line_count = open(file) { |f| f.readlines}.length
+        large_files << file if line_count >= 1000
+        $LOG.debug "#{file}, #{line_count}"
+      end
+    end
+  end
+  $LOG.debug large_files
+  
+  timestamps = Array.new
+  
+  large_files.each do |large_file|
+    timestamps << large_file.gsub(/ECGData_epiRT_/, '')
+  end
+
+  $LOG.debug timestamps
+  
+  return visit_epi_files.zip(timestamps)
+end
+
+def create_spec
+  spec_file = 'respiratory_fixtures.yaml'
+  
+  runs = YAML::load_file(spec_file)
+  
+  runs.each do |run|
+      options = [['--card', run['cardiac_data']], ['--resp', run['respiratory_data']], ['--ox', run['cardiac_trigger']]]
+      system("PhysioNoise.py #{options.flatten.join(" ")}")
+  end
+  
+end
+
+
+if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
+  RDoc::usage() if (ARGV[0] == '-h')
+  path = ARGV[0]
+
+  resp_files = match_respiratory_files(path)
+  resp_files.each do |resp_file|
+    puts "#{resp_file[0]}, #{resp_file[1]}"
+  end
+end

data/lib/nifti_builder.rb

@@ -7,6 +7,10 @@ Builds Nifti files from Dicoms.
 TO3D_CMD = 'to3d'
 
 module UnknownImageDataset
+  # Always set AFNI GE DICOM Fix to "No" before conversion with to3d.
+  ENV['AFNI_SLICE_SPACING_IS_GAP'] == "NO"
+
+  
   def dataset_to_nifti(nifti_output_directory, nifti_filename, input_options = {} )
     if input_options.has_key?(:dicom_files)
       input_files = input_options[:dicom_files].each {|file| file.to_s }.join(' ')

data/lib/raw_image_dataset.rb

@@ -181,7 +181,7 @@ have more component files than shell commands can handle.
 Does same basic string replacements to ensure valid filenames.
 =end
   def escape_filename(filename)
-    filename.mgsub([[/[\s\:\)\(]+/, "-"], [/\*/, "star"]])
+    filename.mgsub([[/[\s\:\)\(\/]+/, "-"], [/\*/, "star"]])
   end
   
 private

data/lib/visit_raw_data_directory.rb

@@ -17,6 +17,7 @@ def flash(msg)
   printf "\t%s\n", Time.now
   puts "+" * 120
   puts
+  $LOG.info msg if $LOG
 end
 
 
@@ -159,7 +160,8 @@ Returns an array of the created nifti files.
       nifti_filename = "#{scanid}_#{dataset.escape_filename(dataset.series_description)}_#{File.basename(dataset.directory)}.nii"
 
       Pathname.new(dataset.directory).all_dicoms do |dicom_files| 
-        nifti_conversion_command, nifti_output_file = dataset.to_nifti!(nifti_output_path, nifti_filename, :input_directory => @working_directory, :append_modality_directory => true)
+        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
@@ -444,19 +446,21 @@ class Pathname
   
   def all_dicoms
     local_copies = []
-    begin
+    Dir.mktmpdir do |tempdir|
+      begin
       
-      entries.each do |leaf|
-        branch = self + leaf
-        if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.0[0-9]+(\.bz2)?$/
-          local_copies << branch.local_copy
+        entries.each do |leaf|
+          branch = self + leaf
+          if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.0[0-9]+(\.bz2)?$/
+            local_copies << branch.local_copy(tempdir)
+          end
         end
-      end
 
-      yield local_copies
+        yield local_copies
 
-    ensure
-      local_copies.each { |lc| lc.delete }
+      ensure
+        local_copies.each { |lc| lc.delete }
+      end
     end
     
     return
@@ -464,9 +468,9 @@ class Pathname
   
   
   
-  def local_copy
+  def local_copy(tempdir = Dir.tmpdir)
     tfbase = self.to_s =~ /\.bz2$/ ? self.basename.to_s.chomp(".bz2") : self.basename.to_s
-    tmpfile = File.join(Dir.tmpdir, tfbase)
+    tmpfile = File.join(tempdir, tfbase)
     if self.to_s =~ /\.bz2$/
       `bunzip2 -k -c #{self.to_s} >> #{tmpfile}`
     else

data/metamri.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.5"
+  s.version = "0.1.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2009-12-18}
+  s.date = %q{2010-01-19}
   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"]
+  s.executables = ["convert_visit.rb", "import_study.rb", "import_visit.rb", "import_respiratory_files.rb"]
   s.extra_rdoc_files = [
     "README.rdoc"
   ]
@@ -23,6 +23,7 @@ Gem::Specification.new do |s|
      "Rakefile",
      "VERSION",
      "bin/convert_visit.rb",
+     "bin/import_respiratory_files.rb",
      "bin/import_study.rb",
      "bin/import_visit.rb",
      "lib/metamri.rb",
@@ -33,6 +34,7 @@ Gem::Specification.new do |s|
      "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_file_test.rb",
@@ -45,11 +47,11 @@ Gem::Specification.new do |s|
   s.rubygems_version = %q{1.3.5}
   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/visit_test.rb"
   ]
 
   if s.respond_to? :specification_version then

data/test/fixtures/respiratory_fixtures.yaml

@@ -0,0 +1,11 @@
+fMRI ASSET RUN 1:
+  cardiac_data: ECGData_epiRT_0210200914_22_58
+  respiratory_data: RespData_epiRT_0210200914_22_58
+  cardiac_trigger: TrigEcg_epiRT_0210200914_22_58
+  respiratory_trigger: TrigResp_epiRT_0210200914_22_58
+
+fMRI ASSET RUN 2:
+  cardiac_data: ECGData_epiRT_0210200914_22_58
+  respiratory_data: RespData_epiRT_0210200914_22_58
+  cardiac_trigger: TrigEcg_epiRT_0210200914_22_58
+  respiratory_trigger: TrigResp_epiRT_0210200914_22_58

data/test/nifti_builder_spec.rb

@@ -59,8 +59,9 @@ describe "Convert Unknown Dicoms to Nifti Files" do
       nifti_conversion_command.should == "to3d -session /tmp -prefix 001.nii /tmp/'*.dcm'"
 
       
+      nifti_input_path = File.dirname(dicom_files.first)
       nifti_conversion_command, nifti_output_file = @dataset.to_nifti(nifti_output_path, nifti_filename, :dicom_files => dicom_files)
-      nifti_conversion_command.should == "to3d -session /tmp -prefix 001.nii #{Dir.tmpdir}/I0001.dcm #{Dir.tmpdir}/I0002.dcm #{Dir.tmpdir}/I0003.dcm #{Dir.tmpdir}/I0004.dcm #{Dir.tmpdir}/I0005.dcm #{Dir.tmpdir}/I0006.dcm #{Dir.tmpdir}/I0007.dcm #{Dir.tmpdir}/I0008.dcm #{Dir.tmpdir}/I0009.dcm #{Dir.tmpdir}/I0010.dcm #{Dir.tmpdir}/I0011.dcm #{Dir.tmpdir}/I0012.dcm #{Dir.tmpdir}/I0013.dcm #{Dir.tmpdir}/I0014.dcm #{Dir.tmpdir}/I0015.dcm"
+      nifti_conversion_command.should == "to3d -session /tmp -prefix 001.nii #{dicom_files.each {|dicom| dicom}.join(" ")}"
 
     end
   end

data/test/visit_test.rb

@@ -10,7 +10,7 @@ require 'logger'
 
 class RawImageFileTest < Test::Unit::TestCase
   DBFILE = '/Users/kris/projects/TransferScans/db/development.sqlite3'
-  LOG = Logger.new('visit_test.log', shift_age = 7, shift_size = 1048576)
+  $LOG = Logger.new('visit_test.log', shift_age = 7, shift_size = 1048576)
   STUDIES = [
     # Pathname.new('/Data/vtrak1/raw/alz_2000'),
     # Pathname.new('/Data/vtrak1/raw/alz_2000'),
@@ -65,8 +65,8 @@ class RawImageFileTest < Test::Unit::TestCase
         rescue Exception => e
           puts "There was a problem scanning a dataset in #{visitdir}... skipping."
           puts "Exception message: #{e.message}"
-          LOG.error "There was a problem scanning a dataset in #{visitdir}... skipping."
-          LOG.error "Exception message: #{e.message}"
+          $LOG.error "There was a problem scanning a dataset in #{visitdir}... skipping."
+          $LOG.error "Exception message: #{e.message}"
         ensure
           v = nil
         end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  version: 0.1.5
+  version: 0.1.6
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -9,16 +9,17 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-12-18 00:00:00 -06:00
+date: 2010-01-19 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: []
 
 extra_rdoc_files: 
@@ -30,6 +31,7 @@ files:
 - Rakefile
 - VERSION
 - bin/convert_visit.rb
+- bin/import_respiratory_files.rb
 - bin/import_study.rb
 - bin/import_visit.rb
 - lib/metamri.rb
@@ -40,6 +42,7 @@ files:
 - 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_file_test.rb
@@ -74,8 +77,8 @@ 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