wadrc-bcp-scripts 0.0.6

data/bin/tensor_transpose.rb

@@ -0,0 +1,45 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'optparse'
+require 'tensor'
+
+def run!
+  # Parse CLI Options and Spec File
+  options = parse_options
+
+  # Create a DTI Preprocessing Flow Task and run it.
+  tensor = Tensor.new(options[:tensor_file])
+  tensor.to_fsl_txt(options[:output_file])
+
+end
+
+def parse_options
+  options = Hash.new
+  
+  parser = OptionParser.new do |opts|
+    opts.banner = "Usage: #{File.basename(__FILE__)} [options] input_tensor output_transposed_tensor"
+
+    # opts.on('-t', '--tensor TENSOR_FILE', "Tensor File.")     do |tensor_file| 
+    #   options[:tensor_file] = tensor_file
+    # end
+    
+    opts.on_tail('-h', '--help',          "Show this message")          { puts(parser); exit }
+    opts.on_tail("Example: #{File.basename(__FILE__)} 40_direction.txt 40_direction_transposed.txt")
+  end
+  parser.parse!(ARGV)
+
+  options[:tensor_file] = ARGV[0]
+  options[:output_file] = ARGV[1]  
+
+  unless ARGV.size == 2
+    puts(parser); exit
+  end
+
+  return options
+end
+
+
+if File.basename(__FILE__) == File.basename($0)
+  run!
+end

data/lib/.svn/entries

@@ -0,0 +1,54 @@
+8
+
+dir
+146
+file:///Data/vtrak1/SysAdmin/lab_repository/trunk/ImageProcessing/lib
+file:///Data/vtrak1/SysAdmin/lab_repository
+
+
+
+2009-05-08T17:32:47.685248Z
+146
+erik
+
+
+svn:special svn:externals svn:needs-lock
+
+
+
+
+
+
+
+
+
+
+
+fd7843e3-2c87-496d-a67a-9fe0c7cb9cb9
+
+dtifit_processing.rb
+file
+
+
+
+
+2009-05-08T17:33:56.000000Z
+b2bef44f643323c28603d4dcb8dd1da8
+2009-05-08T17:32:47.685248Z
+146
+erik
+has-props
+
+dti_wrapper.rb
+file
+
+
+
+
+2009-05-08T17:33:57.000000Z
+22334daf49e150cb1646a6a6ac7a2033
+2009-05-08T17:32:47.685248Z
+146
+erik
+has-props
+

data/lib/.svn/format

@@ -0,0 +1 @@
+8

data/lib/.svn/prop-base/dti_wrapper.rb.svn-base

@@ -0,0 +1,5 @@
+K 14
+svn:executable
+V 0
+
+END

data/lib/.svn/prop-base/dtifit_processing.rb.svn-base

@@ -0,0 +1,5 @@
+K 14
+svn:executable
+V 0
+
+END

data/lib/.svn/text-base/dti_wrapper.rb.svn-base

@@ -0,0 +1,33 @@
+#!/bin/env ruby
+## This is a temporary wrapper to execute DTI data.
+
+require 'dtifit_processing'
+
+=begin rdoc
+This library provides basic processing for Diffusion Tensor Images (DTI)
+This command-line processing script takes raw DTI dicoms and outputs FA, MD &
+associated diffusion maps (eigenvalues & eigenvectors).
+
+Currently, the script assumes raw data are unzipped and the output directory
+exists, the glob and DTI params are constant across DTI series.
+=end
+
+
+#def run!
+#  input_directory = '/Data/vtrak1/raw/wrap140/wrp002_5938_03072008/017'
+#  output_directory = '/Data/vtrak1/preprocessed/visits/wrap140.visit1/wrp002/dti'
+#  subject_prefix = 'wrp002'
+#
+#  ReconstructDTI.reconstruct!(input_directory, output_directory, subject_prefix)
+#end
+#
+#run!
+
+
+if __FILE__ == $0
+  if ARGV.size != 3
+    puts "Usage: dtifit_processing.rb input_directory output_directory subject_prefix"
+  else
+    ReconstructDTI.reconstruct!(ARGV[0], ARGV[1], ARGV[2])
+  end
+end

data/lib/.svn/text-base/dtifit_processing.rb.svn-base

@@ -0,0 +1,95 @@
+#!/bin/env ruby
+
+=begin rdoc
+This library provides basic processing for Diffusion Tensor Images (DTI).
+
+The main function reconstruct! takes 3 arguements: A directory of raw DTI dicoms,
+an output directory and a filename prefix.  A set of batch commands using standard
+imaging tools (AFNI & FSL) are generated and executed to create Fractional 
+Anisotropy (FA), Mean Diffusivity (MD) and associated diffusion maps
+(eigenvalues & eigenvectors) in the output directory.
+
+The script depends on AFNI to be in the path for reconstruction (to3d) and
+FSL to be in the path for DTI Data Fitting (eddy_correct, bet & dtifit)
+
+=end
+
+require 'fileutils'
+
+class ReconstructDTI
+
+	BVECTORS_FILE = '/Data/vtrak1/preprocessed/progs/wrap140.visit1/DTI_Fitting/25_directions_UWhospital_magnet_horizontal_spaces.csv' # Vector directions of the gradient for each of the 25 directtions in this 25-direction DTI sequence.  A 3x26 matrix.
+	BVALUES_FILE = '/Data/vtrak1/preprocessed/progs/wrap140.visit1/DTI_Fitting/25_directions_bvalues.txt' # Magnitude of the direction vectors. A 1x26 matrix of 0 for the first (B0) and then 1000 for each direction afterwards.
+
+	FILE_GLOB = "'I*.dcm'"
+	VOLUMES = 26
+	SLICES_PER_VOLUME = 49
+	SLICE_ORDER = 'altplus'
+
+  # Checks for some required helper applications that must be installed on the
+  # system prior to use.  It returns false if there are no missing
+  # processing program binaries and returns the names of the missing programs.
+  def self.missing_required_binaries?
+    missing_binaries = []
+    ['to3d', 'eddy_correct', 'bet', 'dtifit'].each do |required_binary|
+      if system("which #{required_binary} > /dev/null") == false
+        missing_binaries << required_binary
+      end
+    end
+
+    if missing_binaries.size == 0
+      return false
+    else
+      return missing_binaries
+    end
+
+  end
+
+  # Constructs the commands used in the script from constants and variables
+  # passed in from the command line.
+  def self.construct_commands
+    to3d_recon_options = "-time:zt #{SLICES_PER_VOLUME} #{VOLUMES} 1 #{SLICE_ORDER} #{@@input_directory}/#{FILE_GLOB}"
+
+    recon_cmd = "to3d -prefix #{@@file_prefix}.nii -session #{@@output_directory} #{to3d_recon_options}"
+    eddy_cmd = "eddy_correct #{@@output_directory}/#{@@file_prefix}.nii #{@@output_directory}/#{@@file_prefix}_ecc.nii 0"
+    mask_cmd = "bet #{@@output_directory}/#{@@file_prefix}_ecc  #{@@output_directory}/#{@@file_prefix}_ecc_brain -f 0.1 -g 0 -n -m"
+    dtifit_cmd = "dtifit --data=#{@@output_directory}/#{@@file_prefix}_ecc.nii --out=#{@@output_directory}/#{@@file_prefix}_dti --mask=#{@@output_directory}/#{@@file_prefix}_ecc_brain_mask --bvecs=#{BVECTORS_FILE} --bvals=#{BVALUES_FILE}"
+
+    @@batch_cmd = [recon_cmd, eddy_cmd, mask_cmd, dtifit_cmd].join("; ")
+  end
+
+  # Sets variables passed in from the command-line, constructs the processing
+  # commands and then executes them.
+  #
+  # Throws an IOError if input_directory is not found on the filesystem or
+  # output directory already exists.
+  def self.reconstruct!(input_directory, output_directory, file_prefix)
+    @@input_directory = File.expand_path(input_directory)
+    @@output_directory = File.expand_path(output_directory)
+    @@file_prefix = file_prefix
+
+    if missing_required_binaries?
+      puts "You are missing some required processing programs:"
+      missing_required_binaries?.each { |requirement| puts requirement }
+      puts "Please install the missing programs or run this script from a properly configured workstation."
+      raise(Error)
+    end
+
+    raise(IOError, "#{@@input_directory}: not found.") if not File.directory?(@@input_directory)
+    raise(IOError, "#{@@output_directory} already exists.") if File.directory?(@@output_directory)
+    FileUtils.mkdir_p(@@output_directory)
+
+
+    construct_commands
+
+    puts @@batch_cmd
+    system @@batch_cmd
+  end
+
+end
+
+# Code for when excuting from the command line.
+if __FILE__ == $0
+  puts "Libraries for DTI processing.  To use this with the command-line, use dti_wrapper.rb"
+end
+

data/lib/additions/NetSshConnectionSession.rb

@@ -0,0 +1,20 @@
+# Reopen Net::SSH to allow for a "realtime" ssh run that prints out stdout
+# immediately upon receipt, so you can interactively watch the results.
+class Net::SSH::Connection::Session
+  def exec_realtime(cmd)
+    open_channel do |channel|
+      channel.exec(cmd) do |ch, success|
+        abort "could not execute command: #{cmd}" unless success
+
+        channel.on_data do |ch, data|
+          puts "#{data}"
+        end
+
+        channel.on_extended_data do |ch, type, data|
+          warn "ERROR: #{data}"
+        end
+      end
+    end
+    loop
+  end
+end

data/lib/wadrc-bcp-scripts.rb

@@ -0,0 +1,13 @@
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require 'net/ssh'
+
+require 'wadrc-bcp-scripts/basic_task'
+require 'wadrc-bcp-scripts/dtitask'
+require 'wadrc-bcp-scripts/fieldmap_classes'
+require 'wadrc-bcp-scripts/tensor'
+require 'wadrc-bcp-scripts/version'
+require 'additions/NetSshConnectionSession'
+
+# WADRC Basic Common Processing (BCP) Scripts
+module WadrcBcpScripts; end

data/lib/wadrc-bcp-scripts/basic_task.rb

@@ -0,0 +1,137 @@
+require 'fileutils'
+require 'escoffier'
+
+module WadrcBcpScripts
+
+  # Enviornment and configuration checks common between processing streams.
+  class BasicTask
+    # Task Configuration Options Hash
+    attr_accessor :config
+
+    # Check for some required helper applications that must be installed on the
+    # system prior to use.  It returns true if there are no missing
+    # processing program binaries, otherwise it puts them to the screen and 
+    # raises a ScriptError.
+    def environment_requires(*args)
+      missing_binaries = []
+      args.each do |required_binary|
+        if system("which #{required_binary.to_s} > /dev/null") == false
+          missing_binaries << required_binary
+        end
+      end
+  
+      begin
+        unless missing_binaries.size == 0
+          error = "
+          Warning: The following processing tools weren't found on your system.
+          - #{missing_binaries.join(', ')}
+      
+      
+          Please install the missing programs, run this script from a properly configured workstation,
+          or use the dry_run option to output your script to the terminal.\n "
+          puts error
+          raise(ScriptError, "Missing #{missing_binaries.join(", ")}")
+        end
+      end
+  
+      return
+    end
+
+    # Check for required keys in the @config hash.
+    def config_requires(*args)
+      missing_keys = []
+      args.each do |required_key|
+        unless @config.has_key?(required_key)
+          missing_keys << required_key
+        end
+      end
+  
+      unless missing_keys.size == 0
+        error = "
+        Warning: Misconfiguration detected.
+        You are missing the following keys from your spec file:
+        - #{missing_keys.join(', ')}
+    
+    
+        Please install the missing programs, run this script from a properly configured workstation,
+        or use the dry_run option to output your script to the terminal.\n "
+        puts error
+        raise(ScriptError, "Missing Keys: #{missing_keys.join(", ")}")
+      end
+    end
+
+    # Basic IO Directory Checks
+    def check_setup(input_directory = @input_directory, output_directory = @output_directory)
+      # Check Input Directory
+      raise(IOError, "#{input_directory}: not found.") unless File.directory?(input_directory)
+
+      # Check Gradient Tensor Files
+      ensure_file_exists @config[:bvectors_file], @config[:bvalues_file] 
+  
+      unless @config[:dry_run]
+        # Check Working Input Directory
+        if @config[:force_sandbox]
+          path = Pathname.new(input_directory)
+          # @working_input_directory = path.sandbox(input_directory)
+          @working_input_directory = path.prep_mise(input_directory + '/', Dir.mktmpdir + '/')
+          @working_input_directory = File.join(@working_input_directory, File.basename(input_directory))
+        else
+          @working_input_directory = input_directory
+        end
+  
+        # Check Output Directory and force cleanup if necessary.
+        colliding_files = Dir.glob(File.join(output_directory, @file_prefix) + '*')
+        puts colliding_files
+        if File.directory?(output_directory) && colliding_files.empty? == false
+          if @config[:force_overwrite] then colliding_files.each {|file| puts "Removing #{file}..."; File.delete(file) }
+          else raise(IOError, "#{output_directory} already exists. Set force_overwite in your spec file to overwrite the directory.") 
+          end
+        end
+        FileUtils.mkdir_p(output_directory)
+      else
+        # Use the real input directory if the working directory was not assigned 
+        # (ie during dry run)
+        @working_input_directory = input_directory
+      end
+  
+      # Setup Logging
+      logfile = File.join(output_directory, "#{File.basename(input_directory)}_#{today}.log")
+      if File.writable?(output_directory) && ! @config[:dry_run]
+        $LOG = Logger.new(logfile)
+      else
+        $LOG = Logger.new(STDOUT)
+      end
+  
+      # Switch CWD (default output location for rotbvecs script)
+      @cwd = Dir.pwd
+      Dir.chdir(output_directory) unless @config[:dry_run]
+    end
+
+    def ensure_file_exists(*args)
+      args.each do |file|
+        raise(IOError, "#{file} not found.") unless File.exists?(file)
+      end
+  
+    end
+
+    private
+
+    def cleanup
+      Dir.chdir(@cwd)
+      puts Dir.pwd
+      cleanup_directories
+      # $LOG.close
+    end
+
+    # Cleanup Sandbox Directories
+    def cleanup_directories
+      if File.directory?(@working_input_directory) && (@input_directory != @working_input_directory)
+        FileUtils.rm_r @working_input_directory 
+      end
+    end
+
+    def today
+      [Date.today.month, Date.today.day, Date.today.year].join
+    end
+  end
+end

data/lib/wadrc-bcp-scripts/dtitask.rb

@@ -0,0 +1,156 @@
+module WadrcBcpScripts
+  
+  # This library creates scripts for basic processing for Diffusion Tensor Images 
+  # (DTI).
+  # 
+  # The main function reconstruct! takes 3 arguements: A directory of raw DTI 
+  # dicoms, an output directory and a filename prefix.  A set of batch commands 
+  # using standard imaging tools (AFNI & FSL) are generated and executed to create
+  # Fractional Anisotropy (FA), Mean Diffusivity (MD) and associated diffusion 
+  # maps (eigenvalues & eigenvectors) in the output directory.
+  # 
+  # The script depends on AFNI to be in the path for reconstruction (to3d) and
+  # FSL to be in the path for DTI Data Fitting (eddy_correct, bet & dtifit)
+  class Dtitask < BasicTask
+  
+    # Task Configuration Options Hash
+    attr_accessor :config
+    # Source Directory of DICOMS
+    attr_reader :input_directory
+    # Source Directory of _unzipped_ DICOMS if using a Sandbox (or input_directory if not)
+    attr_reader :working_input_directory
+    # Destination Directory for DTI vectors, values, and maps
+    attr_reader :output_directory
+    # File Prefix to use for processing.
+    attr_reader :file_prefix
+
+
+    # Intialize DTItask with the following options:
+    # 
+    # DTI Options
+    # * bvectors_file : 
+    # * bvalues_file :
+    # * repetition_time : TR in milliseconds, defaults to 8000
+    # 
+    # 
+    # File Conversion Options
+    # * file_glob :
+    # * volumes :
+    # * slices_per_volume :
+    # * slice_order:
+    # 
+    # 
+    # Runtime Options
+    # * dry_run :
+    # * force_overwrite :
+    # * sandbox : Forces copying and unzipping to a temp directory in the case 
+    #             of zipped dicom files.
+    #  
+    def initialize(config = Hash.new)
+      @config = config
+
+      @config[:dry_run] = true if config.empty?
+    
+      begin 
+        # Intialize Settings for File Conversion and Diffusion Directions and Values
+        config_requires :bvectors_file, :bvalues_file, :file_glob, :volumes, 
+        :slices_per_volume, :slice_order
+      
+        # List binaries requried for the script to run.
+        environment_requires :to3d, :eddy_correct, :bet, :dtifit, :rotbvecs
+      rescue ScriptError => e
+        raise e unless @config[:dry_run]
+      end
+    
+    end
+  
+  
+    # Reconstruct creates a script of commands to execute in order to prepare
+    # DTI data for analyses (take a raw directory of DICOMS, convert them to 
+    # nifti, eddy current correct them, and fit them using FSL to create 
+    # eigen vectors and values, and MD and FA maps.
+    #
+    # Throws an IOError if input_directory is not found on the filesystem or
+    # output directory already exists (except during a dry_run).
+    def reconstruct!(input_directory, output_directory, file_prefix = nil)
+      @input_directory = File.expand_path(input_directory)
+      @output_directory = File.expand_path(output_directory)
+      @file_prefix = file_prefix ? file_prefix : File.basename(input_directory)
+    
+      introduction = "Begin processing #{File.join(@input_directory)}"; puts
+      puts "-" * introduction.size
+      puts introduction; puts
+    
+      begin check_setup unless @config[:dry_run]
+      rescue IOError => e
+        puts "Error: #{e}"
+        exit
+      end
+    
+      # Construct the Script, output it and run it.
+      batch_cmd = construct_commands(@working_input_directory, @output_directory, @file_prefix)
+
+      batch_cmd.each do |cmd|
+        puts cmd; $LOG.info cmd
+        puts `#{cmd}` unless @config[:dry_run]
+        puts
+      end
+    
+      cleanup unless @config[:dry_run]
+    
+      puts "Done processing #{@file_prefix}" unless @config[:dry_run]
+    
+    end
+  
+  
+    # Constructs the commands used in the script from constants and variables
+    # set during intialization/configuration and gathered by the main
+    # reconstruct! function.
+    def construct_commands(input_directory, output_directory, file_prefix)
+      rep_time = @config[:repetition_time] ? @config[:repetition_time] : 8000
+      to3d_recon_options = "-time:zt #{@config[:slices_per_volume]} #{@config[:volumes]} #{rep_time} #{@config[:slice_order]} #{input_directory}/#{@config[:file_glob]}"
+    
+      commands = Array.new
+    
+      # Recon
+      commands << "to3d -prefix #{file_prefix}.nii -session #{output_directory} #{to3d_recon_options}"
+    
+      # Eddy Current Correction
+      commands << "eddy_correct #{output_directory}/#{file_prefix}.nii #{output_directory}/#{file_prefix}_ecc.nii 0"
+    
+      if @config[:rotate]
+        # Rotate_bvecs
+        subject_bvectors_file = File.join(output_directory, file_prefix + "_" + File.basename(@config[:bvectors_file]))
+        commands << "rotbvecs #{@config[:bvectors_file]} #{subject_bvectors_file} #{File.join(output_directory, file_prefix)}_ecc.ecclog"
+      else
+        subject_bvectors_file = @config[:bvectors_file]
+      end
+    
+    
+      # Apply Mask
+      if @config[:mask]
+        out = "#{File.join(output_directory, file_prefix)}_ecc_ss"
+        commands << "fslmaths #{@config[:mask]} -mul #{File.join(output_directory, file_prefix)}_ecc #{out}"
+      else
+        out = "#{File.join(output_directory, file_prefix)}_ecc"
+      end
+      commands << "bet #{out} #{out}_brain -f 0.1 -g 0 -n -m"
+    
+      # Run DTI Fit
+      commands << "dtifit --data=#{output_directory}/#{file_prefix}_ecc.nii \
+        --out=#{output_directory}/#{file_prefix}_dti \
+        --mask=#{out}_brain_mask \
+        --bvecs=#{subject_bvectors_file} \
+        --bvals=#{@config[:bvalues_file]}"
+
+      return commands
+    end
+  
+  end
+
+  # Message for when excuting from the command line.
+  if __FILE__ == $0
+    puts "Script generation library for DTI processing.  To use this with the command-line, use preprocess_dti.rb"
+  end
+
+end