wadrc-bcp-scripts 0.0.6

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

@@ -0,0 +1,166 @@
+require 'find'
+require 'tmpdir'
+require 'fileutils'
+require 'rubygems'
+require 'metamri'
+
+module Find
+  def match(path)
+    matched = []
+    find(path) do |p|
+      if yield p
+        if File.file?(p) && File.readable?(path): matched << p; end
+      end  
+    end    
+    return matched
+  end
+  module_function :match
+end
+
+module WadrcBcpScripts
+
+# This library contains tasks for creating Fieldmaps at a remote server
+class FieldmapTask
+  DWELL_TIME = 0.688
+  attr_accessor :log
+  attr_accessor :incoming_tar_file
+
+  def initialize(incoming_tar_file)
+    @log = Logger.new(STDOUT)
+    @log.level = Logger::DEBUG
+    @log.datetime_format = "%Y-%m-%d %H:%M:%S"
+    @incoming_tar_file = incoming_tar_file
+  end
+    
+  def setup_paths
+    @log.debug { %x[set_default_paths.sh] }
+  end
+  
+  def unpack(incoming_tar_file)
+    unpacked_directory = unzip_incoming_tar_file(incoming_tar_file)
+    @log.debug { "Unpacked Directory: #{unpacked_directory}"}
+    fieldmap_directory = File.join(unpacked_directory, 'fieldmap')
+    files_to_fieldmap = Find.match(unpacked_directory) { |f| File.extname(f) == '.nii' }
+    @log.debug {"Files to be fieldmapped: #{files_to_fieldmap.each { |file| File.basename(file) } } " }
+
+    return unpacked_directory, fieldmap_directory, files_to_fieldmap
+  end
+  
+  def unzip_incoming_tar_file(incoming_tar_file, output_directory = nil)
+    unless output_directory
+      # Unless your ruby version is greater than 1.8.7
+      # output_directory = Dir.mktmpdir
+      output_directory = File.join(Dir.tmpdir, File.basename(@incoming_tar_file, '.tar.gz'))
+      Dir.mkdir(output_directory) unless File.exists?(output_directory)
+    end
+    msg = %x[tar --directory #{output_directory} -xzvf #{incoming_tar_file} ]
+    
+    return output_directory
+  end
+
+  def create_fieldmap(fieldmap_directory, output_file = nil)
+    fieldmap_file = output_file ? output_file : 'fmap.nii'
+    make_fmap_cmd = "make_fmap #{fieldmap_directory} #{fieldmap_file}"
+    @log.info make_fmap_cmd
+    system(make_fmap_cmd)
+    #@log.info { %x["#{make_fmap_cmd}"] }
+    return fieldmap_file
+  end
+
+  def apply_fieldmap(fieldmap_file, files_to_fieldmap, output_directory = nil)
+    unless output_directory then output_directory = Dir.pwd; end
+    p files_to_fieldmap
+    fieldmap_correction_cmd = "fieldmap_correction #{fieldmap_file} #{DWELL_TIME} #{output_directory} #{ files_to_fieldmap.join(" ") }"
+    @log.info { fieldmap_correction_cmd }
+    @log.info { %x[#{fieldmap_correction_cmd}] }
+
+=begin    
+    # Pretend fieldmapping works!
+    files_to_fieldmap.each do |f| 
+      fieldmapped_filename = File.join(File.dirname(f), File.basename(f, '.nii') + '_fm.nii')
+      FileUtils.copy(f, fieldmapped_filename) 
+      p fieldmapped_filename
+    end
+=end
+  end
+
+  def zip_up_fieldmapped_files(output_name, fieldmapped_files)
+    tar_and_zip_cmd = "tar -czvf #{output_name} #{fieldmapped_files.join(" ")}"
+    @log.info {tar_and_zip_cmd}
+  end
+  
+  def cleanup(tmpdir)
+
+    output_name='fieldmapped_files.tar.gz'
+    
+    fieldmapped_files = Find.match(tmpdir) { |f| File.fnmatch('*_fm*', f ) }
+    p fieldmapped_files
+    zip_up_fieldmapped_files(output_name, fieldmapped_files)
+    
+    @log.close
+
+  end
+  
+  
+end
+
+class LocalFieldmapSetup
+  attr_accessor :prefix
+  attr_accessor :files_to_fieldmap_directory
+  attr_accessor :dicoms_directory
+  
+  REMOTE_SCRATCH_DIR = '/scratch/johnson_fieldmaps'
+  REMOTE_USER = 'johnson'
+  REMOTE_HOST = 'tezpur'
+  REMOTE_PROCESSING_HOST = 'jaloro'
+  
+  def initialize(prefix, files_to_fieldmap_directory, dicoms_directory)
+    @prefix = prefix
+    @files_to_fieldmap_directory = files_to_fieldmap_directory
+    @dicoms_directory = dicoms_directory
+  end
+  
+  def find_fieldmap_directory(dicoms_directory)
+    visit = VisitRawDataDirectory.new(dicoms_directory)
+    visit.scan
+    visit.datasets.each do |ds|
+      if ds.series_description =~ /.*F Map.*/ then
+        fieldmap_directory = ds.directory
+      end
+    end
+    
+    return fieldmap_directory
+  end
+  
+  def find_files_to_fieldmap(files_to_fieldmap_directory)
+    files_to_fieldmap = Find.match(files_to_fieldmap_directory) { |p| File.fnmatch('r*', p) }
+    return files_to_fieldmap
+  end
+  
+  def create_tarfile(prefix, files_to_fieldmap, fieldmap_directory)
+    local_tarfile = "#{prefix}.tar.gz"
+    system("tar -czvf #{local_tarfile} #{fieldmap_directory} #{files_to_fieldmap.join(" ")}")
+    return local_tarfile
+  end
+
+  def transfer_tarfile_to_move(local_tarfile)
+    remote_tarfile = REMOTE_SCRATCH_DIR + File.basename(tarfile)
+    system("scp #{REMOTE_USER}@#{REMOTE_HOST}:#{remote_tarfile}")
+    return remote_tarfile
+  end
+  
+  def execute_remote_fieldmapping(remote_tarfile)
+    system("ssh johnson@${REMOTE_PROCESSING_HOST} ~/bin/createFieldmap.rb #{remote_tarfile}")
+  end
+  
+  def transfer_tarfile_from_remote
+    system("scp #{REMOTE_USER}@#{REMOTE_HOST}:#{remote_tarfile} .")
+  end
+
+  def unpack_tarfile_locally
+    system("tar -xzvf #{local_tarfile}")
+  end
+  
+end
+
+end

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

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+module WadrcBcpScripts
+  # We want to sample to ASL perfusion data (PET data, or other data) from ROIs,
+  # determined in subject space by running a high-resolution T1 through
+  # Freesurfer. As part of it's recon-all, freesurfer outputs segmentation images
+  # (volume parcellation) that include ~ 100 ROIs for cortical gm, wm and
+  # sub-cortical structures. All we need to do is get that segmentation into a
+  # common space with the image of interest, and then we can sample it to get
+  # meaningful estimates of the data.
+  # 
+  # The Process:
+  # 1) Do Basic Reconstruction for Anatomical Images
+  # 2) Run a high resolution T1 through Freesurfer
+  # 3) Convert the aparc.a2009s+aseg.mgz back to NIfTI in T1 space for sampling.
+  # 4) Rigidly register & reslice Target modality to T1 space 
+  # 5) Sample mean and measures of interest
+  class FreesurferRoiTask < BasicTask
+
+    def initialize(raw_directory, output_directory, config)
+      @config = config
+      @raw_directory = raw_directory
+      @output_directory = output_directory
+      @commands = ShellQueue.new(:dry_run => true)
+    end
+
+    # Do Basic Reconstruction for Anatomical Images
+    def basic_anatomical_reconstruction
+
+      # Create the T1 & other Anatomicals
+      @commands << "convert_visit.rb #{@raw_directory} #{@config[:subj_processed_dir]}"
+
+      # Create the ASL
+      modality_dir = File.join(@config[:subj_processed_dir], @config[:modality])
+      Dir.mkdir_p modality_dir unless File.exists? modality_dir 
+      Dir.chdir modality_dir do
+        # fmap_make /Data/vtrak1/raw/dempsey.plaque.visit1/plq20005_1959_04072011/009
+        #(Or, to search automatically: )
+        @commands << "fmap_make `list_visit #{@raw_directory} -g #{@config[:modality]}`"
+
+        # Link the T1 into the ASL directory for easy visualization if you want.
+
+        # File.symlink("../unknown/plq02002_Ax-FSPGR-BRAVO_003.nii", "plq02002_Ax-FSPGR-BRAVO_003.nii")
+      end
+    end
+
+    # Run a high resolution T1 through Freesurfer
+    def run_t1_through_freesurfer
+      ENV[:SUBJECTS_DIR] = @proc_options[:freesurfer_subjects_dir]
+
+      system("recon-all -all -s #{OPTIONS[:subid]} -i #{File.join(OPTIONS[:subj_raw_dir], OPTIONS[:subid], "003/I0001.dcm")}")
+
+      # This will run for 20 hours, and return a pretty subject directory. See below
+      # for a sample manifest.
+    end
+
+    # Convert the aparc.a2009s+aseg.mgz back to NIfTI in T1 space for sampling.
+    def prepare_segmentation
+      aparc_base = "aparc.a2009s+aseg"
+      freesurfer_subj_mri_dir = File.join(OPTIONS[:freesurfer_subjects_dir], OPTIONS[:subid], "mri")
+
+      Dir.chdir modality_dir do 
+        system("mri_convert #{File.join(freesurfer_subj_mri_dir, aparc_base)}.mgz #{apar_base}.nii")
+
+        # Resample the Segementation image to the T1 space (using nearest neighbor so as
+        # to not change any values):
+        system("
+          flirt -in aparc.a2009s+aseg.nii -ref plq20005_Ax-FSPGR-BRAVO_003.nii \
+          -out raparc.a2009s+aseg.nii -applyxfm -init $FSLDIR/etc/flirtsch/ident.mat \
+          -interp nearestneighbour"
+        )
+      end
+
+      # You could resample with SPM as well (Coregister - Write) but this is a nice
+      # command line option. For the actual registration, we are using SPM because
+      # it's a somewhat better (qualitatively) algorithm.
+    end
+
+    # Rigidly register & reslice Target modality to T1 space 
+    def register_modality_to_t1
+      # For ASL, we ill use the PD image because it's information is closer to
+      # anatomical than the computed flow maps, bringing along the flow maps. 
+
+      # system("spm8")
+      # Click Coregister - Estimate and Reslice
+      # Reference Image: Select the BRAVO
+      # Source Image: Select the PD Map
+      # Other Images: Select the ASL Map
+      # Use other defaults (NMI, etc.) 
+    end
+
+    # Sample mean and measures of interest
+    def sample_roi
+      system("3dROIstats -mask_f2short -mask raparc.a2009s+aseg.nii plq20005_Ax-FSPGR-BRAVO_003.nii rASL_plq20005_fmap.nii > stats.txt")
+    end
+    
+    
+  end
+  
+  # Heroes in a half shell - Turtle Power!
+  # 
+  # Manage a list of shell commands.
+  # q = ShellQueue.new(:dry_run => true)
+  # q << "ls"
+  # q << "time"
+  # q.run!
+  class ShellQueue
+    attr_reader :dry_run, :commands, :completed_commands, :failed_commands
+    
+    # Initialize a queue with an options hash.
+    def initialize(options = {:dry_run => false})
+      @commands = Array.new
+      @dry_run = options[:dry_run]
+    end
+    
+    # Run a queue (or print if dry_run)
+    def run!
+      while @commands.length > 0
+        command = @commands.shift
+        puts command
+        @run_success = run command unless @dry_run
+      end      
+    end
+    
+    def <<(cmd)
+      @commands << cmd
+      run!
+    end
+    
+    # Expose >>, << array methods to commands array.
+    def method_missing(m, *args, &block)
+      @commands.send(m, *args, &block)
+    end
+
+  end
+end

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

@@ -0,0 +1,25 @@
+module WadrcBcpScripts
+
+# A class for manipulating Tensor info for DTI.
+class Tensor
+  attr_accessor :data
+  
+  def initialize(filepath)
+    @data = []
+    open(filepath, 'r').each do |line|
+      @data << line.split(/[\,\:\s]+/).each { |val| val.strip }
+    end
+  end
+  
+  # Write out Data to a file.
+  def to_fsl_txt(output_file = 'out.txt')
+    puts "Writing " + output_file
+    open(output_file, 'w') do |file|
+      @data.transpose.each do |line|
+        file.puts line.join(' ')
+      end
+    end
+  end
+end
+
+end

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

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+module WadrcBcpScripts;   
+  VERSION = '0.0.6'
+end

data/spec/.svn/entries

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+8
+
+dir
+146
+file:///Data/vtrak1/SysAdmin/lab_repository/trunk/ImageProcessing/spec
+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
+

data/spec/.svn/format

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

data/spec/FS_local_recon_spec.rb

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+$:.unshift File.join(File.dirname(__FILE__),'..','bin')
+
+require 'helper_spec'
+load 'FS_local_recon'
+
+describe "Perform local recon" do  
+  
+  # before(:all) do
+  #   @normalizer = Normalizer.new('/tmp/awr011_8414_06182009')
+  # end
+
+  it "should run local recon on a subject" do
+    hostname = 'localhost'
+    subject = "tami99999"
+    options = {:server_analysis_dir => $MRI_DATA, :autorecon_args => ['-autorecon2-wm', '-autorecon3']}
+    lambda { run!(hostname, subject, options) }.should_not raise_error
+  end
+  
+  # after(:each) do
+  # end
+  
+end

data/spec/blueprints.rb

@@ -0,0 +1,12 @@
+require 'machinist/object'
+
+Dtitask.blueprint do
+  config({
+    :bvectors_file=>"/Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvectors.txt",
+    :bvectors_file=>"/Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvectors.txt", 
+    :bvalues_file=>"/Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvalues.txt", 
+    :file_glob=>"'*.dcm'", 
+    :volumes=>26, 
+    :dry_run=>true, 
+    :slices_per_volume=>48 })
+end

data/spec/dtitask_spec.rb

@@ -0,0 +1,95 @@
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'helper_spec'
+require 'wadrc-bcp-scripts/basic_task'
+require 'wadrc-bcp-scripts/dtitask'
+
+describe "Exception Testing for DtiTask" do
+  before(:all) do
+    $LOG = Logger.new(STDOUT)
+  end
+  
+  before(:each) do
+    # @valid_config = {
+    #   :slice_order=>"altplus", 
+    #   :bvectors_file=>"/Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvectors.txt", 
+    #   :bvalues_file=>"/Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvalues.txt", 
+    #   :file_glob=>"'*.dcm'", 
+    #   :force_overwrite=>true, 
+    #   :volumes=>26, 
+    #   :dry_run=>true, 
+    #   :slices_per_volume=>48
+    # }
+    
+    @valid_config = {
+        :slice_order=>"altplus", 
+        :bvectors_file=>"/Data/vtrak1/preprocessed/visits/johnson.alz.snodrest.visit2/DTI_info/preproc_dti/enc12_rows.txt", 
+        :bvalues_file=>"/Data/vtrak1/preprocessed/visits/johnson.alz.snodrest.visit2/DTI_info/preproc_dti/bvalues.txt", 
+        :file_glob=>"'I*'", 
+        :force_overwrite=>true, 
+        :volumes=>13, 
+        :dry_run=>true, 
+        :slices_per_volume=>39,
+        :rotate=>true
+    }
+    @valid_dtitask = WadrcBcpScripts::Dtitask.new(@valid_config)
+    
+    @subid = 'alz021_2'
+    @valid_input_directory = File.join($MRI_DATA, @subid, 'anatomicals', 'S9')
+  end
+
+  it "should raise an IOError if tensor_files do not exist." do
+    File.stub!(:exists?).and_return(false)
+    lambda { @valid_dtitask.ensure_file_exists(@valid_config[:bvectors_file])}.should raise_error(IOError, "#{@valid_config[:bvectors_file]} not found.")
+  end
+  
+  it "should not raise an IOError if tensor_files do exist." do
+    File.stub!(:exists?).and_return(true)
+    lambda { @valid_dtitask.ensure_file_exists(@valid_config[:bvectors_file])}.should_not raise_error(IOError, "#{@valid_config[:bvectors_file]} not found.")
+  end
+  
+  it "should raise an error if required keys are not in config file." do
+    missing_key = :bvectors_file
+    invalid_config = @valid_config
+    invalid_config.delete(missing_key)
+    lambda { WadrcBcpScripts::Dtitask.new(invalid_config).config_requires(missing_key) }.should raise_error(ScriptError, "Missing Keys: #{missing_key}")
+  end
+  
+  it "should create a valid command array when given correct configuration using rotbvecs" do
+    dir = Dir.tmpdir
+    valid_command = [
+      "to3d -prefix #{@subid}.nii -session #{dir} -time:zt #{@valid_config[:slices_per_volume]} #{@valid_config[:volumes]} 8000 altplus #{@valid_input_directory}/#{@valid_config[:file_glob]}", 
+      "eddy_correct #{dir}/#{@subid}.nii #{dir}/#{@subid}_ecc.nii 0", 
+      "rotbvecs #{@valid_config[:bvectors_file]} #{dir}/#{@subid}_#{File.basename(@valid_config[:bvectors_file])} #{dir}/#{@subid}_ecc.ecclog", 
+      "bet #{dir}/#{@subid}_ecc #{dir}/#{@subid}_ecc_brain -f 0.1 -g 0 -n -m", 
+      "dtifit --data=#{dir}/#{@subid}_ecc.nii --out=#{dir}/#{@subid}_dti --mask=#{dir}/#{@subid}_ecc_brain_mask --bvecs=#{dir}/#{@subid}_#{File.basename(@valid_config[:bvectors_file])} --bvals=#{@valid_config[:bvalues_file]}"
+    ]
+    cmd = @valid_dtitask.construct_commands(@valid_input_directory, dir, @subid).collect! {|cmd| cmd.squeeze(" ") }
+    cmd.should == valid_command
+  end
+  
+  it "should create a valid command array when given correct configuration NOT using rotbvecs" do
+    dir = Dir.tmpdir
+    config = @valid_config.dup
+    config[:rotate] = false
+    valid_command = [
+      "to3d -prefix #{@subid}.nii -session #{dir} -time:zt #{@valid_config[:slices_per_volume]} #{@valid_config[:volumes]} 8000 altplus #{@valid_input_directory}/#{@valid_config[:file_glob]}", 
+      "eddy_correct #{dir}/#{@subid}.nii #{dir}/#{@subid}_ecc.nii 0", 
+      "bet #{dir}/#{@subid}_ecc #{dir}/#{@subid}_ecc_brain -f 0.1 -g 0 -n -m", 
+      "dtifit --data=#{dir}/#{@subid}_ecc.nii --out=#{dir}/#{@subid}_dti --mask=#{dir}/#{@subid}_ecc_brain_mask --bvecs=#{@valid_config[:bvectors_file]} --bvals=#{@valid_config[:bvalues_file]}"
+    ]
+    cmd = WadrcBcpScripts::Dtitask.new(config).construct_commands(@valid_input_directory, dir, @subid).collect! {|cmd| cmd.squeeze(" ") }
+    cmd.should == valid_command
+  end
+  
+  it "should sucessfully run through fixture data for johnson.alz.visit2" do
+    Dir.mktmpdir do |dir|
+      cmd = @valid_dtitask.construct_commands(@valid_input_directory, dir, @subid).collect! {|cmd| cmd.squeeze(" ") }
+      puts cmd.join("; ")
+      system(cmd.join("; ")).should == true
+    end
+  end
+  
+  # after(:each) do
+  # end
+end