rpipe 0.0.1

data/rpipe.gemspec

@@ -0,0 +1,177 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{rpipe}
+  s.version = "0.0.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Kristopher Kosmatka", "Erik Kastman"]
+  s.date = %q{2010-07-15}
+  s.description = %q{Neuroimaging preprocessing the Ruby way}
+  s.email = %q{kjkosmatka@gmail.com}
+  s.executables = ["rpipe", "swallow_batch_run.rb", "create_driver.rb"]
+  s.extra_rdoc_files = [
+    "LICENSE",
+     "README",
+     "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+     ".gitignore",
+     "LICENSE",
+     "README",
+     "README.rdoc",
+     "Rakefile",
+     "VERSION",
+     "bin/create_driver.rb",
+     "bin/rpipe",
+     "bin/swallow_batch_run.rb",
+     "lib/core_additions.rb",
+     "lib/custom_methods/JohnsonMerit220Visit1Preproc.m",
+     "lib/custom_methods/JohnsonMerit220Visit1Preproc.rb",
+     "lib/custom_methods/JohnsonMerit220Visit1Preproc_job.m",
+     "lib/custom_methods/JohnsonMerit220Visit1Stats.m",
+     "lib/custom_methods/JohnsonMerit220Visit1Stats.rb",
+     "lib/custom_methods/JohnsonMerit220Visit1Stats_job.m",
+     "lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.m",
+     "lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.rb",
+     "lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc_job.m",
+     "lib/custom_methods/JohnsonTbiLongitudinalSnodStats.m",
+     "lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb",
+     "lib/custom_methods/JohnsonTbiLongitudinalSnodStats_job.m",
+     "lib/custom_methods/ReconWithHello.rb",
+     "lib/default_logger.rb",
+     "lib/default_methods/default_preproc.rb",
+     "lib/default_methods/default_recon.rb",
+     "lib/default_methods/default_stats.rb",
+     "lib/default_methods/recon/physionoise_helper.rb",
+     "lib/default_methods/recon/raw_sequence.rb",
+     "lib/generators/job_generator.rb",
+     "lib/generators/preproc_job_generator.rb",
+     "lib/generators/recon_job_generator.rb",
+     "lib/generators/stats_job_generator.rb",
+     "lib/generators/workflow_generator.rb",
+     "lib/global_additions.rb",
+     "lib/logfile.rb",
+     "lib/matlab_helpers/CreateFunctionalVolumeStruct.m",
+     "lib/matlab_helpers/import_csv.m",
+     "lib/matlab_helpers/matlab_queue.rb",
+     "lib/matlab_helpers/prepare_onsets_xls.m",
+     "lib/rpipe.rb",
+     "rpipe.gemspec",
+     "spec/generators/preproc_job_generator_spec.rb",
+     "spec/generators/recon_job_generator_spec.rb",
+     "spec/generators/stats_job_generator_spec.rb",
+     "spec/generators/workflow_generator_spec.rb",
+     "spec/helper_spec.rb",
+     "spec/integration/johnson.merit220.visit1_spec.rb",
+     "spec/integration/johnson.tbi.longitudinal.snod_spec.rb",
+     "spec/logfile_spec.rb",
+     "spec/matlab_queue_spec.rb",
+     "spec/merit220_stats_spec.rb",
+     "spec/physio_spec.rb",
+     "test/drivers/merit220_workflow_sample.yml",
+     "test/drivers/mrt00000.yml",
+     "test/drivers/mrt00015.yml",
+     "test/drivers/mrt00015_hello.yml",
+     "test/drivers/mrt00015_withphys.yml",
+     "test/drivers/tbi000.yml",
+     "test/drivers/tbi000_separatevisits.yml",
+     "test/drivers/tmp.yml",
+     "test/fixtures/faces3_recognitionA.mat",
+     "test/fixtures/faces3_recognitionA.txt",
+     "test/fixtures/faces3_recognitionA_equal.csv",
+     "test/fixtures/faces3_recognitionA_unequal.csv",
+     "test/fixtures/faces3_recognitionB_incmisses.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3R_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPttl_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3R_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTttl_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3R_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTttl_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RRT_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RVT_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_card_spline_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_resp_spline_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RRT_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RVT_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3R_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTttl_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RRT_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RVT_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_card_spline_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_resp_spline_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_card_spline_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_40.txt",
+     "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_downsampled_40.txt",
+     "test/fixtures/ruport_summary.yml",
+     "test/fixtures/valid_scans.yaml",
+     "test/helper.rb",
+     "test/test_dynamic_method_inclusion.rb",
+     "test/test_includes.rb",
+     "test/test_integrative_johnson.merit220.visit1.rb",
+     "test/test_preproc.rb",
+     "test/test_recon.rb",
+     "test/test_rpipe.rb",
+     "vendor/output_catcher.rb",
+     "vendor/trollop.rb"
+  ]
+  s.homepage = %q{http://github.com/brainmap/rpipe}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{Neuroimaging preprocessing the Ruby way}
+  s.test_files = [
+    "spec/generators/preproc_job_generator_spec.rb",
+     "spec/generators/stats_job_generator_spec.rb",
+     "spec/generators/recon_job_generator_spec.rb",
+     "spec/generators/workflow_generator_spec.rb",
+     "spec/matlab_queue_spec.rb",
+     "spec/logfile_spec.rb",
+     "spec/physio_spec.rb",
+     "spec/integration/johnson.merit220.visit1_spec.rb",
+     "spec/integration/johnson.tbi.longitudinal.snod_spec.rb",
+     "spec/merit220_stats_spec.rb",
+     "spec/helper_spec.rb",
+     "test/helper.rb",
+     "test/test_dynamic_method_inclusion.rb",
+     "test/test_includes.rb",
+     "test/test_integrative_johnson.merit220.visit1.rb",
+     "test/test_preproc.rb",
+     "test/test_recon.rb",
+     "test/test_rpipe.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+      s.add_runtime_dependency(%q<metamri>, [">= 0"])
+      s.add_runtime_dependency(%q<log4r>, [">= 0"])
+      s.add_runtime_dependency(%q<POpen4>, [">= 0"])
+      s.add_runtime_dependency(%q<ruport>, [">= 0"])
+    else
+      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+      s.add_dependency(%q<metamri>, [">= 0"])
+      s.add_dependency(%q<log4r>, [">= 0"])
+      s.add_dependency(%q<POpen4>, [">= 0"])
+      s.add_dependency(%q<ruport>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+    s.add_dependency(%q<metamri>, [">= 0"])
+    s.add_dependency(%q<log4r>, [">= 0"])
+    s.add_dependency(%q<POpen4>, [">= 0"])
+    s.add_dependency(%q<ruport>, [">= 0"])
+  end
+end
+

data/spec/generators/preproc_job_generator_spec.rb

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+require 'helper_spec'
+require 'generators/preproc_job_generator'
+
+describe "PreprocJobGenerator creates a Preproc Job Driver Spec" do
+	before(:all) do
+    @scans = YAML.load_file(File.join(File.dirname(__FILE__), '..', 'fixtures', 'valid_scans.yaml'))
+    @valid_preproc_job_spec = {"step"=>"preprocess", "bold_reps"=>[164, 164, 164]}
+  end
+  
+  it "should create a valid job spec with no custom method" do
+    preproc_job_spec = PreprocJobGenerator.new({'scans' => @scans}).build
+    preproc_job_spec.should == @valid_preproc_job_spec
+  end
+  
+  it "should create a valid job spec with a custom method defined" do
+    valid_preproc_job_spec = @valid_preproc_job_spec.dup
+    valid_preproc_job_spec['method'] = 'Merit220Preprocess'
+    preproc_job_spec = PreprocJobGenerator.new({'method' => 'Merit220Preprocess', 'scans' => @scans}).build
+    preproc_job_spec.should == valid_preproc_job_spec
+  end
+  
+    
+  it "should raise a DriverConfigError if scans are not specified." do
+    lambda { PreprocJobGenerator.new({}).build }.should raise_error DriverConfigError
+  end
+    
+end

data/spec/generators/recon_job_generator_spec.rb

@@ -0,0 +1,33 @@
+require 'helper_spec'
+require 'generators/recon_job_generator'
+
+describe "Recon Job Generator creates a Recon Job Driver Spec" do
+	before(:all) do
+    @rawdir = File.join($MRI_DATA, 'johnson.merit220.visit1', 'mrt00000', 'dicoms')
+    @scans = YAML.load_file(File.join(File.dirname(__FILE__), '..', 'fixtures', 'valid_scans.yaml'))
+    
+    @valid_recon_job_spec = {
+      "step"=>"reconstruct",
+      "scans"=> @scans
+    }
+  end
+  
+  it "should create a valid job spec" do
+    recon_job_spec = ReconJobGenerator.new({'rawdir' => @rawdir}).build
+    recon_job_spec.should == @valid_recon_job_spec
+  end
+  
+  it "should raise an IOError if the raw dir isn't found." do
+    lambda { ReconJobGenerator.new({'rawdir' => '/bad/path/to/raw/dir'}).build }.should raise_error IOError
+  end
+  
+  it "should raise a DriverConfigError if the raw dir isn't specified." do
+    lambda { ReconJobGenerator.new({}).build }.should raise_error DriverConfigError
+  end
+  
+  after(:all) do
+    # FileUtils.rm_r([@valid_workflow_spec['origdir'], @valid_workflow_spec['procdir'], @valid_workflow_spec['statsdir']])
+  end
+  
+  
+end

data/spec/generators/stats_job_generator_spec.rb

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+require 'helper_spec'
+require 'generators/stats_job_generator'
+
+describe "StatsJobGenerator creates a Stats Job Driver Spec" do
+	before(:all) do
+    @subid = 'mrt00000'
+    @scans = YAML.load_file(File.join(File.dirname(__FILE__), '..', 'fixtures', 'valid_scans.yaml'))
+    rootdir = Pathname.new(File.join(File.dirname(__FILE__), '..', '..')).realpath.to_s
+    @valid_stats_job_spec = {
+      "step"=>"stats",
+      "responses"=> {
+        "logfiles" => ["mrt00000_abc_01012010_faces3_recognitionB.txt", "mrt00000_abc_01012010_faces3_recognitionA.txt"],
+        "directory"=> File.join($MRI_DATA, 'responses')
+      },
+      "conditions"=> ["new_correct", "new_incorrect", "old_correct", "old_incorrect"],
+      "regressorsfiles"=> ["rp_amrt00000_EPI-fMRI-Task1.txt", "rp_amrt00000_EPI-fMRI-Task2.txt"],
+      "bold_reps"=>[164, 164]
+    }
+    
+    @valid_options = {
+      'conditions' => ['new_correct', 'new_incorrect', 'old_correct', 'old_incorrect'],
+      'subid' => @subid,
+      'responses_dir' => File.join($MRI_DATA, 'responses'),
+      'scans' => @scans
+    }
+  end
+  
+  it "should create a valid job spec with no custom method" do
+    stats_job_spec = StatsJobGenerator.new(@valid_options).build
+    stats_job_spec.should == @valid_stats_job_spec
+  end
+  
+  it "should create a valid job spec with a custom method defined" do
+    valid_stats_job_spec = @valid_stats_job_spec.dup
+    valid_stats_job_spec['method'] = 'Merit220Preprocess'
+    stats_job_spec = StatsJobGenerator.new(@valid_options.merge({'method' => 'Merit220Preprocess'})).build
+    stats_job_spec.should == valid_stats_job_spec
+  end
+  
+    
+  it "should raise a DriverConfigError if required keys are not specified." do
+    missing_options = ['subid', 'scans', 'conditions'].collect do |key|
+      @valid_options.dup.reject {|k,v| key == k }
+    end
+    missing_options.each do |options|
+      lambda { StatsJobGenerator.new(options).build }.should raise_error DriverConfigError
+    end
+  end
+    
+end

data/spec/generators/workflow_generator_spec.rb

@@ -0,0 +1,97 @@
+require 'helper_spec'
+require 'generators/workflow_generator'
+
+describe "Workflow Generator" do
+	before(:each) do
+	  @fixtures_dir = File.join File.dirname(__FILE__), '..', 'fixtures'
+	  @drivers_dir  = File.join File.dirname(__FILE__), '..', 'drivers'
+    @workflow_driver = YAML.load_file(File.join @drivers_dir, 'merit220_workflow_sample.yml')
+    @rawdir = File.join $MRI_DATA, 'johnson.merit220.visit1', 'mrt00000', 'dicoms'
+    @scans = YAML.load_file(File.join @fixtures_dir, 'valid_scans.yaml')
+    rootdir = Pathname.new(File.join(File.dirname(__FILE__), '..', '..')).realpath.to_s
+    @valid_recon_job_spec = {"step"=>"reconstruct", "scans"=> @scans}
+    @valid_preproc_job_spec = {"step"=>"preprocess", "bold_reps"=>[164, 164, 164], "method" => "JohnsonMerit220Visit1Preproc"}
+    @valid_stats_job_spec = {
+      "step"=>"stats",
+      "responses"=> {
+        "logfiles" => ["mrt00000_abc_01012010_faces3_recognitionB.txt", "mrt00000_abc_01012010_faces3_recognitionA.txt"],
+        "directory"=> File.join($MRI_DATA, 'responses')
+      },
+      "conditions"=> ["new_correct", "new_incorrect", "old_correct", "old_incorrect"],
+      "regressorsfiles"=> ["rp_amrt00000_EPI-fMRI-Task1.txt", "rp_amrt00000_EPI-fMRI-Task2.txt"],
+      "bold_reps"=>[164, 164],
+      "method" => "Merit220Stats"
+    }
+    
+    
+    @valid_job_params = [@valid_recon_job_spec, @valid_preproc_job_spec, @valid_stats_job_spec]	  
+	  
+	  @origdir  = Dir.mktmpdir('orig_')
+	  @procdir  = Dir.mktmpdir('proc_')
+	  @statsdir = Dir.mktmpdir('stats_')
+	  
+	  @valid_workflow_spec = {
+      "study_procedure" => "johnson.merit220.visit1",
+      "subid"     => "mrt00000",
+      "rawdir"    => @rawdir,
+      "origdir"   => @origdir,
+	    "procdir"   => @procdir,
+	    "statsdir"  => @statsdir,
+      "collision" => "destroy",
+      "jobs"      => @valid_job_params
+    }
+	  
+	  @valid_workflow_options = {
+	    'responses_dir' => File.join($MRI_DATA, 'responses')
+	  }.merge @workflow_driver
+    # @valid_pipe = RPipe.new(@valid_workflow_spec)
+    
+    @valid_directory_format = "/Data/vtrak1/preprocessed/visits/johnson.merit220.visit1/<subid>/fmri/orig"
+    @valid_multiple_substitution_directory_format = "/Data/vtrak1/preprocessed/visits/<study_procedure>/<subid>/fmri/orig"
+  end
+  
+  it "should be valid when assigned known directories without study procedure." do
+    options = @valid_workflow_options.merge(
+    {'origdir' => @origdir, 'procdir' => @procdir, 'statsdir' => @statsdir})
+    options.delete('study_procedure')
+    options
+      
+    pp workflow = WorkflowGenerator.new(@rawdir, options).build
+    workflow.should == @valid_workflow_spec
+  end
+  
+  it "should parse directory format with one substitution" do
+    workflow = WorkflowGenerator.new(@rawdir, @valid_workflow_options)
+    dir = workflow.parse_directory_format(@valid_directory_format)
+    dir.should == "/Data/vtrak1/preprocessed/visits/johnson.merit220.visit1/#{@valid_workflow_spec['subid']}/fmri/orig"
+  end
+  
+  it "should parse directory format with multiple substitutions" do
+    workflow = WorkflowGenerator.new(@rawdir, @valid_workflow_options)
+    dir = workflow.parse_directory_format(@valid_multiple_substitution_directory_format)
+    dir.should == "/Data/vtrak1/preprocessed/visits/#{@valid_workflow_spec['study_procedure']}/#{@valid_workflow_spec['subid']}/fmri/orig"    
+  end
+  
+  it "should parse directory format when directories are not explicitly given" do
+    pp options = @valid_workflow_options.dup.delete_if{|key, val| %w{origdir procdir statsdir}.include? key }
+    workflow = WorkflowGenerator.new(@rawdir, options)
+    dir = workflow.parse_directory_format(@valid_directory_format)
+    dir.should == "/Data/vtrak1/preprocessed/visits/#{@valid_workflow_spec['study_procedure']}/#{@valid_workflow_spec['subid']}/fmri/orig"    
+  end
+  
+  it "should guess a properly formed study procedure directory" do
+    workflow = WorkflowGenerator.new(@rawdir, @valid_workflow_options)
+    workflow.guess_study_procedure_from(@rawdir).should == 'johnson.merit220.visit1'
+  end
+  
+  it "should raise a ScriptError if study procedure directory cannot be guessed" do
+    workflow = WorkflowGenerator.new(@rawdir, @valid_workflow_options)
+    lambda {workflow.guess_study_procedure_from('/bad/study/directory')}.should raise_error ScriptError, /Could not guess/
+  end
+  
+  after(:each) do
+    FileUtils.rm_r([@valid_workflow_spec['origdir'], @valid_workflow_spec['procdir'], @valid_workflow_spec['statsdir']])
+  end
+  
+  
+end

data/spec/helper_spec.rb

@@ -0,0 +1,40 @@
+begin
+  require 'spec'
+rescue LoadError
+  require 'rubygems' unless ENV['NO_RUBYGEMS']
+  gem 'rspec'
+  require 'spec'
+end
+
+require 'tmpdir'
+require 'fileutils'
+require 'yaml'
+require 'pp'
+require 'rubygems'
+
+require 'global_additions'
+require 'core_additions'
+
+$MRI_DATA = ENV['MRI_DATA'] || '/Data/vtrak1/raw/test/fixtures/rpipe'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__)))
+$LOAD_PATH.unshift(File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib', 'custom_methods')))
+$LOAD_PATH.unshift(File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib', 'matlab_helpers')))
+
+
+
+#### Add Directory Comparisons to Dir ####
+class Dir
+  def self.compare_directories(dir1, dir2)
+    d1 = Dir.entries(dir1).sort
+    d2 = Dir.entries(dir2).sort
+
+    d1.should == d2
+    d1.each_with_index do |entry, i|
+      next if entry.to_s =~ /\.*/ 
+      File.compare(entry, d2[i]).should be_true
+    end
+
+  end
+end

data/spec/integration/johnson.merit220.visit1_spec.rb

@@ -0,0 +1,47 @@
+require 'helper_spec'
+require 'rpipe'
+
+describe "Integration Processing for Johnson.Merit220" do
+  before(:all) do
+    @driver_file = File.join(File.dirname(__FILE__), '..', 'drivers', 'mrt00000.yml')
+    @driver = YAML.load_file(@driver_file)	  
+    @driver['rawdir']   = File.join($MRI_DATA, 'johnson.merit220.visit1', 'mrt00000', 'dicoms')
+    @driver['origdir']  = Dir.mktmpdir('orig_')
+    @driver['procdir']  = Dir.mktmpdir('proc_')
+    @driver['statsdir'] = Dir.mktmpdir('stats_')
+    @driver['jobs'][2]['responses']['directory'] = File.join($MRI_DATA, 'responses')
+    @valid_responses_options = @driver['jobs'][2]['responses']
+    @pipe = RPipe.new(@driver)
+    @job = @pipe.stats_jobs.first
+    
+    @completed_orig_directory = File.join($MRI_DATA, 'integration', 'mrt00000_orig')
+    @completed_proc_directory = File.join($MRI_DATA, 'integration', 'mrt00000_proc')
+    @completed_stats_directory = File.join($MRI_DATA, 'integration', 'mrt00000_stats')
+    
+  end
+  
+  it "should reconstruct raw data" do
+    pipe = RPipe.new(@driver)
+    p = pipe.recon_jobs.first
+    p.perform
+    @origdir = @driver['origdir'] if Dir.compare_directories(@driver['origdir'], @completed_orig_directory)
+  end
+   
+  it "should preprocess raw data" do
+    @driver['origdir']  = @origdir || Pathname.new(@completed_orig_directory).recursive_local_copy
+    pipe = RPipe.new(@driver)
+    p = pipe.preproc_jobs.first
+    p.perform
+    @procdir = @driver['procdir'] if Dir.compare_directories(@driver['procdir'], @completed_proc_directory)
+  end
+  
+  it "should run stats on processed data" do
+    @driver['procdir'] = @procdir || @completed_proc_directory
+    pipe = RPipe.new(@driver)
+    s = pipe.stats_jobs.first
+    s.perform
+    @statsdir = @driver['statsdir'] if Dir.compare_directories(@driver['statsdir'], @completed_stats_directory)
+  end
+
+end
+

data/spec/integration/johnson.tbi.longitudinal.snod_spec.rb

@@ -0,0 +1,48 @@
+require 'helper_spec'
+require 'rpipe'
+
+describe "Integration Processing for Johnson.Tbi.Longitudinal.Snod" do
+  before(:all) do
+    @driver_file = File.join(File.dirname(__FILE__), '..', 'drivers', 'tbi000.yml')
+
+    @pipe = RPipe.new(@driver_file)
+    @driver = @pipe.workflow_spec
+    
+    @completed_orig_directory = File.join($MRI_DATA, 'integration', 'tbi000_orig')
+    @completed_proc_directory = File.join($MRI_DATA, 'integration', 'tbi000_proc')
+    @completed_stats_directory = File.join($MRI_DATA, 'integration', 'tbi000_stats')
+    
+  end
+  
+  it "should reconstruct raw data" do
+    pipe = RPipe.new(@driver)
+
+    # pipe.recon_jobs.first.perform
+    pipe.recon_jobs.each do |recon_job|
+      recon_job.perform
+    end
+    
+    # Use instance variables to pass on local directories to subsequent tests if this one was successful.
+    @origdir = @driver['origdir'] if Dir.compare_directories(@driver['origdir'], @completed_orig_directory)
+  end
+   
+  it "should preprocess reconstructed data" do
+    # Realignment alters the headers of images during Estimate, so you must
+    # use a local copy that hasn't been run before for correct results.
+    @driver['origdir']  = @origdir || Pathname.new(@completed_orig_directory).recursive_local_copy
+    pipe = RPipe.new(@driver)
+    p = pipe.preproc_jobs.first
+    p.perform
+    @procdir = @driver['procdir'] if Dir.compare_directories(@driver['procdir'], @completed_proc_directory)    
+  end
+  
+  it "should run stats on processed data" do
+    @driver['procdir'] = @procdir || @completed_proc_directory
+    pipe = RPipe.new(@driver)
+    s = pipe.stats_jobs.first
+    s.perform
+    @statsdir = @driver['statsdir'] if Dir.compare_directories(File.join(@driver['statsdir'], 'v1'), @completed_stats_directory)
+  end
+
+end
+

data/spec/logfile_spec.rb

@@ -0,0 +1,96 @@
+require 'helper_spec'
+require 'logfile'
+require 'pp'
+require 'yaml'
+
+describe "Test Logfile Helper" do
+	before(:all) do
+	  @fixture_prefix = 'faces3_recognitionA'
+	  @fixture_prefix_combined = 'faces3_recognitionB_incmisses'
+	  @temp_prefix = 'temp_faces3_recog'
+	  
+	  @textfile = File.join(File.dirname(__FILE__), 'fixtures', @fixture_prefix + '.txt')
+	  @textfile_combined = File.join(File.dirname(__FILE__), 'fixtures', @fixture_prefix_combined + '.txt')
+	  @csvfile_equal =  File.join(File.dirname(__FILE__), 'fixtures', @fixture_prefix + '_equal.csv')
+	  @csvfile_unequal =  File.join(File.dirname(__FILE__), 'fixtures', @fixture_prefix + '_unequal.csv')
+	  @matfile =  File.join(File.dirname(__FILE__), 'fixtures', @fixture_prefix + '.mat')
+	  
+	  @equal_length_conditions = [:new, :old]
+	  @unequal_length_conditions = [:new_correct, :new_incorrect, :old_correct, :old_incorrect]
+	  @collapseable_conditions = [:new_correct, :new_incorrect, :new_misses, :old_correct, :old_incorrect, :old_misses]
+	  @combined_conditions = [:new_correct, :new_incorrect, :old_correct, :old_incorrect, {:misses => [:new_misses, :old_misses]}]
+	  
+	  @ruport_summary = YAML.load_file(File.join(File.dirname(__FILE__), 'fixtures', 'ruport_summary.yml'))
+	  @correct_combined_vectors = {:old_correct=>[8.99945, 13.0001, 18.99695, 22.4986, 34.5006, 49.99595, 53.9966, 59.50275, 88.4972, 91.4998, 103.0028, 120.1117, 137.886, 141.88665, 147.41775], :old_incorrect=>[5.4978, 27.49735, 62.497, 72.50285, 105.99705], :misses=>[116.55185, 123.11425, 131.36515, 135.3575], :new_correct=>[0.0, 2.99425, 15.9938, 25.50115, 30.49995, 36.4968, 40.9965, 46.50265, 56.0011, 65.00055, 69.50025, 74.499, 77.5016, 79.99685, 85.50295, 96.9976, 100.9983, 110.5217, 113.02525, 144.9142, 151.91745, 155.91815, 158.4128], :new_incorrect=>[126.10855]}
+  end
+	  
+  it "should take a text file with vectors of equal length and convert it to a condition csv" do 
+    log = Logfile.new(@textfile, *@equal_length_conditions)
+    puts log.to_csv
+    log.write_csv(@temp_prefix + '.csv')
+    File.exist?(@temp_prefix + '.csv').should be_true
+  end
+	
+	it "should take a text file with vectors of unequal length and convert it to a condition csv" do 
+	  log = Logfile.new(@textfile, *@unequal_length_conditions)
+	  puts log.to_csv
+	  log.write_csv(@temp_prefix + '.csv')
+	  File.exist?(@temp_prefix + '.csv').should be_true
+	  pp log.vectors.values
+	  log.vectors.values.transpose.should have_at_least(10).lines
+	end
+	
+	it "should combine logfile vectors" do 
+	  log = Logfile.new(@textfile, *@collapseable_conditions)
+	  log.combine_vectors(:misses, [:new_misses, :old_misses])
+	  log.write_csv(@temp_prefix + '.csv')
+	  File.exist?(@temp_prefix + '.csv').should be_true
+	  pp log.vectors
+	  log.vectors.values.transpose.should have_at_least(10).lines
+	end
+	
+  
+  it "should take a condition csv with vectors of equal length and convert it to multiple conditions file" do
+    log = Logfile.new(@textfile, *@equal_length_conditions)
+    log.csv_filename = @csvfile_equal # Use CSV Fixture to test only multiple conditions creation.
+    log.write_mat(@temp_prefix)
+    File.exist?(@temp_prefix + '.mat').should be_true
+  end
+  
+  it "should take a condition csv with vectors of unequal length and convert it to multiple conditions file" do
+    log = Logfile.new(@textfile, *@unequal_length_conditions)
+    log.csv_filename = @csvfile_unequal
+    log.write_mat(@temp_prefix)
+    File.exist?(@temp_prefix + '.mat').should be_true
+  end
+  
+  it "should sort logfiles based on file creation time" do
+    [Logfile.new(@textfile), Logfile.new(@textfile)].sort
+  end
+  
+  it "should raise an error if the logfile can't be found" do
+    lambda { Logfile.new('bad_path_to_logfile.csv')}.should raise_error(IOError) 
+  end
+  
+  it "should raise an error if it could not set conditions when they are given" do
+    lambda { Logfile.new(@textfile, nil) }.should raise_error(ScriptError, /Could not set conditions/i)
+  end
+  
+  it "should summarize a directory of logfiles" do
+    summary = Logfile.summarize_directory(File.join(File.dirname(__FILE__), 'fixtures'))
+    summary.column_names.should == ["enum", "task", "version", "ctime", "Total Count", " Hits", " Misses", " Hit%", " Correct", " Incorrect", " Accuracy%", " RT min", " RT max", " RT avg", " RT stdev", " old_stimuli", " old_hits", " old_misses", " old_hit_percent", " old_correct_count", " old_incorrect_count", " old_accuracy", " old_rt_min", " old_rt_max", " old_rt_avg", " old_rt_stdev", " old_correct", " old_correct_rt_min", " old_correct_rt_max", " old_correct_rt_avg", " old_correct_rt_stdev", " old_incorrect", " old_incorrect_rt_min", " old_incorrect_rt_max", " old_incorrect_rt_avg", " old_incorrect_rt_stdev", " new_stimuli", " new_hits", " new_misses", " new_hit_percent", " new_correct_count", " new_incorrect_count", " new_accuracy", " new_rt_min", " new_rt_max", " new_rt_avg", " new_rt_stdev", " new_correct", " new_correct_rt_min", " new_correct_rt_max", " new_correct_rt_avg", " new_correct_rt_stdev", " new_incorrect", " new_incorrect_rt_min", " new_incorrect_rt_max", " new_incorrect_rt_avg", " new_incorrect_rt_stdev", " "]
+    summary.length.should == 2
+    summary.data == @ruport_summary.data
+  end
+  
+  it "should extract combined conditions in a hash" do
+    log = Logfile.new(@textfile_combined, *@combined_conditions)
+    log.conditions.each {|condition| log.condition_vectors[condition.to_s].should == @correct_combined_vectors[condition.to_s] }
+  end
+    
+  after(:each) do
+    ['.txt', '.csv', '.mat'].each do |ext| 
+      File.delete(@temp_prefix + ext) if File.exist?(@temp_prefix + ext)
+    end
+  end
+end

data/spec/matlab_queue_spec.rb

@@ -0,0 +1,40 @@
+require 'helper_spec'
+require 'matlab_queue'
+require 'pp'
+
+describe "Test Matlab Queue Operations" do
+  before(:each) do
+    @q = q = MatlabQueue.new
+  end
+  
+  it "should add a command" do  
+    @q.length.should equal 0
+
+    @q.commands << "1 + 2"
+    @q.length.should equal 1
+    
+    @q.commands << "2 + 3"
+    @q.length.should equal 2
+    
+    @q.to_s.should == "1 + 2; 2 + 3"
+  end
+  
+  it "should add to the path" do
+    @q.paths.length.should equal 0
+    @q.paths << File.dirname(__FILE__)
+    @q.paths.length.should equal 1
+  end
+  
+  it "should generate a good string with paths and commands" do
+    @q.paths << File.dirname(__FILE__)
+    @q.commands << "1 + 2"
+    @q.to_s.should == "addpath(genpath('#{File.dirname(__FILE__)}')); 1 + 2"
+  end
+  
+  it "should run matlab successfully." do
+    @q.paths << File.dirname(__FILE__)
+    @q.commands << "1 + 2"
+    @q.run!.should be_true
+    @q.success.should be_true
+  end
+end