# $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '../../physionoise/lib'))
# 
# require 'helper_spec'
# require 'rpipe'
# require 'physionoise'
# 
# 
# describe "Test Phyiosnoise" do
#   before(:each) do
#     @runs_dir = File.join($MRI_DATA, 'mrt00000', 'dicoms')
#     job_params = {
#       "scans" => [{
#         "label"=>"task1",
#         "dir"=>"s07_epi",
#         "z_slices"=>36, 
#         "rep_time"=>2.0, 
#         "type"=>"func", 
#         "physio_files"=> {
#           :phys_directory       =>  "../cardiac",  # Relative to rawdir
#           :series_description   =>  "EPI  fMRI Task1", 
#           :respiration_signal   =>  "RESPData_epiRT_0211201009_21_22_80", 
#           :respiration_trigger  =>  "RESPTrig_epiRT_0211201009_21_22_80", 
#           :cardiac_signal       =>  "PPGData_epiRT_0211201009_21_22_80", 
#           :cardiac_trigger      =>  "PPGTrig_epiRT_0211201009_21_22_80"
#         }, 
#         "bold_reps"=>167, 
#         "task"=>"Faces3B"
#       }]
#     }
#     
#     workflow_spec = {
#       "subid"=>"mrt00000",
#       "rawdir"=>    @runs_dir,
#       "origdir"=>   Dir.mktmpdir('orig_'),
#       "procdir"=>   Dir.mktmpdir('proc_'),
#       "statsdir"=>  Dir.mktmpdir('stats_'),
#       "collision"=> "destroy"
#     }
#     
#     @valid_physionoise_run_spec = [{
#       :run_directory=> @runs_dir, 
#       :bold_reps=>167, :respiration_signal=>"RESPData_epiRT_0211201009_21_22_80", 
#       :respiration_trigger=>"RESPTrig_epiRT_0211201009_21_22_80", 
#       :cardiac_signal=>"PPGData_epiRT_0211201009_21_22_80", 
#       :cardiac_trigger=>"PPGTrig_epiRT_0211201009_21_22_80", 
#       :phys_directory=> File.join(@runs_dir, '..', 'cardiac'), 
#       :rep_time=>2.0, 
#       :series_description=>"EPI  fMRI Task1"
#     }]
#           
#     @recon_job = Reconstruction.new(workflow_spec, job_params)
#     @scan_spec = @recon_job.scans.first
#     
#     @physionoise_fixture_dir = File.join(File.dirname(__FILE__), 'fixtures', 'physionoise_regressors')
#     
#   end
#     
#   it "should create physionoise regressors from Cardiac and Respiration Data" # do
#     # Dir.chdir @recon_job.origdir do
#     #   @recon_job.create_physiosnoise_regressors(@scan_spec)
#     # end
#     #   
#     # Dir.compare_directories(@recon_job.origdir, @physionoise_fixture_dir).should be_true    
# 
#   # end
#   
#   it "should correctly build a spec for passing to physionoise" # do
#     # @recon_job.build_physionoise_run_spec(@scan_spec).should == @valid_physionoise_run_spec
#   # end
#   
#   it "should correctly build a physionoise python command" # do
#       # @valid_physionoise_run_spec.each do |run|
#       #   puts Physionoise.build_run_cmd(run)
#       # end
#   # end
#   
#   it "should build a 3dRetroicor string" # do
#     # valid_cmd = "3dretroicor -prefix ptask1.nii -card #{@runs_dir}/../cardiac/PPGData_epiRT_0211201009_21_22_80 -resp #{@runs_dir}/../cardiac/RESPData_epiRT_0211201009_21_22_80 task1.nii"
#     # valid_outfile = "p#{@scan_spec['label']}.nii"
#     # test_cmd, test_outfile = @recon_job.build_retroicor_cmd(@scan_spec['physio_files'], "#{@scan_spec['label']}.nii")
#     # 
#     # valid_cmd.should == test_cmd
#     # valid_outfile.should == test_outfile
#   # end
#   
#   it "should raise an error building a 3dRetroicor string if improperly configured" # do
#     # physio_files = @scan_spec['physio_files']
#     # physio_files.delete(:cardiac_signal)
#     # 
#     # lambda {@recon_job.build_retroicor_cmd(physio_files, "#{@scan_spec['label']}.nii") }.should raise_error ScriptError, /Missing .* cardiac/
#   # end
#   
#   it "should raise an IOError building a 3dRetroicor string with bad files"
# 
#   after(:each) do
#     FileUtils.rm_r([@recon_job.origdir, @recon_job.procdir, @recon_job.statsdir])
#   end
# end