spec/physio_spec.rb in rpipe-0.1.6 vs spec/physio_spec.rb in rpipe-0.1.7
- old
+ new
@@ -1,98 +1,98 @@
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '../../physionoise/lib'))
-
-require 'helper_spec'
-require 'rpipe'
-require 'physionoise'
-
-
-describe "Test Phyiosnoise" do
- before(:each) do
- @runs_dir = File.join($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
+# $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '../../physionoise/lib'))
+#
+# require 'helper_spec'
+# require 'rpipe'
+# require 'physionoise'
+#
+#
+# describe "Test Phyiosnoise" do
+# before(:each) do
+# @runs_dir = File.join($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
\ No newline at end of file