rpipe 0.1.6 → 0.1.7

data/lib/default_methods/default_recon.rb

@@ -4,7 +4,8 @@ require 'default_methods/recon/raw_sequence'
 # require 'default_methods/recon/physionoise_helper'
 
 module DefaultRecon
-	
+	DEFAULT_VOLUME_SKIP = 3 # Default number of volumes to strip from beginning of functional scans.
+
 	# Reconstructs, strips, and slice timing corrects all scans specified in the recon_spec.
 	# This function assumes a destination directory is set up in the filesystem and begins writing
 	# to it with no further checking.	 It will overwrite data if it already exists, be careful.
@@ -16,6 +17,9 @@ module DefaultRecon
 			@scans.each_with_index do |scan_spec, i|
 				outfile = "%s_%s.nii" % [@subid, scan_spec['label']]
 				
+        # Set Discarded Acquisitions - Volumes to Skip from Recon Spec, Scan Spec or Default
+				@volumes_to_skip = @volume_skip || scan_spec['volume_skip'] || scan_spec['volumes_to_skip'] || DEFAULT_VOLUME_SKIP
+				
 				reconstruct_scan(scan_spec, outfile)
 				
 				if scan_spec['type'] == "func"
@@ -42,30 +46,16 @@ module DefaultRecon
   # filenaming, I0002.dcm is second file in series,
 	def reconstruct_scan(scan_spec, outfile)	
 		if scan_spec['dir']
-		  sequence = DicomRawSequence.new(scan_spec, @rawdir)
-		  File.delete('tmp.nii') if File.exist? 'tmp.nii'
-		  sequence.prepare('tmp.nii')
-			strip_leading_volumes('tmp.nii', outfile, @volume_skip, scan_spec['bold_reps'])
+		  sequence = DicomRawSequence.new(scan_spec, @rawdir, @volumes_to_skip)
 	  elsif scan_spec['pfile']
-	    sequence = PfileRawSequence.new(scan_spec, @rawdir)
-	    sequence.prepare(outfile)
-    else 
+	    sequence = PfileRawSequence.new(scan_spec, @rawdir, @volumes_to_skip)
+    else
       raise ConfigError, "Scan must list either a pfile or a dicom directory."
     end
+    
+    sequence.prepare(outfile)
 	end
-	
-	# Removes the specified number of volumes from the beginning of a 4D functional nifti file.
-	# In most cases this will be 3 volumes. Writes result in current working directory.
-	def strip_leading_volumes(infile, outfile, volume_skip, bold_reps)
-		$Log.info "Stripping #{volume_skip.to_s} leading volumes: #{infile}"
-		cmd_fmt = "fslroi %s %s %s %s"
-		cmd_options = [infile, outfile, volume_skip.to_s, bold_reps.to_s]
-		cmd = cmd_fmt % cmd_options
-		unless run(cmd)
-		  raise ScriptError, "Failed to strip volumes: #{cmd}"
-	  end
-	end
-	
+		
 	# Uses to3d to slice time correct a 4D functional nifti file.	 Writes result in the current working directory.
 	def slice_time_correct(infile, alt_direction = "alt+z")
 		$Log.info "Slice Timing Correction: #{infile}"

data/lib/default_methods/recon/raw_sequence.rb

@@ -4,10 +4,24 @@ module DefaultRecon
   # them from their raw state (dicoms or pfiles) to Nifti files suitable for
   # processing.
   class RawSequence
-    def initialize(scan_spec, rawdir)
+    def initialize(scan_spec, rawdir, volumes_to_skip)
       @scan_spec = scan_spec
       @rawdir = rawdir
+      @volumes_to_skip = volumes_to_skip
     end
+    
+    # Removes the specified number of volumes from the beginning of a 4D functional nifti file.
+  	# In most cases this will be 3 volumes. Writes result in current working directory.
+  	def strip_leading_volumes(infile, outfile, volume_skip, bold_reps)
+  		$Log.info "Stripping #{volume_skip.to_s} leading volumes: #{infile}"
+  		cmd_fmt = "fslroi %s %s %s %s"
+  		cmd_options = [infile, outfile, volume_skip.to_s, bold_reps.to_s]
+  		cmd = cmd_fmt % cmd_options
+  		unless run(cmd)
+  		  raise ScriptError, "Failed to strip volumes: #{cmd}"
+  	  end
+  	end
+  	
   end
 
   # Manage a folder of Raw Dicoms for Nifti file conversion
@@ -16,9 +30,14 @@ module DefaultRecon
     def prepare_and_convert_sequence(outfile)
       @scandir = File.join(@rawdir, @scan_spec['dir'])
       $Log.info "Dicom Reconstruction: #{@scandir}"
+      
+      File.delete('tmp.nii') if File.exist? 'tmp.nii'
+      
       Pathname.new(@scandir).all_dicoms do |dicoms|
-        convert_sequence(dicoms, outfile)
+        convert_sequence(dicoms, 'tmp.nii')
       end
+      
+      strip_leading_volumes('tmp.nii', outfile, @volumes_to_skip, @scan_spec['bold_reps'])
     end
       
     alias_method :prepare, :prepare_and_convert_sequence
@@ -67,8 +86,8 @@ module DefaultRecon
   # Reconstucts a PFile from Raw to Nifti File
   class PfileRawSequence < RawSequence
     # Create a local unzipped copy of the Pfile and prepare Scanner Reference Data for reconstruction
-    def initialize(scan_spec, rawdir)
-      super(scan_spec, rawdir)
+    def initialize(scan_spec, rawdir, volumes_to_skip)
+      super(scan_spec, rawdir, volumes_to_skip)
       
       base_pfile_path = File.join(@rawdir, @scan_spec['pfile'])
       pfile_path = File.exist?(base_pfile_path) ? base_pfile_path : base_pfile_path + '.bz2'
@@ -86,9 +105,8 @@ module DefaultRecon
     # Outfile may include a '.nii' extension - a nifti file will be constructed
     # directly in this case.
     def reconstruct_sequence(outfile)
-      volumes_to_skip = @scan_spec['volumes_to_skip'] ||= 3
       epirecon_cmd_format = "epirecon_ex -f %s -NAME %s -skip %d -scltype=0"
-      epirecon_cmd_options = [@pfile_data, outfile, volumes_to_skip]
+      epirecon_cmd_options = [@pfile_data, outfile, @volumes_to_skip]
       epirecon_cmd = epirecon_cmd_format % epirecon_cmd_options
 			raise ScriptError, "Problem running #{epirecon_cmd}" unless run(epirecon_cmd)
     end

data/lib/generators/recon_job_generator.rb

@@ -1,5 +1,5 @@
-gem 'activeresource', '<=2.3.8'
-$LOAD_PATH.unshift('~/projects/metamri/lib').unshift('~/code/metamri/lib')
+# gem 'activeresource', '<=2.3.8'
+# $LOAD_PATH.unshift('~/projects/metamri/lib').unshift('~/code/metamri/lib')
 require 'metamri'
 require 'generators/job_generator'
 

data/lib/rpipe.rb

@@ -147,8 +147,6 @@ class Reconstruction < JobStep
 	require 'default_methods/default_recon'
 	include DefaultRecon
 	
-	VOLUME_SKIP = 3 # number of volumes to strip from beginning of functional scans.
-	
 	attr_accessor :scans, :volume_skip
 	
 	# Instances are initialized with a properly configured hash containing all the information needed to drive
@@ -156,7 +154,7 @@ class Reconstruction < JobStep
 	def initialize(workflow_spec, recon_spec)
 		super(workflow_spec, recon_spec)
 		raise ScriptError, "At least one scan must be specified." if @scans.nil?
-		@volume_skip = recon_spec['volume_skip'] || VOLUME_SKIP
+		@volume_skip = recon_spec['volume_skip']
 		
 		job_requires 'rawdir', 'origdir', 'scans'
 	end

data/lib/rpipe/version.rb

@@ -1,3 +1,3 @@
 module Rpipe
-  VERSION = "0.1.6"
-end
+  VERSION = "0.1.7"
+end

data/rpipe.gemspec

@@ -13,6 +13,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/brainmap/rpipe"
 
   s.add_development_dependency "thoughtbot-shoulda", ">= 0"
+  s.add_development_dependency "rspec", "~>1.3.2"
   s.add_dependency "metamri", '~>0.2.9'
   s.add_dependency "log4r", '~>1.1.9'
   s.add_dependency "POpen4", '~>0.1.4'

data/spec/physio_spec.rb

@@ -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

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rpipe
 version: !ruby/object:Gem::Version 
-  hash: 23
+  hash: 21
   prerelease: 
   segments: 
   - 0
   - 1
-  - 6
-  version: 0.1.6
+  - 7
+  version: 0.1.7
 platform: ruby
 authors: 
 - Kristopher Kosmatka
@@ -16,8 +16,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-08-18 00:00:00 -05:00
-default_executable: 
+date: 2012-02-01 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: thoughtbot-shoulda
@@ -34,9 +33,25 @@ dependencies:
   type: :development
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: metamri
+  name: rspec
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 31
+        segments: 
+        - 1
+        - 3
+        - 2
+        version: 1.3.2
+  type: :development
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: metamri
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -48,11 +63,11 @@ dependencies:
         - 9
         version: 0.2.9
   type: :runtime
-  version_requirements: *id002
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: log4r
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -64,11 +79,11 @@ dependencies:
         - 9
         version: 1.1.9
   type: :runtime
-  version_requirements: *id003
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: POpen4
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -80,11 +95,11 @@ dependencies:
         - 4
         version: 0.1.4
   type: :runtime
-  version_requirements: *id004
+  version_requirements: *id005
 - !ruby/object:Gem::Dependency 
   name: ruport
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -96,7 +111,7 @@ dependencies:
         - 3
         version: 1.6.3
   type: :runtime
-  version_requirements: *id005
+  version_requirements: *id006
 description: Functional MRI Processing Pipeline for the WADRC
 email: ekk@medicine.wisc.edu
 executables: 
@@ -217,7 +232,6 @@ files:
 - test/test_rpipe.rb
 - vendor/output_catcher.rb
 - vendor/trollop.rb
-has_rdoc: true
 homepage: http://github.com/brainmap/rpipe
 licenses: []
 
@@ -247,7 +261,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.4.2
+rubygems_version: 1.8.11
 signing_key: 
 specification_version: 3
 summary: Neuroimaging preprocessing the Ruby way