rpipe 0.1.3 → 0.1.4

data/Gemfile

@@ -1,4 +1,4 @@
 source "http://rubygems.org"
 
-# Specify your gem's dependencies in ruby-nifti.gemspec
+# Specify your gem's dependencies in rpipe.gemspec
 gemspec

data/VERSION

@@ -1 +1 @@
-0.1.3
+0.1.4

data/bin/create_driver.rb

@@ -16,15 +16,21 @@ def create!
   workflow_options = workflow_options_defaults.merge(spec_options).merge(cli_options[:config])
 
   # Create a Workflow Generator and use it to create configure job.
-  rawdir = ARGV.pop
-  workflow = WorkflowGenerator.new(rawdir, workflow_options)
-  if cli_options[:dry_run]
-    pp workflow.build
-  else
+  while ARGV.size >= 1
     begin
-      puts write_driver_hash workflow.build, :cli_options => cli_options
-    rescue IOError => e
-      puts e
+      rawdir = ARGV.shift
+      workflow = WorkflowGenerator.new(rawdir, workflow_options)
+      if cli_options[:dry_run]
+        pp workflow.build
+      else
+        begin
+          puts write_driver_hash workflow.build, :cli_options => cli_options
+        rescue IOError => e
+          puts e
+        end
+      end
+    rescue StandardError => e
+      puts "Problem creating driver for #{rawdir}"
     end
   end
 end
@@ -58,7 +64,7 @@ end
 def parse_options
   options = { :config => {} }
   parser = OptionParser.new do |opts|
-    opts.banner = "Usage: #{File.basename(__FILE__)} [options] RAWDIR"
+    opts.banner = "Usage: #{File.basename(__FILE__)} [options] RAWDIR(S)"
 
     opts.on('-s', '--spec SPEC', "Spec File for common study parameters")     do |spec_file| 
       options[:spec_file] = spec_file
@@ -78,6 +84,7 @@ def parse_options
 
     opts.on_tail('-h', '--help', "Show this message")  { puts(parser); exit }
     opts.on_tail("Example: #{File.basename(__FILE__)} mrt00001")
+    opts.on_tail("Example: #{File.basename(__FILE__)} raw/johnson.merit220.visit1/mri/mrt*")
   end
   parser.parse!(ARGV)
 

data/bin/rpipe

@@ -19,18 +19,26 @@ VERSION_LINE = "rpipe %s WADRC Imaging Core" % VERSION_NUMBER
 BANNER = <<-EOS
 A utility for running neuroimaging rpipe jobs.
 
-Usage: rpipe [options] <driver>
+Usage:\trpipe [options] <driver(s)>
+
 EOS
 
 # Main Function for the CLI runner.
 def run!
-  options, driver = setup_options
-  run_with_logging File.basename(driver, File.extname(driver)), options do  
-    $Log.info "Begin Pipelining #{driver} | #{Etc.getlogin} on #{`hostname`}"
-    run_pipe(options, driver)
-    $Log.info "Finished Pipelining #{driver}"
+  options = setup_options
+  drivers = ARGV
+  while drivers.size >= 1    
+    driver = drivers.shift
+    run_with_logging File.basename(driver, File.extname(driver)), options do  
+      begin
+        $Log.info "Begin Pipelining #{driver} | #{Etc.getlogin} on #{`hostname`}"
+        run_pipe(options, driver)
+        $Log.info "Finished Pipelining #{driver}"
+      rescue StandardError => e
+        $Log.error e
+      end
+    end
   end
-
 end
 
 # Perform Each of the Jobs in a Pipe
@@ -72,12 +80,10 @@ def setup_options
   end
 
   Trollop::die "Driver file not given" if (ARGV.size < 1)
-  driver = ARGV.shift
-  Trollop::die "Driver file #{driver} does not exist.  Check the path to that file and try again" unless File.exist?(driver)
 
   pp opts if opts[:debug]
   
-  return opts, driver
+  return opts
 end
 
 # Setup Tee IO's for Out and Error and start logs for them.

data/lib/default_methods/recon/raw_sequence.rb

@@ -14,9 +14,9 @@ module DefaultRecon
   class DicomRawSequence < RawSequence
     # Locally copy and unzip a folder of Raw Dicoms and call convert_sequence on them
     def prepare_and_convert_sequence(outfile)
-      scandir = File.join(@rawdir, @scan_spec['dir'])
-      $Log.info "Dicom Reconstruction: #{scandir}"
-      Pathname.new(scandir).all_dicoms do |dicoms|
+      @scandir = File.join(@rawdir, @scan_spec['dir'])
+      $Log.info "Dicom Reconstruction: #{@scandir}"
+      Pathname.new(@scandir).all_dicoms do |dicoms|
         convert_sequence(dicoms, outfile)
       end
     end
@@ -28,15 +28,23 @@ module DefaultRecon
     # Convert a folder of unzipped Dicom files to outfile
     def convert_sequence(dicoms, outfile)
       local_scandir = File.dirname(dicoms.first)
-      second_file = Dir.glob( File.join(local_scandir, "*0002*") )
-      wildcard = File.join(local_scandir, "*.[0-9]*")
+      second_file = Dir.glob( File.join(local_scandir, "*0002*") ).first
+      glob = case second_file
+      when /.*\.dcm$/
+        "*.dcm"
+      else 
+        "*.[0-9]*"
+      end
+      wildcard = File.join(local_scandir, glob)
+        
+        
     
       recon_cmd_format = 'to3d -skip_outliers %s -prefix tmp.nii "%s"'
 
       timing_opts = timing_options(@scan_spec, second_file)
 
       unless run(recon_cmd_format % [timing_opts, wildcard])
-        raise(IOError,"Failed to reconstruct scan: #{scandir}")
+        raise(IOError,"Failed to reconstruct scan: #{@scandir}")
       end
     end
   

data/lib/generators/workflow_generator.rb

@@ -44,7 +44,7 @@ class WorkflowGenerator < JobGenerator
     jobs = []
     
     # Recon
-    recon_options = {'rawdir' => @rawdir, 'epi_pattern' => /(Resting|Task)/i, }
+    recon_options = {'rawdir' => @rawdir, 'epi_pattern' => /(Rest|Task)/i, }
     config_step_method(recon_options, 'recon') if @config['custom_methods']
     jobs << ReconJobGenerator.new(recon_options).build
     

data/rpipe.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rpipe}
-  s.version = "0.1.3"
+  s.version = "0.1.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher Kosmatka", "Erik Kastman"]
-  s.date = %q{2011-03-24}
+  s.date = %q{2011-03-31}
   s.description = %q{Neuroimaging preprocessing the Ruby way}
   s.email = %q{kjkosmatka@gmail.com}
   s.executables = ["swallow_batch_run.rb", "rpipe", "summarize_responses.rb", "create_driver.rb"]
@@ -157,6 +157,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
       s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+      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"])
@@ -166,6 +167,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
       s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+      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"])
@@ -176,6 +178,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+    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"])

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rpipe
 version: !ruby/object:Gem::Version 
-  hash: 29
+  hash: 19
   prerelease: 
   segments: 
   - 0
   - 1
-  - 3
-  version: 0.1.3
+  - 4
+  version: 0.1.4
 platform: ruby
 authors: 
 - Kristopher Kosmatka
@@ -16,7 +16,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-24 00:00:00 -05:00
+date: 2011-03-31 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -77,8 +77,8 @@ dependencies:
   requirement: *id004
 - !ruby/object:Gem::Dependency 
   prerelease: false
-  name: metamri
-  type: :runtime
+  name: thoughtbot-shoulda
+  type: :development
   version_requirements: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -91,7 +91,7 @@ dependencies:
   requirement: *id005
 - !ruby/object:Gem::Dependency 
   prerelease: false
-  name: log4r
+  name: metamri
   type: :runtime
   version_requirements: &id006 !ruby/object:Gem::Requirement 
     none: false
@@ -105,7 +105,7 @@ dependencies:
   requirement: *id006
 - !ruby/object:Gem::Dependency 
   prerelease: false
-  name: POpen4
+  name: log4r
   type: :runtime
   version_requirements: &id007 !ruby/object:Gem::Requirement 
     none: false
@@ -119,7 +119,7 @@ dependencies:
   requirement: *id007
 - !ruby/object:Gem::Dependency 
   prerelease: false
-  name: ruport
+  name: POpen4
   type: :runtime
   version_requirements: &id008 !ruby/object:Gem::Requirement 
     none: false
@@ -131,6 +131,20 @@ dependencies:
         - 0
         version: "0"
   requirement: *id008
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: ruport
+  type: :runtime
+  version_requirements: &id009 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  requirement: *id009
 description: Neuroimaging preprocessing the Ruby way
 email: kjkosmatka@gmail.com
 executables: