rpipe 0.1.0 → 0.1.1

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/bin/rpipe

@@ -96,7 +96,7 @@ def run_with_logging(logfile_stem, options, &block)
   teeout = Tee.new(out_logfile, :out, 'a')
   teeerr = Tee.new(error_logfile, :err, 'a')
   
-  setup_logger(command_logfile, teeout, teeerr, options)
+  setup_runner_logger(command_logfile, teeout, teeerr, options)
   
   begin
     yield
@@ -112,13 +112,12 @@ def run_with_logging(logfile_stem, options, &block)
 end
 
 # Log Commands to a file and Output to stdout
-def setup_logger(command_logfile, teeout, teeerr, options)
+def setup_runner_logger(command_logfile, teeout, teeerr, options)
   console_pattern = "#{'*' * 10} %m [ %d ]"
   $Log = Log4r::Logger.new('output')
   $Log.level = Log4r::DEBUG
   $Log.add Log4r::IOOutputter.new(:stdout, teeout, :formatter => FlashFormatter.new)
 
-  File.delete command_logfile if File.exist? command_logfile
   $CommandLog = Log4r::Logger.new('command::output')
   $CommandLog.add Log4r::FileOutputter.new(:file, :filename => command_logfile, :trunc => false, :formatter => Log4r::PatternFormatter.new(:pattern => "%m"))
   $CommandLog.add Log4r::IOOutputter.new(:stdout, teeout, :formatter => FlashFormatter.new)

data/lib/custom_methods/JohnsonMerit220Visit1Preproc.rb

@@ -30,6 +30,7 @@ module JohnsonMerit220Visit1Preproc
 
 	  queue = MatlabQueue.new
 	  queue.paths << [
+	    @spmdir,
 	    File.join(@spmdir, 'config'),
 	    File.join(@spmdir, 'matlabbatch'),
 	    File.expand_path(File.join(@libdir, 'custom_methods')), 

data/lib/custom_methods/JohnsonMerit220Visit1Stats.rb

@@ -45,6 +45,7 @@ module JohnsonMerit220Visit1Stats
     
     queue = MatlabQueue.new
 	  queue.paths << [
+	    @spmdir,
 	    File.join(@spmdir, 'config'),
 	    File.join(@spmdir, 'matlabbatch'),
 	    File.expand_path(File.join(@libdir, 'custom_methods')), 

data/lib/default_methods/default_stats.rb

@@ -67,8 +67,14 @@ module DefaultStats
 	  onsets_mat_files = []
 	  wd = Dir.pwd
 	  matching_directories = Dir.glob(responses['directory'])
-	  raise IOError, "Response directory #{responses['directory']} doesn't exist." unless File.directory?(responses['directory'])
-	  raise IOError, "Only one response directory currently accepted (matched directories: #{matching_directories.join(', ')})" unless matching_directories.length == 1
+
+	  case 
+	  when matching_directories.length == 0
+	    raise(IOError, "Response directory #{responses['directory']} doesn't exist or isn't mounted.")
+	  when matching_directories.length > 1
+	    raise IOError, "Only one response directory currently accepted (matched directories: #{matching_directories.join(', ')})"
+    end
+	  
 	  Dir.chdir matching_directories.first  do
 	    responses['logfiles'].each do |logfile|
   	    # Either Strip off the prefix directly without changing the name...

data/lib/generators/workflow_generator.rb

@@ -18,7 +18,7 @@ require 'generators/stats_job_generator'
 #  - statsdir : A directory where stats will be saved.  (This should be a final directory.)
 
 class WorkflowGenerator < JobGenerator
-  attr_reader :spec
+  attr_reader :spec, :config
   
   def initialize(rawdir, config = Hash.new)
     config_defaults = {}
@@ -81,9 +81,15 @@ class WorkflowGenerator < JobGenerator
   # Handle Directory Configuration and Defaults for orig, proc and stats dirs.
   def configure_directories
     processing_dir = @config['processing_dir']
-    @spec['origdir']  = @config['origdir']  || parse_directory_format(@config['directory_formats']['origdir'])  || File.join(processing_dir, @spec['subid'] + '_orig')
-    @spec['procdir']  = @config['procdir']  || parse_directory_format(@config['directory_formats']['procdir'])  || File.join(processing_dir, @spec['subid'] + '_proc')
-    @spec['statsdir'] = @config['statsdir'] || parse_directory_format(@config['directory_formats']['statsdir']) || File.join(processing_dir, @spec['subid'] + '_stats')
+    if @config['directory_formats']
+      @spec['origdir']  = @config['origdir']  || parse_directory_format(@config['directory_formats']['origdir'])  || File.join(processing_dir, @spec['subid'] + '_orig')
+      @spec['procdir']  = @config['procdir']  || parse_directory_format(@config['directory_formats']['procdir'])  || File.join(processing_dir, @spec['subid'] + '_proc')
+      @spec['statsdir'] = @config['statsdir'] || parse_directory_format(@config['directory_formats']['statsdir']) || File.join(processing_dir, @spec['subid'] + '_stats')
+    else
+      @spec['origdir']  = @config['origdir']  || File.join(processing_dir, @spec['subid'] + '_orig')
+      @spec['procdir']  = @config['procdir']  || File.join(processing_dir, @spec['subid'] + '_proc')
+      @spec['statsdir'] = @config['statsdir'] || File.join(processing_dir, @spec['subid'] + '_stats')
+    end
   end
   
   # Replace a directory format string with respective values from the spec.

data/lib/global_additions.rb

@@ -1,4 +1,10 @@
 require 'popen4'
+require 'default_logger'
+include DefaultLogger
+
+unless defined?($Log)
+  DefaultLogger::setup_logger
+end
 
 # Global Method to Log and Run system commands.
 def run(command)

data/lib/matlab_helpers/matlab_queue.rb

@@ -1,3 +1,4 @@
+require 'global_additions'
 require 'default_logger'
 
 # Maintain and run matlab commands and paths.
@@ -11,7 +12,7 @@ class MatlabQueue
     @paths = []
     @commands = []
     @ml_command = "matlab -nosplash -nodesktop"
-    setup_logger
+    setup_logger unless defined?($Log)
   end
   
   def to_s

data/rpipe.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rpipe}
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher Kosmatka", "Erik Kastman"]
-  s.date = %q{2010-09-21}
+  s.date = %q{2010-10-29}
   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.executables = ["swallow_batch_run.rb", "create_driver.rb", "rpipe"]
   s.extra_rdoc_files = [
     "LICENSE",
      "README",

data/spec/generators/workflow_generator_spec.rb

@@ -20,7 +20,7 @@ describe "Workflow Generator" do
       "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"
+      "method" => "JohnsonMerit220Visit1Stats"
     }
     
     

data/spec/matlab_queue_spec.rb

@@ -16,7 +16,7 @@ describe "Test Matlab Queue Operations" do
     @q.commands << "2 + 3"
     @q.length.should equal 2
     
-    @q.to_s.should == "1 + 2; 2 + 3"
+    @q.to_s.should == "1 + 2, 2 + 3"
   end
   
   it "should add to the path" do
@@ -28,7 +28,7 @@ describe "Test Matlab Queue Operations" do
   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"
+    @q.to_s.should == "1 + 2"
   end
   
   it "should run matlab successfully." do

data/spec/physio_spec.rb

@@ -55,40 +55,40 @@ describe "Test Phyiosnoise" do
 	  
   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    
+  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
+  # 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 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 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 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 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"
 

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 0
-  version: 0.1.0
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - Kristopher Kosmatka
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-09-21 00:00:00 -05:00
+date: 2010-10-29 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -81,9 +81,9 @@ dependencies:
 description: Neuroimaging preprocessing the Ruby way
 email: kjkosmatka@gmail.com
 executables: 
-- rpipe
 - swallow_batch_run.rb
 - create_driver.rb
+- rpipe
 extensions: []
 
 extra_rdoc_files: