rpipe 0.0.1

data/test/fixtures/ruport_summary.yml

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+--- !ruby/object:Ruport::Data::Table 
+column_names: &id001 
+  - enum
+  - task
+  - version
+  - ctime
+  - Total Count
+  - " Hits"
+  - " Misses"
+  - " Hit%"
+  - " Correct"
+  - " Incorrect"
+  - " Accuracy%"
+  - " RT min"
+  - " RT max"
+  - " RT avg"
+  - " RT stdev"
+  - " old_stimuli"
+  - " old_hits"
+  - " old_misses"
+  - " old_hit_percent"
+  - " old_correct_count"
+  - " old_incorrect_count"
+  - " old_accuracy"
+  - " old_rt_min"
+  - " old_rt_max"
+  - " old_rt_avg"
+  - " old_rt_stdev"
+  - " old_correct"
+  - " old_correct_rt_min"
+  - " old_correct_rt_max"
+  - " old_correct_rt_avg"
+  - " old_correct_rt_stdev"
+  - " old_incorrect"
+  - " old_incorrect_rt_min"
+  - " old_incorrect_rt_max"
+  - " old_incorrect_rt_avg"
+  - " old_incorrect_rt_stdev"
+  - " new_stimuli"
+  - " new_hits"
+  - " new_misses"
+  - " new_hit_percent"
+  - " new_correct_count"
+  - " new_incorrect_count"
+  - " new_accuracy"
+  - " new_rt_min"
+  - " new_rt_max"
+  - " new_rt_avg"
+  - " new_rt_stdev"
+  - " new_correct"
+  - " new_correct_rt_min"
+  - " new_correct_rt_max"
+  - " new_correct_rt_avg"
+  - " new_correct_rt_stdev"
+  - " new_incorrect"
+  - " new_incorrect_rt_min"
+  - " new_incorrect_rt_max"
+  - " new_incorrect_rt_avg"
+  - " new_incorrect_rt_stdev"
+  - " "
+data: 
+- !ruby/object:Ruport::Data::Record 
+  attributes: *id001
+  data: 
+    " ": 
+    " new_rt_stdev": "393.78058"
+    " new_rt_avg": "1451.43333"
+    " new_rt_min": "945.6"
+    " new_hits": "24"
+    " old_incorrect_rt_avg": "1614.75"
+    " old_incorrect_rt_min": "1150.3"
+    " old_correct_rt_max": "1801.4"
+    " Hit%": "100"
+    " Misses": "0"
+    " new_correct_rt_stdev": "414.191973"
+    " new_correct_rt_avg": "1464.65333"
+    " new_correct_rt_min": "1087.9"
+    " new_incorrect_count": "9"
+    " old_correct": "20"
+    " old_rt_avg": "1306.27083"
+    " old_rt_min": "799.4"
+    " old_correct_count": "20"
+    " RT stdev": "357.924556"
+    " old_hit_percent": "100"
+    enum: faces3
+    " new_incorrect_rt_max": "2123.4"
+    " new_correct": "15"
+    " new_accuracy": "62.5"
+    " old_incorrect": "4"
+    " old_correct_rt_avg": "1244.575"
+    " old_correct_rt_min": "799.4"
+    " old_misses": "0"
+    " old_hits": "24"
+    " Hits": "48"
+    " new_correct_count": "15"
+    " new_stimuli": "24"
+    " Accuracy%": "72.9166667"
+    " Incorrect": "13"
+    " new_incorrect": "9"
+    " old_correct_rt_stdev": "241.838353"
+    " RT max": "2400.8"
+    version: 
+    " new_incorrect_rt_stdev": "356.089861"
+    " new_incorrect_rt_avg": "1429.4"
+    " new_incorrect_rt_min": "945.6"
+    " old_incorrect_rt_stdev": "370.275982"
+    " old_incorrect_rt_max": "2067.6"
+    ctime: 2010-05-27 18:23:44 -05:00
+    task: 
+    " new_rt_max": "2400.8"
+    " new_hit_percent": "100"
+    " old_rt_stdev": "301.032812"
+    " old_accuracy": "83.3333333"
+    " new_correct_rt_max": "2400.8"
+    " new_misses": "0"
+    " old_rt_max": "2067.6"
+    " old_incorrect_count": "4"
+    " RT avg": "1378.85208"
+    " RT min": "799.4"
+    " old_stimuli": "24"
+    " Correct": "35"
+    Total Count: "48"
+record_class: Ruport::Data::Record

data/test/fixtures/valid_scans.yaml

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+--- 
+- label: EPI-fMRI-Task1
+  dir: s07_epi
+  type: func
+  z_slices: 36
+  rep_time: 2.0
+  bold_reps: 167
+  volumes_to_skip: 3
+  # task: "?"
+  # physio_files: "#TODO"
+  # physio_files: 
+  #   phys_directory: "../cardiac"
+  #   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"  
+- label: EPI-fMRI-Task2
+  dir: s08_epi
+  type: func
+  z_slices: 36
+  rep_time: 2.0
+  bold_reps: 167
+  volumes_to_skip: 3
+  # task: "?"
+  # physio_files: "#TODO"
+- label: EPI-Resting-fMRI
+  dir: s09_epi
+  type: func
+  z_slices: 36
+  rep_time: 2.0
+  bold_reps: 167
+  volumes_to_skip: 3
+  # task: "?"
+  # physio_files: "#TODO"

data/test/helper.rb

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+require 'rubygems'
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rpipe'
+
+class Test::Unit::TestCase
+end

data/test/test_dynamic_method_inclusion.rb

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+require 'helper'
+require 'pp'
+
+class TestDynamicMethodInclusion < Test::Unit::TestCase
+  should "include a dynamic method for recon" do
+    pipe = RPipe.new(File.join(File.dirname(__FILE__), 'drivers', 'mrt00015_hello.yml'))
+		r = pipe.recon_jobs.first
+		assert_equal "=== Hello World! ===", r.hello
+  end
+end

data/test/test_includes.rb

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+require 'helper'
+
+class TestIncludes < Test::Unit::TestCase
+  should "include the standard implementation of reconstruction" do
+		r = Reconstruction.new(
+			{ 'subid' => 'swallow001', 'rawdir' => nil, 'origdir' => nil, 'procdir' => nil },
+			{ 'scans' => nil, 'source' => nil, 'method' => nil }
+		)
+		assert_equal "swallow001", r.subid
+  end
+end

data/test/test_integrative_johnson.merit220.visit1.rb

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+require 'helper'
+require 'pp'
+
+# class TestJohnsonMerit220Preproc < Test::Unit::TestCase
+#   should "preprocess raw data" do
+#     pipe = RPipe.new('drivers/mrt00015.yml')
+#     p = pipe.preproc_jobs.first
+#     p.preproc_visit
+#   end
+# end
+
+# class TestJohnsonMerit220Stats < Test::Unit::TestCase
+#   should "run stats on processed data" do
+#     pipe = RPipe.new('drivers/mrt00015.yml')
+#     s = pipe.stats_jobs.first
+#     s.run_first_level_stats
+#   end
+# end
+
+class TestJohnsonMerit220Integrative < Test::Unit::TestCase
+  should "run through a subject." do
+    pipe = RPipe.new(File.join(File.dirname(__FILE__), 'drivers', '/mrt00015_hello.yml'))
+
+    # Run Each Job
+    pipe.jobs.each do |job|
+      job.perform
+    end
+
+  end
+end
+

data/test/test_preproc.rb

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+require 'helper'
+require 'pp'
+
+class TestRecon < Test::Unit::TestCase
+  should "preprocess raw data" do
+		driver = ARGV[0] ||= File.join(File.dirname(__FILE__), 'drivers', 'mrt00015.yml')
+    pipe = RPipe.new(driver)
+		p = pipe.preproc_jobs.first
+		p.preproc_visit
+  end
+end

data/test/test_recon.rb

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+require 'helper'
+require 'pp'
+
+class TestRecon < Test::Unit::TestCase
+  should "reconstruct raw data" do
+		driver = ARGV[0] ||= File.join(File.dirname(__FILE__), 'drivers', 'mrt00015.yml')
+    pipe = RPipe.new(driver)
+		r = pipe.recon_jobs.first
+		r.recon_visit
+  end
+end

data/test/test_rpipe.rb

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+require 'helper'
+
+class TestRPipe < Test::Unit::TestCase
+  should "initialize a pipe from a yml spec file" do
+    pipe = RPipe.new(File.join(File.dirname(__FILE__), 'drivers', 'mrt00015.yml'))
+
+		assert_not_nil pipe.recon_jobs
+		assert_not_nil pipe.preproc_jobs
+		assert_not_nil pipe.stats_jobs
+
+    assert_equal 'mrt00015', pipe.jobs.first.subid
+    assert_equal '/tmp/mrt00015', pipe.jobs.first.rawdir
+    assert_equal '/tmp/mrt00015_orig',  pipe.jobs.first.origdir
+    assert_equal '/tmp/mrt00015_proc',  pipe.jobs.first.procdir
+    assert_equal '/tmp/mrt00015_stats', pipe.jobs.first.statsdir
+    assert_equal :destroy, pipe.jobs.first.collision_policy
+    
+  end
+end

data/vendor/output_catcher.rb

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+=begin rdoc
+
+= OutputCatcher
+
+by Matthias Hennemeyer <mhennemeyer@gmail.com>
+
+== Introduction
+
+OutputCatcher is available as a Rails plugin and as a gem.
+It provides a way to capture the standard out($stdout) or standard error($stderr) of your code without pain
+and suppresses the output of the 'err' or 'out' stream.
+
+
+== Usage
+
+  OutputCatcher knows only two methods: .catch_err and .catch_out
+
+  To capture the stderr of your code:
+
+  err = OutputCatcher.catch_err do
+    $stderr << "error error"
+  end
+  err #=> "error error"
+
+
+  To capture the stdout of your code:
+
+  out = OutputCatcher.catch_out do
+    puts "Hello Hello"
+  end
+  out #=> "Hello Hello"
+
+== INSTALL:
+Rails:
+
+  $ ruby script/plugin install git://github.com/mhennemeyer/output_catcher.git
+
+Gem:
+
+  $ gem install mhennemeyer-output_catcher
+
+
+Copyright (c) 2008 Matthias Hennemeyer, released under the MIT license
+
+=end
+
+require 'stringio'
+
+class OutputCatcher
+  class << self
+    
+    def catch_io(post, &block)
+      original = eval("$std" + post)
+      fake = StringIO.new
+      eval("$std#{post} = fake")
+      begin
+        yield
+      ensure
+        eval("$std#{post} = original")
+      end
+      fake.string
+    end
+    
+    def catch_out(&block)
+      catch_io("out", &block)
+    end
+    
+    def catch_err(&block)
+      catch_io("err", &block)
+    end
+    
+  end
+end
+
+class Tee < IO
+  FILE_DESC = {:in => 0, :out => 1, :err => 2}
+  
+  def initialize(filename, post = :out, mode_string = 'w')
+    super(FILE_DESC[post], mode_string)
+    @file = File.open(filename, 'w')
+    eval("$std#{post} = self")
+  end
+  
+  def write(string)
+    STDOUT.write string
+    @file.puts string
+    @file.flush
+  end
+  
+  def self.open(filename, post, mode_string, &block)
+    
+  end
+end