optimus-ep 0.5 → 0.5.5

data/GPL.txt

@@ -0,0 +1,280 @@
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+
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+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
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+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
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data/History.txt

@@ -0,0 +1,19 @@
+== 0.5.5 7/09/2008
+* New features:
+  * Supports making multiple passes through data, to allow extracting multiple
+    stimuli that occur on the same row
+  * Created a general-purpose stimulus extractor to pull data out in the
+    format:
+    stimulus \t onset__time \t offset__time
+* Architectural changes:
+  * Created a BasicTransformer that performs all of the basic operations to
+    datasets: column calculation, row filtering, and multipass
+  * Moved ColumnCalculator, RowFilter, and Multipasser into a Transformers
+    module
+  * Support release via hoe / rubygems
+
+== 0.5.0 6/26/2008
+
+* First public gem release
+  * Supports converting general Eprime files into tab-delimited files
+  * Supports converting Eprime files into AFNI stim_times files

data/License.txt

@@ -0,0 +1,17 @@
+Optimus: Libraries and utilities for interacting with E-Prime data files
+Copyright (C) 2008 Board of Regents of the University of Wisconsin System
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of version 2 of the GNU General Public
+License as published by the Free Software Foundation.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+E-Prime is a registered trademark of Psychology Software Tools, Inc.

data/Manifest.txt

@@ -0,0 +1,47 @@
+GPL.txt
+History.txt
+License.txt
+Manifest.txt
+README.txt
+Rakefile
+bin/eprime2tabfile
+lib/calculator.rb
+lib/eprime.rb
+lib/eprime_data.rb
+lib/eprime_reader.rb
+lib/eprimetab_parser.rb
+lib/excel_parser.rb
+lib/log_file_parser.rb
+lib/tabfile_parser.rb
+lib/tabfile_writer.rb
+lib/transformers/basic_transformer.rb
+lib/transformers/column_calculator.rb
+lib/transformers/multipasser.rb
+lib/transformers/row_filter.rb
+lib/transformers/timing_extractor.rb
+lib/version.rb
+lib/writers/stimtimes_writer.rb
+spec/calculator_spec.rb
+spec/eprime_data_spec.rb
+spec/eprime_reader_spec.rb
+spec/eprimetab_parser_spec.rb
+spec/excel_parser_spec.rb
+spec/log_file_parser_spec.rb
+spec/samples/bad_excel_tsv.txt
+spec/samples/corrupt_log_file.txt
+spec/samples/eprime_tsv.txt
+spec/samples/excel_tsv.txt
+spec/samples/optimus_log.txt
+spec/samples/short_columns.txt
+spec/samples/sorted_columns.txt
+spec/samples/std_columns.txt
+spec/samples/unknown_type.txt
+spec/samples/unreadable_file
+spec/spec_helper.rb
+spec/tabfile_parser_spec.rb
+spec/tabfile_writer_spec.rb
+spec/transformers/basic_transformer_spec.rb
+spec/transformers/column_calculator_spec.rb
+spec/transformers/multipasser_spec.rb
+spec/transformers/row_filter_spec.rb
+spec/writers/stimtimes_writer_spec.rb

data/README.txt

@@ -0,0 +1,45 @@
+= optimus-ep
+
+* FIX (url)
+
+== DESCRIPTION:
+
+FIX (describe your package)
+
+== FEATURES/PROBLEMS:
+
+* FIX (list of features or problems)
+
+== SYNOPSIS:
+
+  FIX (code sample of usage)
+
+== REQUIREMENTS:
+
+* FIX (list of requirements)
+
+== INSTALL:
+
+* FIX (sudo gem install, anything else)
+
+== LICENSE:
+
+(The GNU Public License, Version 2)
+
+Optimus: Libraries and utilities for interacting with E-Prime data files
+Copyright (C) 2008 Board of Regents of the University of Wisconsin System
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of version 2 of the GNU General Public
+License as published by the Free Software Foundation.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+E-Prime is a registered trademark of Psychology Software Tools, Inc.

data/Rakefile

@@ -1,9 +1,11 @@
 require 'rake'
 require 'spec/rake/spectask'
+require 'config/requirements'
+require 'config/hoe' # setup Hoe + all gem configuration
+
+Dir['tasks/**/*.rake'].each { |rake| load rake }
 
 desc "Run specs"
 Spec::Rake::SpecTask.new('default') do |t|
   t.spec_files = FileList['spec/**/*.rb']
 end
-
-

data/lib/calculator.rb

@@ -31,8 +31,9 @@ module Eprime
         prefix(char('-') >> Neg, 60)
       expr = nil
       float_parser = number.map(&To_f)
+      string_parser = regexp(/[_a-z]\S*/i)
       grouping_parser = char('(') >>(lazy{expr})<< char(')')
-      term = alt(float_parser, grouping_parser)
+      term = alt(float_parser, grouping_parser, string_parser)
       delim = whitespace.many_
       expr = delim >> Expressions.build(term, ops, delim)
       @parser = expr << eof
@@ -40,6 +41,7 @@ module Eprime
     
     def compute(expression)
       ans = @parser.parse(expression)
+      return ans if ans.is_a?(String)
       if (ans - ans.to_i) == 0
         ans = ans.to_i
       end

data/lib/eprime.rb

@@ -9,6 +9,7 @@
 $: << File.expand_path(File.join(File.dirname(__FILE__), "..", "lib"))
 
 require 'eprime_data'
+require 'version'
 require 'tabfile_writer'
 require 'eprime_reader'
 

data/lib/eprime_data.rb

@@ -71,14 +71,21 @@ module Eprime
       datasets.each do |source|
         source.each do |row|
           r = self.add_row
-          source.columns.each do |col|
+          row.columns.each do |col|
             r[col] = row[col]
           end
+          r.sort_value = row.sort_value
         end
       end
       return self
     end
     
+    def dup
+      Eprime::Data.new().merge!(self)
+    end
+    
+    alias :to_eprime_data :dup
+    
     # We mostly delegate to our rows array
     def method_missing(method, *args, &block)
       @rows.send method, *args, &block
@@ -115,9 +122,13 @@ module Eprime
     end
     
     class Row
+      attr_accessor :sort_value
+      
       def initialize(parent)
         @data = []
         @parent = parent
+        # Ensure it's comparable
+        @sort_value = 1
       end
       
       def [](index)
@@ -136,6 +147,10 @@ module Eprime
         @data[num_index] = value
       end
       
+      def <=>(other)
+        @sort_value <=> other.sort_value
+      end
+      
       def columns
         @parent.columns
       end

data/lib/transformers/basic_transformer.rb

@@ -0,0 +1,103 @@
+# Part of the Optimus package for managing E-Prime data
+# 
+# Copyright (C) 2008 Board of Regents of the University of Wisconsin System
+# 
+# Written by Nathan Vack <njvack@wisc.edu>, at the Waisman Laborotory for Brain
+# Imaging and Behavior, University of Wisconsin - Madison
+#
+# This is a complete general eprime transforer -- it supports computed columns
+# row filters, and multipass operation. In general, once you've read a file in,
+# this is probably what you want to use.
+# Essentially, this is just a wrapper around the ColumnCalculator,
+# RowFilter, and Multipasser classes
+
+require 'eprime'
+require 'transformers/column_calculator'
+require 'transformers/row_filter'
+require 'transformers/multipasser'
+
+module Eprime
+  module Transformers
+    class BasicTransformer
+      def initialize(data)
+        @computed_columns = []
+        @copydown_columns = []
+        @counter_columns = []
+        @row_filter = lambda {|r| true}
+        @passes = []
+        self.data = data
+      end
+      
+      # Delegate to our processed object for... anything we can't already do.
+      def method_missing(m, *args, &block)
+        processed.send(m, *args, &block)
+      end
+      
+      def data=(data)
+        reset!
+        @data = Eprime::Data.new.merge(data)
+      end
+      
+      def computed_column(*args)
+        reset!
+        @computed_columns << args
+      end
+      
+      def copydown_column(*args)
+        reset!
+        @copydown_columns << args
+      end
+      
+      def counter_column(*args)
+        reset!
+        @counter_columns << args
+      end
+      
+      def row_filter=(filter)
+        reset!
+        @row_filter = filter
+      end
+      
+      def add_pass(*args)
+        reset!
+        p = Multipasser::Pass.new(*args)
+        yield p if block_given?
+        @passes << p
+        return p
+      end
+      
+      private
+      
+      # This method should be used instead of accessing @processed directly
+      def processed
+        compute! and return @processed
+      end
+      
+      def reset!
+        @processed = nil
+        return true
+      end
+      
+      def compute!
+        return @processed if @processed
+        cc = ColumnCalculator.new
+        cc.data = @data
+        @computed_columns.each do |c|
+          cc.computed_column *c
+        end
+        @copydown_columns.each do |c|
+          cc.copydown_column *c
+        end
+        @counter_columns.each do |c|
+          cc.counter_column *c
+        end
+        filtered = RowFilter.new(cc, @row_filter)
+        multi = Multipasser.new(filtered)
+        @passes.each do |p|
+          multi.add_pass(p)
+        end
+        @processed = Eprime::Data.new.merge(multi)
+      end
+    end
+  end
+end