nifti 0.0.1 → 0.0.2

data/.gitignore

@@ -1,6 +1,21 @@
-pkg/*
 *.gem
+*.rbc
 .bundle
-._*
-doc/*
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+.DS_Store
+.ruby-version
+.ruby-gemset
 

data/CHANGELOG

@@ -1,3 +1,13 @@
+= 0.0.2
+
+=== (Updates from Rafael Reggiani Manzo) March, 2014
+
+* Add Gzip Read/Write Support
+* Ruby 2.0 Compatibility
+* New NImage convenience class to index into NArray Image Data
+* Cleaned up the gemspec
+
+
 = 0.0.1
 
 === (In Development) February, 2011

data/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
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+other than an Application or a Combined Work as defined below.
+
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+of using an interface provided by the Library.
+
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+
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+       a copy of the Library already present on the user's computer
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+   be required to provide such information under section 6 of the
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+   you use option 4d0, the Installation Information must accompany
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+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
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+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
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+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
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+
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data/README.markdown

@@ -3,10 +3,10 @@ RUBY NIfTI
 
 Ruby NIfTI is a pure-ruby library for handling NIfTI data in Ruby. NIfTI
 [(Neuroimaging Informatics Technology Initiative)](http://nifti.nimh.nih.gov/)
-is an image format designed primarily for storing and analyzing MRI & PET
+is an image format designed primarily for the storage and analysis of MRI & PET
 imaging data.
 
-Ruby NIfTI currently only supports basic access to NIfTI files, including
+Ruby NIfTI currently supports basic access to NIfTI files, including
 basic and extended header information, as well as image information. It
 doesn't attempt to touch the image data (rotate it, etc.), but it does provide
 access to qform and sform orientation matrices. Nonetheless it does provide a
@@ -24,21 +24,36 @@ INSTALLATION
 BASIC USAGE
 -----------
 
+Initialize the library:
+
     require "nifti"
-    # Read file:
+
+Read file:
+
     obj = NIFTI::NObject.new("some_file.nii")
-    # Display some key information about the file:
+
+Display some key information about the file:
+
 	  puts obj.header['sform_code_descr']
     => "NIFTI_XFORM_SCANNER_ANAT"
-    # Retrieve the pixel data in a Ruby Array:
+
+Retrieve the pixel data in a Ruby Array:
+
     image = obj.get_image
-    # Load the pixel data to an NArray image object and display it on the screen:
+
+Load the pixel data to an NArray image object and display it on the screen:
+
     image = obj.get_image_narray
 
+Or load the pixel data into an NImage (for easier indexing):
+
+    image = obj.get_nimage
+    
+
 LIMITATIONS
 -----------
 
-There are plenty of NIfTI libraries around (the canonical
+There are several good NIfTI libraries around (the canonical
 [nifticlib](http://niftilib.sourceforge.net/), which includes c, python and
 matlab interfaces, and Matlab interfaces in the Mathworks image processing
 toolbox (IPT) and [Toolbox for
@@ -48,12 +63,13 @@ by Jimmy Shen.
 This library does not intend to replace them, but rather to provide a few ruby
 convenience methods for quickly accessing imaging data from ruby without
 having to call out to external programs, as well as write custom extensions to
-the NIfTI header. At current, it doesn't do much more than byte parsing and
-providing access to the header, and its quite slow when compared to existing
-libraries. However, [narray](http://narray.rubyforge.org/) is picking up and
-its possible that people would want to have some easy way to access NIfTI info
-using custom ruby libraries.
+the NIfTI header.
+
+GETTING HELP
+------------
 
+Feel free to use the [github issue tracker](https://github.com/brainmap/nifti/issues) 
+to post any questions, or email me directly.
 
 CREDIT
 ------
@@ -67,9 +83,8 @@ wouldn't exist without his examples.
 RESOURCES
 ---------
 
-* [Official home page](http://brainmap.wisc.edu/pages/10-RUBY-NIFTI)
-* [Development / Source code repository](https://github.com/brainmap/ruby-nifti)
-* [Documentation](http://rdoc.info/github/brainmap/ruby-nifti/master/frames)
+* [Development / Source code](https://github.com/brainmap/nifti)
+* [Documentation](http://rdoc.info/github/brainmap/nifti/master/frames)
 
 
 Examples
@@ -105,22 +120,3 @@ want to take find the mean and std dev of the entire image.
 
 If you don't have narray installed, you could still use obj.image as a ruby
 array, but you'd have to collect the summary stats yourself.
-
-
-COPYRIGHT
----------
-
-Copyright 2011 Erik Kastman
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-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, see http://www.gnu.org/licenses/ .

data/Rakefile

@@ -1,2 +1,18 @@
 require 'bundler'
 Bundler::GemHelper.install_tasks
+
+begin
+
+  require 'rspec'
+  require 'rspec/core/rake_task'
+  
+  
+  desc  "Run RSpec code examples"
+  RSpec::Core::RakeTask.new(:spec) do |t|
+    t.rcov = true
+    t.rcov_opts = %w{--exclude osx\/objc,gems\/,spec\/,features\/}
+  end
+
+rescue LoadError => e
+  puts e
+end

data/features/n_image.feature

@@ -0,0 +1,18 @@
+Feature: Image data interface with NImage
+  In Order to able manipulate the image data
+  As a developer
+  I want to access it as a multidimensional array
+
+  @clean_saved_files
+  Scenario: reading and writing
+    Given I have a NObject loaded
+    And I have the NImage representation of the image
+    When I get the value at ("64", "64", "35", "3")
+    # I know the dataset, so we know this value
+    Then the value should be equals to "2.4997341632843018"
+    When I set the value at ("64", "64", "35", "3") to "2.0"
+    And I save the NImage as new file
+    And I load the new file
+    And I have the NImage representation of the image
+    And I get the value at ("64", "64", "35", "3")
+    Then the value should be equals to "2.0"

data/features/step_definitions/n_image_steps.rb

@@ -0,0 +1,33 @@
+Given(/^I have a NObject loaded$/) do
+  @n_object = NIFTI::NObject.new(File.join(File.dirname(__FILE__), '..', 'support', 'fixtures', 'brain_dti.nii.gz'))
+end
+
+Given(/^I have the NImage representation of the image$/) do
+  @n_image = @n_object.get_nimage
+end
+
+When(/^I get the value at \("(.*?)", "(.*?)", "(.*?)", "(.*?)"\)$/) do |x, y, z, t|
+  @value = @n_image[x.to_i][y.to_i][z.to_i][t.to_i]
+end
+
+When(/^I set the value at \("(.*?)", "(.*?)", "(.*?)", "(.*?)"\) to "(.*?)"$/) do |x, y, z, t, val|
+  @n_image[x.to_i][y.to_i][z.to_i][t.to_i] = val.to_f
+end
+
+When(/^I save the NImage as new file$/) do
+  obj = NIFTI::NObject.new
+  obj.header = @n_object.header
+  obj.extended_header = @n_object.extended_header
+  obj.image = @n_image.array_image
+
+  writer = NIFTI::NWrite.new(obj, "test.nii.gz")
+  writer.write
+end
+
+When(/^I load the new file$/) do
+  @n_object = NIFTI::NObject.new('test.nii.gz')
+end
+
+Then(/^the value should be equals to "(.*?)"$/) do |val|
+  @value.should eq(val.to_f)
+end

data/features/support/env.rb

@@ -0,0 +1,11 @@
+# SimpleCov for test coverage report
+require 'simplecov'
+SimpleCov.start do
+  add_filter "/spec/"
+  add_filter "/features/"
+
+  coverage_dir 'coverage/cucumber'
+end
+
+# The gem itself
+require 'nifti'

data/features/support/hooks.rb

@@ -0,0 +1,3 @@
+After('@clean_saved_files') do
+  File.delete('test.nii.gz') if File.exist?('test.nii.gz')
+end

data/lib/nifti.rb

@@ -12,6 +12,7 @@ module NIFTI; end
 require 'nifti/n_object'
 require 'nifti/n_read'
 require 'nifti/n_write'
+require 'nifti/n_image'
 require 'nifti/stream'
 require 'nifti/constants'
 

data/lib/nifti/n_image.rb

@@ -0,0 +1,110 @@
+module NIFTI
+  # The NImage class is a container for the "raw" NIFTI image data making easier to deal with them.
+
+  class NImage
+    attr_reader :array_image, :dim, :previous_indexes
+
+    # Creates an NImage instance.
+    #
+    # The NImages instance provides a user friendly interface to the NIFTI Image
+    # A NImage is typically built by NObject instance
+    #
+    # === Parameters
+    #
+    # * <tt>array_image</tt> -- The NIFTI image contained on and one dimensional array
+    # * <tt>dim</tt> -- The dimensions array from the NIFTI header.
+    #
+    # === Examples
+    #
+    #   # Creates an NImage to deal with an 9 position array that represents a 3x3 matrix
+    #   img = Nimage.new(Array.new(9,0.0), [2,3,3])
+    #
+    def initialize(array_image, dim, previous_indexes=[])
+      @array_image = array_image
+      @dim = dim
+      @previous_indexes = previous_indexes
+    end
+
+    # Retrieves an element or partition of the dataset
+    #
+    # === Parameters
+    #
+    # * <tt>index</tt> -- The desired index on the dataset
+    #
+    # === Options
+    #
+    # === Examples
+    #
+    #   img[0][0]
+    #   img[0][0..1]
+    #
+    def [](index)
+      # Dealing with Ranges is useful when the image represents a tensor
+      if (index.is_a?(Fixnum) && index >= self.shape[0]) || (index.is_a?(Range) && index.last >= self.shape[0])
+        raise IndexError.new("Index over bounds")
+      elsif self.shape.count == 1
+        if index.is_a?(Range)
+          value = []
+          index.each { |i| value << self.array_image[get_index_value(i)] }
+          value
+        else
+          self.array_image[get_index_value(index)]
+        end
+      else
+        NImage.new(self.array_image, self.dim, self.previous_indexes.clone << index)
+      end
+    end
+
+    # Set the value for an element of the dataset
+    #
+    # === Parameters
+    #
+    # * <tt>index</tt> -- The desired index on the dataset
+    # * <tt>value</tt> -- The value that the will be set
+    #
+    # === Options
+    #
+    # === Examples
+    #
+    #   img[0][0] = 1.0
+    #
+    def []=(index,value)
+      if self.shape.count != 1 or index >= self.shape[0]
+        raise IndexError.new("You can only set values for array values")
+      else
+        @array_image[get_index_value(index)] = value
+      end
+    end
+
+    # Dataset shape
+    #
+    # === Examples
+    #
+    #   img.shape
+    #
+    def shape
+      start_index = 1
+      self.previous_indexes.each {start_index += 1}
+      self.dim[start_index..self.dim[0]]
+    end
+
+    private
+
+    def get_index_value(current_index)
+      reverse_dim = self.dim.take(self.dim[0] + 1).reverse
+      step = (reverse_dim.inject(:*)/self.dim[0])/reverse_dim[0]
+
+      index_value = current_index*step
+      step /= reverse_dim[1]
+      dim_index = 1
+
+      self.previous_indexes.reverse_each do |previous_index|
+        index_value += step*previous_index
+        dim_index += 1
+        step /= reverse_dim[dim_index] if dim_index < (reverse_dim.count - 1)
+      end
+
+      index_value
+    end
+  end
+end