c_nifti 0.0.1

data/ext/nifticlib/nifticlib.c

@@ -0,0 +1,107 @@
+#include <ruby.h> // Ruby C extensions
+#include <nifti1_io.h> // standard NIfTI C library
+#include <string.h>
+#include <stdio.h>
+
+#include <nifti_image.h>
+#include <nifti_image_converters.h>
+
+// DATA types
+VALUE mNIfTICLib;
+VALUE cNIfTIImage;
+
+/*********************/
+/* NIfTICLib Methods */
+/*********************/
+
+static VALUE nifti_image_read_wrapper(VALUE self, VALUE rb_input_file_path){
+  VALUE rb_img;
+  char *input_file_path = NULL;
+  nifti_image *img = NULL;
+
+  StringValue(rb_input_file_path);
+  input_file_path = StringValuePtr(rb_input_file_path);
+
+  img = nifti_image_read(input_file_path, 1);
+  if(!img) {
+    rb_raise(rb_eRuntimeError, "Failed to read NIfTI image from '%s'\n", input_file_path);
+  }
+
+  rb_img = Data_Wrap_Struct(cNIfTIImage, NULL, nifti_image_free, img);
+
+  return rb_img;
+}
+
+VALUE nifti_image_write_wrapper(VALUE self, VALUE rb_nifti_image, VALUE rb_output_file_path){
+  VALUE rb_img = Qnil;
+  char *output_file_path = NULL;
+  char *original_file_path = NULL;
+  nifti_image *img = to_nifti_image(rb_nifti_image);
+  FILE *output_file = NULL;
+
+  StringValue(rb_output_file_path);
+  output_file_path = StringValuePtr(rb_output_file_path);
+  output_file = fopen(output_file_path, "r");
+
+  if(output_file){
+    rb_raise(rb_eRuntimeError, "File %s already exists", output_file_path);
+    fclose(output_file);
+  }else{
+    original_file_path = malloc(RSTRING_LEN(rb_output_file_path)*sizeof(char));
+
+    strcpy(original_file_path,img->fname);
+    nifti_set_filenames(img, output_file_path, 1, 1);
+
+    nifti_image_write(img);
+    nifti_set_filenames(img, original_file_path, 0, 1);
+
+    rb_img = Data_Wrap_Struct(cNIfTIImage, NULL, nifti_image_free, nifti_image_read(output_file_path, 1));
+
+    return rb_img;
+  }
+}
+
+/******************/
+/* New NIfTIImage */
+/******************/
+
+VALUE nifti_image_new(VALUE self, VALUE r_dims, VALUE r_datatype, VALUE r_data_fill){
+  int i = 0;
+  int *dims = NULL;
+  int datatype = 0;
+  int data_fill = 0;
+  nifti_image *img = NULL;
+
+  dims = malloc(RARRAY_LEN(r_dims)*sizeof(int));
+
+  for(i = 0; i < RARRAY_LEN(r_dims); i++){
+    dims[i] = NUM2INT(rb_ary_entry(r_dims, i));
+  }
+
+  datatype = NUM2INT(r_datatype);
+
+  data_fill = NUM2INT(r_data_fill);
+
+  img = nifti_make_new_nim(dims, datatype, data_fill);
+
+  free(dims);
+
+  return  Data_Wrap_Struct(cNIfTIImage, NULL, nifti_image_free, img);
+}
+
+/********/
+/* Init */
+/********/
+
+void Init_nifticlib(void){
+  // NIfTICLib module
+  mNIfTICLib = rb_define_module("NIfTICLib");
+
+  // NIfTICLib methods
+  rb_define_singleton_method(mNIfTICLib, "read", nifti_image_read_wrapper, 1);
+  rb_define_singleton_method(mNIfTICLib, "write", nifti_image_write_wrapper, 2);
+
+  cNIfTIImage = init_nifti_image(mNIfTICLib);
+  // New
+  rb_define_singleton_method(cNIfTIImage, "new", nifti_image_new, 3);
+}

data/ext/nifticlib/patches/nifticlib_fpic.patch

@@ -0,0 +1,13 @@
+diff --git Makefile Makefile
+index bcb059c..1c40db2 100644
+--- Makefile
++++ Makefile
+@@ -24,7 +24,7 @@ RANLIB  = ranlib
+ DEPENDFLAGS	=	-MM
+ GNU_ANSI_FLAGS	= 	-Wall -ansi -pedantic
+ ANSI_FLAGS	= 	${GNU_ANSI_FLAGS}
+-CFLAGS		=	$(ANSI_FLAGS)
++CFLAGS		=	$(ANSI_FLAGS) -fPIC
+ 
+ ## Command defines
+ ## gmake does not work on MacOSX or some versions of linux MAKE  = gmake 

data/features/read_modify_write.feature

@@ -0,0 +1,11 @@
+Feature: Read, Modify and Write
+  In order to be able to work NIfTI images
+  As a developer
+  I want to read a image, modify it and save the modification
+
+  Scenario: with a existing image
+    Given I have opened the image at "features/support/fixtures/sample.nii.gz"
+    When I modify the image data at "0" "0" "0" setting it to "0"
+    And I save the image to "/tmp/c_nifti_test.nii.gz"
+    And I have opened the image at "/tmp/c_nifti_test.nii.gz"
+    Then I should get the data value "0" at the position "0" "0" "0"

data/features/step_definitions/nifti_image_steps.rb

@@ -0,0 +1,16 @@
+Given(/^I have opened the image at "(.*?)"$/) do |path|
+  @img = CNifti::Image.new.open(path)
+end
+
+When(/^I modify the image data at "(.*?)" "(.*?)" "(.*?)" setting it to "(.*?)"$/) do |x, y, z, value|
+  @img.data[x.to_i][y.to_i][z.to_i] = value.to_i
+end
+
+When(/^I save the image to "(.*?)"$/) do |path|
+  File.delete(path) if File.exists?(path)
+  @img.save_as(path)
+end
+
+Then(/^I should get the data value "(.*?)" at the position "(.*?)" "(.*?)" "(.*?)"$/) do |value, x, y, z|
+  expect(@img.data[x.to_i][y.to_i][z.to_i]).to eq(value.to_i)
+end

data/features/support/env.rb

@@ -0,0 +1,14 @@
+# 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 'c_nifti'
+
+require 'factory_girl'
+FactoryGirl.find_definitions

data/lib/c_nifti.rb

@@ -0,0 +1,9 @@
+require "c_nifti/version"
+require 'c_nifti/header_element'
+require 'c_nifti/header'
+require 'c_nifti/data'
+require 'c_nifti/image'
+
+module CNifti
+  # Your code goes here...
+end

data/lib/c_nifti/data.rb

@@ -0,0 +1,70 @@
+module CNifti
+  class Data
+    def initialize(nifti_image, previous_indexes=[])
+      @nifti_image = nifti_image
+      @previous_indexes = previous_indexes
+    end
+
+    def raw
+      @nifti_image.data
+    end
+
+    def set_raw(index, value)
+      @nifti_image.set_data(index, value)
+    end
+
+    def get_raw(index)
+      @nifti_image.get_data(index)
+    end
+
+    def shape
+      start_index = 1
+      @previous_indexes.each {start_index += 1}
+      @nifti_image.dim[start_index..@nifti_image.dim[0]]
+    end
+
+    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.get_raw(get_index_value(i)) }
+          value
+        else
+          self.get_raw(get_index_value(index))
+        end
+      else
+        Data.new(@nifti_image, @previous_indexes.clone << index)
+      end
+    end
+
+    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
+        self.set_raw(get_index_value(index), value)
+      end
+    end
+
+    private
+
+    def get_index_value(current_index)
+      reverse_dim = @nifti_image.dim.take(@nifti_image.dim[0] + 1).reverse
+      step = (reverse_dim.inject(:*)/@nifti_image.dim[0])/reverse_dim[0]
+
+      index_value = current_index*step
+      step /= reverse_dim[1]
+      dim_index = 1
+
+      @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

data/lib/c_nifti/header.rb

@@ -0,0 +1,16 @@
+module CNifti
+  class Header
+    include HeaderElement::Metadata
+    include HeaderElement::Dimensions
+    include HeaderElement::Intents
+    include HeaderElement::Quaternions
+    include HeaderElement::Spacings
+    include HeaderElement::Timings
+    include HeaderElement::Transforms
+    include HeaderElement::Miscellaneous
+
+    def initialize(nifti_image)
+      @nifti_image = nifti_image
+    end
+  end
+end

data/lib/c_nifti/header_element.rb

@@ -0,0 +1,13 @@
+require 'c_nifti/header_element/datatype'
+require 'c_nifti/header_element/metadata'
+require 'c_nifti/header_element/dimensions'
+require 'c_nifti/header_element/intents'
+require 'c_nifti/header_element/quaternions'
+require 'c_nifti/header_element/spacings'
+require 'c_nifti/header_element/timings'
+require 'c_nifti/header_element/transforms'
+require 'c_nifti/header_element/miscellaneous'
+
+module CNifti
+  module HeaderElement; end
+end

data/lib/c_nifti/header_element/datatype.rb

@@ -0,0 +1,49 @@
+require 'c_nifti/header_element/datatype/binary'
+require 'c_nifti/header_element/datatype/double'
+require 'c_nifti/header_element/datatype/float'
+require 'c_nifti/header_element/datatype/long_double'
+require 'c_nifti/header_element/datatype/long_long'
+require 'c_nifti/header_element/datatype/signed_char'
+require 'c_nifti/header_element/datatype/signed_int'
+require 'c_nifti/header_element/datatype/signed_short'
+require 'c_nifti/header_element/datatype/unsigned_char'
+require 'c_nifti/header_element/datatype/unsigned_int'
+require 'c_nifti/header_element/datatype/unsigned_long_long'
+require 'c_nifti/header_element/datatype/unsigned_short'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      def self.to_datatype(value)
+        case value
+        when Binary.to_i
+          return Binary
+        when Double.to_i
+          return Double
+        when Float.to_i
+          return Float
+        when LongDouble.to_i
+          return LongDouble
+        when LongLong.to_i
+          return LongLong
+        when SignedChar.to_i
+          return SignedChar
+        when SignedInt.to_i
+          return SignedInt
+        when SignedShort.to_i
+          return SignedShort
+        when UnsignedChar.to_i
+          return UnsignedChar
+        when UnsignedInt.to_i
+          return UnsignedInt
+        when UnsignedLongLong.to_i
+          return UnsignedLongLong
+        when UnsignedShort.to_i
+          return UnsignedShort
+        else
+          raise TypeError.new("Datatype #{value} unsupported")
+        end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/base.rb

@@ -0,0 +1,9 @@
+module CNifti
+  module HeaderElement
+    module Datatype
+      class Base
+        def self.to_i; raise NotImplementedError; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/binary.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class Binary < Base
+        def self.to_i; 1; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/double.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class Double < Base
+        def self.to_i; 64; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/float.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class Float < Base
+        def self.to_i; 16; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/long_double.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class LongDouble < Base
+        def self.to_i; 1538; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/long_long.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class LongLong < Base
+        def self.to_i; 1024; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/signed_char.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class SignedChar < Base
+        def self.to_i; 256; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/signed_int.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class SignedInt < Base
+        def self.to_i; 8; end
+      end
+    end
+  end
+end

data/lib/c_nifti/header_element/datatype/signed_short.rb

@@ -0,0 +1,11 @@
+require 'c_nifti/header_element/datatype/base'
+
+module CNifti
+  module HeaderElement
+    module Datatype
+      class SignedShort < Base
+        def self.to_i; 4; end
+      end
+    end
+  end
+end