c_nifti 0.0.1

data/COPYING.lesser

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+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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+
+
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+

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in c_nifti.gemspec
+gemspec

data/README.md

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+# CNifti
+
+Currently under development and not realeased yet! But should be ready for reading NIfTI image and header
+
+CNifti is a wrapper for the standard C NIfTI 1 library found at http://afni.nimh.nih.gov/pub/dist/src/nifti/
+
+## Installation
+
+Add this line to your application's Gemfile (not working before release):
+
+    gem 'c_nifti'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as  (not working before release):
+
+    $ gem install c_nifti
+
+## Usage
+
+    image_path = "image.nii.gz"
+    img = CNifti::Image.open(image_path)
+
+    img.header.ndim
+    img.header.nx
+    img.header.ny
+    img.header.nz
+    img.header.nt
+    img.header.nu
+    img.header.nv
+    img.header.nw
+    img.header.dim
+    img.header.nvox
+    img.header.nbyper
+    img.header.datatype
+    img.header.dx
+    img.header.dy
+    img.header.dz
+    img.header.dt
+    img.header.du
+    img.header.dv
+    img.header.dw
+    img.header.pixdim
+    img.header.scl_slope
+    img.header.scl_inter
+    img.header.cal_min
+    img.header.cal_max
+    img.header.qform_code
+    img.header.sform_code
+    img.header.freq_dim
+    img.header.phase_dim
+    img.header.slice_dim
+    img.header.slice_code
+    img.header.slice_start
+    img.header.slice_end
+    img.header.slice_duration
+    img.header.quatern_b
+    img.header.quatern_c
+    img.header.quatern_d
+    img.header.qoffset_x
+    img.header.qoffset_y
+    img.header.qoffset_z
+    img.header.qfac
+    img.header.qto_xyz
+    img.header.qto_ijk
+    img.header.sto_xyz
+    img.header.sto_ijk
+    img.header.toffset
+    img.header.xyz_units
+    img.header.time_units
+    img.header.nifti_type
+    img.header.intent_code
+    img.header.intent_p1
+    img.header.intent_p2
+    img.header.intent_p3
+    img.header.intent_name
+    img.header.descrip
+    img.header.aux_file
+    img.header.file_name
+    img.header.image_name
+    img.header.image_name_offset
+    img.header.swapsize
+    img.header.byteorder
+    img.header.analyze75_orient
+
+    img.header.description = "description"
+    img.header.aux_file = "aux_file"
+    img.header.file_name = "new_image.nii.gz" # resets the fname, iname and iname_offset of NIfTI
+
+    img.data.raw # returns the data into a unidimensional array
+    img.data.get_raw(0) # returns the data at index 0 from the unidimensional array
+    img.data.set_raw(0,1) # sets the data at index 0 from the unidimensional array to 1
+    img.data.shape # like img.header.dim but without the first element
+    img.data[0][0][0] # Supposing the data has 3 dimensions, returns its value
+    img.data[0][0][0] = 1 # Supposing the data has 3 dimensions, sets its value at position (0,0,0) to 1
+
+    img.save_as("out_#{image_path})
+
+### Not supported data types
+* DT_COMPLEX
+* DT_RGB
+* DT_ALL
+* DT_COMPLEX128
+* DT_COMPLEX256
+* DT_RGBA32
+
+### NIfTI extensions are not supported
+
+## Contributing
+
+1. Fork it ( https://github.com/rafamanzo/c_nifti/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+require 'rake/extensiontask'
+
+Rake::ExtensionTask.new('nifticlib') do |ext|
+  ext.lib_dir = "lib/nifticlib"
+end

data/c_nifti.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'c_nifti/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "c_nifti"
+  spec.version       = CNifti::VERSION
+  spec.authors       = ["Rafael Reggiani Manzo"]
+  spec.email         = ["rr.manzo@gmail.com"]
+  spec.summary       = "NIfTI 1 and ANALYZE 7.5 medical image formats IO"
+  spec.description   = "CNifti is a wrapper for the standard C NIfTI 1 library found at http://afni.nimh.nih.gov/pub/dist/src/nifti/"
+  spec.homepage      = "https://github.com/rafamanzo/c_nifti"
+  spec.license       = "LGPLv3"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.extensions = %w[ext/nifticlib/extconf.rb]
+
+  spec.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rake-compiler"
+  spec.add_development_dependency "rspec", "~> 3.0.0"
+  spec.add_development_dependency "mocha", "~> 1.1.0"
+  spec.add_development_dependency "simplecov"
+  spec.add_development_dependency "factory_girl", "~> 4.4.0"
+  spec.add_development_dependency "cucumber", "~> 1.3.16"
+end

data/ext/nifticlib/extconf.rb

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+require 'mkmf'
+
+find_executable('make')
+find_executable('csh')
+
+puts "Compiling standard C NIfTI library..."
+Dir.chdir("#{File.dirname(__FILE__)}/nifticlib-2.0.0") do
+  `patch -p0 < ../patches/nifticlib_fpic.patch`
+  `make all`
+end
+puts "Compiling standard C NIfTI library... Compiled!"
+
+find_library('niftiio', nil, "#{File.dirname(__FILE__)}/nifticlib-2.0.0/lib")
+find_library('znz', nil, "#{File.dirname(__FILE__)}/nifticlib-2.0.0/lib")
+have_library('m')
+have_library('z')
+find_header('nifti1_io.h', "#{File.dirname(__FILE__)}/nifticlib-2.0.0/include")
+find_header('nifti_image.h', "#{File.dirname(__FILE__)}/include")
+find_header('nifti_image_converters.h', "#{File.dirname(__FILE__)}/include")
+find_header('nifti_image_dimensions.h', "#{File.dirname(__FILE__)}/include")
+find_header('nifti_image_spacings.h', "#{File.dirname(__FILE__)}/include")
+find_header('nifti_image_timings.h', "#{File.dirname(__FILE__)}/include")
+find_header('nifti_image_quaternions.h', "#{File.dirname(__FILE__)}/include")
+find_header('nifti_image_transforms.h', "#{File.dirname(__FILE__)}/include")
+find_header('nifti_image_intents.h', "#{File.dirname(__FILE__)}/include")
+find_header('nifti_image_metadata.h', "#{File.dirname(__FILE__)}/include")
+
+$LIBS << " -lznz" # For some reason znz is not linked without this
+
+create_makefile 'nifticlib/nifticlib'

data/ext/nifticlib/include/nifti_image.h

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+VALUE nifti_image_data(VALUE self);
+VALUE init_nifti_image(VALUE module);

data/ext/nifticlib/include/nifti_image_converters.h

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+VALUE voxel_data_to_value(nifti_image *img, int index);
+nifti_image * to_nifti_image(VALUE rb_nifti_image);
+VALUE mat44_to_rb_array(mat44 matrix);

data/ext/nifticlib/include/nifti_image_dimensions.h

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+VALUE nifti_image_dimensions_init(VALUE klass);

data/ext/nifticlib/include/nifti_image_intents.h

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+VALUE nifti_image_intents_init(VALUE klass);

data/ext/nifticlib/include/nifti_image_metadata.h

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+VALUE nifti_image_metadata_init(VALUE klass);

data/ext/nifticlib/include/nifti_image_quaternions.h

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+VALUE nifti_image_quaternions_init(VALUE klass);

data/ext/nifticlib/include/nifti_image_spacings.h

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+VALUE nifti_image_spacings_init(VALUE klass);

data/ext/nifticlib/include/nifti_image_timings.h

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+VALUE nifti_image_timings_init(VALUE klass);

data/ext/nifticlib/include/nifti_image_transforms.h

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+VALUE nifti_image_transforms_init(VALUE klass);

data/ext/nifticlib/nifti_image.c

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+#include <ruby.h> // Ruby C extensions
+#include <nifti1_io.h> // standard NIfTI C library
+#include <stdbool.h> // Boolean type handling
+
+#include <nifti_image.h>
+#include <nifti_image_converters.h>
+#include <nifti_image_dimensions.h>
+#include <nifti_image_spacings.h>
+#include <nifti_image_timings.h>
+#include <nifti_image_quaternions.h>
+#include <nifti_image_transforms.h>
+#include <nifti_image_intents.h>
+#include <nifti_image_metadata.h>
+
+/***********/
+/* Scaling */
+/***********/
+
+VALUE nifti_image_scl_slope(VALUE self){
+  nifti_image *img = to_nifti_image(self);
+
+  return rb_float_new((double) img->scl_slope);
+}
+
+VALUE nifti_image_scl_inter(VALUE self){
+  nifti_image *img = to_nifti_image(self);
+
+  return rb_float_new((double) img->scl_inter);
+}
+
+/***************/
+/* Calibration */
+/***************/
+
+VALUE nifti_image_cal_min(VALUE self){
+  nifti_image *img = to_nifti_image(self);
+
+  return rb_float_new((double) img->cal_min);
+}
+
+VALUE nifti_image_cal_max(VALUE self){
+  nifti_image *img = to_nifti_image(self);
+
+  return rb_float_new((double) img->cal_max);
+}
+
+/********/
+/* Data */
+/********/
+
+VALUE nifti_image_data(VALUE self){
+  int i = 0;
+  nifti_image *img = to_nifti_image(self);
+
+  VALUE rb_data = rb_ary_new2(img->nvox);
+
+  for(i = 0; i < ((int) img->nvox); i++){
+    rb_ary_store(rb_data, i, voxel_data_to_value(img, i));
+  }
+
+  return rb_data;
+}
+
+VALUE nifti_image_set_data(VALUE self, VALUE r_index, VALUE r_value){
+  char *str_value;
+  nifti_image *img = to_nifti_image(self);
+  int index = NUM2INT(r_index);
+
+  // Types nifti1.h
+  switch(img->datatype){
+    case DT_BINARY: // DT_UINT8
+      if (r_value == Qtrue){
+        ((bool *) img->data)[index] = true;
+      }else{
+        ((bool *) img->data)[index] = false;
+      }
+      break;
+    case DT_UNSIGNED_CHAR:
+      Check_Type(r_value, T_STRING);
+      StringValue(r_value);
+      str_value = StringValuePtr(r_value);
+
+      ((unsigned char *) img->data)[index] = ((unsigned char) str_value[0]);
+      break;
+    case DT_SIGNED_SHORT: // DT_INT16
+      ((short *) img->data)[index] = ((short) NUM2INT(r_value));
+      break;
+    case DT_SIGNED_INT: // DT_INT32
+      ((int *) img->data)[index] = NUM2INT(r_value);
+      break;
+    case DT_FLOAT: // DT_FLOAT32
+      ((float *) img->data)[index] = ((float) NUM2DBL(r_value));
+      break;
+    case DT_DOUBLE: // DT_FLOAT64
+      ((double *) img->data)[index] = NUM2DBL(r_value);
+      break;
+    case DT_INT8:
+      Check_Type(r_value, T_STRING);
+      StringValue(r_value);
+      str_value = StringValuePtr(r_value);
+
+      ((char *) img->data)[index] = ((char) str_value[0]);
+      break;
+    case DT_UINT16:
+      ((unsigned short *) img->data)[index] = ((unsigned short) NUM2INT(r_value));
+      break;
+    case DT_UINT32:
+      ((unsigned int *) img->data)[index] = ((unsigned int) NUM2INT(r_value));
+      break;
+    case DT_INT64:
+      ((long long *) img->data)[index] = ((long long) NUM2LONG(r_value));
+      break;
+    case DT_UINT64:
+      ((unsigned long long *) img->data)[index] = ((unsigned long long) NUM2LONG(r_value));
+      break;
+    case DT_FLOAT128:
+      ((long double *) img->data)[index] = ((long double) NUM2DBL(r_value));
+      break;
+    default: // Unsupported types: DT_COMPLEX, DT_RGB, DT_ALL, DT_COMPLEX128, DT_COMPLEX256, DT_RGBA32
+      rb_raise(rb_eTypeError, "Unsupported datatype");
+  }
+
+  return r_value;
+}
+
+VALUE nifti_image_get_data(VALUE self, VALUE r_index){
+  nifti_image *img = to_nifti_image(self);
+
+  return voxel_data_to_value(img, NUM2INT(r_index));
+}
+/********/
+/* Type */
+/********/
+
+VALUE nifti_image_nifti_type(VALUE self){
+  nifti_image *img = to_nifti_image(self);
+
+  return INT2NUM(img->nifti_type);
+}
+
+/********/
+/* Init */
+/********/
+
+VALUE init_nifti_image(VALUE module){
+  VALUE cNIfTIImage = rb_define_class_under(module, "NIfTIImage", rb_cObject);
+
+  cNIfTIImage = nifti_image_dimensions_init(cNIfTIImage);
+  cNIfTIImage = nifti_image_spacings_init(cNIfTIImage);
+  // Scaling methods
+  rb_define_method(cNIfTIImage, "scl_slope", nifti_image_scl_slope, 0);
+  rb_define_method(cNIfTIImage, "scl_inter", nifti_image_scl_inter, 0);
+  // Calibration methods
+  rb_define_method(cNIfTIImage, "cal_min", nifti_image_cal_min, 0);
+  rb_define_method(cNIfTIImage, "cal_max", nifti_image_cal_max, 0);
+  cNIfTIImage = nifti_image_timings_init(cNIfTIImage);
+  cNIfTIImage = nifti_image_quaternions_init(cNIfTIImage);
+  cNIfTIImage = nifti_image_transforms_init(cNIfTIImage);
+  // Data methods
+  rb_define_method(cNIfTIImage, "data", nifti_image_data, 0);
+  rb_define_method(cNIfTIImage, "set_data", nifti_image_set_data, 2);
+  rb_define_method(cNIfTIImage, "get_data", nifti_image_get_data, 1);
+  // Type methods
+  rb_define_method(cNIfTIImage, "nifti_type", nifti_image_nifti_type, 0);
+  cNIfTIImage = nifti_image_intents_init(cNIfTIImage);
+  cNIfTIImage = nifti_image_metadata_init(cNIfTIImage);
+
+  return cNIfTIImage;
+}