nifti 0.0.1 → 0.0.2

data/spec/custom_matchers.rb

@@ -1,3 +1,4 @@
+require 'rspec'
 require 'digest/md5'
 
 # Source: Matt Wynne; https://gist.github.com/736421

data/spec/nifti/n_image_spec.rb

@@ -0,0 +1,76 @@
+require 'spec_helper'
+
+describe NIFTI::NImage do
+  let!(:image_array) { Array.new(27,0.0) }
+  let!(:dim) { [3, 3, 3, 3, 1, 1, 1] }
+
+  describe 'shape' do
+    it 'should disconsider the first (number of dimensions) and three last elements of dim' do
+      NImage.new(image_array, dim).shape.should eq([3,3,3])
+    end
+  end
+
+  describe '[]' do
+    subject { NImage.new(image_array, dim) }
+
+    context 'with a Fixnum' do
+      context 'with a index out of range' do
+        it 'should raise a IndexError' do
+          expect{ subject[2][2][3] }.to raise_error(IndexError)
+        end
+      end
+
+      context 'with a valid index' do
+        it 'should return the value' do
+          mod_image_array = image_array
+          mod_image_array[26] = 1.0
+          n_image = NImage.new(mod_image_array, dim)
+
+          n_image[2][2][2].should eq(1.0)
+        end
+      end
+    end
+
+    context 'with a Range' do
+      context 'with a index out of range' do
+        it 'should raise a IndexError' do
+          expect{ subject[2][2][0..3] }.to raise_error(IndexError)
+        end
+      end
+
+      context 'with a valid index' do
+        it 'should return the value' do
+          mod_image_array = image_array
+          mod_image_array[26] = 1.0
+          n_image = NImage.new(mod_image_array, dim)
+
+          n_image[2][2][0..2].should eq([0.0, 0.0, 1.0])
+        end
+      end
+    end
+  end
+
+  describe '[]=' do
+    subject { NImage.new(image_array, dim) }
+
+    context 'when setting value for a non Fixnum' do
+      it 'should raise an error' do
+        expect { subject[2]=1.0}.to raise_error(IndexError)
+      end
+    end
+
+    context 'with an invalid index' do
+      it 'should raise an error' do
+        expect { subject[2][2][3]=1.0}.to raise_error(IndexError)
+      end
+    end
+
+    context 'with a valid index' do
+      it 'should set the value' do
+        subject[2][2][2] = 1.0
+
+        image_array[26].should eq(1.0)
+      end
+    end
+  end
+end

data/spec/nifti/n_object_spec.rb

@@ -26,36 +26,36 @@ describe NIFTI::NObject do
       "intent_p3"=>0.0, "regular"=>"r"
     }
   end
-  
+
   # Think of these more as integration tests, since the actual reading
   # is done and tested in the NRead spec
   it "should read a nifti file and correctly initialize header and image" do
     obj = NObject.new(NIFTI_TEST_FILE1)
-    
+
     obj.header.should == @valid_header
     obj.extended_header.should_not be_empty
     obj.extended_header.first[:esize].should == 5680
     obj.extended_header.first[:ecode].should == 4
     obj.extended_header.first[:data].length.should == @fixture_afni_extension_length
     obj.image.should be_nil
-    
+
   end
 
   it "should read a binary string and correctly initialize header and image" do
     obj = NObject.new(@string, :bin => true)
-    
+
     obj.header.should == @valid_header
     obj.extended_header.should_not be_empty
     obj.extended_header.first[:esize].should == 5680
     obj.extended_header.first[:ecode].should == 4
     obj.extended_header.first[:data].length.should == @fixture_afni_extension_length
     obj.image.should be_nil
-        
+
   end
-  
+
   it "should read a nifti file with image" do
     obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
-    
+
     obj.header.should == @valid_header
     obj.extended_header.should_not be_empty
     obj.extended_header.first[:esize].should == 5680
@@ -63,12 +63,12 @@ describe NIFTI::NObject do
     obj.extended_header.first[:data].length.should == @fixture_afni_extension_length
     obj.image.should_not be_nil
     obj.image.length.should == @fixture_image_length
-    
+
   end
-  
+
   it "should read a nifti file with image as narray" do
     obj = NObject.new(NIFTI_TEST_FILE1, :image => true, :narray => true)
-    
+
     obj.header.should == @valid_header
     obj.extended_header.should_not be_empty
     obj.extended_header.first[:esize].should == 5680
@@ -77,33 +77,38 @@ describe NIFTI::NObject do
     obj.image.should_not be_nil
     obj.image.class.should == NArray
     obj.image.dim.should == 3
-    
+
   end
-  
+
   it "should retrieve image data when requested" do
     obj = NObject.new(NIFTI_TEST_FILE1)
     obj.get_image.length.should == @fixture_image_length
   end
-  
-  
+
+
   it "should raise an error if initialized with bad argument" do
     lambda {
       NObject.new(12345)
     }.should raise_error ArgumentError, /Invalid argument/
   end
-  
+
   it "should sucessfully write a NIfTI file" do
     obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
     obj.write(@new_fixture_file_name)
     File.exist?(@new_fixture_file_name).should be_true
     obj.write_success.should be_true
   end
-  
-  it "should be able to assign an image" do 
+
+  it "should be able to assign an image" do
     obj = NObject.new(@string, :bin => true, :image => true)
     obj.image = [0] * @fixture_image_length
   end
-  
+
+  it 'should retrieve an NImage' do
+    obj = NObject.new(NIFTI_TEST_FILE1)
+    obj.get_nimage.should be_a(NImage)
+  end
+
   after :each do
     File.delete @new_fixture_file_name if File.exist? @new_fixture_file_name
   end

data/spec/nifti/n_read_spec.rb

@@ -1,9 +1,7 @@
 require 'spec_helper'
 
 describe NIFTI::NRead do
-  before :all do
-    @string = File.open(NIFTI_TEST_FILE1, 'rb').read
-    @stream = Stream.new(@string, false)
+  before do
     @fixture_image_length = 983040
     @fixture_afni_extension_length = 5661
     @valid_header = {
@@ -25,65 +23,133 @@ describe NIFTI::NRead do
       "cal_max"=>0.0, "vox_offset"=>6032.0, "slice_start"=>0,
       "intent_p3"=>0.0, "regular"=>"r"
     }
-    @n_read_obj = NRead.new(@string, :bin => true)
   end
-  
-  it "should read a binary string and correctly return header variables" do
-    NRead.new(@string, :bin => true).hdr.should == @valid_header
-  end
-  
-  it "should read a nifti file and correctly return header variables" do
-    NRead.new(NIFTI_TEST_FILE1).hdr.should == @valid_header
-  end
-  
-  it "should raise IOError if header size != 348." do
-    str = @string.dup
-    str[0..4] = [0].pack("N*")
-    lambda {
-      NRead.new(str, :bin => true).hdr
-    }.should raise_error IOError, /Header appears to be malformed/
-  end
-  
-  it "should raise IOError if magic != ni1 or n+1." do
-    str = @string.dup
-    str[344..348] = ["NOPE"].pack("a*")
-    lambda {
-      NRead.new(str, :bin => true).hdr
-    }.should raise_error IOError, /Header appears to be malformed/
-  end
-  
-  it "should read image data correctly if :image option is true" do
-    obj = NRead.new(@string, :bin => true, :image => true)
-    obj.image_rubyarray.class.should == Array
-    obj.image_rubyarray.length.should == @fixture_image_length
-    # Since this is a fixture, we know exactly what the values are.
-    # Pick some from the middle of the string and test them.
-    obj.image_rubyarray[(@fixture_image_length / 2)..(@fixture_image_length/2 + 100)].should == [0, 0, 0, 0, 18, 36, 25, 23, 19, 23, 13, 14, 16, 16, 12, 16, 22, 17, 13, 17, 19, 24, 19, 14, 11, 16, 49, 81, 129, 194, 216, 175, 130, 128, 146, 154, 159, 205, 304, 391, 414, 380, 320, 281, 297, 343, 358, 322, 287, 339, 450, 493, 426, 344, 310, 285, 275, 290, 282, 283, 310, 278, 268, 222, 49, 284, 235, 172, 116, 108, 115, 112, 135, 176, 196, 200, 216, 207, 86, 30, 152, 161, 138, 117, 81, 47, 73, 207, 381, 459, 415, 346, 353, 429, 490, 503, 492, 454, 379, 304, 275]
-    obj.image_narray.should be_nil
-  end
-  
-  it "should return an narray if requested" do
-    obj = NRead.new(@string, :bin => true, :narray => true)
-    obj.image_narray.should_not be_nil
+
+  context 'with an uncompressed file' do
+    before do
+      @string = File.open(NIFTI_TEST_FILE1, 'rb').read
+      @stream = Stream.new(@string, false)
+      @n_read_obj = NRead.new(@string, :bin => true)
+    end
+
+    it "should read a binary string and correctly return header variables" do
+      NRead.new(@string, :bin => true).hdr.should == @valid_header
+    end
+
+    it "should read a nifti file and correctly return header variables" do
+      NRead.new(NIFTI_TEST_FILE1).hdr.should == @valid_header
+    end
+
+    it "should raise IOError if header size != 348." do
+      str = @string.dup
+      str[0..4] = [0].pack("N*")
+      lambda {
+        NRead.new(str, :bin => true).hdr
+      }.should raise_error IOError, /Header appears to be malformed/
+    end
+
+    it "should raise IOError if magic != ni1 or n+1." do
+      str = @string.dup
+      str[344..348] = ["NOPE"].pack("a*")
+      lambda {
+        NRead.new(str, :bin => true).hdr
+      }.should raise_error IOError, /Header appears to be malformed/
+    end
+
+    it "should read image data correctly if :image option is true" do
+      obj = NRead.new(@string, :bin => true, :image => true)
+      obj.image_rubyarray.class.should == Array
+      obj.image_rubyarray.length.should == @fixture_image_length
+      # Since this is a fixture, we know exactly what the values are.
+      # Pick some from the middle of the string and test them.
+      obj.image_rubyarray[(@fixture_image_length / 2)..(@fixture_image_length/2 + 100)].should == [0, 0, 0, 0, 18, 36, 25, 23, 19, 23, 13, 14, 16, 16, 12, 16, 22, 17, 13, 17, 19, 24, 19, 14, 11, 16, 49, 81, 129, 194, 216, 175, 130, 128, 146, 154, 159, 205, 304, 391, 414, 380, 320, 281, 297, 343, 358, 322, 287, 339, 450, 493, 426, 344, 310, 285, 275, 290, 282, 283, 310, 278, 268, 222, 49, 284, 235, 172, 116, 108, 115, 112, 135, 176, 196, 200, 216, 207, 86, 30, 152, 161, 138, 117, 81, 47, 73, 207, 381, 459, 415, 346, 353, 429, 490, 503, 492, 454, 379, 304, 275]
+      obj.image_narray.should be_nil
+    end
+
+    it "should return an narray if requested" do
+      obj = NRead.new(@string, :bin => true, :narray => true)
+      obj.image_narray.should_not be_nil
+    end
+
+    it "should add an NArray Install message and not set the image_narray if NArray was not available" do
+      Object.expects(:const_defined?).with('NArray').returns(false)
+      obj = NRead.new(@string, :bin => true, :narray => true)
+      obj.msg.should_not be_empty
+      obj.msg.grep(/Please `gem install narray`/).empty?.should be_false
+      obj.image_narray.should be_nil
+      obj.image_rubyarray.size.should == @fixture_image_length
+    end
+
+    it "should read extended header attributes" do
+      @n_read_obj.extended_header.should_not be_empty
+      @n_read_obj.extended_header.first[:esize].should == 5680
+      @n_read_obj.extended_header.first[:ecode].should == 4
+      @n_read_obj.extended_header.first[:data].length.should == @fixture_afni_extension_length
+      @n_read_obj.extended_header.first[:data].should == "<?xml version='1.0' ?>\n<AFNI_attributes\n  self_idcode=\"XYZ_Fk5B7fY4srOPxYrGolqMIg\"\n  NIfTI_nums=\"256,256,15,1,1,4\"\n  ni_form=\"ni_group\" >\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"HISTORY_NOTE\" >\n \"[erik@nelson.medicine.wisc.edu: Fri Jan 21 10:24:14 2011] to3d -prefix 3plLoc.nii I0001.dcm I0002.dcm I0003.dcm ... I0014.dcm I0015.dcm\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"TYPESTRING\" >\n \"3DIM_HEAD_ANAT\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"IDCODE_STRING\" >\n \"XYZ_Fk5B7fY4srOPxYrGolqMIg\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"IDCODE_DATE\" >\n \"Fri Jan 21 10:24:15 2011\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"SCENE_DATA\" >\n 0\n 0\n 0\n -999\n -999\n -999\n -999\n -999\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"LABEL_1\" >\n \"3plLoc.nii+orig\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"LABEL_2\" >\n \"Viggo!\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"DATASET_NAME\" >\n \"./3plLoc.nii+orig\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"3\"\n  atr_name=\"ORIENT_SPECIFIC\" >\n 0\n 3\n 4\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"3\"\n  atr_name=\"ORIGIN\" >\n -119.531\n -159.531\n -25\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"3\"\n  atr_name=\"DELTA\" >\n 0.9375\n 0.9375\n 12.5\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"12\"\n  atr_name=\"IJK_TO_DICOM\" >\n 0.9375\n 0.9375\n 0.9375\n -360\n 0\n 0\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"12\"\n  atr_name=\"IJK_TO_DICOM_REAL\" >\n 0.9375\n 0\n 0\n -119.531\n 0\n 0.9375\n 0\n -159.531\n 0\n 0\n 12.5\n -25\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"30\"\n  atr_name=\"MARKS_XYZ\" >\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"MARKS_LAB\" >\n \"AC superior edge~~~~AC posterior margin~PC inferior edge~~~~First mid-sag pt~~~~Another mid-sag pt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"3\"\n  atr_name=\"MARKS_HELP\" >\n \"This is the uppermost point&#x0a;on the anterior commisure,&#x0a;in the mid-sagittal plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~This is the rearmost point&#x0a;on the anterior commisure,&#x0a;in the mid-sagittal plane.&#x0a;[Just a couple mm behind and&#x0a; below the AC superior edge.]~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~This is the bottommost point&#x0a;on the posterior commissure,&#x0a;in the mid-sagittal plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~You must also specify two other points in the&#x0a;mid-sagittal plane, ABOVE the corpus callosum&#x0a;(i.e., in the longitudinal fissure).  These&#x0a;points are needed to define the vertical plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n \"~~~~~~~~~~~~~~~~~~~~~~~~You must also specify two other points in the&#x0a;mid-sagittal plane, ABOVE the corpus callosum&#x0a;(i.e., in the longitudinal fissure).  These&#x0a;points are needed to define the vertical plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n \"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"MARKS_FLAGS\" >\n 1\n 1\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"2\"\n  atr_name=\"BRICK_STATS\" >\n 0\n 2402\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"DATASET_RANK\" >\n 3\n 1\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"5\"\n  atr_name=\"DATASET_DIMENSIONS\" >\n 256\n 256\n 15\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"1\"\n  atr_name=\"BRICK_TYPES\" >\n 1\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"1\"\n  atr_name=\"BRICK_FLOAT_FACS\" >\n 0\n</AFNI_atr>\n\n</AFNI_attributes>\n"
+    end
   end
-  
-  it "should add an NArray Install message and not set the image_narray if NArray was not available" do
-    Object.send(:remove_const, :NArray)
-    obj = NRead.new(@string, :bin => true, :narray => true)
-    obj.msg.should_not be_empty
-    obj.msg.grep(/Please `gem install narray`/).empty?.should be_false
-    obj.image_narray.should be_nil
-    obj.image_rubyarray.size.should == @fixture_image_length
-    require 'narray'
+
+  context 'with an gzip compressed file' do
+    before do
+      @string = File.open(NIFTI_TEST_FILE1_GZ, 'rb').read
+      @stream = Stream.new(@string, false)
+      @n_read_obj = NRead.new(NIFTI_TEST_FILE1_GZ)
+    end
+
+    it "should read a nifti file and correctly return header variables" do
+      NRead.new(NIFTI_TEST_FILE1_GZ).hdr.should == @valid_header
+    end
+
+    it "should raise IOError if header size != 348." do
+      str = @string.dup
+      str[0..4] = [0].pack("N*")
+      lambda {
+        NRead.new(str, :bin => true).hdr
+      }.should raise_error IOError, /Header appears to be malformed/
+    end
+
+    it "should raise IOError if magic != ni1 or n+1." do
+      str = @string.dup
+      str[344..348] = ["NOPE"].pack("a*")
+      lambda {
+        NRead.new(str, :bin => true).hdr
+      }.should raise_error IOError, /Header appears to be malformed/
+    end
+
+    it "should read image data correctly if :image option is true" do
+      obj = NRead.new(NIFTI_TEST_FILE1_GZ, :image => true)
+      obj.image_rubyarray.class.should == Array
+      obj.image_rubyarray.length.should == @fixture_image_length
+      # Since this is a fixture, we know exactly what the values are.
+      # Pick some from the middle of the string and test them.
+      obj.image_rubyarray[(@fixture_image_length / 2)..(@fixture_image_length/2 + 100)].should == [0, 0, 0, 0, 18, 36, 25, 23, 19, 23, 13, 14, 16, 16, 12, 16, 22, 17, 13, 17, 19, 24, 19, 14, 11, 16, 49, 81, 129, 194, 216, 175, 130, 128, 146, 154, 159, 205, 304, 391, 414, 380, 320, 281, 297, 343, 358, 322, 287, 339, 450, 493, 426, 344, 310, 285, 275, 290, 282, 283, 310, 278, 268, 222, 49, 284, 235, 172, 116, 108, 115, 112, 135, 176, 196, 200, 216, 207, 86, 30, 152, 161, 138, 117, 81, 47, 73, 207, 381, 459, 415, 346, 353, 429, 490, 503, 492, 454, 379, 304, 275]
+      obj.image_narray.should be_nil
+    end
+
+    it "should return an narray if requested" do
+      obj = NRead.new(NIFTI_TEST_FILE1_GZ, :narray => true)
+      obj.image_narray.should_not be_nil
+    end
+
+    it "should add an NArray Install message and not set the image_narray if NArray was not available" do
+      Object.expects(:const_defined?).with('NArray').returns(false)
+      obj = NRead.new(NIFTI_TEST_FILE1_GZ, :narray => true)
+      obj.msg.should_not be_empty
+      obj.msg.grep(/Please `gem install narray`/).empty?.should be_false
+      obj.image_narray.should be_nil
+      obj.image_rubyarray.size.should == @fixture_image_length
+    end
+
+    it "should read extended header attributes" do
+      @n_read_obj.extended_header.should_not be_empty
+      @n_read_obj.extended_header.first[:esize].should == 5680
+      @n_read_obj.extended_header.first[:ecode].should == 4
+      @n_read_obj.extended_header.first[:data].length.should == @fixture_afni_extension_length
+      @n_read_obj.extended_header.first[:data].should == "<?xml version='1.0' ?>\n<AFNI_attributes\n  self_idcode=\"XYZ_Fk5B7fY4srOPxYrGolqMIg\"\n  NIfTI_nums=\"256,256,15,1,1,4\"\n  ni_form=\"ni_group\" >\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"HISTORY_NOTE\" >\n \"[erik@nelson.medicine.wisc.edu: Fri Jan 21 10:24:14 2011] to3d -prefix 3plLoc.nii I0001.dcm I0002.dcm I0003.dcm ... I0014.dcm I0015.dcm\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"TYPESTRING\" >\n \"3DIM_HEAD_ANAT\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"IDCODE_STRING\" >\n \"XYZ_Fk5B7fY4srOPxYrGolqMIg\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"IDCODE_DATE\" >\n \"Fri Jan 21 10:24:15 2011\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"SCENE_DATA\" >\n 0\n 0\n 0\n -999\n -999\n -999\n -999\n -999\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"LABEL_1\" >\n \"3plLoc.nii+orig\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"LABEL_2\" >\n \"Viggo!\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"DATASET_NAME\" >\n \"./3plLoc.nii+orig\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"3\"\n  atr_name=\"ORIENT_SPECIFIC\" >\n 0\n 3\n 4\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"3\"\n  atr_name=\"ORIGIN\" >\n -119.531\n -159.531\n -25\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"3\"\n  atr_name=\"DELTA\" >\n 0.9375\n 0.9375\n 12.5\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"12\"\n  atr_name=\"IJK_TO_DICOM\" >\n 0.9375\n 0.9375\n 0.9375\n -360\n 0\n 0\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"12\"\n  atr_name=\"IJK_TO_DICOM_REAL\" >\n 0.9375\n 0\n 0\n -119.531\n 0\n 0.9375\n 0\n -159.531\n 0\n 0\n 12.5\n -25\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"30\"\n  atr_name=\"MARKS_XYZ\" >\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"MARKS_LAB\" >\n \"AC superior edge~~~~AC posterior margin~PC inferior edge~~~~First mid-sag pt~~~~Another mid-sag pt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"3\"\n  atr_name=\"MARKS_HELP\" >\n \"This is the uppermost point&#x0a;on the anterior commisure,&#x0a;in the mid-sagittal plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~This is the rearmost point&#x0a;on the anterior commisure,&#x0a;in the mid-sagittal plane.&#x0a;[Just a couple mm behind and&#x0a; below the AC superior edge.]~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~This is the bottommost point&#x0a;on the posterior commissure,&#x0a;in the mid-sagittal plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~You must also specify two other points in the&#x0a;mid-sagittal plane, ABOVE the corpus callosum&#x0a;(i.e., in the longitudinal fissure).  These&#x0a;points are needed to define the vertical plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n \"~~~~~~~~~~~~~~~~~~~~~~~~You must also specify two other points in the&#x0a;mid-sagittal plane, ABOVE the corpus callosum&#x0a;(i.e., in the longitudinal fissure).  These&#x0a;points are needed to define the vertical plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n \"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"MARKS_FLAGS\" >\n 1\n 1\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"2\"\n  atr_name=\"BRICK_STATS\" >\n 0\n 2402\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"DATASET_RANK\" >\n 3\n 1\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"5\"\n  atr_name=\"DATASET_DIMENSIONS\" >\n 256\n 256\n 15\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"1\"\n  atr_name=\"BRICK_TYPES\" >\n 1\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"1\"\n  atr_name=\"BRICK_FLOAT_FACS\" >\n 0\n</AFNI_atr>\n\n</AFNI_attributes>\n"
+    end
   end
-  
-  it "should read extended header attributes" do
-    @n_read_obj.extended_header.should_not be_empty
-    @n_read_obj.extended_header.first[:esize].should == 5680
-    @n_read_obj.extended_header.first[:ecode].should == 4
-    @n_read_obj.extended_header.first[:data].length.should == @fixture_afni_extension_length
-    @n_read_obj.extended_header.first[:data].should == "<?xml version='1.0' ?>\n<AFNI_attributes\n  self_idcode=\"XYZ_Fk5B7fY4srOPxYrGolqMIg\"\n  NIfTI_nums=\"256,256,15,1,1,4\"\n  ni_form=\"ni_group\" >\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"HISTORY_NOTE\" >\n \"[erik@nelson.medicine.wisc.edu: Fri Jan 21 10:24:14 2011] to3d -prefix 3plLoc.nii I0001.dcm I0002.dcm I0003.dcm ... I0014.dcm I0015.dcm\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"TYPESTRING\" >\n \"3DIM_HEAD_ANAT\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"IDCODE_STRING\" >\n \"XYZ_Fk5B7fY4srOPxYrGolqMIg\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"IDCODE_DATE\" >\n \"Fri Jan 21 10:24:15 2011\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"SCENE_DATA\" >\n 0\n 0\n 0\n -999\n -999\n -999\n -999\n -999\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"LABEL_1\" >\n \"3plLoc.nii+orig\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"LABEL_2\" >\n \"Viggo!\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"DATASET_NAME\" >\n \"./3plLoc.nii+orig\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"3\"\n  atr_name=\"ORIENT_SPECIFIC\" >\n 0\n 3\n 4\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"3\"\n  atr_name=\"ORIGIN\" >\n -119.531\n -159.531\n -25\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"3\"\n  atr_name=\"DELTA\" >\n 0.9375\n 0.9375\n 12.5\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"12\"\n  atr_name=\"IJK_TO_DICOM\" >\n 0.9375\n 0.9375\n 0.9375\n -360\n 0\n 0\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"12\"\n  atr_name=\"IJK_TO_DICOM_REAL\" >\n 0.9375\n 0\n 0\n -119.531\n 0\n 0.9375\n 0\n -159.531\n 0\n 0\n 12.5\n -25\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"30\"\n  atr_name=\"MARKS_XYZ\" >\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n -999999\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"1\"\n  atr_name=\"MARKS_LAB\" >\n \"AC superior edge~~~~AC posterior margin~PC inferior edge~~~~First mid-sag pt~~~~Another mid-sag pt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"String\"\n  ni_dimen=\"3\"\n  atr_name=\"MARKS_HELP\" >\n \"This is the uppermost point&#x0a;on the anterior commisure,&#x0a;in the mid-sagittal plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~This is the rearmost point&#x0a;on the anterior commisure,&#x0a;in the mid-sagittal plane.&#x0a;[Just a couple mm behind and&#x0a; below the AC superior edge.]~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~This is the bottommost point&#x0a;on the posterior commissure,&#x0a;in the mid-sagittal plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~You must also specify two other points in the&#x0a;mid-sagittal plane, ABOVE the corpus callosum&#x0a;(i.e., in the longitudinal fissure).  These&#x0a;points are needed to define the vertical plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n \"~~~~~~~~~~~~~~~~~~~~~~~~You must also specify two other points in the&#x0a;mid-sagittal plane, ABOVE the corpus callosum&#x0a;(i.e., in the longitudinal fissure).  These&#x0a;points are needed to define the vertical plane.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n \"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\"\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"MARKS_FLAGS\" >\n 1\n 1\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"2\"\n  atr_name=\"BRICK_STATS\" >\n 0\n 2402\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"8\"\n  atr_name=\"DATASET_RANK\" >\n 3\n 1\n 0\n 0\n 0\n 0\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"5\"\n  atr_name=\"DATASET_DIMENSIONS\" >\n 256\n 256\n 15\n 0\n 0\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"int\"\n  ni_dimen=\"1\"\n  atr_name=\"BRICK_TYPES\" >\n 1\n</AFNI_atr>\n\n<AFNI_atr\n  ni_type=\"float\"\n  ni_dimen=\"1\"\n  atr_name=\"BRICK_FLOAT_FACS\" >\n 0\n</AFNI_atr>\n\n</AFNI_attributes>\n"
+
+  context 'without narray' do
+
   end
-  
-  
 end

data/spec/nifti/n_write_spec.rb

@@ -3,7 +3,6 @@ require 'spec_helper'
 describe NIFTI::NWrite do
   before :all do
     @n_object = NObject.new(NIFTI_TEST_FILE1)
-    @new_fixture_file_name = '5PlLoc.nii'
     @fixture_image_length = 983040
     @fixture_afni_extension_length = 5661
     @valid_header = {
@@ -26,31 +25,77 @@ describe NIFTI::NWrite do
       "intent_p3"=>0.0, "regular"=>"r"
     }
   end
-  
-  it "should write a NIfTI file" do
-    obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
-    w = NWrite.new(obj, @new_fixture_file_name)
-    w.write
-    w.msg.should be_empty
-    File.exist? @new_fixture_file_name.should be_true
-  end
-  
-  it "should write back an identical file if no changes were made" do
-    obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
-    w = NWrite.new(obj, @new_fixture_file_name)
-    w.write
-    @new_fixture_file_name.should be_same_file_as NIFTI_TEST_FILE1
-  end
-  
-  it "should write a new image after changing some variables" do
-    obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
-    obj.header['qoffset_x'] = obj.header['qoffset_x'] + 1
-    w = NWrite.new(obj, @new_fixture_file_name)
-    w.write
-    @new_fixture_file_name.should_not be_same_file_as NIFTI_TEST_FILE1
+
+  context 'writing to an uncompressed file' do
+    before do
+      @new_fixture_file_name = '5PlLoc.nii'
+    end
+
+    it "should write a NIfTI file" do
+      obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
+      w = NWrite.new(obj, @new_fixture_file_name)
+      w.write
+      w.msg.should be_empty
+      File.exist?(@new_fixture_file_name).should be_true
+    end
+
+    it "should write back an identical file if no changes were made" do
+      obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
+      w = NWrite.new(obj, @new_fixture_file_name)
+      w.write
+      @new_fixture_file_name.should be_same_file_as NIFTI_TEST_FILE1
+    end
+
+    it "should write a new image after changing some variables" do
+      obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
+      obj.header['qoffset_x'] = obj.header['qoffset_x'] + 1
+      w = NWrite.new(obj, @new_fixture_file_name)
+      w.write
+      @new_fixture_file_name.should_not be_same_file_as NIFTI_TEST_FILE1
+    end
+
+    after :each do
+      File.delete @new_fixture_file_name if File.exist? @new_fixture_file_name
+    end
   end
-  
-  after :each do
-    File.delete @new_fixture_file_name if File.exist? @new_fixture_file_name
+
+  context 'writing to a compressed file' do
+    before do
+      @new_fixture_file_name = '5PlLoc.nii.gz'
+    end
+
+    it "should write a NIfTI file" do
+      obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
+      w = NWrite.new(obj, @new_fixture_file_name)
+      w.write
+      w.msg.should be_empty
+      File.exist?(@new_fixture_file_name).should be_true
+    end
+
+    it "should write back an identical file if no changes were made" do
+      obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
+
+      w = NWrite.new(obj, @new_fixture_file_name)
+      w.write
+      writen_obj = NObject.new(@new_fixture_file_name, :image => true)
+
+      # for some reason be_same_file_as fails for gziped images
+      # but we can make sure of it opening the file again and comparing the data
+      writen_obj.get_image.should eq(obj.get_image)
+      writen_obj.header.should eq(obj.header)
+      writen_obj.extended_header.should eq(obj.extended_header)
+    end
+
+    it "should write a new image after changing some variables" do
+      obj = NObject.new(NIFTI_TEST_FILE1, :image => true)
+      obj.header['qoffset_x'] = obj.header['qoffset_x'] + 1
+      w = NWrite.new(obj, @new_fixture_file_name)
+      w.write
+      @new_fixture_file_name.should_not be_same_file_as NIFTI_TEST_FILE1_GZ
+    end
+
+    after :each do
+      File.delete @new_fixture_file_name if File.exist? @new_fixture_file_name
+    end
   end
 end