nifti 0.0.1 → 0.0.2

data/lib/nifti/n_object.rb

@@ -1,7 +1,7 @@
 module NIFTI
   # The NObject class is the main class for interacting with the NIFTI object.
   # Reading from and writing to files is executed from instances of this class.
-  # 
+  #
   class NObject
     # An array which contain any notices/warnings/errors that have been recorded for the NObject instance.
     attr_reader :errors
@@ -65,9 +65,16 @@ module NIFTI
       elsif not string == nil
         raise ArgumentError, "Invalid argument. Expected String (or nil), got #{string.class}."
       end
-      
     end
-    
+
+    # Reopen the NIFTI File and retrieve image data, returning, if the retrieval was successful, it as an NImage object
+    def get_nimage
+      image = self.get_image
+      if !image.nil?
+        NImage.new(image, self.header["dim"])
+      end
+    end
+
     # Reopen the NIFTI File and retrieve image data
     def get_image
       r = NRead.new(@string, :image => true)
@@ -75,7 +82,7 @@ module NIFTI
         @image = r.image_rubyarray
       end
     end
-    
+
     # Passes the NObject to the DWrite class, which writes out the header and image to the specified file.
     #
     # === Parameters
@@ -101,10 +108,10 @@ module NIFTI
         raise ArgumentError, "Invalid file_name. Expected String, got #{file_name.class}."
       end
     end
-    
+
     # Following methods are private:
-    private 
-    
+    private
+
     # Returns a NIFTI object by reading and parsing the specified file.
     # This is accomplished by initializing the NRead class, which loads NIFTI information.
     #
@@ -112,7 +119,7 @@ module NIFTI
     #
     # This method is called automatically when initializing the NObject class with a file parameter,
     # and in practice should not be called by users.
-    # 
+    #
     def read(string, options={})
       if string.is_a?(String)
         @string = string
@@ -124,7 +131,7 @@ module NIFTI
           @header = r.hdr
           @extended_header = r.extended_header
           if r.image_narray
-            @image = r.image_narray 
+            @image = r.image_narray
           elsif r.image_rubyarray
             @image = r.image_rubyarray
           end
@@ -150,6 +157,6 @@ module NIFTI
       @errors << msg
       @errors.flatten
     end
-    
+
   end
 end

data/lib/nifti/n_read.rb

@@ -1,6 +1,8 @@
+require 'zlib'
+
 module NIFTI
   # The NRead class parses the NIFTI data from a binary string.
-  # 
+  #
   class NRead
     # An array which records any status messages that are generated while parsing the DICOM string.
     attr_reader :msg
@@ -14,14 +16,14 @@ module NIFTI
     attr_reader :image_rubyarray
     # A narray of image values reshapred to image dimensions
     attr_reader :image_narray
-    
+
     # Valid Magic codes for the NIFTI Header
     MAGIC = %w{ni1 n+1}
-    
+
     # Create a NRead object to parse a nifti file or binary string and set header and image info instance variables.
     #
     # The nifti header will be checked for validity (header size and magic number) and will raise an IOError if invalid.
-    # 
+    #
     # NIFTI header extensions are not yet supported and are not included in the header.
     #
     # The header and image are accessible via the hdr and image instance variables.  An optional narray matrix may also be available in image_narray if desired by passing in :narray => true as an option.
@@ -43,18 +45,18 @@ module NIFTI
       @success = false
       set_stream(source, options)
       parse_header(options)
-      
+
       return self
     end
-    
+
     # Unpack an image array from vox_offset to the end of a nifti file.
-    # 
+    #
     # === Parameters
     #
     # There are no parameters - this reads from the binary string in the @string instance variable.
-    # 
+    #
     # This sets @image_rubyarray to the image data vector and also returns it.
-    # 
+    #
     def read_image
       raw_image = []
       @stream.index = @hdr['vox_offset']
@@ -62,25 +64,25 @@ module NIFTI
       format = @stream.format[type]
       @image_rubyarray = @stream.decode(@stream.rest_length, type)
     end
-    
-    # Create an narray if the NArray is available 
+
+    # Create an narray if the NArray is available
     # Tests if a file is readable, and if so, opens it.
     #
     # === Parameters
     #
     # * <tt>image_array</tt> -- Array. A vector of image data.
     # * <tt>dim</tt> -- Array. The dim array from the nifti header, specifing number of dimensions (dim[0]) and dimension length of other dimensions to reshape narray into.
-    # 
+    #
     def get_image_narray(image_array, dim)
-      if defined? NArray
+      if Object.const_defined?('NArray')
         @image_narray = pixel_data = NArray.to_na(image_array).reshape!(*dim[1..dim[0]])
       else
         add_msg "Can't find NArray, no image_narray created.  Please `gem install narray`"
       end
     end
-    
+
     private
-    
+
     # Initializes @stream from a binary string or filename
     def set_stream(source, options)
       # Are we going to read from a file, or read from a binary string?
@@ -101,65 +103,65 @@ module NIFTI
           @file.close
         end
       end
-      
+
       # Create a Stream instance to handle the decoding of content from this binary string:
       @file_endian = false
       @stream = Stream.new(@str, false)
     end
-    
+
     # Parse the NIFTI Header.
     def parse_header(options = {})
       check_header
       @hdr = parse_basic_header
       @extended_header = parse_extended_header
-      
+
       # Optional image gathering
-      read_image if options[:image] 
+      read_image if options[:image]
       get_image_narray(@image_rubyarray, @hdr['dim']) if options[:narray]
-      
+
       @success = true
     end
-    
+
     # NIFTI uses the header length (first 4 bytes) to be 348 number of "ni1\0"
     # or "n+1\0" as the last 4 bytes to be magic numbers to validate the header.
-    # 
+    #
     # The header is usually checked before any data is read, but can be
     # checked at any point in the process as the stream index is reset to its
     # original position after validation.
-    # 
-    # There are no options - the method will raise an IOError if any of the 
+    #
+    # There are no options - the method will raise an IOError if any of the
     # magic numbers are not valid.
     def check_header
       begin
         starting_index = @stream.index
-        
+
         # Check sizeof_hdr
-        @stream.index = 0; 
+        @stream.index = 0;
         sizeof_hdr = @stream.decode(4, "UL")
         raise IOError, "Bad Header Length #{sizeof_hdr}" unless sizeof_hdr == 348
-            
+
         # Check magic
-        @stream.index = 344; 
+        @stream.index = 344;
         magic = @stream.decode(4, "STR")
         raise IOError, "Bad Magic Code #{magic} (should be ni1 or n+1)" unless MAGIC.include?(magic)
-        
+
       rescue IOError => e
         raise IOError, "Header appears to be malformed: #{e}"
       else
         @stream.index = starting_index
-      end        
+      end
     end
 
     # Read the nifti header according to its byte signature.
-    # The file stream will be left open and should be positioned at the end of the 348 byte header. 
+    # The file stream will be left open and should be positioned at the end of the 348 byte header.
     def parse_basic_header
       # The HEADER_SIGNATURE is defined in NIFTI::Constants and used for both reading and writing.
       header = {}
-      HEADER_SIGNATURE.each do |header_item| 
+      HEADER_SIGNATURE.each do |header_item|
         name, length, type = *header_item
         header[name] = @stream.decode(length, type)
       end
-      
+
       # Extract Freq, Phase & Slice Dimensions from diminfo
       if header['dim_info']
         header['freq_dim'] = dim_info_to_freq_dim(header['dim_info'])
@@ -168,7 +170,7 @@ module NIFTI
       end
       header['sform_code_descr'] = XFORM_CODES[header['sform_code']]
       header['qform_code_descr'] = XFORM_CODES[header['qform_code']]
-            
+
       return header
     end
 
@@ -201,7 +203,7 @@ module NIFTI
       end
       return extended
     end
-    
+
     # Tests if a file is readable, and if so, opens it.
     #
     # === Parameters
@@ -213,7 +215,11 @@ module NIFTI
         if File.readable?(file)
           if not File.directory?(file)
             if File.size(file) > 8
-              @file = File.new(file, "rb")
+              begin
+                @file = Zlib::GzipReader.new(File.new(file, "rb"))
+              rescue Zlib::GzipFile::Error
+                @file = File.new(file, "rb")
+              end
             else
               @msg << "Error! File is too small to contain DICOM information (#{file})."
             end
@@ -227,38 +233,38 @@ module NIFTI
         @msg << "Error! The file you have supplied does not exist (#{file})."
       end
     end
-        
+
     # Bitwise Operator to extract Frequency Dimension
     def dim_info_to_freq_dim(dim_info)
       extract_dim_info(dim_info, 0)
     end
-    
-    # Bitwise Operator to extract Phase Dimension 
+
+    # Bitwise Operator to extract Phase Dimension
     def dim_info_to_phase_dim(dim_info)
       extract_dim_info(dim_info, 2)
     end
-    
+
     # Bitwise Operator to extract Slice Dimension
     def dim_info_to_slice_dim(dim_info)
       extract_dim_info(dim_info, 4)
     end
-    
+
     # Bitwise Operator to extract Frequency, Phase & Slice Dimensions from 2byte diminfo
     def extract_dim_info(dim_info, offset = 0)
       (dim_info >> offset) & 0x03
     end
-    
+
     # Bitwise Operator to encode Freq, Phase & Slice into Diminfo
     def fps_into_dim_info(frequency_dim, phase_dim, slice_dim)
-      ((frequency_dim & 0x03 ) << 0 ) | 
-      ((phase_dim & 0x03) << 2 ) | 
+      ((frequency_dim & 0x03 ) << 0 ) |
+      ((phase_dim & 0x03) << 2 ) |
       ((slice_dim & 0x03) << 4 )
     end
-    
+
     # Add a message (TODO: and maybe print to screen if verbose)
     def add_msg(msg)
       @msg << msg
     end
-    
+
   end
 end

data/lib/nifti/n_write.rb

@@ -1,3 +1,5 @@
+require 'zlib'
+
 module NIFTI
 
   # The NWrite class handles the encoding of an NObject instance to a valid NIFTI string.
@@ -9,7 +11,7 @@ module NIFTI
     attr_reader :msg
     # A boolean which reports whether the DICOM string was encoded/written successfully (true) or not (false).
     attr_reader :success
-    
+
     # Creates an NWrite instance.
     #
     # === Parameters
@@ -26,7 +28,7 @@ module NIFTI
       # Array for storing error/warning messages:
       @msg = Array.new
     end
-    
+
     # Handles the encoding of NIfTI information to string as well as writing it to file.
     def write
       # Check if we are able to create given file:
@@ -40,7 +42,7 @@ module NIFTI
         @stream = Stream.new(nil, @file_endian)
         # Tell the Stream instance which file to write to:
         @stream.set_file(@file)
-        
+
         # Write Header and Image
         write_basic_header
         write_extended_header
@@ -51,9 +53,9 @@ module NIFTI
         # Mark this write session as successful:
         @success = true
       end
-      
+
     end
-    
+
     # Write Basic Header
     def write_basic_header
       HEADER_SIGNATURE.each do |header_item|
@@ -72,7 +74,7 @@ module NIFTI
         end
       end
     end
-    
+
     # Write Extended Header
     def write_extended_header
       unless @obj.extended_header.empty?
@@ -85,16 +87,14 @@ module NIFTI
       else
         @stream.write @stream.encode([0,0,0,0], "BY")
       end
-      
-      
     end
-    
+
     # Write Image
     def write_image
       type = NIFTI_DATATYPES[@obj.header['datatype']]
       @stream.write @stream.encode(@obj.image, type)
     end
-    
+
     # Tests if the path/file is writable, creates any folders if necessary, and opens the file for writing.
     #
     # === Parameters
@@ -106,7 +106,7 @@ module NIFTI
       if File.exist?(file)
         # Is it writable?
         if File.writable?(file)
-          @file = File.new(file, "wb")
+          @file = get_new_file_writer(file)
         else
           # Existing file is not writable:
           @msg << "Error! The program does not have permission or resources to create the file you specified: (#{file})"
@@ -127,16 +127,31 @@ module NIFTI
           end
         end
         # The path to this non-existing file is verified, and we can proceed to create the file:
-        @file = File.new(file, "wb")
+        @file = get_new_file_writer(file)
       end
     end
-  
+
     # Creates various variables used when encoding the DICOM string.
     #
     def init_variables
       # Until a DICOM write has completed successfully the status is 'unsuccessful':
       @success = false
     end
-    
+
+    private
+
+    # Opens the file according to it's extension (gziped or uncompressed)
+    #
+    # === Parameters
+    #
+    # * <tt>file</tt> -- A path/file string.
+    #
+    def get_new_file_writer(file)
+      if File.extname(file) == '.gz'
+        Zlib::GzipWriter.new(File.new(file, 'wb'))
+      else
+        File.new(file, 'wb')
+      end
+    end
   end
 end

data/lib/nifti/version.rb

@@ -1,4 +1,4 @@
 module NIFTI
   # Current Version of NIFTI
-  VERSION = "0.0.1"
+  VERSION = "0.0.2"
 end

data/nifti.gemspec

@@ -7,18 +7,21 @@ Gem::Specification.new do |s|
   s.version     = NIFTI::VERSION
   s.platform    = Gem::Platform::RUBY
   s.authors     = ["Erik Kastman"]
-  s.email       = ["ekk@medicine.wisc.edu"]
-  s.homepage    = ""
+  s.email       = ["erik.kastman@gmail.com"]
+  s.homepage    = "https://github.com/brainmap/nifti"
   s.summary     = %q{A pure Ruby API to the NIfTI Neuroimaging Format}
   s.description = %q{A pure Ruby API to the NIfTI Neuroimaging Format}
 
-  s.rubyforge_project = "nifti"
+  s.required_ruby_version     = '>= 1.8'
 
   s.files         = `git ls-files`.split("\n")
   s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
   s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
   s.require_paths = ["lib"]
+  s.license       = 'LGPLv3'
   s.add_development_dependency "rspec"
   s.add_development_dependency "mocha"
+  s.add_development_dependency "cucumber"
   s.add_development_dependency "narray"
+  s.add_development_dependency "simplecov"
 end