nmatrix 0.0.3 → 0.0.4

data/ext/nmatrix/data/complex.h

@@ -9,8 +9,8 @@
 //
 // == Copyright Information
 //
-// SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-// NMatrix is Copyright (c) 2012, Ruby Science Foundation
+// SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
+// NMatrix is Copyright (c) 2013, Ruby Science Foundation
 //
 // Please see LICENSE.txt for additional copyright notices.
 //
@@ -132,23 +132,23 @@ class Complex {
 	
 	template <typename OtherType>
 	inline Complex<Type> operator*(const Complex<OtherType>& other) const {
-		return Complex<Type>(this->r * other.r - this->i * other.i, this->r * other.i - this->i * other.r);
+		return Complex<Type>(this->r * other.r - this->i * other.i, this->r * other.i + this->i * other.r);
 	}
 
   template <typename OtherType>
   inline Complex<Type>& operator*=(const Complex<OtherType>& other) {
     this->r = this->r * other.r - this->i * other.i;
-    this->i = this->r * other.i - this->i * other.r;
+    this->i = this->r * other.i + this->i * other.r;
     return *this;
   }
 
 	template <typename OtherType>
 	inline Complex<Type> operator/(const Complex<OtherType>& other) const {
 		Type new_r, new_i;
-		Type denom = this->i * this->i + other.r * other.r;
+		Type denom = other.i * other.i + other.r * other.r;
 		
 		new_r = (this->r * other.r + this->i * other.i) / denom;
-		new_i = (this->r * other.i - this->i * other.r) / denom;
+		new_i = (this->i * other.r - this->r * other.i) / denom;
 		
 		return Complex<Type>(new_r, new_i);
 	}
@@ -199,7 +199,7 @@ class Complex {
 	
 	template <typename RationalType>
 	inline Complex<Type> operator-(const Rational<RationalType>& other) const {
-		return *this * Complex<Type>(other);
+		return *this - Complex<Type>(other);
 	}
 	
 	template <typename RationalType>

data/ext/nmatrix/data/data.cpp

@@ -9,8 +9,8 @@
 //
 // == Copyright Information
 //
-// SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-// NMatrix is Copyright (c) 2012, Ruby Science Foundation
+// SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
+// NMatrix is Copyright (c) 2013, Ruby Science Foundation
 //
 // Please see LICENSE.txt for additional copyright notices.
 //
@@ -36,13 +36,8 @@
  */
 
 #include "types.h"
-
 #include "data.h"
 
-/*
- * Macros
- */
-
 /*
  * Global Variables
  */

data/ext/nmatrix/data/data.h

@@ -9,8 +9,8 @@
 //
 // == Copyright Information
 //
-// SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-// NMatrix is Copyright (c) 2012, Ruby Science Foundation
+// SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
+// NMatrix is Copyright (c) 2013, Ruby Science Foundation
 //
 // Please see LICENSE.txt for additional copyright notices.
 //
@@ -107,7 +107,8 @@ namespace nm {
 		fun<nm::Complex128>,																\
 		fun<nm::Rational32>,																\
 		fun<nm::Rational64>,																\
-		fun<nm::Rational128> 																\
+		fun<nm::Rational128>, 															\
+		fun<nm::RubyObject>                                 \
 	};
 
 #define NAMED_DTYPE_TEMPLATE_TABLE_NO_ROBJ(name, fun, ret, ...) \
@@ -123,7 +124,7 @@ namespace nm {
 		fun<nm::Complex128>,																\
 		fun<nm::Rational32>,																\
 		fun<nm::Rational64>,																\
-		fun<nm::Rational128>,																\
+		fun<nm::Rational128>																\
 	};
 
 /*
@@ -615,6 +616,8 @@ namespace nm {
 {fun<nm::EW_GEQ, uint32_t, uint8_t>,fun<nm::EW_GEQ, uint32_t, int8_t>,fun<nm::EW_GEQ, uint32_t, int16_t>,fun<nm::EW_GEQ, uint32_t, int32_t>,fun<nm::EW_GEQ, uint32_t, int64_t>,fun<nm::EW_GEQ, uint32_t, float32_t>,fun<nm::EW_GEQ, uint32_t, float64_t>,fun<nm::EW_GEQ, uint32_t, nm::Complex64>,fun<nm::EW_GEQ, uint32_t, nm::Complex128>,fun<nm::EW_GEQ, uint32_t, nm::Rational32>,fun<nm::EW_GEQ, uint32_t, nm::Rational64>,fun<nm::EW_GEQ, uint32_t, nm::Rational128>,fun<nm::EW_GEQ, uint32_t, nm::RubyObject>},\
 {fun<nm::EW_GEQ, uint64_t, uint8_t>,fun<nm::EW_GEQ, uint64_t, int8_t>,fun<nm::EW_GEQ, uint64_t, int16_t>,fun<nm::EW_GEQ, uint64_t, int32_t>,fun<nm::EW_GEQ, uint64_t, int64_t>,fun<nm::EW_GEQ, uint64_t, float32_t>,fun<nm::EW_GEQ, uint64_t, float64_t>,fun<nm::EW_GEQ, uint64_t, nm::Complex64>,fun<nm::EW_GEQ, uint64_t, nm::Complex128>,fun<nm::EW_GEQ, uint64_t, nm::Rational32>,fun<nm::EW_GEQ, uint64_t, nm::Rational64>,fun<nm::EW_GEQ, uint64_t, nm::Rational128>,fun<nm::EW_GEQ, uint64_t, nm::RubyObject>}}};
 
+
+
 /*
  * Defines a static array that holds function pointers to left dtype, right
  * dtype, and itype templated versions of the specified function.

data/ext/nmatrix/data/rational.h

@@ -9,8 +9,8 @@
 //
 // == Copyright Information
 //
-// SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-// NMatrix is Copyright (c) 2012, Ruby Science Foundation
+// SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
+// NMatrix is Copyright (c) 2013, Ruby Science Foundation
 //
 // Please see LICENSE.txt for additional copyright notices.
 //

data/ext/nmatrix/data/ruby_object.h

@@ -9,8 +9,8 @@
 //
 // == Copyright Information
 //
-// SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-// NMatrix is Copyright (c) 2012, Ruby Science Foundation
+// SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
+// NMatrix is Copyright (c) 2013, Ruby Science Foundation
 //
 // Please see LICENSE.txt for additional copyright notices.
 //
@@ -50,17 +50,10 @@
 	if (TYPE(val) != T_DATA || (RDATA(val)->dfree != (RUBY_DATA_FUNC)nm_delete && RDATA(val)->dfree != (RUBY_DATA_FUNC)nm_delete_ref)) \
 		rb_raise(rb_eTypeError, "Expected NMatrix on left-hand side of operation.");
 
-/*
- * Types
- */
-
-/*
- * Data
- */
-
 /*
  * Classes and Functions
  */
+
 namespace nm {
 template<typename T, typename U>
 struct made_from_same_template : std::false_type {}; 

data/ext/nmatrix/extconf.rb

@@ -8,8 +8,8 @@
 #
 # == Copyright Information
 #
-# SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-# NMatrix is Copyright (c) 2012, Ruby Science Foundation
+# SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
+# NMatrix is Copyright (c) 2013, Ruby Science Foundation
 #
 # Please see LICENSE.txt for additional copyright notices.
 #
@@ -29,7 +29,7 @@ require "mkmf"
 
 
 # Function derived from NArray's extconf.rb.
-def have_type(type, header=nil)
+def have_type(type, header=nil) #:nodoc:
   printf "checking for %s... ", type
   STDOUT.flush
 
@@ -60,31 +60,36 @@ SRC
 end
 
 # Function derived from NArray's extconf.rb.
-def create_conf_h(file)
+def create_conf_h(file) #:nodoc:
   print "creating #{file}\n"
   File.open(file, 'w') do |hfile|
-  	header_guard = file.upcase.sub(/\s|\./, '_')
-		
-		hfile.puts "#ifndef #{header_guard}"
-		hfile.puts "#define #{header_guard}"
-		hfile.puts
-		
-		for line in $defs
-		  line =~ /^-D(.*)/
-		  hfile.printf "#define %s 1\n", $1
-		end
-		
-		hfile.puts
-		hfile.puts "#endif"
+    header_guard = file.upcase.sub(/\s|\./, '_')
+
+    hfile.puts "#ifndef #{header_guard}"
+    hfile.puts "#define #{header_guard}"
+    hfile.puts
+
+    # FIXME: Find a better way to do this:
+    if RUBY_VERSION >= '2.0'
+      hfile.puts "#define RUBY_2 1"
+    end
+
+    for line in $defs
+      line =~ /^-D(.*)/
+      hfile.printf "#define %s 1\n", $1
+    end
+
+    hfile.puts
+    hfile.puts "#endif"
   end
 end
 
 if RUBY_VERSION < '1.9'
-  raise(NotImplementedError, "Sorry, you need Ruby 1.9!")
+  raise(NotImplementedError, "Sorry, you need at least Ruby 1.9!")
 else
   $INSTALLFILES = [['nmatrix.h', '$(archdir)'], ['nmatrix.hpp', '$(archdir)'], ['nmatrix_config.h', '$(archdir)']]
   if /cygwin|mingw/ =~ RUBY_PLATFORM
-	 $INSTALLFILES << ['libnmatrix.a', '$(archdir)']
+    $INSTALLFILES << ['libnmatrix.a', '$(archdir)']
   end
 end
 
@@ -96,24 +101,28 @@ $DEBUG = true
 $CFLAGS = ["-Wall ",$CFLAGS].join(" ")
 
 $srcs = [
-	'nmatrix.cpp',
-	'ruby_constants.cpp',
-
-	'data/data.cpp',
-	'util/math.cpp',
-  'util/sl_list.cpp',
-  'util/io.cpp',
-  'storage/common.cpp',
-	'storage/storage.cpp',
-	'storage/dense.cpp',
-  'storage/yale.cpp',
-  'storage/list.cpp'
-]
+         'nmatrix.cpp',
+         'ruby_constants.cpp',
+
+         'data/data.cpp',
+         'util/math.cpp',
+         'util/sl_list.cpp',
+         'util/io.cpp',
+         'storage/common.cpp',
+         'storage/storage.cpp',
+         'storage/dense.cpp',
+         'storage/yale.cpp',
+         'storage/list.cpp'
+        ]
 # add smmp in to get generic transp; remove smmp2 to eliminate funcptr transp
 
-# The next line allows the user to supply --with-atlas-include=/usr/local/atlas, for example,
-# and tell the compiler where to look for ATLAS.
-dir_config("atlas")
+# The next line allows the user to supply --with-atlas-dir=/usr/local/atlas,
+# --with-atlas-lib or --with-atlas-include and tell the compiler where to look
+# for ATLAS. The same for all the others
+#
+#dir_config("clapack", ["/usr/local/atlas/include"], [])
+#
+#
 
 # Is g++ having trouble finding your header files?
 # Try this:
@@ -121,15 +130,31 @@ dir_config("atlas")
 #   export CPLUS_INCLUDE_PATH=/usr/local/atlas/include
 # (substituting in the path of your cblas.h and clapack.h for the path I used). -- JW 8/27/12
 
-find_library("lapack", "clapack_dgetrf", "/usr/local/lib", "/usr/local/atlas/lib")
-find_header("clapack.h", "/usr/local/atlas/include")
-have_header("clapack.h")
 
-find_library("cblas", "cblas_dgemm", "/usr/local/lib", "/usr/local/atlas/lib")
-find_library("atlas", "ATL_dgemmNN", "/usr/local/lib", "/usr/local/atlas/lib", "/usr/lib")
-find_header("cblas.h", "/usr/local/atlas/include")
+unless have_library("lapack")
+  dir_config("lapack", ["/usr/include/atlas"], ["/usr/local/lib", "/usr/local/atlas/lib"])
+end
+
+unless have_library("cblas")
+  dir_config("cblas", ["/usr/local/atlas/include", "/usr/include/atlas"], ["/usr/local/lib", "/usr/local/atlas/lib"])
+end
+
+unless have_library("atlas")
+  dir_config("atlas", ["/usr/local/atlas/include", "/usr/include/atlas"], ["/usr/local/atlas/lib", "/usr/local/lib", "/usr/lib"])
+end
+
+#find_library("lapack", "clapack_dgetrf")
+have_header("clapack.h")
 have_header("cblas.h")
 
+have_func("clapack_dgetrf", "clapack.h")
+
+
+#find_library("cblas", "cblas_dgemm")
+#find_library("atlas", "ATL_dgemmNN")
+
+have_func("cblas_dgemm", "cblas.h")
+
 # Order matters here: ATLAS has to go after LAPACK: http://mail.scipy.org/pipermail/scipy-user/2007-January/010717.html
 $libs += " -llapack -lcblas -latlas "
 
@@ -138,8 +163,8 @@ $objs = %w{nmatrix ruby_constants data/data util/io util/math util/sl_list stora
 #CONFIG['CXX'] = 'clang++'
 CONFIG['CXX'] = 'g++'
 
-def find_newer_gplusplus
-  [7,6,5,4,3].each do |minor|
+def find_newer_gplusplus #:nodoc:
+  [8,7,6,5,4,3].each do |minor|
     result = `which g++-4.#{minor}`
     next if result.empty?
     CONFIG['CXX'] = "g++-4.#{minor}"
@@ -148,16 +173,16 @@ def find_newer_gplusplus
   false
 end
 
-def gplusplus_version
-  `#{CONFIG['CXX']} -v 2>&1`.lines.to_a.last.match(/gcc\sversion\s(\d\.\d.\d)/).captures.first
+def gplusplus_version #:nodoc:
+  `LANG="en_US" #{CONFIG['CXX']} -v 2>&1`.lines.to_a.last.match(/gcc\sversion\s(\d\.\d.\d)/).captures.first
 end
 
 
 if CONFIG['CXX'] == 'clang++'
-	$CPP_STANDARD = 'c++11'
+  $CPP_STANDARD = 'c++11'
 
 else
-	version = gplusplus_version
+  version = gplusplus_version
   if version < '4.3.0' && CONFIG['CXX'] == 'g++'  # see if we can find a newer G++, unless it's been overridden by user
     if !find_newer_gplusplus
       raise("You need a version of g++ which supports -std=c++0x or -std=c++11. If you're on a Mac and using Homebrew, we recommend using mac-brew-gcc.sh to install a more recent g++.")
@@ -165,16 +190,16 @@ else
     version = gplusplus_version
   end
 
-	if version < '4.7.0'
-		$CPP_STANDARD = 'c++0x'
-	else
-		$CPP_STANDARD = 'c++11'
-	end
+  if version < '4.7.0'
+    $CPP_STANDARD = 'c++0x'
+  else
+    $CPP_STANDARD = 'c++11'
+  end
 end
 
 # For release, these next two should both be changed to -O3.
-$CFLAGS += " -O0 "
-$CPPFLAGS += " -O0 -std=#{$CPP_STANDARD} " #-fmax-errors=10 -save-temps
+$CFLAGS += " -O0 -g "
+$CPPFLAGS += " -O0 -g -std=#{$CPP_STANDARD} " #-fmax-errors=10 -save-temps
 
 CONFIG['warnflags'].gsub!('-Wshorten-64-to-32', '') # doesn't work except in Mac-patched gcc (4.2)
 CONFIG['warnflags'].gsub!('-Wdeclaration-after-statement', '')

data/ext/nmatrix/new_extconf.rb

@@ -31,26 +31,25 @@ $CFLAGS							= '-I. -fPIC -Wall -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fst
 CONFIG['CXXFLAGS']	= '-std=c++11'
 
 if clang_path = find_executable('clang') and clang_pp_path = find_executable('clang++')
-	CONFIG['CC']	= clang_path
-	CONFIG['CXX']	= clang_pp_path
+  CONFIG['CC']	= clang_path
+  CONFIG['CXX']	= clang_pp_path
 end
 
 # Necessary header files.
-find_header('ruby/config.h') 
+find_header('ruby/config.h')
 
 # List the source files that need to be compiled.
 $srcs = [
-#	'nmatrix.cpp',
-	'ruby_constants.cpp',
-	
-	'data/data.cpp',
-	'math.cpp',
-	'storage/storage.cpp',
-	'storage/dense.cpp'
-]
+         #	'nmatrix.cpp',
+         'ruby_constants.cpp',
+
+         'data/data.cpp',
+         'math.cpp',
+         'storage/storage.cpp',
+         'storage/dense.cpp'
+        ]
 
 $objs = $srcs.map { |f| f.sub('.cpp', '.o') }
 
 # Create the actual Makefile.
 create_makefile('NMatrix')
-

data/ext/nmatrix/nmatrix.cpp

@@ -9,8 +9,8 @@
 //
 // == Copyright Information
 //
-// SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-// NMatrix is Copyright (c) 2012, Ruby Science Foundation
+// SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
+// NMatrix is Copyright (c) 2013, Ruby Science Foundation
 //
 // Please see LICENSE.txt for additional copyright notices.
 //
@@ -23,9 +23,9 @@
 //
 // == nmatrix.cpp
 //
-// Main C++ source file for NMatrix. Contains Init_nmatrix and most Ruby instance and
-// class methods for NMatrix. Also responsible for calling Init methods on related
-// modules.
+// Main C++ source file for NMatrix. Contains Init_nmatrix and most Ruby
+// instance and class methods for NMatrix. Also responsible for calling Init
+// methods on related modules.
 
 /*
  * Standard Includes
@@ -44,6 +44,7 @@ extern "C" {
 /*
  * Project Includes
  */
+
 #include "types.h"
 #include "data/data.h"
 #include "util/math.h"
@@ -58,26 +59,11 @@ extern "C" {
  * Macros
  */
 
-/*
- * If no block is given, return an enumerator. This copied straight out of ruby's include/ruby/intern.h.
- *
- * rb_enumeratorize is located in enumerator.c.
- *
- *    VALUE rb_enumeratorize(VALUE obj, VALUE meth, int argc, VALUE *argv) {
- *      return enumerator_init(enumerator_allocate(rb_cEnumerator), obj, meth, argc, argv);
- *    }
- */
-#define RETURN_ENUMERATOR(obj, argc, argv) do {				            \
-	if (!rb_block_given_p())					                              \
-	  return rb_enumeratorize((obj), ID2SYM(rb_frame_this_func()),  \
-				    (argc), (argv));			                                \
-  } while (0)
 
 /*
  * Global Variables
  */
 
-
 namespace nm {
 
   /*
@@ -144,7 +130,6 @@ namespace nm {
     return bytes_written;
   }
 
-
   /*
    * We need to specialize for Hermitian matrices. The next six functions accomplish that specialization, basically
    * by ensuring that non-complex matrices cannot read or write hermitians (which would cause big problems).
@@ -187,7 +172,6 @@ namespace nm {
     }
   }
 
-
   /*
    * Read the elements of a dense storage matrix from a binary file, padded to 64-bits.
    *
@@ -259,8 +243,6 @@ namespace nm {
     if (bytes_read % 8) f.ignore(bytes_read % 8);
   }
 
-
-
   template <typename DType, typename IType>
   void write_padded_yale_elements(std::ofstream& f, YALE_STORAGE* storage, size_t length, nm::symm_t symm) {
     if (symm != nm::NONSYMM) rb_raise(rb_eNotImpError, "Yale matrices can only be read/written in full form");
@@ -299,8 +281,6 @@ namespace nm {
     f.read(reinterpret_cast<char*>(&padding), bytes_read % 8);
   }
 
-
-
   /*
    * Write the elements of a dense storage matrix to a binary file, padded to 64-bits.
    */
@@ -340,7 +320,6 @@ namespace nm {
 
 } // end of namespace nm
 
-
 extern "C" {
 
 /*
@@ -365,6 +344,7 @@ static VALUE nm_dim(VALUE self);
 static VALUE nm_shape(VALUE self);
 static VALUE nm_capacity(VALUE self);
 static VALUE nm_each(VALUE nmatrix);
+static VALUE nm_each_stored_with_indices(VALUE nmatrix);
 
 static SLICE* get_slice(size_t dim, VALUE* c, VALUE self);
 static VALUE nm_xslice(int argc, VALUE* argv, void* (*slice_func)(STORAGE*, SLICE*), void (*delete_func)(NMATRIX*), VALUE self);
@@ -429,16 +409,11 @@ static VALUE nm_upcast(VALUE self, VALUE t1, VALUE t2);
 static double get_time(void);
 #endif
 
-/*
- * Functions
- */
-
 ///////////////////
 // Ruby Bindings //
 ///////////////////
 
 void Init_nmatrix() {
-	
 	///////////////////////
 	// Class Definitions //
 	///////////////////////
@@ -447,8 +422,16 @@ void Init_nmatrix() {
 	cNVector = rb_define_class("NVector", cNMatrix);
 	
 	// Special exceptions
-	nm_eDataTypeError    = rb_define_class("DataTypeError",			rb_eStandardError);
-	nm_eStorageTypeError = rb_define_class("StorageTypeError",	rb_eStandardError);
+	
+	/*
+	 * Exception raised when there's a problem with data.
+	 */
+	nm_eDataTypeError    = rb_define_class("DataTypeError", rb_eStandardError);
+	
+	/*
+	 * Exception raised when something goes wrong with the storage of a matrix.
+	 */
+	nm_eStorageTypeError = rb_define_class("StorageTypeError", rb_eStandardError);
 
 	///////////////////
 	// Class Methods //
@@ -487,8 +470,8 @@ void Init_nmatrix() {
 	rb_define_method(cNMatrix, "is_ref?", (METHOD)nm_is_ref, 0);
 	rb_define_method(cNMatrix, "dimensions", (METHOD)nm_dim, 0);
 
-	rb_define_method(cNMatrix, "to_hash", (METHOD)nm_to_hash, 0);
-	rb_define_alias(cNMatrix,  "to_h",    "to_hash");
+	rb_define_protected_method(cNMatrix, "to_hash_c", (METHOD)nm_to_hash, 0); // handles list and dense, which are n-dimensional
+	//rb_define_alias(cNMatrix,  "to_h",    "to_hash");
 
 	rb_define_method(cNMatrix, "shape", (METHOD)nm_shape, 0);
 	rb_define_method(cNMatrix, "det_exact", (METHOD)nm_det_exact, 0);
@@ -496,6 +479,7 @@ void Init_nmatrix() {
 	rb_define_method(cNMatrix, "complex_conjugate!", (METHOD)nm_complex_conjugate_bang, 0);
 
 	rb_define_method(cNMatrix, "each", (METHOD)nm_each, 0);
+	rb_define_method(cNMatrix, "each_stored_with_indices", (METHOD)nm_each_stored_with_indices, 0);
 
 	rb_define_method(cNMatrix, "==",	  (METHOD)nm_eqeq,				1);
 
@@ -574,8 +558,6 @@ static VALUE nm_alloc(VALUE klass) {
   return Data_Wrap_Struct(klass, NULL, nm_delete, mat);
 }
 
-
-
 /*
  * Find the capacity of an NMatrix. The capacity only differs from the size for
  * Yale matrices, which occasionally allocate more space than they need. For
@@ -629,6 +611,9 @@ static void nm_delete_ref(NMATRIX* mat) {
 }
 
 /*
+ * call-seq:
+ *     dtype -> Symbol
+ *
  * Get the data type (dtype) of a matrix, e.g., :byte, :int8, :int16, :int32,
  * :int64, :float32, :float64, :complex64, :complex128, :rational32,
  * :rational64, :rational128, or :object (the last is a Ruby object).
@@ -638,8 +623,10 @@ static VALUE nm_dtype(VALUE self) {
   return ID2SYM(dtype);
 }
 
-
 /*
+ * call-seq:
+ *     itype -> Symbol or nil
+ *
  * Get the index data type (dtype) of a matrix. Defined only for yale; others return nil.
  */
 static VALUE nm_itype(VALUE self) {
@@ -650,7 +637,6 @@ static VALUE nm_itype(VALUE self) {
   return Qnil;
 }
 
-
 /*
  * Get the index data type (dtype) of a matrix. Defined only for yale; others return nil.
  */
@@ -665,8 +651,10 @@ static VALUE nm_itype_by_shape(VALUE self, VALUE shape_arg) {
   return ID2SYM(itype_id);
 }
 
-
 /*
+ * call-seq:
+ *     upcast(first_dtype, second_dtype) ->
+ *
  * Given a binary operation between types t1 and t2, what type will be returned?
  *
  * This is a singleton method on NMatrix, e.g., NMatrix.upcast(:int32, :int64)
@@ -680,62 +668,11 @@ static VALUE nm_upcast(VALUE self, VALUE t1, VALUE t2) {
 }
 
 
-/*
- * Each: Yield objects directly (suitable only for a dense matrix of Ruby objects).
- */
-static VALUE nm_dense_each_direct(VALUE nm) {
-  DENSE_STORAGE* s = NM_STORAGE_DENSE(nm);
-
-  RETURN_ENUMERATOR(nm, 0, 0);
-
-  for (size_t i = 0; i < nm_storage_count_max_elements(s); ++i)
-    rb_yield( reinterpret_cast<VALUE*>(s->elements)[i] );
-
-  return nm;
-}
-
-/*
- * Each: Copy matrix elements into Ruby VALUEs before operating on them (suitable for a dense matrix).
- */
-static VALUE nm_dense_each_indirect(VALUE nm) {
-  DENSE_STORAGE* s = NM_STORAGE_DENSE(nm);
-
-  RETURN_ENUMERATOR(nm, 0, 0);
-
-  for (size_t i = 0; i < nm_storage_count_max_elements(s); ++i) {
-    VALUE v = rubyobj_from_cval((char*)(s->elements) + i*DTYPE_SIZES[NM_DTYPE(nm)], NM_DTYPE(nm)).rval;
-    rb_yield( v ); // yield to the copy we made
-  }
-
-  return nm;
-}
-
 
 /*
- * Borrowed this function from NArray. Handles 'each' iteration on a dense
- * matrix.
+ * call-seq:
+ *     each -> 
  *
- * Additionally, handles separately matrices containing VALUEs and matrices
- * containing other types of data.
- */
-static VALUE nm_dense_each(VALUE nmatrix) {
-  volatile VALUE nm = nmatrix; // Not sure this actually does anything.
-
-  if (NM_DTYPE(nm) == nm::RUBYOBJ) {
-
-    // matrix of Ruby objects -- yield those objects directly
-    return nm_dense_each_direct(nm);
-
-  } else {
-
-    // We're going to copy the matrix element into a Ruby VALUE and then operate on it. This way user can't accidentally
-    // modify it and cause a seg fault.
-    return nm_dense_each_indirect(nm);
-  }
-}
-
-
-/*
  * Iterate over the matrix as you would an Enumerable (e.g., Array).
  *
  * Currently only works for dense.
@@ -751,6 +688,26 @@ static VALUE nm_each(VALUE nmatrix) {
   }
 }
 
+/*
+ * Iterate over the sparse entries of any matrix. For dense and yale, this iterates over non-zero
+ * entries; for list, this iterates over non-default entries. Yields dim+1 values for each entry:
+ * i, j, ..., and the entry itself.
+ */
+static VALUE nm_each_stored_with_indices(VALUE nmatrix) {
+  volatile VALUE nm = nmatrix;
+
+  switch(NM_STYPE(nm)) {
+  case nm::YALE_STORE:
+    return nm_yale_each_stored_with_indices(nm);
+  case nm::DENSE_STORE:
+    return nm_dense_each_with_indices(nm);
+  case nm::LIST_STORE:
+    return nm_list_each_stored_with_indices(nm);
+  default:
+    rb_raise(nm_eDataTypeError, "Not a proper storage type");
+  }
+}
+
 
 
 /*
@@ -803,6 +760,9 @@ DEF_ELEMENTWISE_RUBY_ACCESSOR(LT, lt)
 DEF_ELEMENTWISE_RUBY_ACCESSOR(GT, gt)
 
 /*
+ * call-seq:
+ *     hermitian? -> Boolean
+ *
  * Is this matrix hermitian?
  *
  * Definition: http://en.wikipedia.org/wiki/Hermitian_matrix
@@ -814,6 +774,9 @@ static VALUE nm_hermitian(VALUE self) {
 }
 
 /*
+ * call-seq:
+ * complex_conjugate -> NMatrix
+ *
  * Transform the matrix (in-place) to its complex conjugate. Only works on complex matrices.
  *
  * FIXME: For non-complex matrices, someone needs to implement a non-in-place complex conjugate (which doesn't use a bang).
@@ -860,7 +823,6 @@ static VALUE nm_complex_conjugate_bang(VALUE self) {
   return self;
 }
 
-
 /*
  * Helper function for creating a matrix. You have to create the storage and pass it in, but you don't
  * need to worry about deleting it.
@@ -875,6 +837,9 @@ NMATRIX* nm_create(nm::stype_t stype, STORAGE* storage) {
 }
 
 /*
+ * call-seq:
+ *     new -> NMatrix
+ *
  * Create a new NMatrix.
  *
  * There are several ways to do this. At a minimum, dimensions and either a dtype or initial values are needed, e.g.,
@@ -999,7 +964,7 @@ static VALUE nm_init(int argc, VALUE* argv, VALUE nm) {
   		break;
   		
   	case nm::YALE_STORE:
-  		nmatrix->storage = (STORAGE*)nm_yale_storage_create(dtype, shape, dim, init_cap);
+  		nmatrix->storage = (STORAGE*)nm_yale_storage_create(dtype, shape, dim, init_cap, nm::UINT8);
   		nm_yale_storage_init((YALE_STORAGE*)(nmatrix->storage));
   		break;
   }
@@ -1007,11 +972,13 @@ static VALUE nm_init(int argc, VALUE* argv, VALUE nm) {
   return nm;
 }
 
-
 /*
+ * call-seq:
+ *     to_hash -> Hash
+ * 
  * Create a Ruby Hash from an NMatrix.
  *
- * Currently only works for list storage.
+ * This is an internal C function which handles list stype only.
  */
 static VALUE nm_to_hash(VALUE self) {
   if (NM_STYPE(self) != nm::LIST_STORE) {
@@ -1021,7 +988,6 @@ static VALUE nm_to_hash(VALUE self) {
   return nm_list_storage_to_hash(NM_STORAGE_LIST(self), NM_DTYPE(self));
 }
 
-
 /*
  * Copy constructor for changing dtypes and stypes.
  */
@@ -1046,7 +1012,6 @@ static VALUE nm_init_cast_copy(VALUE self, VALUE new_stype_symbol, VALUE new_dty
   return Data_Wrap_Struct(CLASS_OF(self), mark[lhs->stype], nm_delete, lhs);
 }
 
-
 /*
  * Copy constructor for transposing.
  */
@@ -1066,7 +1031,6 @@ static VALUE nm_init_transposed(VALUE self) {
   return Data_Wrap_Struct(CLASS_OF(self), mark[lhs->stype], nm_delete, lhs);
 }
 
-
 /*
  * Copy constructor for no change of dtype or stype (used for #initialize_copy hook).
  */
@@ -1089,7 +1053,6 @@ static VALUE nm_init_copy(VALUE copy, VALUE original) {
   return copy;
 }
 
-
 /*
  * Get major, minor, and release components of NMatrix::VERSION. Store in function parameters.
  */
@@ -1339,7 +1302,7 @@ static VALUE nm_read(int argc, VALUE* argv, VALUE self) {
     f.read(reinterpret_cast<char*>(&ndnz),     sizeof(uint32_t));
     f.read(reinterpret_cast<char*>(&length),   sizeof(uint32_t));
 
-    s = nm_yale_storage_create(dtype, shape, dim, length); // set length as init capacity
+    s = nm_yale_storage_create(dtype, shape, dim, length, itype); // set length as init capacity
 
     read_padded_yale_elements(f, reinterpret_cast<YALE_STORAGE*>(s), length, symm, dtype, itype);
   } else {
@@ -1402,9 +1365,10 @@ static VALUE nm_is_ref(VALUE self) {
   return Qfalse;
 }
 
-
-
 /*
+ * call-seq:
+ *     slice -> ...
+ *
  * Access the contents of an NMatrix at given coordinates, using copying.
  *
  *     n.slice(3,3)  # => 5.0
@@ -1422,6 +1386,9 @@ static VALUE nm_mget(int argc, VALUE* argv, VALUE self) {
 }
 
 /*
+ * call-seq:
+ *     matrix[indexes] -> ...
+ *
  * Access the contents of an NMatrix at given coordinates by reference.
  *
  *     n[3,3]  # => 5.0
@@ -1528,9 +1495,10 @@ static VALUE nm_multiply(VALUE left_v, VALUE right_v) {
   return Qnil;
 }
 
-
-
 /*
+ * call-seq:
+ *     matrix.factorize_lu -> ...
+ *
  * LU factorization of a matrix.
  *
  * FIXME: For some reason, getrf seems to require that the matrix be transposed first -- and then you have to transpose the
@@ -1573,6 +1541,9 @@ static VALUE nm_factorize_lu(VALUE self) {
 }
 
 /*
+ * call-seq:
+ *     dim -> Integer
+ *
  * Get the number of dimensions of a matrix.
  *
  * In other words, if you set your matrix to be 3x4, the dim is 2. If the
@@ -1586,6 +1557,9 @@ static VALUE nm_dim(VALUE self) {
 }
 
 /*
+ * call-seq:
+ *     shape -> Array
+ *
  * Get the shape (dimensions) of a matrix.
  */
 static VALUE nm_shape(VALUE self) {
@@ -1601,6 +1575,9 @@ static VALUE nm_shape(VALUE self) {
 }
 
 /*
+ * call-seq:
+ *     stype -> Symbol
+ *
  * Get the storage type (stype) of a matrix, e.g., :yale, :dense, or :list.
  */
 static VALUE nm_stype(VALUE self) {
@@ -1609,6 +1586,9 @@ static VALUE nm_stype(VALUE self) {
 }
 
 /*
+ * call-seq:
+ *     symmetric? -> Boolean
+ *
  * Is this matrix symmetric?
  */
 static VALUE nm_symmetric(VALUE self) {
@@ -1665,7 +1645,6 @@ static VALUE elementwise_op(nm::ewop_t op, VALUE left_val, VALUE right_val) {
 		nm_dense_storage_ew_op,
 		nm_list_storage_ew_op,
 		nm_yale_storage_ew_op
-//		NULL
 	};
 	
 	NMATRIX *result = ALLOC(NMATRIX), *left;
@@ -1708,10 +1687,15 @@ static VALUE elementwise_op(nm::ewop_t op, VALUE left_val, VALUE right_val) {
     }
   }
 
-	return Data_Wrap_Struct(cNMatrix, mark[result->stype], nm_delete, result);
-}
+	VALUE result_val = Data_Wrap_Struct(CLASS_OF(left_val), mark[result->stype], nm_delete, result);
 
+	// If we're dealing with a vector, need to make sure the @orientation matches.
+	// FIXME: Eventually we probably need to make this an internal property of NVector.
+	if (CLASS_OF(left_val) == cNVector)
+	  rb_iv_set(result_val, "@orientation", rb_iv_get(left_val, "@orientation"));
 
+	return result_val;
+}
 
 /*
  * Check to determine whether matrix is a reference to another matrix.
@@ -1751,7 +1735,6 @@ static VALUE is_symmetric(VALUE self, bool hermitian) {
   return Qfalse;
 }
 
-
 ///////////////////////
 // Utility Functions //
 ///////////////////////
@@ -1996,12 +1979,10 @@ static nm::stype_t interpret_stype(VALUE arg) {
   }
 }
 
-
 //////////////////
 // Math Helpers //
 //////////////////
 
-
 STORAGE* matrix_storage_cast_alloc(NMATRIX* matrix, nm::dtype_t new_dtype) {
   if (matrix->storage->dtype == new_dtype && !is_ref(matrix))
     return matrix->storage;
@@ -2010,7 +1991,6 @@ STORAGE* matrix_storage_cast_alloc(NMATRIX* matrix, nm::dtype_t new_dtype) {
   return cast_copy_storage[matrix->stype][matrix->stype](matrix->storage, new_dtype);
 }
 
-
 STORAGE_PAIR binary_storage_cast_alloc(NMATRIX* left_matrix, NMATRIX* right_matrix) {
   STORAGE_PAIR casted;
   nm::dtype_t new_dtype = Upcast[left_matrix->storage->dtype][right_matrix->storage->dtype];
@@ -2021,7 +2001,6 @@ STORAGE_PAIR binary_storage_cast_alloc(NMATRIX* left_matrix, NMATRIX* right_matr
   return casted;
 }
 
-
 static VALUE matrix_multiply_scalar(NMATRIX* left, VALUE scalar) {
   rb_raise(rb_eNotImpError, "matrix-scalar multiplication not implemented yet");
   return Qnil;
@@ -2070,10 +2049,6 @@ static VALUE matrix_multiply(NMATRIX* left, NMATRIX* right) {
   return Qnil; // Only if we try to multiply list matrices should we return Qnil.
 }
 
-
-
-
-
 /*
  * Calculate the exact determinant of a dense matrix.
  *
@@ -2093,14 +2068,10 @@ static VALUE nm_det_exact(VALUE self) {
   return rubyobj_from_cval(result, NM_DTYPE(self)).rval;
 }
 
-
-
-
 /////////////////
 // Exposed API //
 /////////////////
 
-
 /*
  * Create a dense matrix. Used by the NMatrix GSL fork. Unlike nm_create, this one copies all of the
  * arrays and such passed in -- so you don't have to allocate and pass a new shape object for every
@@ -2142,7 +2113,6 @@ VALUE rb_nmatrix_dense_create(nm::dtype_t dtype, size_t* shape, size_t dim, void
   return Data_Wrap_Struct(klass, nm_dense_storage_mark, nm_dense_storage_delete, nm);
 }
 
-
 /*
  * Create a dense vector. Used by the NMatrix GSL fork.
  *
@@ -2158,4 +2128,3 @@ VALUE rb_nvector_dense_create(nm::dtype_t dtype, void* elements, size_t length)
 }
 
 } // end of extern "C"
-