numo-narray-alt 0.9.4 → 0.9.5

data/ext/numo/narray/step.c

@@ -36,7 +36,9 @@ static ID id_beg, id_end, id_len, id_step;
  *  <i>array_sizse</i> is given, negative array index is considered.
  */
 
-void nary_step_array_index(VALUE obj, size_t ary_size, size_t* plen, ssize_t* pbeg, ssize_t* pstep) {
+void nary_step_array_index(
+  VALUE obj, size_t ary_size, size_t* plen, ssize_t* pbeg, ssize_t* pstep
+) {
   size_t len;
   ssize_t beg = 0, step = 1;
   VALUE vbeg, vend, vstep, vlen;
@@ -178,7 +180,10 @@ void nary_step_array_index(VALUE obj, size_t ary_size, size_t* plen, ssize_t* pb
   // puts("pass 2");
 
   if (beg < 0 || beg >= (ssize_t)ary_size || end < 0 || end >= (ssize_t)ary_size) {
-    rb_raise(rb_eRangeError, "beg=%" SZF "d,end=%" SZF "d is out of array size (%" SZF "u)", beg, end, ary_size);
+    rb_raise(
+      rb_eRangeError, "beg=%" SZF "d,end=%" SZF "d is out of array size (%" SZF "u)", beg, end,
+      ary_size
+    );
   }
   if (plen) *plen = len;
   if (pbeg) *pbeg = beg;

data/ext/numo/narray/struct.c

@@ -167,7 +167,10 @@ static VALUE nst_field_view(VALUE self, VALUE idx) {
   def = nst_definition(self, idx);
   if (!RTEST(def)) {
     idx = rb_funcall(idx, rb_intern("to_s"), 0);
-    rb_raise(rb_eTypeError, "Invalid field: '%s' for struct %s", StringValuePtr(idx), rb_class2name(rb_obj_class(self)));
+    rb_raise(
+      rb_eTypeError, "Invalid field: '%s' for struct %s", StringValuePtr(idx),
+      rb_class2name(rb_obj_class(self))
+    );
   }
   type = RARRAY_AREF(def, 1);
   ofs = RARRAY_AREF(def, 2);
@@ -268,7 +271,6 @@ static VALUE nst_s_new(int argc, VALUE* argv, VALUE klass) {
 
   size = rb_iv_get(st, "__offset__");
   members = rb_iv_get(st, "__members__");
-  // printf("size=%d\n",NUM2INT(size));
   rb_define_const(st, CONTIGUOUS_STRIDE, size);
   rb_define_const(st, ELEMENT_BYTE_SIZE, size);
   rb_define_const(st, ELEMENT_BIT_SIZE, rb_funcall(size, '*', 1, INT2FIX(8)));
@@ -344,7 +346,9 @@ static VALUE nstruct_add_type(VALUE type, int argc, VALUE* argv, VALUE nst) {
 
   size = rb_funcall(type, rb_intern("byte_size"), 0);
   rb_iv_set(nst, "__offset__", rb_funcall(ofs, '+', 1, size));
-  rb_ary_push(rb_iv_get(nst, "__members__"), rb_ary_new3(4, name, type, ofs, size)); // <- field definition
+  rb_ary_push(
+    rb_iv_get(nst, "__members__"), rb_ary_new3(4, name, type, ofs, size)
+  ); // <- field definition
   return Qnil;
 }
 
@@ -421,9 +425,9 @@ static VALUE nst_create_member_views(VALUE self) {
 
 static VALUE nary_struct_to_a(VALUE self) {
   volatile VALUE opt;
-  ndfunc_arg_in_t ain[3] = {{Qnil, 0}, {sym_loop_opt}, {sym_option}};
-  ndfunc_arg_out_t aout[1] = {{rb_cArray, 0}}; // dummy?
-  ndfunc_t ndf = {iter_nstruct_to_a, NO_LOOP, 3, 1, ain, aout};
+  ndfunc_arg_in_t ain[3] = { { Qnil, 0 }, { sym_loop_opt }, { sym_option } };
+  ndfunc_arg_out_t aout[1] = { { rb_cArray, 0 } }; // dummy?
+  ndfunc_t ndf = { iter_nstruct_to_a, NO_LOOP, 3, 1, ain, aout };
 
   opt = nst_create_member_views(self);
   return na_ndloop_cast_narray_to_rarray(&ndf, self, opt);
@@ -581,19 +585,14 @@ static VALUE nary_struct_cast_array(VALUE klass, VALUE rary) {
   narray_t* na;
   // na_compose_t *nc;
   VALUE opt;
-  ndfunc_arg_in_t ain[3] = {{OVERWRITE, 0}, {rb_cArray, 0}, {sym_option}};
-  ndfunc_t ndf = {iter_nstruct_from_a, NO_LOOP, 3, 0, ain, 0};
-
-  // fprintf(stderr,"rary:");rb_p(rary);
-  // fprintf(stderr,"class_of(rary):");rb_p(rb_obj_class(rary));
+  ndfunc_arg_in_t ain[3] = { { OVERWRITE, 0 }, { rb_cArray, 0 }, { sym_option } };
+  ndfunc_t ndf = { iter_nstruct_from_a, NO_LOOP, 3, 0, ain, 0 };
 
   // vnc = na_ary_composition_for_struct(klass, rary);
   // Data_Get_Struct(vnc, na_compose_t, nc);
   // nary = nary_new(klass, nc->ndim, nc->shape);
   nary = na_s_new_like(klass, rary);
   GetNArray(nary, na);
-  // fprintf(stderr,"na->size=%lu\n",na->size);
-  // fprintf(stderr,"na->ndim=%d\n",na->ndim);
   if (na->size > 0) {
     opt = nst_create_member_views(nary);
     rb_funcall(nary, rb_intern("allocate"), 0);
@@ -657,8 +656,8 @@ static void iter_struct_store_struct(na_loop_t* const lp) {
 }
 
 static VALUE nary_struct_store_struct(VALUE self, VALUE obj) {
-  ndfunc_arg_in_t ain[2] = {{OVERWRITE, 0}, {Qnil, 0}};
-  ndfunc_t ndf = {iter_struct_store_struct, FULL_LOOP, 2, 0, ain, 0};
+  ndfunc_arg_in_t ain[2] = { { OVERWRITE, 0 }, { Qnil, 0 } };
+  ndfunc_t ndf = { iter_struct_store_struct, FULL_LOOP, 2, 0, ain, 0 };
 
   na_ndloop(&ndf, 2, self, obj);
   return self;
@@ -683,8 +682,10 @@ static VALUE nary_struct_store(VALUE self, VALUE obj) {
     nary_struct_store_struct(self, obj);
     return self;
   }
-  rb_raise(nary_eCastError, "unknown conversion from %s to %s", rb_class2name(rb_obj_class(obj)),
-           rb_class2name(rb_obj_class(self)));
+  rb_raise(
+    nary_eCastError, "unknown conversion from %s to %s", rb_class2name(rb_obj_class(obj)),
+    rb_class2name(rb_obj_class(self))
+  );
   return self;
 }
 
@@ -741,10 +742,10 @@ static VALUE nst_s_add_type(int argc, VALUE* argv, VALUE mod) {
   return Qnil;
 }
 
-#define NST_TYPEDEF(tpname, tpclass)                                                                                           \
-  static VALUE nst_s_##tpname(int argc, VALUE* argv, VALUE mod) {                                                              \
-    nstruct_add_type(tpclass, argc, argv, mod);                                                                                \
-    return Qnil;                                                                                                               \
+#define NST_TYPEDEF(tpname, tpclass)                              \
+  static VALUE nst_s_##tpname(int argc, VALUE* argv, VALUE mod) { \
+    nstruct_add_type(tpclass, argc, argv, mod);                   \
+    return Qnil;                                                  \
   }
 
 NST_TYPEDEF(int8, numo_cInt8)
@@ -760,7 +761,8 @@ NST_TYPEDEF(dcomplex, numo_cDComplex)
 NST_TYPEDEF(sfloat, numo_cSFloat)
 NST_TYPEDEF(scomplex, numo_cSComplex)
 
-#define rb_define_singleton_alias(klass, name1, name2) rb_define_alias(rb_singleton_class(klass), name1, name2)
+#define rb_define_singleton_alias(klass, name1, name2) \
+  rb_define_alias(rb_singleton_class(klass), name1, name2)
 
 void Init_nary_struct(void) {
   cT = rb_define_class_under(mNumo, "Struct", numo_cNArray);

data/lib/numo/narray/extra.rb

@@ -1086,7 +1086,7 @@ module Numo
               if am > nx && an > nx && bm > nx && bn > nx &&
                  size > ns && b.size > ns
                 @@warn_slow_dot = true
-                warn "\nwarning: Built-in matrix dot is slow. Consider installing Numo::Linalg.\n\n"
+                warn "\nwarning: Built-in matrix dot is slow. Consider installing numo-linalg-alt gem.\n\n"
               end
             end
             self[false, :new].mulsum(b[false, :new, true, true], axis: -2)
@@ -1209,8 +1209,37 @@ module Numo
       (self[*adim] * b[*bdim]).reshape(*shpr)
     end
 
-    # under construction
-    def cov(y = nil, ddof: 1, fweights: nil, aweights: nil)
+    # Compute a covariance matrix.
+    #
+    # @param y [Numo::NArray] (optional) If not nil, the covariance matrix of `self` and `y` is computed.
+    # @param ddof [Integer] (optional) Delta degrees of freedom. The divisor used in calculations is `N - ddof`,
+    #   where `N` represents the number of observations.
+    # @param fweights [Numo::NArray] (optional) 1-D array of integer frequency weights.
+    # @param aweights [Numo::NArray] (optional) 1-D array of observation vector weights.
+    # @return [Numo::NArray]  return covariance matrix
+    #
+    # @example
+    #   x = Numo::DFloat[4, 5, 6]
+    #   x.cov
+    #   # => 1.0
+    #
+    #   x = Numo::DFloat[[4, 5, 6], [3, 2, 1]]
+    #   x.cov
+    #   # => Numo::DFloat#shape=[2,2]
+    #   # [[1, -1],
+    #   #  [-1, 1]]
+    #
+    #   y = Numo::DFloat[7, 9, 8]
+    #   x.cov(y)
+    #   # => Numo::DFloat#shape=[3,3]
+    #   # [[1, -1, 0.5],
+    #   #  [-1, 1, -0.5],
+    #   #  [0.5, -0.5, 1]]
+    def cov(y = nil, ddof: 1, fweights: nil, aweights: nil) # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity, Metrics/PerceivedComplexity
+      raise Numo::NArray::ShapeError, 'ndim must be <= 2' if ndim > 2
+      raise Numo::NArray::ShapeError, 'y.ndim must be <= 2' if !y.nil? && (y.ndim > 2)
+      raise ArgumentError, 'ddof must be 0 or 1' unless [0, 1].include?(ddof)
+
       m = if y
             NArray.vstack([self, y])
           else
@@ -1218,36 +1247,48 @@ module Numo
           end
       w = nil
       if fweights
-        f = fweights
-        w = f
+        fweights = Numo::NArray.cast(fweights) unless fweights.is_a?(Numo::NArray)
+        raise ArgumentError, 'fweights must be 1-D array' unless fweights.ndim == 1
+        raise ArgumentError, 'fweights size is wrong' unless fweights.size == m.shape[1]
+        raise ArgumentError, 'fweights must be non-negative' if (fweights < 0).any?
+        raise ArgumentError, 'fweights must be integer' unless fweights == fweights.floor
+
+        w = fweights
       end
       if aweights
-        a = aweights
-        w = w ? w * a : a
-      end
-      if w
-        w_sum = w.sum(axis: -1, keepdims: true)
-        if ddof == 0
-          fact = w_sum
-        elsif aweights.nil?
-          fact = w_sum - ddof
+        aweights = Numo::NArray.cast(aweights) unless aweights.is_a?(Numo::NArray)
+        raise ArgumentError, 'aweights must be 1-D array' unless aweights.ndim == 1
+        raise ArgumentError, 'aweights size is wrong' unless aweights.size == m.shape[1]
+        raise ArgumentError, 'aweights must be non-negative' if (aweights < 0).any?
+
+        if w.nil?
+          w = aweights
         else
-          wa_sum = (w * a).sum(axis: -1, keepdims: true)
-          fact = w_sum - (ddof * wa_sum / w_sum)
+          w *= aweights
         end
-        raise StandardError, 'Degrees of freedom <= 0 for slice' if (fact <= 0).any?
-      else
-        fact = m.shape[-1] - ddof
       end
-      if w
-        m -= (m * w).sum(axis: -1, keepdims: true) / w_sum
-        mw = m * w
-      else
+      fact = if w.nil?
+               m.shape[-1] - ddof
+             elsif ddof == 0
+               w.sum
+             elsif aweights.nil?
+               w.sum - ddof
+             else
+               w_sum = w.sum
+               w_sum - (ddof * (w * aweights).sum / w_sum)
+             end
+      if fact <= 0
+        warn('Degrees of freedom <= 0 for slice')
+        fact = 0.0
+      end
+      if w.nil?
         m -= m.mean(axis: -1, keepdims: true)
         mw = m
+      else
+        m -= (m * w).sum(axis: -1, keepdims: true) / w.sum
+        mw = m * w
       end
-      mt = m.ndim < 2 ? m : m.swapaxes(-2, -1)
-      mw.dot(mt.conj) / fact
+      m.dot(mw.transpose.conj) / fact
     end
 
     private

data/numo-narray-alt.gemspec

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+require 'English'
+
+lib = File.expand_path('lib', __dir__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+
+open('ext/numo/narray/numo/narray.h') do |f|
+  f.each_line do |l|
+    if /NARRAY_VERSION "([\d.]+)"/ =~ l
+      NARRAY_VERSION = Regexp.last_match(1)
+      break
+    end
+  end
+end
+
+Gem::Specification.new do |spec|
+  spec.name          = 'numo-narray-alt'
+  spec.version       = NARRAY_VERSION
+  spec.authors       = ['yoshoku']
+  spec.email         = ['yoshoku@outlook.com']
+  spec.description   = 'Numo::NArray Alternative is an experimental project forked from Numo::NArray.'
+  spec.summary       = 'Numo::NArray Alternative is an experimental project forked from Numo::NArray.'
+  spec.homepage      = 'https://github.com/yoshoku/numo-narray-alt'
+  spec.license       = 'BSD-3-Clause'
+  spec.required_ruby_version = '>= 2.2'
+
+  spec.metadata['homepage_uri'] = spec.homepage
+  spec.metadata['source_code_uri'] = spec.homepage
+  spec.metadata['changelog_uri'] = "#{spec.homepage}/blob/main/CHANGELOG.md"
+  spec.metadata['documentation_uri'] = "https://gemdocs.org/gems/#{spec.name}/#{spec.version}/"
+
+  spec.files         = `git ls-files Gemfile LICENSE README.md Rakefile lib ext numo-narray-alt.gemspec`.split($INPUT_RECORD_SEPARATOR) # rubocop:disable Layout/LineLength
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib']
+  spec.extensions    = ['ext/numo/narray/extconf.rb']
+  spec.metadata['rubygems_mfa_required'] = 'true'
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: numo-narray-alt
 version: !ruby/object:Gem::Version
-  version: 0.9.4
+  version: 0.9.5
 platform: ruby
 authors:
 - yoshoku
@@ -70,6 +70,7 @@ files:
 - ext/numo/narray/src/t_int32.c
 - ext/numo/narray/src/t_int64.c
 - ext/numo/narray/src/t_int8.c
+- ext/numo/narray/src/t_mean.c
 - ext/numo/narray/src/t_robject.c
 - ext/numo/narray/src/t_scomplex.c
 - ext/numo/narray/src/t_sfloat.c
@@ -81,10 +82,15 @@ files:
 - ext/numo/narray/struct.c
 - lib/numo/narray.rb
 - lib/numo/narray/extra.rb
+- numo-narray-alt.gemspec
 homepage: https://github.com/yoshoku/numo-narray-alt
 licenses:
 - BSD-3-Clause
 metadata:
+  homepage_uri: https://github.com/yoshoku/numo-narray-alt
+  source_code_uri: https://github.com/yoshoku/numo-narray-alt
+  changelog_uri: https://github.com/yoshoku/numo-narray-alt/blob/main/CHANGELOG.md
+  documentation_uri: https://gemdocs.org/gems/numo-narray-alt/0.9.5/
   rubygems_mfa_required: 'true'
 rdoc_options: []
 require_paths: