carray 1.3.5 → 1.5.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/LICENSES

@@ -0,0 +1,22 @@
+Copyright (c) 2020 Hiroki Motoyoshi.
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -3,41 +3,38 @@ Ruby/CArray
 
 Ruby/CArray is an extension library for the multi-dimensional array class.
 
+Features
+--------
+
+* Multidimensional array for storing uniform data
+* Various ways to access data elements
+* Masks for each element to handle missing values
+* Element-wise operations and mathematical functions
+* Statistical functions for the elements
+* Indirect data manipulation for original array by virtual array 
+* Special iterators (dimension, block, window, categorical)
+* User-defined array
+* Storing fixed length data with data_class
+* Memory sharing with other objects (Experimental)
+
 Requirements
 ------------
 
-* Ruby 2.2.0 or later
+* Ruby 2.4.0 or later
 * C compiler 
   + IEEE754 floating point number
   + C99 complex number
-* Optionally required gems
-  + narray
-  + narray_miss
-  + axlsx
-  + spreadsheet
-  + sqlite3
-* Optional command
-  + Gnuplot
-  + ImageMagick (stream, convert, display, identify)
 
 Directories
 -----------
 
     .         - Ruby/CArray extension source codes
     lib       - Ruby/CArray standard library in Ruby
-    ext       - optional extension libraries for Ruby/CArray
-    examples  - some examples
     test      - some unit tests (incomplete)
     spec      - some rspec (incomplete)
     utils     - support tools for development.
 
-Author
-------
-
-Hiroki Motoyoshi 
-
-Copying
--------
+Licenses
+--------
 
-You can redistribute this library package and/or modify it under the terms of
-the Ruby Licence. See the file 'COPYING' in this directory.
+MIT (after version 1.5.0)

data/Rakefile

@@ -2,12 +2,43 @@
 #
 #
 
+GEMSPEC = "carray.gemspec"
+
+task :install do
+  spec = eval File.read(GEMSPEC)
+  version_h = `ruby ext/version.rb`.chomp
+  if spec.version.to_s != version_h
+    STDERR.puts "Mismatch in version between carray.gemspec and version.h"
+    STDERR.puts "  carray.gemspec - #{spec.version.to_s }"
+    STDERR.puts "  version.h      - #{version_h}"
+    STDERR.puts "Please check!"
+    exit(1)
+  end
+  system %{
+    gem build #{GEMSPEC}; gem install #{spec.full_name}.gem
+  }
+end
+
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new
+
+
+__END__
 require 'rake'
 require 'rake/testtask'
 require 'rspec/core/rake_task'
 
 task :default => :test
 
+GEMSPEC = "carray.gemspec"
+
+task :install do
+  spec = eval File.read(GEMSPEC)
+  system %{
+    gem build #{GEMSPEC}; gem install #{spec.full_name}.gem
+  }
+end
+
 desc "Run the tests"
 Rake::TestTask::new(:test) do |t|
   t.test_files = FileList['test/test_ALL.rb']

data/carray.gemspec

@@ -1,21 +1,18 @@
-
-
 Gem::Specification::new do |s|
-  require_relative "./version"
-  
-  version, date = carray_version()
+
+  version = "1.5.1"
 
   files = Dir.glob("**/*") - [ 
-                            Dir.glob("vendor"),
-                            Dir.glob("ext/**/{Makefile,mkmf.log}"),
-                            Dir.glob("**/*.{o,so,bundle}"),
-                            Dir.glob("**/*~"),
-                            Dir.glob("carray-*.gem"), 
-                           ].flatten
+                               Dir.glob("carray-*.gem"), 
+                               Dir.glob("ext/**/{Makefile,mkmf.log}"),
+                               Dir.glob("**/*.{o,so,bundle}"),
+                               Dir.glob("**/*~"),
+                               Dir.glob("doc/**/*"),
+                             ].flatten
 
   s.platform    = Gem::Platform::RUBY
   s.name        = "carray"
-  s.summary     = "Multi-dimesional array class"
+  s.summary     = "Multi-dimesional array class for Ruby"
   s.description = <<-HERE
     CArray is a uniform multi-dimensional rectangular array class.
     It provides the various types of sub-arrays and references
@@ -25,20 +22,10 @@ Gem::Specification::new do |s|
   s.version     = version
   s.author      = "Hiroki Motoyoshi"
   s.email       = ""
+  s.licenses    = ['MIT']
   s.homepage    = 'https://github.com/himotoyoshi/carray'
   s.files       = files
-  s.extensions  = [ "extconf.rb" ] + 
-                     Dir["ext/*/extconf.rb"].select{|f| File.exist?(f) }
-  s.rdoc_options = [
-		"-m rdoc_main.rb", 
-		"rdoc_main.rb", 
-		"rdoc_ext.rb",
-		"rdoc_math.rb", 
-		"rdoc_stat.rb", 
-		Dir.glob("lib/carray/**/*.rb"),
-	].flatten
-  s.required_ruby_version = ">= 1.8.1"
-  s.add_runtime_dependency 'narray', '~> 0.6.1.1'
-  s.add_runtime_dependency 'narray_miss', '~> 1.3'
-  s.add_runtime_dependency 'sqlite3', '~> 1.3'
+  s.extensions  = [ "ext/extconf.rb" ] 
+  s.required_ruby_version = ">= 2.4.0"
 end
+

data/{ca_iter_block.c → ext/ca_iter_block.c}

@@ -23,7 +23,7 @@ VALUE rb_cCABlockIterator;
 typedef struct {
   int16_t   obj_type;
   int8_t    data_type;
-  int8_t    rank;
+  int8_t    ndim;
   int32_t   flags;
   ca_size_t   bytes;
   ca_size_t   elements;
@@ -42,11 +42,11 @@ typedef struct {
   ca_size_t  *step;
   ca_size_t  *count;
   ca_size_t  *size0;
-} CABlock;                  // 68 + 20*(rank) (bytes) 
+} CABlock;                  // 68 + 20*(ndim) (bytes) 
 */
 
 typedef struct {
-  int8_t  rank;
+  int8_t  ndim;
   ca_size_t dim[CA_RANK_MAX];
   CArray *reference;
   CArray * (*kernel_at_addr)(void *, ca_size_t, CArray *);
@@ -73,14 +73,14 @@ ca_bi_kernel_at_index (void *it, ca_size_t *idx, CArray *ref)
   else {
     CABlock *ck = (CABlock *)bit->kernel;
     kernel = ca_block_new(ref,
-                          ck->rank, ck->size0,
+                          ck->ndim, ck->size0,
                           ck->start, ck->step, ck->count,
                           ck->offset);
   }
 
   ca_update_mask(kernel);
 
-  for (i=0; i<kernel->rank; i++) {
+  for (i=0; i<kernel->ndim; i++) {
     j = idx[i];
     CA_CHECK_INDEX(j, bit->dim[i]);
     kernel->start[i] += j * kernel->dim[i];
@@ -99,7 +99,7 @@ ca_bi_kernel_at_addr (void *it, ca_size_t addr, CArray *ref)
   ca_size_t *dim = bit->dim;
   ca_size_t idx[CA_RANK_MAX];
   int8_t i;
-  for (i=bit->rank-1; i>=0; i--) {
+  for (i=bit->ndim-1; i>=0; i--) {
     idx[i] = addr % dim[i];
     addr  /= dim[i];
   }
@@ -117,7 +117,7 @@ ca_bi_kernel_move_to_index (void *it, ca_size_t *idx, CArray *kern)
 
   ca_update_mask(kernel);
 
-  for (i=0; i<kernel->rank; i++) {
+  for (i=0; i<kernel->ndim; i++) {
     j = idx[i];
     CA_CHECK_INDEX(j, bit->dim[i]);
     kernel->start[i] = j * kernel->dim[i];
@@ -136,7 +136,7 @@ ca_bi_kernel_move_to_addr (void *it, ca_size_t addr, CArray *ref)
   ca_size_t *dim = bit->dim;
   ca_size_t idx[CA_RANK_MAX];
   int8_t i;
-  for (i=bit->rank-1; i>=0; i--) {
+  for (i=bit->ndim-1; i>=0; i--) {
     idx[i] = addr % dim[i];
     addr  /= dim[i];
   }
@@ -158,11 +158,11 @@ ca_bi_setup (VALUE self, VALUE rref, VALUE rker)
   Data_Get_Struct(rref, CArray, ref);
   Data_Get_Struct(rker, CABlock, ker);
 
-  if ( ref->rank != ker->rank ) {
-    rb_raise(rb_eRuntimeError, "rank mismatch between reference and kernel");
+  if ( ref->ndim != ker->ndim ) {
+    rb_raise(rb_eRuntimeError, "ndim mismatch between reference and kernel");
   }
 
-  for (i=0; i<ref->rank; i++) {
+  for (i=0; i<ref->ndim; i++) {
     if ( ker->step[i] != 1 ) {
       rb_raise(rb_eRuntimeError, "block should be contiguous");
     }
@@ -174,8 +174,8 @@ ca_bi_setup (VALUE self, VALUE rref, VALUE rker)
     */
   }
 
-  it->rank      = ref->rank;
-  memcpy(it->dim, dim, it->rank * sizeof(ca_size_t));
+  it->ndim      = ref->ndim;
+  memcpy(it->dim, dim, it->ndim * sizeof(ca_size_t));
   it->reference = ref;
   it->kernel    = ker;
   it->kernel_at_addr  = ca_bi_kernel_at_addr;

data/{ca_iter_dimension.c → ext/ca_iter_dimension.c}

@@ -21,7 +21,7 @@ VALUE rb_cCADimIterator;
 */
 
 typedef struct {
-  int8_t  rank;
+  int8_t  ndim;
   ca_size_t dim[CA_RANK_MAX];
   CArray *reference;
   CArray * (*kernel_at_addr)(void *, ca_size_t, CArray *);
@@ -50,14 +50,14 @@ ca_di_kernel_at_index (void *it, ca_size_t *idx, CArray *ref)
   else {
     CABlock *ck = (CABlock *)dit->kernel;
     kernel = ca_block_new(ref,
-                          ck->rank, ck->size0,
+                          ck->ndim, ck->size0,
                           ck->start, ck->step, ck->count,
                           ck->offset);
   }
 
   ca_update_mask(kernel);
 
-  for (i=0; i<dit->rank; i++) {
+  for (i=0; i<dit->ndim; i++) {
     val = idx[i];
     CA_CHECK_INDEX(val, dit->dim[i]);
     kernel->start[dit->symindex[i]] = val * kernel->step[dit->symindex[i]];
@@ -77,7 +77,7 @@ ca_di_kernel_at_addr (void *it, ca_size_t addr, CArray *ref)
   ca_size_t *dim = dit->dim;
   ca_size_t idx[CA_RANK_MAX];
   int8_t i;
-  for (i=dit->rank-1; i>=0; i--) {
+  for (i=dit->ndim-1; i>=0; i--) {
     idx[i] = addr % dim[i];
     addr  /= dim[i];
   }
@@ -94,7 +94,7 @@ ca_di_kernel_move_to_index (void *it, ca_size_t *idx, CArray *kern)
 
   ca_update_mask(kernel);
 
-  for (i=0; i<dit->rank; i++) {
+  for (i=0; i<dit->ndim; i++) {
     val = idx[i];
     CA_CHECK_INDEX(val, dit->dim[i]);
     kernel->start[dit->symindex[i]] = val * kernel->step[dit->symindex[i]];
@@ -114,7 +114,7 @@ ca_di_kernel_move_to_addr (void *it, ca_size_t addr, CArray *ref)
   ca_size_t *dim = dit->dim;
   ca_size_t idx[CA_RANK_MAX];
   int8_t i;
-  for (i=dit->rank-1; i>=0; i--) {
+  for (i=dit->ndim-1; i>=0; i--) {
     idx[i] = addr % dim[i];
     addr  /= dim[i];
   }
@@ -129,7 +129,7 @@ ca_di_setup (VALUE self, VALUE rref, CAIndexInfo *info)
   volatile VALUE rindex, rker, rsymtbl;
   CADimIterator *it;
   CAIndexInfo blk_spec;
-  int8_t rank;
+  int8_t ndim;
   int i, j, k;
 
   Data_Get_Struct(self, CADimIterator, it);
@@ -142,7 +142,7 @@ ca_di_setup (VALUE self, VALUE rref, CAIndexInfo *info)
 
   blk_spec      = *info;
   blk_spec.type = CA_REG_BLOCK;
-  for (i=0; i<info->rank; i++) {
+  for (i=0; i<info->ndim; i++) {
     if ( info->index_type[i] == CA_IDX_SYMBOL ) {
       blk_spec.index_type[i] = CA_IDX_ALL;
       rb_hash_aset(rsymtbl, ID2SYM(blk_spec.index[i].symbol.id), INT2NUM(i));
@@ -151,13 +151,13 @@ ca_di_setup (VALUE self, VALUE rref, CAIndexInfo *info)
 
   rref = rb_ca_ref_block(rref, &blk_spec);
 
-  rindex = rb_ary_new2(info->rank);
-  rank = 0;
+  rindex = rb_ary_new2(info->ndim);
+  ndim = 0;
 
   j = 0;
   k = 0;
 
-  for (i=0; i<info->rank; i++) {
+  for (i=0; i<info->ndim; i++) {
     if ( info->index_type[i] == CA_IDX_SCALAR ) {
       rb_ary_store(rindex, i, SIZE2NUM(info->index[i].scalar));
       continue; /* escape from j++ */
@@ -165,8 +165,8 @@ ca_di_setup (VALUE self, VALUE rref, CAIndexInfo *info)
     else if ( info->index_type[i] == CA_IDX_SYMBOL ) {
       rb_ary_store(rindex, i, rb_ary_new3(1, SIZE2NUM(0)));
       it->symflag[j]       = 1;
-      it->symindex[rank] = j;
-      rank++;
+      it->symindex[ndim] = j;
+      ndim++;
     }
     else if ( info->index_type[i] == CA_IDX_ALL ) {
       rb_ary_store(rindex, i, Qnil);
@@ -184,7 +184,7 @@ ca_di_setup (VALUE self, VALUE rref, CAIndexInfo *info)
 
   rker = rb_apply(rref, rb_intern("[]"), rindex);
 
-  it->rank = rank;
+  it->ndim = ndim;
   Data_Get_Struct(rref, CArray, it->reference);
   Data_Get_Struct(rker, CArray, it->kernel);
   it->kernel_at_addr  = ca_di_kernel_at_addr;
@@ -192,7 +192,7 @@ ca_di_setup (VALUE self, VALUE rref, CAIndexInfo *info)
   it->kernel_move_to_addr  = ca_di_kernel_move_to_addr;
   it->kernel_move_to_index = ca_di_kernel_move_to_index;
 
-  for (i=0; i<it->rank; i++) {
+  for (i=0; i<it->ndim; i++) {
     it->dim[i] = it->reference->dim[it->symindex[i]];
   }
 
@@ -239,7 +239,7 @@ rb_ca_dim_iterator (int argc, VALUE *argv, VALUE self)
 
   Data_Get_Struct(self, CArray, ca);
 
-  rb_ca_scan_index(ca->rank, ca->dim, ca->elements, argc, argv, &info);
+  rb_ca_scan_index(ca->ndim, ca->dim, ca->elements, argc, argv, &info);
 
   obj = rb_di_s_allocate(rb_cCADimIterator);
   ca_di_setup(obj, self, &info);

data/{ca_iter_window.c → ext/ca_iter_window.c}

@@ -13,7 +13,7 @@
 #include "carray.h"
 
 typedef struct {
-  int8_t  rank;
+  int8_t  ndim;
   ca_size_t dim[CA_RANK_MAX];
   CArray *reference;
   CArray * (*kernel_at_addr)(void *, ca_size_t, CArray *);
@@ -59,7 +59,7 @@ ca_vi_kernel_at_index (void *it, ca_size_t *idx, CArray *ref)
 
   ca_update_mask(kernel);
 
-  for (i=0; i<kernel->rank; i++) {
+  for (i=0; i<kernel->ndim; i++) {
     j = idx[i];
     CA_CHECK_INDEX(j, vit->dim[i]);
     kernel->start[i] = j - vit->offset[i];
@@ -78,7 +78,7 @@ ca_vi_kernel_at_addr (void *it, ca_size_t addr, CArray *ref)
   ca_size_t *dim = vit->dim;
   ca_size_t idx[CA_RANK_MAX];
   int8_t i;
-  for (i=vit->rank-1; i>=0; i--) {
+  for (i=vit->ndim-1; i>=0; i--) {
     idx[i] = addr % dim[i];
     addr  /= dim[i];
   }
@@ -97,7 +97,7 @@ ca_vi_kernel_move_to_index (void *it, ca_size_t *idx, CArray *kern)
 
   ca_update_mask(kernel);
 
-  for (i=0; i<kernel->rank; i++) {
+  for (i=0; i<kernel->ndim; i++) {
     j = idx[i];
     CA_CHECK_INDEX(j, dim[i]);
     kernel->start[i] = j - offset[i];
@@ -116,7 +116,7 @@ ca_vi_kernel_move_to_addr (void *it, ca_size_t addr, CArray *ref)
   ca_size_t *dim = vit->dim;
   ca_size_t idx[CA_RANK_MAX];
   int8_t i;
-  for (i=vit->rank-1; i>=0; i--) {
+  for (i=vit->ndim-1; i>=0; i--) {
     idx[i] = addr % dim[i];
     addr  /= dim[i];
   }
@@ -136,12 +136,12 @@ ca_vi_setup (VALUE self, VALUE rref, VALUE rker)
   Data_Get_Struct(rref, CArray, ref);
   Data_Get_Struct(rker, CArray, ker);
 
-  if ( ref->rank != ker->rank ) {
-    rb_raise(rb_eRuntimeError, "rank mismatch between reference and kernel");
+  if ( ref->ndim != ker->ndim ) {
+    rb_raise(rb_eRuntimeError, "ndim mismatch between reference and kernel");
   }
 
-  it->rank      = ref->rank;
-  memcpy(it->dim, ref->dim, it->rank * sizeof(ca_size_t));
+  it->ndim      = ref->ndim;
+  memcpy(it->dim, ref->dim, it->ndim * sizeof(ca_size_t));
   it->reference = ref;
   it->kernel    = ker;
   it->kernel_at_addr  = ca_vi_kernel_at_addr;
@@ -149,7 +149,7 @@ ca_vi_setup (VALUE self, VALUE rref, VALUE rker)
   it->kernel_move_to_addr  = ca_vi_kernel_move_to_addr;
   it->kernel_move_to_index = ca_vi_kernel_move_to_index;
 
-  for (i=0; i<it->rank; i++) {
+  for (i=0; i<it->ndim; i++) {
     it->offset[i] = -(((CAWindow*)ker)->start[i]);
   }