OpenMatriX 0.1.0

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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/.rspec

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+--format documentation
+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.1.7
+before_install: gem install bundler -v 1.10.6

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in OpenMatriX.gemspec
+gemspec

data/LICENSE.md

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data/OpenMatriX.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'OpenMatriX/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "OpenMatriX"
+  spec.version       = OpenMatriX::VERSION
+  spec.authors       = ["Andrew Rohne"]
+  spec.email         = ["arohne@oki.org"]
+  spec.licenses      = ["Apache-2.0"]
+  spec.summary       = %q{Open Matrix support for Ruby}
+  spec.description   = %q{Open Matrix Ruby API}
+  spec.homepage      = "https://github.com/okiandrew/OpenMatriX"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.10"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.3"
+
+  spec.add_dependency "ffi", "~> 1.9"
+  spec.add_dependency "narray", "~> 0.6"
+end

data/README.md

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+# OpenMatriX
+
+OpenMatriX is a Ruby Gem to read (Open Matrix files)[https://sites.google.com/site/openmodeldata/]. This was built for use on the web and to eventually have APIs that can return values from a matrix.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'OpenMatriX'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install OpenMatriX
+
+## Usage
+
+```ruby
+# Open file
+# OMX::OMXFile.new(filename)
+file = OMX::OMXFile.new('filename.omx')
+
+# Get the attributes from the file
+at = OMX::OMXAttr.new(file)
+puts "Version: #{at.getVersion()}"
+puts "Zones: #{at.getZones()}"
+
+# Get the tables from the file
+t = OMX::OMXTables.new(file)
+puts "Tables: #{t.getNTables()}"
+puts "Table Names: #{t.getTableNames()}"
+
+# Get data from the file
+# OMX::OMXData.new(file,"Tablename", nZones)
+tt = OMX::OMXData.new(file,"DIST",at.getZones())
+puts tt.getJ(5)
+
+# Close the file
+file.close()
+```
+
+## Important Concepts for Non-Travel-Modelers
+
+Note that our use of matrices may be a little different from others', and we
+have some of our own nomenclature.
+
+The use of the term "zone" refers to a geographic location called a Traffic
+Analysis Zone, or TAZ.  These TAZs are created by the model "owner", which
+differs by state and jurisdiction.
+
+Zones are generally sequentially numbered starting with 1.  OMX files, depending
+on how they are viewed and/or accessed likely start at 0, so increments/decrements
+are fairly common in code.
+
+In travel modeling, there is a nomenclature that I is a production or origin
+zone and J is an attraction or destination zone.  "Production" and "Attraction"
+are not the same as "Origin" and "Destination".  We treat I as the matrix ROW and
+J as the matrix COLUMN.  So I=10, J=20 would be row 10 (1-based, row 9 if 0-based)
+and column 20 (1-based, column 19 of 0-based).
+
+## Contributing
+
+This is still under some development.  Bug reports and pull requests are welcome on GitHub at https://github.com/okiandrew/OpenMatriX.  
+
+## Contact
+
+Old School Email: arohne (at) oki (dot) org
+
+Twitter: @okiAndrew

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "OpenMatriX"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

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+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/OpenMatriX/version.rb

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+module OpenMatriX
+  VERSION = "0.1.0"
+end

data/lib/OpenMatriX.rb

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+require "OpenMatriX/version"
+
+module OMX
+
+  # Lots of this was built upon the work at https://github.com/edmundhighcock/hdf5
+  require 'ffi'
+  require 'narray'
+  class NArray
+    # Returns an FFI::Pointer which points to the location
+    # of the actual data array in memory.
+    def ffi_pointer
+      FFI::Pointer.new(Hdf5.narray_data_address(self))
+    end
+  end
+
+  class Array
+    # Allocate an integer64 chunk of memory, copy the contents of
+    # the array into it and return an FFI::MemoryPointer to the memory.
+    # The memory will be garbage collected when the pointer goes out of
+    # scope. Obviously the array should contain only integers. This method
+    # is not fast and shouldn't be used for giant arrays.
+    def ffi_mem_pointer_int64
+      raise TypeError.new("Array must contain only integers.") if self.find{|el| not el.kind_of? Integer}
+      ptr = FFI::MemoryPointer.new(:int64, size)
+      ptr.write_array_of_int64(self)
+      ptr
+    end
+
+    # This method currently assumes that hsize_t is an int64... this needs
+    # to be generalised ASAP.
+    def ffi_mem_pointer_hsize_t
+      ffi_mem_pointer_int64
+    end
+  end
+
+  # This is a module for reading and manipulating HDF5 (Hierarchical Data Format)
+  # files. At the current time (July 2014) it is capable of basic reading operations.
+  # However, its use of the FFI library means that extending its capabilities is easy
+  # and quick. For a basic example see the test file.
+  # Basic usage:
+  #     file = OMX::OMXile.new('filename.omx')
+  #     file.close
+  #module OpenMatriX
+
+    # A module containing functions for relating HDF5 types to the appropriate
+    # FFI symbol. At the moment these are set by hand, but at some point in the
+    # future they should be set dynamically by interrogation of the the library.
+    module H5Types
+      extend FFI::Library
+      class << self
+        def herr_t
+          :int
+        end
+        def hid_t
+          :int
+        end
+        def hbool_t
+          :uint
+        end
+        def htri_t
+          :int
+        end
+        def hsize_t
+          :size_t
+        end
+        def h5t_class_t
+          enum [
+            :h5t_no_class         , -1,  #*error                                      */
+            :h5t_integer          , 0,   #*integer types                              */
+            :h5t_float            , 1,   #*floating-point types                       */
+            :h5t_time             , 2,   #*date and time types                        */
+            :h5t_string           , 3,   #*character string types                     */
+            :h5t_bitfield         , 4,   #*bit field types                            */
+            :h5t_opaque           , 5,   #*opaque types                               */
+            :h5t_compound         , 6,   #*compound types                             */
+            :h5t_reference        , 7,   #*reference types                            */
+            :h5t_enum    , 8, #*enumeration types                          */
+            :h5t_vlen    , 9, #*variable-length types                      */
+            :h5t_array           , 10,  #*array types                                */
+
+            :h5t_nclasses                #*this must be last                          */
+          ]
+        end
+        def H5T_C_S1
+          :string
+        end
+        def H5G_obj_t
+          enum [:H5G_UNKNOWN, :H5G_GROUP, :H5G_DATASET, :H5G_TYPE, :H5G_LINK,
+            :H5G_UDLINK, :H5G_RESERVED_5,	:H5G_RESERVED_6, :H5G_RESERVED_7]
+        end
+        def time_t
+          :int
+        end
+        def size_t
+          :int
+        end
+      end
+    end
+
+    # A module for dynamically interrogating the environment and the library
+    # and providing the correct library path etc. Currently very dumb!
+    module H5Library
+      class << self
+        # The location of the hdf5 library. Currently it is assumed to be in
+        # the default linker path.
+        def library_path
+          'hdf5'
+        end
+      end
+    end
+
+    extend  FFI::Library
+    ffi_lib H5Library.library_path
+    attach_function :group_open, :H5Fopen, [H5Types.hid_t, :string, H5Types.hid_t], H5Types.hid_t
+    attach_function :get_type, :H5Iget_type, [H5Types.hid_t], H5Types.hid_t
+    #
+    # Object for wrapping an OMX file. Basic usage:
+    #     file = OMX::OMXFile.new('filename.omx')
+    # => Do stuff
+    #     file.close
+    #
+    class OMXFile
+      class InvalidFile < StandardError; end
+      extend  FFI::Library
+      ffi_lib H5Library.library_path
+
+      #htri_t H5Fis_hdf5(const char *name )
+      attach_function :basic_is_hdf5, :H5Fis_hdf5, [:string], H5Types.htri_t
+
+      #hid_t H5Fopen( const char *name, unsigned flags, hid_t fapl_id )
+      attach_function :basic_open, :H5Fopen, [:string, :uint, H5Types.hid_t], H5Types.hid_t
+
+      #herr_t H5Fclose( hid_t file_id )
+      attach_function :basic_close, :H5Fclose, [H5Types.hid_t], H5Types.herr_t
+
+      #hid_t H5Aopen( hid_t obj_id, const char *attr_name, hid_t aapl_id )
+      #attach_function :basic_openattr, :H5Aopen, [H5Types.hid_t, :string], H5Types.hid_t
+
+      attr_reader :id
+      # Open the file with the given filename. Currently read only
+      def initialize(filename)
+        raise Errno::ENOENT.new("File #{filename} does not exist") unless FileTest.exist?(filename)
+        raise InvalidFile.new("File #{filename} is not a valid hdf5 file") unless basic_is_hdf5(filename) > 0
+        @filename = filename
+        @id = basic_open(filename, 0x0000, 0)
+        raise InvalidFile.new("An unknown problem occured opening #{filename}") if @id < 0
+      end
+      # Is the file a valid hdf5 file
+      def is_hdf5?
+        basic_is_hdf5(@filename) > 0
+      end
+      # Close the file
+      def close
+        basic_close(@id)
+      end
+      # Return a group object with the given name
+      # (relative to the root of the file)
+      def group(name)
+        return H5Group.open(@id, name)
+      end
+      # Return a dataset object with the given name
+      # (relative to the root of the file)
+      def dataset(name)
+        return H5Dataset.open2(@id, name)
+      end
+    end #Class OMXile
+
+    # A Class to read and return the OMX version and shape (number of zones) attribute
+    class OMXAttr
+      class InvalidFile < StandardError; end
+      extend  FFI::Library
+      ffi_lib H5Library.library_path
+
+      #herr_t H5Aread(hid_t attr_id, hid_t mem_type_id, void *buf )
+      attach_function :basic_readattr, :H5Aread, [H5Types.hid_t, H5Types.hid_t, :pointer], H5Types.herr_t
+
+      #hid_t H5Aget_type(hid_t attr_id)
+      attach_function :get_type, :H5Aget_type, [H5Types.hid_t], H5Types.hid_t
+
+      #hid_t H5Aopen_name( hid_t loc_id, const char *name )
+      attach_function :basic_openattr, :H5Aopen, [H5Types.hid_t, :string], H5Types.hid_t
+
+      #hid_t H5Tcopy( hid_t dtype_id )
+      attach_function :h5t_copy, :H5Tcopy, [H5Types.hid_t], H5Types.hid_t
+
+      attach_variable :H5T_C_S1_g, :int
+
+      def initialize(file)
+        @id = file.id
+      end
+
+      # A function to return the OMX Version number
+      def getVersion()
+        aid = basic_openattr(@id,"OMX_VERSION")
+        attrOut = FFI::MemoryPointer.new(H5Types.hsize_t)
+        sv = get_type(aid)
+        oo = basic_readattr(aid,sv,attrOut)
+        raise InvalidFile.new("OMX_VERSION Attribute not found") if oo < 0
+        return(attrOut.read_string())
+      end
+
+      # A function to return the number of zones
+      def getZones()
+        aid = basic_openattr(@id,"SHAPE")
+        attrOut = FFI::MemoryPointer.new(H5Types.hsize_t)
+        sv = get_type(aid)
+        oo = basic_readattr(aid,sv,attrOut)
+        raise InvalidFile.new("SHAPE Attribute not found") if oo < 0
+        return(attrOut.read_int())
+      end
+
+    end #Class OMXAttr
+
+    # A class to return the tables in the OMX file
+    class OMXTables
+      class InvalidFile < StandardError; end
+      extend  FFI::Library
+      ffi_lib H5Library.library_path
+
+      #hid_t H5Dopen( hid_t loc_id, const char *name )
+      attach_function :gOpen, :H5Gopen1, [H5Types.hid_t, :string], H5Types.hid_t
+
+      #herr_t H5Gget_num_objs(hid_t loc_id, hsize_t* num_obj)
+      attach_function :nTables, :H5Gget_num_objs, [H5Types.hid_t, :pointer], H5Types.herr_t
+
+      #ssize_t H5Gget_objname_by_idx(hid_t loc_id, hsize_t idx, char *name, size_t size )
+      attach_function :tNames, :H5Gget_objname_by_idx, [H5Types.hid_t, :int, :pointer, :int], :int
+
+      def initialize(file)
+        @id = file.id
+        @gId = gOpen(@id, "data")
+      end
+
+      # A function to return the number of matrix tables. Returns an integer value
+      # of the number of tables in the matrix
+      def getNTables()
+        nObjs = FFI::MemoryPointer.new(H5Types.hsize_t)
+        nT = nTables(@gId, nObjs)
+        return(nObjs.read_int())
+      end
+
+      # A function to get the table info... kind of a useless function for now
+      # TODO: Can this be removed?
+      def getTableInfo()
+        sb = Statbuf.new
+        oi = tInfo(@id, "data", 0, sb)
+        puts sb[:nlink]
+        return(oi)
+      end
+
+      # A function to get the table names. Returns a string array of table names.
+      def getTableNames()
+        nT = self.getNTables()-1
+
+        tN ||= []
+        for t in 0..nT
+          tName = FFI::MemoryPointer.new(:string)
+          tno = tNames(@gId,t,tName,100)
+          tN << tName.read_string()
+        end
+        return(tN)
+      end
+
+    end #class OMXTables
+
+    #Class to read the data from the OMX file
+    class OMXData
+      class InvalidFile < StandardError; end
+      extend  FFI::Library
+      ffi_lib H5Library.library_path
+
+      #hid_t H5Dopen2( hid_t loc_id, const char *name, hid_t dapl_id )
+      attach_function :basic_open, :H5Dopen1, [H5Types.hid_t, :string], H5Types.hid_t
+
+      #herr_t H5Dread( hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_plist_id, void * buf )
+      attach_function :h5dRead, :H5Dread, [H5Types.hid_t, H5Types.hid_t, H5Types.hid_t, H5Types.hid_t, H5Types.hid_t, :pointer], H5Types.herr_t
+
+      #hid_t H5Dget_type(hid_t dataset_id )
+      attach_function :h5dtype, :H5Dget_type, [H5Types.hid_t], H5Types.hid_t
+
+      #hid_t H5Dget_space( hid_t dataset_id )
+      attach_function :h5dspace, :H5Dget_space, [H5Types.hid_t], H5Types.hid_t
+
+      #int H5Sget_simple_extent_ndims( hid_t space_id )
+      attach_function :h5sN, :H5Sget_simple_extent_ndims, [H5Types.hid_t], :int
+
+      #int H5Sget_simple_extent_dims(hid_t space_id, hsize_t *dims, hsize_t *maxdims )
+      attach_function :h5sD, :H5Sget_simple_extent_dims, [H5Types.hid_t, :pointer, :pointer], :int
+
+      attach_function :h5dpl, :H5Dget_create_plist, [H5Types.hid_t], :int
+
+      attach_function :h5pLayout, :H5Pget_layout, [H5Types.hid_t], :bool
+
+      #int H5Pget_chunk(hid_t plist, int max_ndims, hsize_t * dims )
+      attach_function :h5pGetChunk, :H5Pget_chunk, [H5Types.hid_t, :int, :pointer], :int
+
+      #hid_t H5Screate_simple( int rank, const hsize_t * current_dims, const hsize_t * maximum_dims )
+      attach_function :h5sCreate, :H5Screate_simple, [:int, :pointer, :pointer], H5Types.hid_t
+
+      def initialize(file, table, zones)
+        @id = file.id
+        @gId = OMXTables::gOpen(@id,"data")
+        @zones = zones
+        b = basic_open(@gId,table)
+        filespace = h5dspace(b)
+        rank = h5sN(filespace)
+        dims = FFI::MemoryPointer.new(H5Types.hsize_t)
+        maxdims = FFI::MemoryPointer.new(H5Types.hsize_t)
+        status_n = h5sD(filespace,dims,maxdims)
+        cparms = h5dpl(b)
+        if h5pLayout(cparms)
+          chunk_dims = FFI::MemoryPointer.new(H5Types.hsize_t)
+          rank_chunk = h5pGetChunk(cparms, maxdims.read_int(), chunk_dims)
+        end
+        memspace = h5sCreate(2, dims, nil)
+        type = h5dtype(b)
+        buffer = FFI::MemoryPointer.new(type,2)
+        c = h5dRead(b, type, memspace, filespace, 0, buffer)
+        ask_zones = zones * zones
+        @outAry = buffer.get_array_of_double(0,ask_zones)
+      end
+
+      def getI(zone)
+        return(@outAry[(zone-1)*@zones,@zones])
+      end
+
+      def getIJ(i,j)
+        a = @outAry[(i-1)*@zones,@zones]
+        return(a[j-1])
+      end
+
+      def getJ(j)
+        out ||= []
+        for i in 0..@zones-1
+          x = @outAry[i*@zones,j]
+          out << x[j-1]
+        end
+        return(out)
+      end
+
+    end #Class OMXData
+  end
+#end

metadata

@@ -0,0 +1,126 @@
+--- !ruby/object:Gem::Specification
+name: OpenMatriX
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Andrew Rohne
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2015-10-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.9'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.9'
+- !ruby/object:Gem::Dependency
+  name: narray
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+description: Open Matrix Ruby API
+email:
+- arohne@oki.org
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.md
+- OpenMatriX.gemspec
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/OpenMatriX.rb
+- lib/OpenMatriX/version.rb
+homepage: https://github.com/okiandrew/OpenMatriX
+licenses:
+- Apache-2.0
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.5
+signing_key: 
+specification_version: 4
+summary: Open Matrix support for Ruby
+test_files: []