Class: MDArray

Inherits:
Object
  • Object
show all
Includes:
Enumerable, GenericFunctions
Defined in:
lib/mdarray.rb,
lib/mdarray/views.rb,
lib/mdarray/access.rb,
lib/mdarray/counter.rb,
lib/mdarray/section.rb,
lib/mdarray/creation.rb,
lib/mdarray/printing.rb,
lib/mdarray/lazy_mdarray.rb,
lib/mdarray/ruby_generic_functions.rb

Direct Known Subclasses

NonNumericalMDArray, NumericalMDArray

Defined Under Namespace

Classes: Counter, IteratorFast, IteratorFastBoolean, IteratorFastByte, IteratorFastChar, IteratorFastDouble, IteratorFastFloat, IteratorFastInt, IteratorFastLong, IteratorFastShort, Section

Class Attribute Summary collapse

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from FunctionCreation

#make_binary_op, #make_unary_op

Methods included from RubyFunctions

#make_binary_operator, #make_binary_operators, #make_comparison_operator, #make_unary_operator, #make_unary_operators, #ruby_binary_function, #ruby_unary_function

Constructor Details

#initialize(type, storage, section = false) ⇒ MDArray

Initializes an MDArray

Parameters:

  • type (String) —

    the type of the mdarray: boolean, byte, int, short, long, float, double

  • storage (Array) —

    a ruby array with the initialization data to the MDArray

  • section (defaults to: false) —

    True if this is an mdarray section



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# File 'lib/mdarray.rb', line 115

def initialize(type, storage, section = false)
  
  @id = (0..8).map{MDArray.characters.sample}.join
  @type = type
  @nc_array = storage
  @local_index = Counter.new(self)
  @local_iterator = nil
  @section = section
  @coerced = false            # should never be set by the user! For internal use only!
  @binary_operator = nil
  @unary_operator = nil

  # initialize printing defaults
  printing_defaults

end

Class Attribute Details

.binary_operator ⇒ Object

Returns the value of attribute binary_operator.



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# File 'lib/mdarray.rb', line 97

def binary_operator
  @binary_operator
end

.characters ⇒ Object (readonly)

Returns the value of attribute characters.



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# File 'lib/mdarray.rb', line 101

def characters
  @characters
end

.function_map ⇒ Object

Returns the value of attribute function_map.



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# File 'lib/mdarray.rb', line 94

def function_map
  @function_map
end

.functions ⇒ Object

Returns the value of attribute functions.



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# File 'lib/mdarray.rb', line 93

def functions
  @functions
end

.non_numerical ⇒ Object (readonly)

Returns the value of attribute non_numerical.



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# File 'lib/mdarray.rb', line 96

def non_numerical
  @non_numerical
end

.numerical ⇒ Object (readonly)

Returns the value of attribute numerical.



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# File 'lib/mdarray.rb', line 95

def numerical
  @numerical
end

.previous_binary_operator ⇒ Object

Returns the value of attribute previous_binary_operator.



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# File 'lib/mdarray.rb', line 99

def previous_binary_operator
  @previous_binary_operator
end

.previous_unary_operator ⇒ Object

Returns the value of attribute previous_unary_operator.



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# File 'lib/mdarray.rb', line 100

def previous_unary_operator
  @previous_unary_operator
end

.unary_operator ⇒ Object

Returns the value of attribute unary_operator.



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# File 'lib/mdarray.rb', line 98

def unary_operator
  @unary_operator
end

Instance Attribute Details

#binary_operator ⇒ Object

binary_operator and unary_operator are instance variables that allow overwriting the class variables binary_operator and unary_operator



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# File 'lib/mdarray.rb', line 77

def binary_operator
  @binary_operator
end

#coerced ⇒ Object

Returns the value of attribute coerced.



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# File 'lib/mdarray.rb', line 79

def coerced
  @coerced
end

#float_output_precision=(value) ⇒ Object (writeonly)

Sets the attribute float_output_precision

Parameters:

  • value —

    the value to set the attribute float_output_precision to.



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# File 'lib/mdarray/printing.rb', line 40

def float_output_precision=(value)
  @float_output_precision = value
end

#float_output_suppress_small=(value) ⇒ Object (writeonly)

Sets the attribute float_output_suppress_small

Parameters:

  • value —

    the value to set the attribute float_output_suppress_small to.



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# File 'lib/mdarray/printing.rb', line 41

def float_output_suppress_small=(value)
  @float_output_suppress_small = value
end

#formatter=(value) ⇒ Object (writeonly)

Sets the attribute formatter

Parameters:

  • value —

    the value to set the attribute formatter to.



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# File 'lib/mdarray/printing.rb', line 37

def formatter=(value)
  @formatter = value
end

#id ⇒ Object (readonly)

an array identifier



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# File 'lib/mdarray.rb', line 70

def id
  @id
end

#inf_str=(value) ⇒ Object (writeonly)

Sets the attribute inf_str

Parameters:

  • value —

    the value to set the attribute inf_str to.



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# File 'lib/mdarray/printing.rb', line 30

def inf_str=(value)
  @inf_str = value
end

#int_output_size=(value) ⇒ Object (writeonly)

Sets the attribute int_output_size

Parameters:

  • value —

    the value to set the attribute int_output_size to.



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# File 'lib/mdarray/printing.rb', line 39

def int_output_size=(value)
  @int_output_size = value
end

#local_index ⇒ Object (readonly)

internal helper index for this array



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# File 'lib/mdarray.rb', line 73

def local_index
  @local_index
end

#local_iterator ⇒ Object (readonly)

Returns the value of attribute local_iterator.



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# File 'lib/mdarray.rb', line 74

def local_iterator
  @local_iterator
end

#max_line_width=(value) ⇒ Object (writeonly)

Sets the attribute max_line_width

Parameters:

  • value —

    the value to set the attribute max_line_width to.



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# File 'lib/mdarray/printing.rb', line 34

def max_line_width=(value)
  @max_line_width = value
end

#nan_str=(value) ⇒ Object (writeonly)

attributes necessary for printing



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# File 'lib/mdarray/printing.rb', line 29

def nan_str=(value)
  @nan_str = value
end

#nc_array ⇒ Object (readonly)

Returns the value of attribute nc_array.



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# File 'lib/mdarray.rb', line 72

def nc_array
  @nc_array
end

#prefix=(value) ⇒ Object (writeonly)

Sets the attribute prefix

Parameters:

  • value —

    the value to set the attribute prefix to.



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# File 'lib/mdarray/printing.rb', line 36

def prefix=(value)
  @prefix = value
end

#separator=(value) ⇒ Object (writeonly)

Sets the attribute separator

Parameters:

  • value —

    the value to set the attribute separator to.



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# File 'lib/mdarray/printing.rb', line 35

def separator=(value)
  @separator = value
end

#summary_edge_items=(value) ⇒ Object (writeonly)

Sets the attribute summary_edge_items

Parameters:

  • value —

    the value to set the attribute summary_edge_items to.



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# File 'lib/mdarray/printing.rb', line 31

def summary_edge_items=(value)
  @summary_edge_items = value
end

#summary_threshold=(value) ⇒ Object (writeonly)

Sets the attribute summary_threshold

Parameters:

  • value —

    the value to set the attribute summary_threshold to.



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# File 'lib/mdarray/printing.rb', line 32

def summary_threshold=(value)
  @summary_threshold = value
end

#type ⇒ Object (readonly)

Returns the value of attribute type.



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# File 'lib/mdarray.rb', line 71

def type
  @type
end

#unary_operator ⇒ Object

Returns the value of attribute unary_operator.



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# File 'lib/mdarray.rb', line 78

def unary_operator
  @unary_operator
end

Class Method Details

.arange(*args) ⇒ Object

Return evenly spaced values within a given interval. Values are generated within the half-open interval [start, stop) (in other words, the interval including start but excluding stop). For integer arguments the function is equivalent to the Python built-in range function, but returns an mdarray rather than a list. When using a non-integer step, such as 0.1, the results will often not be consistent. It is better to use linspace for these cases.

Parameters:

  • start
  • stop
  • step

Returns:

  • int mdarray



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# File 'lib/mdarray/creation.rb', line 313

def self.arange(*args)

  case args.size
  when 1
    start = 0
    last = args[0]
    stride = 1
  when 2
    start = args[0]
    last = args[1]
    stride = 1
  when 3
    start = args[0]
    last = args[1]
    stride = args[2]
  else
    raise "Method arange can have at most 3 arguments"
  end

  arr = Array.new
  (start...last).step(stride) { |val| arr << val }
  self.build("int", [arr.size], arr)

end

.boolean(shape, storage = nil, layout = :row) ⇒ Object

Builds a boolean mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 141

def self.boolean(shape, storage = nil, layout = :row)
  self.build("boolean", shape, storage, layout)
end

.build(type, shape, storage = nil, layout = :row) ⇒ Object

Builds a new MDArray

Parameters:

  • type —

    the type of the new mdarray to build, could be boolean, byte, short, int, long, float, double, string, structure

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 63

def self.build(type, shape, storage = nil, layout = :row)

  if (shape.is_a? String)
    # building from csv
    # using shape as filename
    # using storage as flag for headers
    storage = (storage)? storage : false
    parameters = Csv.read_numeric(shape, storage)
    shape=[parameters[0], parameters[1]]
    storage = parameters[2]
  end

  # Java-NetCDF creates an ArrayObject when given type string.  It should create an
  # ArrayString instead.  Some string methods in Java-NetCDF expect an ArrayObject
  # instead of an ArrayString, however, other libraries actually expect an ArrayString,
  # so we know have two type: "string" stores internally the data as an ArrayObject, 
  # "rstring" stores data internally as an ArrayString
  rtype = (type == "rstring")? "string" : type
  dtype = DataType.valueOf(rtype.upcase)

  jshape = shape.to_java :int

  if (storage)
    jstorage = storage.to_java rtype.downcase.to_sym
    if (type == "rstring")
      # circunvent bug in Java-NetCDF.  Type rstring is actually type string but should
      # and should build and ArrayString and not an ObjectString which is currently being
      # build.
      index = Java::UcarMa2.Index.factory(jshape)
      nc_array = Java::UcarMa2.ArrayString.factory(index, jstorage)
    else
      nc_array = Java::UcarMa2.Array.factory(dtype, jshape, jstorage)
    end
  else
    nc_array = Java::UcarMa2.Array.factory(dtype, jshape)
  end

  klass = Object.const_get("#{rtype.capitalize}MDArray")
  return klass.new(rtype, nc_array)

end

.build_from_nc_array(type, nc_array, section = false) ⇒ Object 



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# File 'lib/mdarray/creation.rb', line 127

def self.build_from_nc_array(type, nc_array, section = false)
  if (!type)
    type = MDArray.get_ncarray_type(nc_array)
  end
  klass = Object.const_get("#{type.capitalize}MDArray")
  return klass.new(type, nc_array, section)
end

.byte(shape, storage = nil, layout = :row) ⇒ Object

Builds a byte mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 151

def self.byte(shape, storage = nil, layout = :row)
  self.build("byte", shape, storage, layout)
end

.calc_value(given_type, function_type, match, partial_match, no_match) ⇒ Object 



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# File 'lib/mdarray.rb', line 321

def self.calc_value(given_type, function_type, match, partial_match, no_match)

  if (given_type == function_type)
    match
  elsif ((function_type == "*") || (given_type == "*"))
    partial_match
  else
    no_match
  end

end

.char(shape, storage = nil, layout = :row) ⇒ Object

Builds a char mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 161

def self.char(shape, storage = nil, layout = :row)
  self.build("char", shape, storage, layout)
end

.double(shape, storage = nil, layout = :row) ⇒ Object

Builds a double mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 213

def self.double(shape, storage = nil, layout = :row)
  self.build("double", shape, storage, layout)
end

.float(shape, storage = nil, layout = :row) ⇒ Object

Builds a float mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 203

def self.float(shape, storage = nil, layout = :row)
  self.build("float", shape, storage, layout)
end

.from_jstorage(type, shape, jstorage, section = false) ⇒ Object 



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# File 'lib/mdarray/creation.rb', line 109

def self.from_jstorage(type, shape, jstorage, section = false)

  if (shape.size == 1 && shape[0] == 0)
    return nil
  end

  dtype = DataType.valueOf(type.upcase)
  jshape = shape.to_java :int
  nc_array = Java::UcarMa2.Array.factory(dtype, jshape, jstorage)
  klass = Object.const_get("#{type.capitalize}MDArray")
  return klass.new(type, nc_array, section)

end

.fromfunction(type, shape, &block) ⇒ Object

Construct an array by executing a function over each coordinate. The resulting array therefore has a value “fn(x, y, z)“ at coordinate “(x, y, z)“. Parameters

Parameters:

  • type —

    : data-type, optional Data-type of the coordinate arrays passed to ‘fn`

  • shape —

    : (N,) tuple of ints Shape of the output array, which also determines the shape of the coordinate arrays passed to ‘fn`.

  • &block: —

    a block to be executed The block is called with N parameters, each of which represents the coordinates of the array varying along a specific axis. For example, if ‘shape` were “(2, 2)“, then the parameters would be two arrays, “[[0, 0], [1, 1]]“ and “[[0, 1], [0, 1]]“. `fn` must be capable of operating on arrays, and should return a scalar value.



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# File 'lib/mdarray/creation.rb', line 270

def self.fromfunction(type, shape, &block)

  dtype = DataType.valueOf(type.upcase)
  jshape = shape.to_java :int
  arr = self.build(type, shape)
  arr.dim_set(nil, block)
  return arr

end

.function_map_to_csv ⇒ Object

Prints a list of all available functions know to MDArray is csv. Should be reimplemented. For debuging only for now.



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# File 'lib/mdarray.rb', line 243

def self.function_map_to_csv

  p "scope, short name, long name, return type, input1 type, input2 type" 
  
  MDArray.function_map.each_pair do |key, value|
    value.each do |func|
      p "#{func.scope}, #{key}, #{func.long_name}, #{func.return_type}, #{func.input1_type}, #{func.input2_type}"
    end
  end
    
end

.init_with(type, shape, value) ⇒ Object

Build mdarray and fills it with the given value

Parameters:

  • type —

    type of the mdarray

  • shape
  • value —

    the given value to fill in the mdarray



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# File 'lib/mdarray/creation.rb', line 287

def self.init_with(type, shape, value)

  size = 1
  shape.each do |val|
    size = size * val
  end

  storage = Array.new(size, value)    
  self.build(type, shape, storage)

end

.int(shape, storage = nil, layout = :row) ⇒ Object

Builds an int mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 182

def self.int(shape, storage = nil, layout = :row)
  self.build("int", shape, storage, layout)
end

.lazy=(flag) ⇒ Object 



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# File 'lib/mdarray/lazy_mdarray.rb', line 309

def self.lazy=(flag)
  set_lazy(flag)
end

.linspace(type, start, stop, number) ⇒ Object 



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# File 'lib/mdarray/creation.rb', line 380

def self.linspace(type, start, stop, number)
  
  arr = (start..stop).step((stop-start).to_f/(number-1)).map{|x| x }
  self.build(type, [arr.size], arr)
  
end

.long(shape, storage = nil, layout = :row) ⇒ Object

Builds a long mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 193

def self.long(shape, storage = nil, layout = :row)
  self.build("long", shape, storage, layout)
end

.make_binary_op(name, exec_type, func, helper_class, force_type = nil, pre_condition = nil, post_condition = nil) ⇒ Object

Makes a new binary operator for this MDArray. All binary operators are created using this method or the one in module FunctionCreation.

Parameters:

  • name (String) —

    name of the new binary operator

  • exec_type —

    execution type of the binary operator. Existing execution types at present are: :default, :fill, :in_place, :reduce.

  • func —

    the function to be applied for this binary operator. For instance, lets say we are build the “add” binary operator. exec_type is :default, func is a ruby proc Proc.new { |val1, val2| val1 + val2 }

  • force_type (defaults to: nil) —

    forces the type of the resulting array after executing the binary operator. For instance, if we force type “int”, then even adding two double arrays the resulting array will be of type int

  • pre_condition (defaults to: nil) —

    Proc to be executed before the operator’s execution

  • post_condition (defaults to: nil) —

    Proc to be executed after the operator’s execution



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# File 'lib/mdarray.rb', line 271

def self.make_binary_op(name, exec_type, func, helper_class, force_type = nil, 
                        pre_condition = nil, post_condition = nil)

  define_method(name) do |op2, requested_type = nil, *args|
    if (@type == "lazy" || ((op2.is_a? MDArray) && op2.type == "lazy"))
      binary_op = LazyBinaryOperator
    else
      binary_op = get_binary_op
    end
    op = binary_op.new(name, exec_type, force_type, pre_condition, post_condition)
    op.exec(self, op2, requested_type, *args)
  end

  MDArray.register_function(name, func, 2, helper_class)

end

.make_unary_op(name, exec_type, func, helper_class, force_type = nil, pre_condition = nil, post_condition = nil) ⇒ Object

Makes a new unary operator for this MDArray. All unary operators are created using this method or the one in module FunctionCreation.

Parameters:

  • name (String) —

    name of the new binary operator

  • exec_type —

    execution type of the binary operator. Existing execution types at present are: :default, :fill, :in_place, :reduce.

  • func —

    the function to be applied for this binary operator. For instance, lets say we are build the “add” binary operator. exec_type is :default, func is a ruby proc Proc.new { |val1, val2| val1 + val2 }

  • force_type (defaults to: nil) —

    forces the type of the resulting array after executing the binary operator. For instance, if we force type “int”, then even adding two double arrays the resulting array will be of type int

  • pre_condition (defaults to: nil) —

    Proc to be executed before the operator’s execution

  • post_condition (defaults to: nil) —

    Proc to be executed after the operator’s execution



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# File 'lib/mdarray.rb', line 304

def self.make_unary_op(name, exec_type, func, helper_class, force_type = nil, 
                       pre_condition = nil, post_condition = nil)
  
  define_method(name) do |requested_type = nil, *args|
    unary_op = get_unary_op
    op = unary_op.new(name, exec_type, force_type, pre_condition, post_condition)
    op.exec(self, requested_type, *args)
  end

  MDArray.register_function(name, func, 1, helper_class)

end

.ones(type, shape) ⇒ Object 



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# File 'lib/mdarray/creation.rb', line 391

def self.ones(type, shape)
  init_with(type, shape, 1)
end

.print_function_map ⇒ Object

Prints a list of all available functions know to MDArray. Should be reimplemented. For debuging only for now.



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# File 'lib/mdarray.rb', line 224

def self.print_function_map

  MDArray.function_map.each_pair do |key, value|

    value.each do |func|

      p "package: #{func.package}, short name: #{key}, long name: #{func.long_name}, return type: #{func.return_type}, input1 type: #{func.input1_type}, input2 type: #{func.input2_type}"

    end

  end
    
end

.register_function(name, fmap, arity, helper_class) ⇒ Object

fmap is an array with the following data: long_name, scope, function, return_type, input1_type, input2_type



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# File 'lib/mdarray/creation.rb', line 400

def self.register_function(name, fmap, arity, helper_class)
  
  if ((list = MDArray.function_map[name]) == nil)
    list = (MDArray.function_map[name] = Array.new)
  end
  list << FunctionMap.new(name, fmap[0], fmap[1], fmap[2], fmap[3], fmap[4], fmap[5],
                          arity, helper_class)

end

.rstring(shape, storage = nil, layout = :row) ⇒ Object

Builds a string mdarray. Really builds an string array. Only exists to fix the Java-NetCDF issue described above.

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 236

def self.rstring(shape, storage = nil, layout = :row)
  self.build("rstring", shape, storage, layout)
end

.select_function(name, package = nil, return_type = nil, input1_type = nil, input2_type = nil) ⇒ Object

Selects the best function to use at execution time for a given operation. MDArray allow for many implementations of the same function. For instance, one could implement the add operation as a ruby proc Proc.new { |val1, val2| val1 + val2 } or as a Java method. At execution time the system will select the best function to execute given a set of decision paramenters. At this time, this method needs to be improved.

Parameters:

  • name —

    the name of the function

  • scope (String) —

    a given scope defined by the user, used as a decision parameter

  • return_type (defaults to: nil) —

    the return type of the function

  • input1_type (defaults to: nil) —

    the type of the first argument to the function

  • input2_type (defaults to: nil) —

    the type of the second argument to the function



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# File 'lib/mdarray.rb', line 347

def self.select_function(name, package = nil, return_type = nil, input1_type = nil, 
                         input2_type = nil)


=begin
  p "selecting function: #{name}"
  p "return_type: #{return_type}"
  p "input1_type: #{input1_type}"
  p "input2_type: #{input2_type}"
=end

  list = MDArray.function_map[name]
  best_value = -1
  func = nil

  list.each do |function|
    value = (package == function.package)? 2 : 1
    # p "package: #{package}; function package: #{function.package}"
    # p value
    value *= calc_value(return_type, function.return_type, 32, 16, 0)
    # p "return_type: #{return_type}; func_ret_type: #{function.return_type}"
    # p value
    value *= calc_value(input1_type, function.input1_type, 8, 4, 0)
    # p "input1_type: #{input1_type}; func_input1_type: #{function.input1_type}"
    # p value
    value *= calc_value(input2_type, function.input2_type, 2, 1, 0)
    # p "input2_type: #{input2_type}; func_input2_type: #{function.input2_type}"
    # p value
    if (value == 0)
      next
    elsif (value > best_value)
      func = function
      best_value = value
    end
  end

=begin
  p "MDArray.select_function"
  p "selected function #{func.function}"
=end

  if (best_value > 0)
    func
  else
    raise "No method to process operator: #{name}"
  end

end

.set_lazy(flag = true) ⇒ Object 



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# File 'lib/mdarray/lazy_mdarray.rb', line 289

def self.set_lazy(flag = true)

  if (flag)
    if (MDArray.binary_operator != LazyBinaryOperator)
      MDArray.previous_binary_operator = MDArray.binary_operator
      MDArray.previous_unary_operator = MDArray.unary_operator
    end
    MDArray.binary_operator = LazyBinaryOperator
    MDArray.unary_operator = LazyUnaryOperator
  else
    MDArray.binary_operator = MDArray.previous_binary_operator if MDArray.previous_binary_operator != nil
    MDArray.unary_operator = MDArray.previous_unary_operator if MDArray.previous_unary_operator != nil
  end

end

.short(shape, storage = nil, layout = :row) ⇒ Object

Builds a byte mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 172

def self.short(shape, storage = nil, layout = :row)
  self.build("short", shape, storage, layout)
end

.string(shape, storage = nil, layout = :row) ⇒ Object

Builds a string mdarray. Java-NetCDF does not actuallly build a string array when type string is passed, it builds an object array. This is an open issue with Java-NetCDF.

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 225

def self.string(shape, storage = nil, layout = :row)
  self.build("string", shape, storage, layout)
end

.structure(shape, storage = nil, layout = :row) ⇒ Object

Builds a structure mdarray

Parameters:

  • shape (Array) —

    the shape of the mdarray as a ruby array

  • storage (Array) (defaults to: nil) —

    a ruby array with the initialization data



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# File 'lib/mdarray/creation.rb', line 246

def self.structure(shape, storage = nil, layout = :row)
  self.build("structure", shape, storage, layout)
end

.typed_arange(type, *args) ⇒ Object

Return evenly spaced values within a given interval. Values are generated within the half-open interval [start, stop) (in other words, the interval including start but excluding stop). For integer arguments the function is equivalent to the Python built-in range function, but returns an mdarray rather than a list.

Parameters:

  • type —

    the desired type of the new mdarray

  • start
  • stop
  • step 


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# File 'lib/mdarray/creation.rb', line 351

def self.typed_arange(type, *args)

  case args.size
  when 1
    start = 0
    last = args[0]
    stride = 1
  when 2
    start = args[0]
    last = args[1]
    stride = 1
  when 3
    start = args[0]
    last = args[1]
    stride = args[2]
  else
    raise "Method arange can have at most 3 arguments"
  end

  arr = Array.new
  (start...last).step(stride) { |val| arr << val }
  self.build(type, [arr.size], arr)

end

.upcast(type1, type2) ⇒ Object

Given two types returns the upcasted one



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# File 'lib/mdarray/creation.rb', line 32

def self.upcast(type1, type2)

  type1_i = MDArray.numerical.index(type1)
  type2_i = MDArray.numerical.index(type2)
  type_i = (type1_i < type2_i)? type2_i : type1_i
  type = MDArray.numerical.at(type_i)

end

Instance Method Details

#[](*index) ⇒ Object

When get is used to retrieve an element, it is assumed that the index does not need correction, for instance, no negative index is allowed. If one wants to use negative indexes, then method [] should be used. So mat.get([-1, 0, 0]) raises an exception while mat[-1, 0, 0] gets the last value for the first dimension.



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# File 'lib/mdarray/access.rb', line 53

def [](*index)

  if (index.size != 0)
    @local_index[*index]
  elsif (@local_iterator)
    @local_iterator.get_current
  else
    raise "No iterator defined! Cannot get element"
  end

end

#[]=(*index, value) ⇒ Object 



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# File 'lib/mdarray/access.rb', line 118

def []=(*index, value)

  if (index.size != 0)
    @local_index[index] = value
  elsif (@local_iterator)
    @local_iterator.set_current(value)
  else
    raise "No iterator defined! Cannot set element value"
  end

end

#apply_over_axes(axes) ⇒ Object 



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# File 'lib/mdarray/printing.rb', line 168

def apply_over_axes(axes)

  counter = Counter.new(self)
  # find the axes and sizes 
  slice = Array.new(rank, 0)
  sizes = Array.new(rank, 1)
  (0..rank).each do |i|
    if (axes[i] != i)
      sizes[i] = shape[i]
    end
  end

  counter.each_along_axes(axes) do |ct, axis|
    section(ct, sizes)
  end
  
end

#compatible(array) ⇒ Object

Checks to see if this array is compatible with another array. Two arrays are compatible if they have the same shape and have operatable types.



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# File 'lib/mdarray.rb', line 215

def compatible(array)
  (get_shape == array.get_shape)? true : false
end

#copy ⇒ Object

Create a copy of this Array, copying the data so that physical order is the same as logical order



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# File 'lib/mdarray/views.rb', line 29

def copy
  MDArray.build_from_nc_array(@type, @nc_array.copy())
end

#csv1d ⇒ Object 



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# File 'lib/mdarray/printing.rb', line 99

def csv1d
  
  each_with_counter do |elmt, index|
    if (!is_zero?(index))
      Kernel.print @separator
    end
    Kernel.printf @formatter.call(elmt)
  end
  Kernel.print "\n"

end

#dtype ⇒ Object

Gets the element type of this array



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# File 'lib/mdarray.rb', line 171

def get_element_type
  @nc_array.getElementType().toString()
end

#each ⇒ Object 



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# File 'lib/mdarray/access.rb', line 185

def each
  
  iterator = get_iterator_fast
  while (iterator.has_next?)
    yield iterator.get_next if block_given?
  end
  
end

#each_cont ⇒ Object

Continues a each from the position the @local_iterator is in. each_cont cannot be called from multiple threads as there is only one @local_iterator.



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# File 'lib/mdarray/access.rb', line 218

def each_cont

  while (elmt = self.next)
    yield elmt if block_given?
  end

end

#each_slice(axes, reduce = true) ⇒ Object 



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# File 'lib/mdarray/views.rb', line 254

def each_slice(axes, reduce = true)
  
  counter = Counter.new(self)

  sizes = Array.new
  (0..rank - 1).each do |axis|
    if (axes.include?(axis))
      sizes[axis] = 1
    else
      sizes[axis] = shape[axis]
    end
  end

  counter.each_along_axes(axes) do |ct|
    yield section(ct, sizes, reduce) if block_given?
  end

end

#each_with_counter ⇒ Object

Cycles through the whole list of elements yielding to a block (if given) the next element and its index. The index is a ruby array.



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# File 'lib/mdarray/access.rb', line 204

def each_with_counter

  iterator = get_iterator_fast
  while (iterator.has_next?)
    yield iterator.get_next, iterator.get_current_counter if block_given?
  end
  
end

#flip(dim) ⇒ Object 



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# File 'lib/mdarray/views.rb', line 37

def flip(dim)
  MDArray.build_from_nc_array(@type, @nc_array.flip(dim))
end

#get(index = nil) ⇒ Object

When get is used to retrieve an element, it is assumed that the index does not need correction, for instance, no negative index is allowed. If one wants to use negative indexes, then method [] should be used. So mat.get([-1, 0, 0]) raises an exception while mat[-1, 0, 0] gets the last value for the first dimension.



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# File 'lib/mdarray/access.rb', line 72

def get(index = nil)
  @local_index.get(index)
end

#get_as(type, counter = nil) ⇒ Object 



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# File 'lib/mdarray/access.rb', line 80

def get_as(type, counter = nil)
  @local_index.get_as(type, counter)
end

#get_binary_op ⇒ Object 



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# File 'lib/mdarray/creation.rb', line 45

def get_binary_op
  (@binary_operator)? @binary_operator : MDArray.binary_operator
end

#get_counter ⇒ Object 



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# File 'lib/mdarray/access.rb', line 169

def get_counter
  Counter.new(self)
end

#get_current_index ⇒ Object 



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# File 'lib/mdarray/access.rb', line 28

def get_current_index
  @local_iterator.get_current_index
end

#get_element_type ⇒ Object

Gets the element type of this array



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# File 'lib/mdarray.rb', line 167

def get_element_type
  @nc_array.getElementType().toString()
end

#get_index ⇒ Object 



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# File 'lib/mdarray/counter.rb', line 33

def get_index
  MDArray::Counter.new(self)
end

#get_iterator_fast ⇒ Object

Returns:

  • IteratorFast a fast iterator onto the this array.



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# File 'lib/mdarray.rb', line 406

def get_iterator_fast
  
  case type
  when "boolean"
    IteratorFastBoolean.new(self)
  when "char"
    IteratorFastChar.new(self)
  when "short"
    IteratorFastShort.new(self)
  when "int"
    IteratorFastInt.new(self)
  when "long"
    IteratorFastLong.new(self)
  when "float"
    IteratorFastFloat.new(self)
  when "double"
    IteratorFastDouble.new(self)
  else
    IteratorFast.new(self)
  end

end

#get_next ⇒ Object

Gets the next element of the local iterator



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# File 'lib/mdarray/access.rb', line 104

def get_next

  if (@local_iterator)
    @local_iterator.get_next
  else
    raise "No iterator defined! Cannot get next element"
  end

end

#get_rank ⇒ Object 

Get the number of dimensions of the array.



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# File 'lib/mdarray.rb', line 136

def get_rank
  @nc_array.getRank()
end

#get_scalar ⇒ Object

Sets a value for a scalar D0 array



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# File 'lib/mdarray/access.rb', line 88

def get_scalar
  @local_index.get_scalar
end

#get_shape ⇒ Object

Gets the shape of the array



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# File 'lib/mdarray.rb', line 157

def get_shape
  @nc_array.getShape().to_a
end

#get_size ⇒ Object

Gets the size of the array.



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# File 'lib/mdarray.rb', line 147

def get_size
  @nc_array.getSize()
end

#get_unary_op ⇒ Object 



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# File 'lib/mdarray/creation.rb', line 49

def get_unary_op
  (@unary_operator)? @unary_operator : MDArray.unary_operator
end

#immutable ⇒ Object

Given an MDArray, makes it immutable. Renjin data cannot be changed as Renjin assumes it can delay processing.



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# File 'lib/mdarray/access.rb', line 231

def immutable

  instance_eval { def set(name, value) raise "Array is immutable" end }
  instance_eval { def set_scalar(name, value) raise "Array is immutable" end }
  instance_eval { def set_next(value) raise "Array is immutable" end }
  instance_eval { def []=(name, value) raise "Array is immutable" end }

end

#jget(index = nil) ⇒ Object 



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# File 'lib/mdarray/access.rb', line 96

def jget(index = nil)
  @local_index.jget(index)
end

#ndenumerate ⇒ Object

Method to print all elements of the array for debuging purposes only. Does not need to be very efficient.



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# File 'lib/mdarray.rb', line 200

def ndenumerate
  
  reset_traversal
  while (@local_iterator.has_next?) do
    @local_iterator.next
    print "#{get_current_index} #{@local_iterator.get_current}\n"
  end
  
end

#ndim ⇒ Object 

Get the number of dimensions of the array.



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# File 'lib/mdarray.rb', line 140

def get_rank
  @nc_array.getRank()
end

#next ⇒ Object

Returns the next element of the local_iterator or nil if no next element available



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# File 'lib/mdarray/access.rb', line 36

def next

  if (@local_iterator && @local_iterator.has_next?)
    @local_iterator.get_next
  else
    nil
  end

end

#permute(indices) ⇒ Object

Create a new Array using same backing store as this Array, by permuting the indices. Parameters: indices the old index dims becomes the new kth index. Returns: the new Array Throws: IllegalArgumentException: - wrong rank or dim not valid



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# File 'lib/mdarray/views.rb', line 106

def permute(indices)

  ind = indices.to_java :int
  
  begin
    perm = @nc_array.permute(ind)
  rescue # should catch IllegalArgumentException
    raise "Illegal argument"
  end

  MDArray.build_from_nc_array(@type, perm)

end

#print ⇒ Object 



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# File 'lib/mdarray/printing.rb', line 81

def print

  case rank
  when 0
    print0d
  when 1
    print1d
  else
    printnd
  end
  Kernel.print "\n"

end

#print0d ⇒ Object 



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# File 'lib/mdarray/printing.rb', line 143

def print0d
  Kernel.print(@nc_array.get())
end

#print1d ⇒ Object 



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# File 'lib/mdarray/printing.rb', line 151

def print1d
  
  Kernel.print "["
  each_with_counter do |elmt, index|
    if (!is_zero?(index))
      Kernel.print @separator
    end
    Kernel.printf @formatter.call(elmt)
  end
  Kernel.print "]"
  
end

#printing_defaults ⇒ Object 



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# File 'lib/mdarray/printing.rb', line 47

def printing_defaults

  @nan_str = "nan"
  @inf_str = "inf"
  @summary_edge_items = 3     # repr N leading and trailing items of each dimension
  @summary_threshold = 1000   # total items > triggers array summarization
  
  @max_line_width = 80
  @separator = " "
  @prefix = " "
  
  @int_output_size = 2
  @float_output_precision = 2
  @float_output_suppress_small = false

  case type
  when "int"
    @formatter = method(:integer_formatter)
  when "float"
    @formatter = method(:float_formatter)
  when "double"
    @formatter = method(:float_formatter)
  when "string"
    @formatter = method(:string_formatter)
  else
    @formatter = method(:default_formatter)
  end

end

#rank ⇒ Object 

Get the number of dimensions of the array.



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# File 'lib/mdarray.rb', line 141

def get_rank
  @nc_array.getRank()
end

#reduce(dim = nil) ⇒ Object 



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# File 'lib/mdarray/views.rb', line 83

def reduce(dim = nil)

  if (dim)
    nc_array = @nc_array.reduce(dim.to_java :int)
  else
    nc_array = @nc_array.reduce
  end
  
  shape = MDArray.get_shape(nc_array)
  MDArray.build_from_nc_array(@type, nc_array)
  
end

#region(*args) ⇒ Object

Gets a region from this array. Region is the same as section but using a different interface. parameters that can be given shape origin size stride range section spec



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# File 'lib/mdarray/views.rb', line 205

def region(*args)
  
  opts = Map.options(args)
  reduce = opts.getopt(:reduce)
  sec = MDArray::Section.build(*args)

  if (reduce)
    arr = @nc_array.section(sec.netcdf_elmt.getRanges())
  else
    arr = @nc_array.sectionNoReduce(sec.netcdf_elmt.getRanges())
  end

  # Build the new array as a section from the given one.  Last argument to build is
  # "true" indicating this is a section.
  section = MDArray.build_from_nc_array(@type, arr, true)
  copy_print_parameters(section)
  return section

end

#reset_traversal ⇒ Object 



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# File 'lib/mdarray/access.rb', line 177

def reset_traversal
  @local_iterator = get_iterator_fast
end

#reshape(shape, copy = false) ⇒ Object 



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# File 'lib/mdarray/views.rb', line 45

def reshape(shape, copy = false)

  new_shape = shape.to_java :int

  if (copy)
    nc_array = @nc_array.reshape(new_shape)
  else
    nc_array = @nc_array.reshapeNoCopy(new_shape)
  end

  MDArray.build_from_nc_array(@type, nc_array)

end

#reshape!(shape) ⇒ Object

This method fixes a bug in netcdf-java!!! 



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# File 'lib/mdarray/views.rb', line 63

def reshape!(shape)
  new_shape = shape.to_java :int
  # Netcdf-Java bug... reshape of ArrayString becomes an ArrayObject.  In principle
  # should not require comparison with ArrayString here
  if (@nc_array.is_a? ArrayString)
    @nc_array = Java::UcarMa2.ArrayString.factory(@nc_array.getIndex(), 
      @nc_array.getStorage())
  else
    @nc_array = @nc_array.reshapeNoCopy(new_shape)
  end
  # when we reshape an array we need to re-initialize its index and local_iterator
  @local_index = Counter.new(self)
  @local_iterator = nil
  @self
end

#section(origin, shape, reduce = false) ⇒ Object

Create a new Array as a subsection of this Array, without rank reduction. No data is moved, so the new Array references the same backing store as the original. Throws: InvalidRangeException - if ranges is invalid

Parameters:

  • origin —

    ruby array specifying the starting index. Must be same rank as original Array.

  • shape —

    ruby array specifying the extents in each dimension. This becomes the shape of the returned Array. Must be same rank as original Array.

  • reduce (defaults to: false) —

    true if the array should be reduced by removing dimensions of size 1



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# File 'lib/mdarray/views.rb', line 133

def section(origin, shape, reduce = false)

  jorigin = origin.to_java :int
  jshape = shape.to_java :int

  if (reduce)
    arr = @nc_array.section(jorigin, jshape)
  else
    arr = @nc_array.sectionNoReduce(jorigin, jshape, nil)
  end

  # this is an array section, set it to true
  if (arr.rank == 0)
    return arr.get()
  end

  # Build the new array as a section from the given one.  Last argument to build is
  # "true" indicating this is a section.
  section = MDArray.build_from_nc_array(@type, arr, true)
  copy_print_parameters(section)
  return section

end

#section? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mdarray/views.rb', line 229

def section?
  @section
end

#section_with_stride(origin, shape, stride, reduce = false) ⇒ Object

Create a new Array as a subsection of this Array, without rank reduction. No data is moved, so the new Array references the same backing store as the original. Throws: InvalidRangeException - if ranges is invalid

Parameters:

  • origin —

    ruby array specifying the starting index. Must be same rank as original Array.

  • shape —

    ruby array specifying the extents in each dimension. This becomes the shape of the returned Array. Must be same rank as original Array.

  • stride —

    array specifying the strides in each dimension. If null, assume all ones.

  • reduce (defaults to: false) —

    true if the array should be reduced by removing dimensions of size 1



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# File 'lib/mdarray/views.rb', line 172

def section_with_stride(origin, shape, stride, reduce = false)

  jorigin = origin.to_java :int
  jshape = shape.to_java :int
  jstride = stride.to_java :int

  if (reduce)
    arr = @nc_array.section(jorigin, jshape, jstride)
  else
    arr = @nc_array.sectionNoReduce(jorigin, jshape, jstride)
  end

  # Build the new array as a section from the given one.  Last argument to build is
  # "true" indicating this is a section.
  section = MDArray.build_from_nc_array(@type, arr, true)
  copy_print_parameters(section)
  return section

end

#set(index, value) ⇒ Object

When set is used to assign to an element, it is assumed that the index does not need correction, for instance, no negative index is allowed. If one wants to use negative indexes, then method [] should be used. So mat.set([-1, 0, 0], 10), raises an exection while mat[-1, 0, 0] = 10 sets the last value for the first dimension. *index: array with the index position *value: value to be set



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# File 'lib/mdarray/access.rb', line 139

def set(index, value)
  @local_index.set(index, value)
end

#set_next(value) ⇒ Object 



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# File 'lib/mdarray/access.rb', line 155

def set_next(value)

  if (@local_iterator)
    @local_iterator.set_next(value)
  else
    raise "No iterator defined! Cannot set element value"
  end
  
end

#set_scalar(value) ⇒ Object

Sets a value for a scalar D0 array



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# File 'lib/mdarray/access.rb', line 147

def set_scalar(value)
  @local_index.set_scalar(value)
end

#shape ⇒ Object

Gets the shape of the array



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# File 'lib/mdarray.rb', line 161

def get_shape
  @nc_array.getShape().to_a
end

#size ⇒ Object

Gets the size of the array.



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# File 'lib/mdarray.rb', line 151

def get_size
  @nc_array.getSize()
end

#slice(dim, val) ⇒ Object

Create a new Array using same backing store as this Array, by fixing the specified dimension at the specified index value. This reduces rank by 1.

Parameters:

  • dim —

    dimension to fix

  • val —

    value in which to fix the dimension

Returns:

  • new array sliced at the given dimension on the specified value



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# File 'lib/mdarray/views.rb', line 241

def slice(dim, val)
  
  arr = @nc_array.slice(dim, val)
  slice = MDArray.build_from_nc_array(@type, arr, true)
  copy_print_parameters(slice)
  return slice

end

#to_csv ⇒ Object 



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# File 'lib/mdarray/printing.rb', line 115

def to_csv

  @separator = ", "

  counter = Counter.new(self)
  # find the axes and sizes 
  axes = Array.new
  sizes = Array.new
  (0..(rank - 2)).each do |val|
    axes << val
    sizes << 1
  end
  sizes << shape[rank - 1]

  counter.each_along_axes(axes) do |ct, axis|
    (0..ct.size - 2).each do |i|
      Kernel.print ct[i] 
      Kernel.print @separator
    end
    section(ct, sizes).csv1d
  end
  
end

#to_s ⇒ Object

Prints the array



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# File 'lib/mdarray.rb', line 191

def to_s
  self.print
end

#to_string(max_size = 3) ⇒ Object

Prints the content of the netcdf_array. Mainly for debugging purposes.

Parameters:

  • max_size (int) (defaults to: 3) 


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# File 'lib/mdarray.rb', line 178

def to_string(max_size = 3)
  if (size > max_size * 2)
    @nc_array.toString()
  else
    @nc_array.toString()
  end

end

#transpose(dim1, dim2) ⇒ Object

Create a new Array using same backing store as this Array, by transposing two of the indices.

Parameters:

  • dim1 —

    first dimension index

  • dim2 —

    second dimension index

Returns:

  • new array with dimensions transposed



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# File 'lib/mdarray/views.rb', line 281

def transpose(dim1, dim2)

  arr = @nc_array.transpose(dim1, dim2)
  transpose = MDArray.build_from_nc_array(@type, arr, true)
  copy_print_parameters(transpose)
  return transpose

end