Module: RBridge

Extended by:
FFI::Library
Defined in:
lib/r_bridge.rb,
lib/r_bridge/version.rb,
lib/r_bridge/r_bridge_ffi.rb,
lib/r_bridge/r_bridge_lazyfunc_ext.rb

Defined Under Namespace

Classes: Error, LazyFunc, RInstPrevious, RNameContainer, RParamManager, RParamName, RPointerManager, RResultManager, RResultName, RResultNameArray, RResultPrevious, SignR, SymbolR

Constant Summary collapse

VERSION = 
"0.5.7"

Class Method Summary collapse

Class Method Details

.array_depth(ary) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 308

def self.array_depth (ary)
  return 0 unless ary.is_a?(Array)
  return 1 + ary.map(){|elem| array_depth(elem) }.max()
end

.assoc_array?(ary) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/r_bridge/r_bridge_ffi.rb', line 313

def self.assoc_array?(ary)
  if ary.map(){|elem| elem.size }.uniq == [2]
    true
  else
    false
  end
end

.convert_to_r_object(value) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 237

def self.convert_to_r_object(value)
  case
  when [String, Integer, Float , TrueClass, FalseClass].include?( value.class )
    r_obj = RBridge.create_vec( [ value ] )
  when value.class == Array
    if value[0].class == RBridge::SymbolR
      ary = value.map(){|elem| 
        if(value.val == "TRUE" || value.val == "T") 
          true
        elsif(value.val == "FALSE" || value.val == "F") 
          false
        else
          raise "Array of symbols is not accepted except TRUE(T) or FALSE(F) array" 
        end
      }
      r_obj = RBridge.create_vec( ary )
    else
      r_obj = RBridge.create_vec( value )
    end
  when value.class == RBridge::SymbolR  # SymbolR with name of T, F, TRUE and FALSE
    if value.val == "TRUE" || value.val == "T"
      r_obj = RBridge.create_vec( [true] )
    elsif value.val == "FALSE" || value.val == "F"
      r_obj = RBridge.create_vec( [false] )
    else
      r_obj = value.to_r_symbol
    end
  when value.class == NilClass
    r_obj = RBridge.r_nil
  end
  return r_obj
end

.create_assign_function(var_name, r_obj) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 104

def self.create_assign_function( var_name, r_obj )
  raise "create_assign_function should take an String argument for variable name" if(var_name.class != String)
  r_var_name = create_strvec ([var_name])
  r_create_formula = create_function_call( "assign" , {"x" => r_var_name , "value" => r_obj })
  return r_create_formula
end

.create_dataframe(hash) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 77

def self.create_dataframe( hash )
  vec_size_array = hash.map(){|key, val|
    val.size
  }
  if vec_size_array.uniq.size != 1
    raise "For data.frame, all the element vectors should have the same length."
  end

  r_list = create_list(hash)
  r_df = r_list_to_dataframe(r_list)
  return r_df 
end

.create_env_function_call(env, fname, hash_like) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 373

def self.create_env_function_call( env, fname, hash_like )
  raise "create_env_function_call should take String for env" if(env.class != String) 
  raise "create_env_function_call should take String for function name" if(fname.class != String) 
  raise "create_env_function_call should take Hash like structure for function arguments" if(hash_like.class != Hash && hash_like.class != Array)
  lcons_args = hash_to_lcons_args( hash_like )

  new_function_call = r_lang_create_env_fcall(env, fname, lcons_args)
  ptr_manager_add_ptr_to_current( new_function_call )
  return new_function_call
end

.create_env_lazy_function(env, fname, hash_like, param_manager) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_lazyfunc_ext.rb', line 11

def self.create_env_lazy_function( env, fname, hash_like , param_manager)
  raise "create_env_lazy_function should take String for environment" if(env.class != String) 
  raise "create_env_lazy_function should take String for function name" if(fname.class != String) 
  raise "create_env_lazy_function should take Hash like structure for function arguments" if(hash_like.class != Hash && hash_like.class != Array)
  return LazyFunc.new( nil, env, fname, hash_like, param_manager)
end

.create_extptr(ffi_pointer) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 299

def self.create_extptr( ffi_pointer )
  raise "create_extptr should take a FFI::Pointer argument" if(ffi_pointer.class != FFI::Pointer)

  extptr = r_lang_create_extptr(ffi_pointer)

  ptr_manager_add_ptr_to_current( extptr )
  return extptr
end

.create_formula_from_syms(ary) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 90

def self.create_formula_from_syms( ary )
  raise "create_formula_from_syms should take an Array argument" if(ary.class != Array) 
  raise "Array has an(some) elemnt(s) that are not SymbolR" if(! ary.all? {|i| i.is_a?(SymbolR) || i.is_a?(SignR) }) 

  str = ary.map(){|sym| sym.val}.join(" ")
  r_strvec = create_strvec([str])

  r_create_formula = create_function_call( "as.formula" , {"object" => r_strvec})

  r_formula_ptr = exec_function( r_create_formula ) # No need to add_ptr b/c exec_function adds this pointer to ptr_manager.

  return r_formula_ptr
end

.create_function_call(fname, hash_like) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 384

def self.create_function_call( fname,  hash_like )
  raise "create_function_call should take String for function name" if(fname.class != String) 
  raise "create_function_call should take Hash like structure for function arguments" if(hash_like.class != Hash && hash_like.class != Array)
  lcons_args = hash_to_lcons_args( hash_like )

  new_function_call = r_lang_create_fcall(fname, lcons_args)
  ptr_manager_add_ptr_to_current( new_function_call )
  return new_function_call
end

.create_function_call_from_lazy_function_attrs(ns, env, fname, fargs, param_manager, result_manager) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_lazyfunc_ext.rb', line 24

def self.create_function_call_from_lazy_function_attrs( ns, env, fname, fargs, param_manager, result_manager)

  new_arg_assoc_array = []
  fargs.each(){|key, val|

    if val.is_a? RResultPrevious
      r_previous = result_manager.get_previous() # if r_nil (i.e. 1st instruction or no previous result-store instructions) we need to use default one.
      if ! RBridge::is_r_nil?(r_previous)  # When previous result exists
        new_arg_assoc_array << [key, r_previous]
        next
      else  # When previous result does not exist
        val = val.default
      end
    end

    case val
    when LazyFunc then
      new_arg_assoc_array << [key, create_function_call_from_lazy_function_attrs( val.ns, val.env, val.fname, val.args , param_manager, result_manager )]
    when RResultName , RResultNameArray then 
      new_arg_assoc_array << [key, result_manager.get_last_for( val )]
    when RParamName then
      new_arg_assoc_array << [key, param_manager.get_r_object( val )]
    when RNameContainer then
      idx = 0
      while idx < val.elems.size do
        elem = val.elems[idx]
        case elem
        when RResultName, RResultNameArray then 
          result = result_manager.get_last_for( elem )
          if( ! RBridge::is_r_nil?(result) )
            new_arg_assoc_array << [key, result]
            break
          end
        when RParamName then
          result = param_manager.get_r_object( elem )
          if( ! RBridge::is_r_nil?(result) )
            new_arg_assoc_array << [key, result]
            break
          end
        else  # R object
          new_arg_assoc_array << [key, val]
          break
        end
        idx = idx + 1
      end
      if(idx == val.elems.size ) # Not found
        new_arg_assoc_array << [key, RBridge::r_nil()]
      end
    when RInstPrevious
      new_arg_assoc_array << [key, result_manager.get_previous_inst_name() ]
    else  # R object
      new_arg_assoc_array << [key, val]
    end
  }
  if( ns.nil? )
    if( env.nil? )
      return create_function_call( fname, new_arg_assoc_array )
    else
      return create_env_function_call( env, fname, new_arg_assoc_array )
    end
  else
    if( env.nil? )
      return create_ns_function_call( ns, fname, new_arg_assoc_array )
    else
      raise "namespace and environment are not allowed to be specified at the same time."
    end
  end
end

.create_intvec(ary) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 140

def self.create_intvec( ary )
  raise "create_intvec should take an Array argument" if(ary.class != Array) 
  raise "Array has an(some) elemnt(s) that are not Integer" if(! ary.all? {|i| i.is_a?(Integer) }) 
  r_intvec_ptr = r_vec_create_int(ary.size)
  int_values = FFI::MemoryPointer.new(:int, ary.size) # This is garbage collected by FFI
  int_values.put_array_of_int(0, ary)
  r_vec_set_int( r_intvec_ptr, int_values , ary.size)
 
  ptr_manager_add_ptr_to_current( r_intvec_ptr )
  return r_intvec_ptr
end

.create_lazy_function(fname, hash_like, param_manager) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_lazyfunc_ext.rb', line 18

def self.create_lazy_function( fname, hash_like , param_manager)
  raise "create_lazy_function should take String for function name" if(fname.class != String) 
  raise "create_lazy_function should take Hash like structure for function arguments" if(hash_like.class != Hash && hash_like.class != Array)
  return LazyFunc.new( nil, nil, fname, hash_like, param_manager)
end

.create_lglvec(ary) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 164

def self.create_lglvec( ary )
  raise "create_lglvec should take an Array argument" if(ary.class != Array)
  raise "Array has an(some) elemnt(s) that are not true or false" if(! ary.all? {|i| [true, false].include?(i) })
  ary = ary.map{|elem| elem ? 1 : 0 }

  r_lglvec_ptr = r_vec_create_lgl(ary.size)
  lgl_values = FFI::MemoryPointer.new(:int, ary.size) # This is garbage collected by FFI
  lgl_values.put_array_of_int(0, ary)
  r_vec_set_lgl( r_lglvec_ptr, lgl_values , ary.size)
 
  ptr_manager_add_ptr_to_current( r_lglvec_ptr )
  return r_lglvec_ptr
end

.create_library_function(lib_name) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 111

def self.create_library_function( lib_name )
  raise "create_library_function should take an String argument for variable name" if(lib_name.class != String)
  r_lib_name = create_strvec([lib_name])
  func = create_function_call( "library", {"package" => r_lib_name})
  return func    
end

.create_list(hash) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 63

def self.create_list( hash )
  size = hash.size
  r_name_vec = create_strvec(hash.keys)

  r_list = r_list_create(r_name_vec, size)
  ptr_manager_add_ptr_to_current( r_list )

  hash.values.each_with_index(){|v, idx|
    r_vec = create_vec( v )
    r_list_set_elem( r_list, idx, r_vec )
  }
  return r_list
end

.create_ns_function_call(ns, fname, hash_like) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 362

def self.create_ns_function_call( ns, fname, hash_like )
  raise "create_ns_function_call should take String for namespace" if(ns.class != String) 
  raise "create_ns_function_call should take String for function name" if(fname.class != String) 
  raise "create_ns_function_call should take Hash like structure for function arguments" if(hash_like.class != Hash && hash_like.class != Array)
  lcons_args = hash_to_lcons_args( hash_like )

  new_function_call = r_lang_create_ns_fcall(ns, fname, lcons_args)
  ptr_manager_add_ptr_to_current( new_function_call )
  return new_function_call
end

.create_ns_lazy_function(ns, fname, hash_like, param_manager) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_lazyfunc_ext.rb', line 4

def self.create_ns_lazy_function( ns, fname, hash_like , param_manager)
  raise "create_ns_lazy_function should take String for namespace" if(ns.class != String) 
  raise "create_ns_lazy_function should take String for function name" if(fname.class != String) 
  raise "create_ns_lazy_function should take Hash like structure for function arguments" if(hash_like.class != Hash && hash_like.class != Array)
  return LazyFunc.new( ns, nil, fname, hash_like, param_manager)
end

.create_realvec(ary) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 152

def self.create_realvec( ary )
  raise "create_realvec should take an Array argument" if(ary.class != Array)
  raise "Array has an(some) elemnt(s) that are not Float" if(! ary.all? {|i| i.is_a?(Float) })
  r_realvec_ptr = r_vec_create_real(ary.size)
  dbl_values = FFI::MemoryPointer.new(:double, ary.size) # This is garbage collected by FFI
  dbl_values.put_array_of_double(0, ary)
  r_vec_set_real( r_realvec_ptr, dbl_values , ary.size)
 
  ptr_manager_add_ptr_to_current( r_realvec_ptr )
  return r_realvec_ptr
end

.create_strvec(ary) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 118

def self.create_strvec( ary )
  raise "create_strvec should take an Array argument" if(ary.class != Array) 
  raise "Array has an(some) elemnt(s) that are not String" if(! ary.all? {|i| i.is_a?(String) }) 

  r_strvec_ptr = r_vec_create_str(ary.size )

  str_values = FFI::MemoryPointer.new(:pointer, ary.size ) # This is garbage collected by FFI
  
  strptrs = []
  ary.each(){|str_elem|
    strptrs << FFI::MemoryPointer.from_string(str_elem) # Make cstring pointer managed via FFI::MemoryPointer
  }
  strptrs.each_with_index do |p, i|
      str_values[i].put_pointer(0,  p)
  end

  r_vec_set_str( r_strvec_ptr, str_values , ary.size )
 
  ptr_manager_add_ptr_to_current( r_strvec_ptr )
  return r_strvec_ptr
end

.create_vec(ary) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 178

def self.create_vec( ary )
  raise "create_vec should take an Array argument" if(ary.class != Array)
  # (SymbolR >) String > Real > Int > Logical
  
  type_ary = ary.map(){|elem|
    case elem
    when String
      4
    when Float
      3
    when Integer
      2
    when TrueClass
      1
    when FalseClass
      1
    else
      raise " The current elemnt is not supported to convert to R vector : " + elem
    end
  }

  max_type = type_ary.max()

  converted_ary = ary.each_with_index.map(){|elem, idx|
    if type_ary[idx] != max_type
      case max_type
      when 4
          converted = ary[idx].to_s
      when 3
        if(type_ary[idx] == 2)
          converted = ary[idx].to_f
        else # 1 : boolean
          converted = ary[idx] ? 1 : 0
        end
      when 2
        converted = ary[idx].to_i
      when 1
        raise "All the elements shold be true/false. Current value: " + ary[idx]
      end
      converted
    else
      ary[idx]
    end
  }

  case max_type
  when 4
    new_r_vec = create_strvec( converted_ary )
  when 3
    new_r_vec = create_realvec( converted_ary )
  when 2
    new_r_vec = create_intvec( converted_ary )
  when 1
    new_r_vec = create_lglvec( converted_ary )
  end

  return new_r_vec
end

.end_embedded_r ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 59

def self.end_embedded_r()
  r_embedded_end()
end

.exec_function(func, allow_nil_result: false) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 394

def self.exec_function( func , allow_nil_result: false )
  result = r_eval( func )
  if ( ! allow_nil_result ) && ( is_r_nil?( result ))  
    raise "Return value of R's function is unintentioanlly nil"
  end

  if ( ! is_r_nil?( result ) )
    # if the result is nil, this pointer needs no tracking (for GC)
    ptr_manager_add_ptr_to_current( result )
  end
  return result
end

.exec_function_no_return(func) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 407

def self.exec_function_no_return( func )
  r_eval_no_return( func )
  return nil
end

.exec_lazy_function(lazy_func, result_manager, allow_nil_result: false) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_lazyfunc_ext.rb', line 93

def self.exec_lazy_function( lazy_func , result_manager , allow_nil_result: false )
  raise "exec_lazy_function should take LazyFunc object" if(lazy_func.class != LazyFunc) 
  raise "exec_lazy_function should take RResultManager or Nil for 2nd argment: " + result_manager.class.to_s  if(! [RResultManager, NilClass].include?(result_manager.class) )
  ns = lazy_func.ns
  env = lazy_func.env
  fname = lazy_func.fname
  arg_hash = lazy_func.args
  param_manager = lazy_func.param_manager

  func = create_function_call_from_lazy_function_attrs(ns, env, fname, arg_hash, param_manager, result_manager)
  result = exec_function( func , allow_nil_result: allow_nil_result )
  return result
end

.gc_all ⇒ Object

public



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 541

def self.gc_all()
  num_of_objs_by_ptr_managers = @ptr_managers.map(){|key,r_obj| r_obj}.reduce(0){| result, elem | result + elem.ptr_num() }
  if(@gc_counter != num_of_objs_by_ptr_managers)
    puts "RBridge internal error: R object counting and tracking mismatch"
    puts "GC counter: #{@gc_counter}  Num of objects under ptr managers: #{num_of_objs_by_ptr_managers}"
  end

  r_ptr_gc( @gc_counter )
  @gc_counter = 0
end

.hash_to_lcons_args(hash_like) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 321

def self.hash_to_lcons_args( hash_like )
  if hash_like.class == Hash
    # hash
  elsif hash_like.class == Array
    if array_depth(hash_like) == 2 && assoc_array?(hash_like)
      # association array
    else
      raise "hash_to_lcons_args should take Hash argument (or Association Array argument)"
    end
  else
    raise "hash_to_lcons_args should take Hash argument (or Association Array argument)"
  end

  if(hash_like.size == 0)
    lcons_args = r_lang_nil()
  elsif(hash_like.size == 1)
    tag = hash_like.first[0]
    val = hash_like.first[1]
    lcons_args = lcons_gen( val )
    if( tag != "" )
      set_tag_to_lcons( lcons_args, tag )
    end
  else
    idx = 0
    hash_like.reverse_each(){|arg|
      tag = arg[0]
      val = arg[1]
      if(idx == 0 )
        lcons_args = lcons_gen( val )
      else
        lcons_args = lcons( val, lcons_args )
      end
      if( tag != "" )
        set_tag_to_lcons( lcons_args, tag )
      end
      idx = idx + 1
    }
  end
  return lcons_args
end

.init_embedded_r(unlimited_cstack: false) ⇒ Object

From here, Ruby interface



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 52

def self.init_embedded_r( unlimited_cstack: false )
  if(unlimited_cstack.class != TrueClass && unlimited_cstack.class != FalseClass)
    raise "init_embedded_r() can take true or false for unlimited C stack size. true: unlimited, false: default." 
  end
  r_embedded_init( unlimited_cstack )
end

.is_pointer?(val) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/r_bridge/r_bridge_ffi.rb', line 46

def self.is_pointer?(val)
  return val.is_a? FFI::Pointer
end

.is_r_nil?(obj) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/r_bridge/r_bridge_ffi.rb', line 286

def self.is_r_nil?( obj )
  result = r_is_nil( obj )
  if(result == 1)
      return true
  else
      return false
  end
end

.lcons(car, cdr) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 270

def self.lcons( car, cdr )
  new_lcons = r_lang_cons(car, cdr)
  ptr_manager_add_ptr_to_current( new_lcons )
  return new_lcons
end

.lcons_gen(car) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 276

def self.lcons_gen( car )
  new_lcons = r_lang_cons_gen(car )
  ptr_manager_add_ptr_to_current( new_lcons )
  return new_lcons
end

.ptr_manager_close(ptr_manager_name) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 500

def self.ptr_manager_close( ptr_manager_name )
  raise "RPointerManager(" + ptr_manager_name + ") does not exist"  if ! @ptr_managers.keys.include?( ptr_manager_name )
  raise "RPointerManager with empty string name should never be closed." if ptr_manager_name == ""

  @gc_counter = @gc_counter - (@ptr_managers[ptr_manager_name]).ptr_num()
  @ptr_managers[ptr_manager_name].close()

  @ptr_managers.delete(ptr_manager_name)
  @ptr_manager_stack.delete(ptr_manager_name)
end

.ptr_manager_open(ptr_manager_name) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 485

def self.ptr_manager_open( ptr_manager_name )
  if block_given?
    ptr_manager_create_or_switch( ptr_manager_name )
    begin
      yield
    rescue => e
      raise e
    ensure
      ptr_manager_close( ptr_manager_name )  # This part is always conducted at the end of block or when error raised within block 
    end
  else
    ptr_manager_create_or_switch( ptr_manager_name )
  end
end

.ptr_manager_switch(ptr_manager_name) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 511

def self.ptr_manager_switch( ptr_manager_name )
  raise "ptr_manager_name does not exit yet: #{ptr_manager_name}" if ! @ptr_managers.keys.include?( ptr_manager_name )
  raise "ptr_manager_name does not exit yet: #{ptr_manager_name}" if ! @ptr_manager_stack.include?( ptr_manager_name )

  # put the specified name on top(last) of stack
  @ptr_manager_stack.delete( ptr_manager_name ) && ( @ptr_manager_stack << ptr_manager_name )
end

.r_nil ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 282

def self.r_nil()
  return r_lang_nil()
end

.set_tag_to_lcons(lcons, tag_name) ⇒ Object 



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# File 'lib/r_bridge/r_bridge_ffi.rb', line 295

def self.set_tag_to_lcons( lcons, tag_name )
  r_lang_set_tag( lcons, tag_name )
end