mdarray 0.5.3-java → 0.5.4-java

data/lib/netcdf/cdm_node.rb

@@ -0,0 +1,71 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+class NetCDF
+
+  #=======================================================================================
+  # Define a superclass for all the CDM node classes: Group, Dimension, etc. Define the 
+  # sort of the node CDMSort so that we can 1. do true switching on node type 2. avoid use 
+  # of instanceof 3. Use container classes that have more than one kind of node
+  #
+  # Also move various common fields and methods to here.
+  #=======================================================================================
+
+  class CDMNode
+
+    attr_reader :netcdf_elmt
+
+    #------------------------------------------------------------------------------------
+    # Initializes a CDMNode with a java CDMNode
+    #------------------------------------------------------------------------------------
+
+    def initialize(netcdf_cdmnode)
+      @netcdf_elmt = netcdf_cdmnode
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def get_full_name
+      @netcdf_elmt.getFullName()
+    end
+
+    alias :get_full_name_escaped :get_full_name
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def get_short_name
+      @netcdf_elmt.getShortName()
+    end
+
+    alias :name :get_short_name
+
+  end
+
+end
+
+require_relative 'group'
+require_relative 'dimension'
+require_relative 'variable'
+require_relative 'attribute'

data/lib/netcdf/dimension.rb

@@ -0,0 +1,146 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+class NetCDF
+
+  #=======================================================================================
+  # A Dimension is used to define the array shape of a Variable. It may be shared among 
+  # Variables, which provides a simple yet powerful way of associating Variables. When a 
+  # Dimension is shared, it has a unique name within its Group. It may have a coordinate 
+  # Variable, which gives each index a coordinate value. A private Dimension cannot have a 
+  # coordinate Variable, so use shared dimensions with coordinates when possible. The 
+  # Dimension length must be > 0, except for an unlimited dimension which may have 
+  # length = 0, and a vlen Dimension has length = -1.
+  # Immutable if setImmutable() was called, except for an Unlimited Dimension, whose size 
+  # can change.
+  #=======================================================================================
+
+  class Dimension < CDMNode
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def get_length
+      @netcdf_elmt.getLength()
+    end
+
+    alias :length :get_length
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def shared?
+      @netcdf_elmt.isShared()
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def unlimited?
+      @netcdf_elmt.isUnlimited()
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def variable_length?
+      @netcdf_elmt.isVariableLength()
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def group
+      NetCDF::Group.new(@netcdf_elmt.getGroup())
+    end
+
+  end # Dimension
+
+  #=======================================================================================
+  #
+  #=======================================================================================
+
+  class DimensionWriter < Dimension
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def set_immutable
+      @netcdf_elmt.setImmutable()
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def length=(val)
+      @netcdf_elmt.setLength(val)
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def name=(name)
+      @netcdf_elmt.setName(name)
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def shared=(bool)
+      @netcdf_elmt.setShared(bool)
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def unlimited=(bool)
+      @netcdf_elmt.setUnlimited(bool)
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def variable_length=(bool)
+      @netcdf_elmt.setVariableLength(bool)
+    end
+
+    #------------------------------------------------------------------------------------
+    #
+    #------------------------------------------------------------------------------------
+
+    def group=(group)
+      @netcdf_elmt.setGroup(group.netcdf_elmt)
+    end
+
+  end # DimensionWriter
+
+end # NetCDF

data/lib/netcdf/file.rb

@@ -0,0 +1,253 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'java'
+
+#======================================================================================
+#
+#======================================================================================
+
+class NetCDF
+  
+  #=======================================================================================
+  # Parent File for the file hierarchy that includes File and FileWriter.  
+  #=======================================================================================
+
+  class FileParent
+
+    attr_reader :home_dir
+    attr_reader :file_name
+    attr_reader :netcdf_elmt
+    attr_reader :outside_scope
+    attr_reader :root_group
+
+    #------------------------------------------------------------------------------------
+    # NetCDF File
+    #------------------------------------------------------------------------------------
+    
+    def initialize(home_dir, name, outside_scope = nil)
+      @home_dir = home_dir
+      @file_name = "#{home_dir}/#{name}.nc"
+      @outside_scope = outside_scope
+    end
+    
+    #------------------------------------------------------------------------------------
+    # Gets a list of all global attributes, i.e, all attributes in the root group
+    #------------------------------------------------------------------------------------
+
+    def global_attributes
+      @root_group.attributes
+    end
+
+  end # FileParent
+
+  #=======================================================================================
+  # Read-only scientific datasets that are accessible through the netCDF API. Immutable 
+  # after setImmutable() is called. However, reading data is not thread-safe.
+  #=======================================================================================
+
+  class File < FileParent
+    include_package "ucar.nc2"
+
+    #------------------------------------------------------------------------------------
+    # Opens a file for reading
+    #------------------------------------------------------------------------------------
+
+    def open
+      @netcdf_elmt = NetcdfFile.open(@file_name)
+      @root_group = @netcdf_elmt.findGroup(nil)
+    end
+
+    #------------------------------------------------------------------------------------
+    # Find out if the file can be opened, but dont actually open it.
+    #------------------------------------------------------------------------------------
+
+    def can_open?
+      @netcdf_elmt.canOpen(@file_name)
+    end
+
+    #------------------------------------------------------------------------------------
+    # closes the file
+    #------------------------------------------------------------------------------------
+    
+    def close
+      @netcdf_elmt.close()
+    end
+
+    #------------------------------------------------------------------------------------
+    # Completely empty the objects in the netcdf file.
+    #------------------------------------------------------------------------------------
+    
+    def empty
+      @netcdf_elmt.empty()
+    end
+
+    #------------------------------------------------------------------------------------
+    # Find a Group, with the specified (full) name.
+    #------------------------------------------------------------------------------------
+
+    def find_group(name)
+      NetCDF::Group.new(@netcdf_elmt.findGroup(name))
+    end
+
+    #------------------------------------------------------------------------------------
+    # Find an attribute, with the specified (escaped full) name.
+    #------------------------------------------------------------------------------------
+
+    def find_attribute(name)
+      NetCDF::Attribute.new(@netcdf_elmt.findAttribute(name))
+    end
+
+    #------------------------------------------------------------------------------------
+    # Find an global attribute, with the specified (full) name.
+    #------------------------------------------------------------------------------------
+
+    def find_global_attribute(name, ignore_case = false)
+      if (ignore_case)
+        NetCDF::Attribute.new(@netcdf_elmt.findGlobalAttributeIgnoreCase(name))
+      else
+        NetCDF::Attribute.new(@netcdf_elmt.findGlobalAttribute(name))
+      end
+    end
+
+    #------------------------------------------------------------------------------------
+    # Finds a dimension by full name
+    #------------------------------------------------------------------------------------
+    
+    def find_dimension(name)
+      NetCDF::Dimension.new(@netcdf_elmt.findDimension(name))
+    end
+
+    #------------------------------------------------------------------------------------
+    # Return the unlimited (record) dimension, or null if not exist. If there are 
+    # multiple unlimited dimensions, it will return the first one.
+    # <tt>Returns:</tt> the unlimited Dimension, or null if none.
+    #------------------------------------------------------------------------------------
+
+    def find_unlimited_dimension
+      NetCDF::Dimension.new(@netcdf_elmt.getUnlimitedDimension())
+    end
+
+    # Don't know the difference between find and get methods on the original NetCDF API
+    alias :get_unlimited_dimension :find_unlimited_dimension
+
+
+    #------------------------------------------------------------------------------------
+    # Finds a variable by name
+    #------------------------------------------------------------------------------------
+
+    def find_variable(name)
+      NetCDF::Variable.new(@netcdf_elmt.findVariable(name))
+    end
+
+
+
+
+    #------------------------------------------------------------------------------------
+    # Outputs the data CDL to an output stream
+    # * TODO: allow writing to other output streams.  Need to interface with java streams
+    # * <tt>strict</tt> if true, make it stricly CDL, otherwise, add a little extra info
+    #------------------------------------------------------------------------------------
+    
+    def write_cdl(out = $stdout, strict = false)
+      @netcdf_elmt.writeCDL(out.to_outputstream, strict)
+    end
+
+    #------------------------------------------------------------------------------------
+    # Find all dimensions in the file
+    #------------------------------------------------------------------------------------
+
+    def detail_info
+      @netcdf_elmt.getDetailInfo()
+    end
+
+    #------------------------------------------------------------------------------------
+    # Get a human-readable description for this file type.
+    #------------------------------------------------------------------------------------
+
+    def file_type_description
+      @netcdf_elmt.getFileTypeDescription()
+    end
+
+    #------------------------------------------------------------------------------------
+    # Get the file type id for the underlying data source.
+    #------------------------------------------------------------------------------------
+
+    def file_type_id
+      @netcdf_elmt.getFileTypeId()
+    end
+
+    #------------------------------------------------------------------------------------
+    # Get the globally unique dataset identifier, if it exists.
+    #------------------------------------------------------------------------------------
+
+    def id
+      @netcdf_elmt.getId()
+    end
+
+    #------------------------------------------------------------------------------------
+    # 
+    #------------------------------------------------------------------------------------
+
+    def last_modified
+      @netcdf_elmt.getLastModified() 
+    end
+
+    #------------------------------------------------------------------------------------
+    # Get the NetcdfFile location.
+    #------------------------------------------------------------------------------------
+
+    def location
+      @netcdf_elmt.getLocation() 
+    end
+
+    #------------------------------------------------------------------------------------
+    # Get the human-readable title, if it exists.
+    #------------------------------------------------------------------------------------
+
+    def title
+      @netcdf_elmt.getTitle() 
+    end
+
+    #------------------------------------------------------------------------------------
+    # Get the human-readable title, if it exists.
+    #------------------------------------------------------------------------------------
+
+    def unlimited_dimension?
+      @netcdf_elmt.hasUnlimitedDimension() 
+    end
+
+
+
+
+    #------------------------------------------------------------------------------------
+    # Find all dimensions in the file
+    #------------------------------------------------------------------------------------
+
+    def get_dimensions
+      @netcdf_elmt.getDimensions()
+    end
+
+  end # File
+
+end # NetCDF
+
+require_relative 'file_writer'