mdarray 0.5.3-java → 0.5.4-java
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- data/README.md +325 -70
- data/doc/20130625 MDArray Internals.docx +0 -0
- data/lib/colt/colt.rb +2 -0
- data/lib/colt/matrix/colt_matrix.rb +365 -0
- data/lib/colt/matrix/matrix2D_floating_algebra.rb +325 -0
- data/lib/colt/matrix/matrix_hierarchy.rb +258 -0
- data/lib/mdarray.rb +54 -3
- data/lib/mdarray/access.rb +16 -0
- data/lib/mdarray/counter.rb +16 -0
- data/lib/mdarray/creation.rb +13 -1
- data/lib/mdarray/lazy_mdarray.rb +6 -2
- data/lib/mdarray/lazy_operators.rb +8 -0
- data/lib/mdarray/printing.rb +18 -3
- data/lib/mdarray/section.rb +101 -0
- data/lib/netcdf/attribute.rb +154 -0
- data/lib/netcdf/cdm_node.rb +71 -0
- data/lib/netcdf/dimension.rb +146 -0
- data/lib/netcdf/file.rb +253 -0
- data/lib/netcdf/file_writer.rb +474 -0
- data/lib/netcdf/group.rb +205 -0
- data/lib/netcdf/netcdf.rb +151 -0
- data/lib/netcdf/variable.rb +520 -0
- data/test/colt/test_complete.rb +1 -2
- data/test/colt/test_double_matrix2d.rb +186 -0
- data/test/colt/test_float_matrix2d.rb +171 -0
- data/test/colt/test_math.rb +21 -0
- data/test/colt/test_matrix.rb +172 -0
- data/test/complete.rb +9 -1
- data/test/env.rb +11 -1
- data/test/mdarray/test_complete.rb +2 -0
- data/test/mdarray/test_creation.rb +19 -28
- data/test/mdarray/test_non_numeric.rb +97 -0
- data/test/mdarray/test_sections.rb +94 -0
- data/test/mdarray/test_views.rb +23 -1
- data/test/netcdf/netcdfwriter.rb +197 -0
- data/test/netcdf/test_complete.rb +27 -0
- data/test/netcdf/test_netcdf.rb +331 -0
- data/test/netcdf/test_redefine.rb +120 -0
- data/vendor/incanter.jar +0 -0
- data/vendor/{netcdfAll-4.3.16.jar → netcdfAll-4.3.18.jar} +0 -0
- data/version.rb +1 -1
- metadata +44 -26
- data/vendor/parallelcolt-0.10.0.jar +0 -0
data/lib/netcdf/group.rb
ADDED
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# -*- coding: utf-8 -*-
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##########################################################################################
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# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify,
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# and distribute this software and its documentation, without fee and without a signed
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# licensing agreement, is hereby granted, provided that the above copyright notice, this
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# paragraph and the following two paragraphs appear in all copies, modifications, and
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# distributions.
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#
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# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL,
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# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF
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# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE
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# POSSIBILITY OF SUCH DAMAGE.
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#
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# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
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# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
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# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS".
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# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS,
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# OR MODIFICATIONS.
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##########################################################################################
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class NetCDF
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########################################################################################
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# A Group is a logical collection of Variables. The Groups in a Dataset form a
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# hierarchical tree, like directories on a disk. A Group has a name and optionally a
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# set of Attributes. There is always at least one Group in a dataset, the root Group,
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# whose name is the empty string.
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#
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# Immutable if setImmutable() was called.
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########################################################################################
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class Group < CDMNode
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def common_parent(group)
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@netcdf_elmt.commomParent(group.netcdf_elmt)
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def find_attribute(name, ignore_case = false)
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if (ignore_case)
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NetCDF::Attribute.new(@netcdf_elmt.findAttributeIgnoreCase(name))
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else
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NetCDF::Attribute.new(@netcdf_elmt.findAttribute(name))
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end
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end
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#------------------------------------------------------------------------------------
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# Retrieve a Dimension using its (short) name. If local is true, then
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# retrieve a Dimension using its (short) name, in this group only.
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#------------------------------------------------------------------------------------
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def find_dimension(name, local = false)
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if (local)
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NetCDF::Dimension.new(@netcdf_elmt.findDimensionLocal(name))
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else
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NetCDF::Dimension.new(@netcdf_elmt.findDimension(name))
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end
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end
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#------------------------------------------------------------------------------------
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# Retrieve the Group with the specified (short) name.
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#------------------------------------------------------------------------------------
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def find_group(name)
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NetCDF::Group.new(@netcdf_elmt.findGroup(name))
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def find_variable(name, local = true)
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if (local)
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NetCDF::Variable.new(@netcdf_elmt.findVariable(name))
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else
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NetCDF::Variable.new(@netcdf_elmt.findVariableOrInParent(name))
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end
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def attributes
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java_attributes = @netcdf_elmt.getAttributes()
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attributes = Array.new
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java_attributes.each do |att|
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attributes << NetCDF::Attribute.new(att)
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end
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attributes
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def to_string
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@netcdf_elmt.toString()
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end
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end
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#=======================================================================================
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# GroupWriter is a group that allows for writing data on it.
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#=======================================================================================
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class GroupWriter < Group
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def add_attribute(attribute)
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@netcdf_elmt.addAttribute(attribute.netcdf_elmt)
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def add_dimension(dimension)
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@netcdf_elmt.addDimension(dimension.netcdf_elmt)
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def add_dimension_if_not_exists(dimension)
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@netcdf_elmt.addDimensionIfNotExists(dimension.netcdf_elmt)
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def add_group(group)
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@netcdf_elmt.addGroup(group.netcdf_elmt)
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def add_variable(variable)
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@netcdf_elmt.addVariable(variable.netcdf_elmt)
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def remove(elmt)
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@netcdf_elmt.remove(elmt.netcdf_elmt)
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end
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#------------------------------------------------------------------------------------
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# remove a Dimension using its name, in this group only
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#------------------------------------------------------------------------------------
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def remove_dimension(name)
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@netcdf_elmt.removeDimension(name)
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end
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#------------------------------------------------------------------------------------
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# remove a Variable using its (short) name, in this group only
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#------------------------------------------------------------------------------------
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def remove_variable(name)
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@netcdf_elmt.removeVariable(name)
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def name=(name)
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@netcdf_elmt.setName(name)
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end
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#------------------------------------------------------------------------------------
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# Set the Group's parent Group
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#------------------------------------------------------------------------------------
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def parent_group=(parent)
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@netcdf_elmt.setParentGroup(parent.netcdf_elmt)
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end
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end # GroupWriter
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end
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@@ -0,0 +1,151 @@
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# -*- coding: utf-8 -*-
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##########################################################################################
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# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify,
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5
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+
# and distribute this software and its documentation, without fee and without a signed
|
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+
# licensing agreement, is hereby granted, provided that the above copyright notice, this
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# paragraph and the following two paragraphs appear in all copies, modifications, and
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# distributions.
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#
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# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL,
|
11
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# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF
|
12
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# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE
|
13
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+
# POSSIBILITY OF SUCH DAMAGE.
|
14
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#
|
15
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# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
|
16
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+
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
|
17
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+
# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS".
|
18
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+
# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS,
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# OR MODIFICATIONS.
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##########################################################################################
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#======================================================================================
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#
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#======================================================================================
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class NetCDF
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include_package "ucar.nc2"
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include_package "ucar.ma2"
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def self.define(home_dir, file_name, version, outside_scope = nil, &block)
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writer = NetCDF::FileWriter.new_file(home_dir, file_name, version, outside_scope)
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begin
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writer.open
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writer.instance_eval(&block)
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writer.create
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writer.close
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writer
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rescue
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writer.close
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raise "Illegal opperation occured on file: #{writer.file_name}"
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end
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def self.redefine(home_dir, file_name, outside_scope = nil, &block)
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writer = NetCDF::FileWriter.existing_file(home_dir, file_name, outside_scope)
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begin
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writer.open
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writer.redefine = true
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# we are not really adding a root group, but actually getting the root group
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# can only be done in define mode
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writer.add_root_group
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writer.instance_eval(&block)
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writer.redefine = false
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writer.close
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writer
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rescue Exception =>e
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writer.close
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p e.message
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# p e.backtrace.inspect
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# raise "Illegal opperation occured on file: #{writer.file_name}"
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raise e
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end
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def self.write(home_dir, file_name, outside_scope = nil, &block)
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writer = NetCDF::FileWriter.existing_file(home_dir, file_name, outside_scope)
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85
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begin
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writer.open
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writer.instance_eval(&block)
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writer.close
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writer
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rescue Exception => e
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writer.close
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# raise "Illegal opperation occured on file: #{file_name}"
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raise e
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end
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end
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#------------------------------------------------------------------------------------
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#
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#------------------------------------------------------------------------------------
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def self.read(home_dir, file_name, outside_scope = nil, &block)
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reader = NetCDF::File.new(home_dir, file_name, outside_scope)
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begin
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reader.open
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reader.instance_eval(&block)
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reader.close
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reader
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rescue Exception => e
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reader.close
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p e.message
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114
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# raise "Illegal opperation occured on file: #{file_name}"
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raise e
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+
end
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+
|
118
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end
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119
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+
|
120
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#------------------------------------------------------------------------------------
|
121
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# Outputs the data format
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122
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#------------------------------------------------------------------------------------
|
123
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+
|
124
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def self.output(file_name)
|
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print `ncdump #{file_name}`
|
126
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+
end
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127
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+
|
128
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#------------------------------------------------------------------------------------
|
129
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+
#
|
130
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#------------------------------------------------------------------------------------
|
131
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+
|
132
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def self.get_dtype(type)
|
133
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+
DataType.valueOf(type.upcase)
|
134
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+
end
|
135
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+
|
136
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#------------------------------------------------------------------------------------
|
137
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+
#
|
138
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+
#------------------------------------------------------------------------------------
|
139
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+
|
140
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+
def self.writer_version(name)
|
141
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+
NetcdfFileWriter::Version.valueOf(name)
|
142
|
+
end
|
143
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+
|
144
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#------------------------------------------------------------------------------------
|
145
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+
#
|
146
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+
#------------------------------------------------------------------------------------
|
147
|
+
|
148
|
+
end # NetCDF
|
149
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+
|
150
|
+
require_relative 'cdm_node'
|
151
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+
require_relative 'file'
|
@@ -0,0 +1,520 @@
|
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1
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+
# -*- coding: utf-8 -*-
|
2
|
+
|
3
|
+
##########################################################################################
|
4
|
+
# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify,
|
5
|
+
# and distribute this software and its documentation, without fee and without a signed
|
6
|
+
# licensing agreement, is hereby granted, provided that the above copyright notice, this
|
7
|
+
# paragraph and the following two paragraphs appear in all copies, modifications, and
|
8
|
+
# distributions.
|
9
|
+
#
|
10
|
+
# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL,
|
11
|
+
# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF
|
12
|
+
# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE
|
13
|
+
# POSSIBILITY OF SUCH DAMAGE.
|
14
|
+
#
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# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
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# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
|
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# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS".
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# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS,
|
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+
# OR MODIFICATIONS.
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##########################################################################################
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+
|
22
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class NetCDF
|
23
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+
|
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#=======================================================================================
|
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# A Variable is a logical container for data. It has a dataType, a set of Dimensions
|
26
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# that define its array shape, and optionally a set of Attributes. The data is a
|
27
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# multidimensional array of primitive types, Strings, or Structures. Data access is
|
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# done through the read() methods, which return a memory resident Array.
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# Immutable if setImmutable() was called.
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#=======================================================================================
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+
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class Variable < CDMNode
|
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+
|
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attr_reader :attributes
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attr_reader :dimensions
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attr_reader :index_iterator
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+
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#------------------------------------------------------------------------------------
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+
#
|
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+
#------------------------------------------------------------------------------------
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+
|
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def extra_info
|
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+
@netcdf_elmt.extraInfo()
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+
end
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+
|
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+
#------------------------------------------------------------------------------------
|
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# Create a new data cache, use this when you dont want to share the cache.
|
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+
#------------------------------------------------------------------------------------
|
49
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+
|
50
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+
def create_new_cache
|
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+
@netcdf_elmt.createNewCache()
|
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+
end
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53
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+
|
54
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+
#------------------------------------------------------------------------------------
|
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# Finds an attribute by name
|
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+
#------------------------------------------------------------------------------------
|
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+
|
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def find_attribute(name, ignore_case = false)
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+
|
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if (ignore_case)
|
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@netcdf_elmt.findAttributeIgnoreCase(name)
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else
|
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@netcdf_elmt.findAttribute(name)
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+
end
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+
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+
end
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67
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+
|
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#------------------------------------------------------------------------------------
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# Find the index of the named Dimension in this Variable.
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#------------------------------------------------------------------------------------
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71
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+
|
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def find_dimension_index(name)
|
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@netcdf_elmt.findDimensionIndex(name)
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+
end
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75
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+
|
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#------------------------------------------------------------------------------------
|
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# Returns the set of attributes for this variable.
|
78
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#------------------------------------------------------------------------------------
|
79
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+
|
80
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+
def find_attributes
|
81
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+
|
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attributes = @netcdf_elmt.getAttributes()
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atts = Array.new
|
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attributes.each do |att|
|
85
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+
atts << NetCDF::Attribute.new(att)
|
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+
end
|
87
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+
atts
|
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+
|
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|
+
end
|
90
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+
|
91
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+
#------------------------------------------------------------------------------------
|
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|
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# Gets the variable data_type
|
93
|
+
#------------------------------------------------------------------------------------
|
94
|
+
|
95
|
+
def get_data_type
|
96
|
+
@netcdf_elmt.getDataType().toString()
|
97
|
+
end
|
98
|
+
|
99
|
+
#------------------------------------------------------------------------------------
|
100
|
+
# Get the description of the Variable.
|
101
|
+
#------------------------------------------------------------------------------------
|
102
|
+
|
103
|
+
def get_description
|
104
|
+
@netcdf_elmt.getDescription()
|
105
|
+
end
|
106
|
+
|
107
|
+
#------------------------------------------------------------------------------------
|
108
|
+
# Get the ith dimension.
|
109
|
+
#------------------------------------------------------------------------------------
|
110
|
+
|
111
|
+
def get_dimension(index)
|
112
|
+
@netcdf_elmt.getDimension(index)
|
113
|
+
end
|
114
|
+
|
115
|
+
#------------------------------------------------------------------------------------
|
116
|
+
# Get the list of dimensions used by this variable.
|
117
|
+
#------------------------------------------------------------------------------------
|
118
|
+
|
119
|
+
def find_dimensions
|
120
|
+
|
121
|
+
dimensions = @netcdf_elmt.getDimensions()
|
122
|
+
dims = Array.new
|
123
|
+
dimensions.each do |dim|
|
124
|
+
dims << NetCDF::Dimension.new(dim)
|
125
|
+
end
|
126
|
+
dims
|
127
|
+
|
128
|
+
end
|
129
|
+
|
130
|
+
#------------------------------------------------------------------------------------
|
131
|
+
# Get the list of Dimension names, space delineated.
|
132
|
+
#------------------------------------------------------------------------------------
|
133
|
+
|
134
|
+
def get_dimensions_string
|
135
|
+
@netcdf_elmt.getDimensionsString()
|
136
|
+
end
|
137
|
+
|
138
|
+
#------------------------------------------------------------------------------------
|
139
|
+
# Get the number of bytes for one element of this Variable.
|
140
|
+
#------------------------------------------------------------------------------------
|
141
|
+
|
142
|
+
def get_element_size
|
143
|
+
@netcdf_elmt.getElementSize()
|
144
|
+
end
|
145
|
+
|
146
|
+
#------------------------------------------------------------------------------------
|
147
|
+
# Get the display name plus the dimensions, eg 'float name(dim1, dim2)'
|
148
|
+
#------------------------------------------------------------------------------------
|
149
|
+
|
150
|
+
def get_name_and_dimensions
|
151
|
+
@netcdf_elmt.getNameAndDimensions()
|
152
|
+
end
|
153
|
+
|
154
|
+
#------------------------------------------------------------------------------------
|
155
|
+
# Get the number of dimensions of the Variable.
|
156
|
+
#------------------------------------------------------------------------------------
|
157
|
+
|
158
|
+
def get_rank
|
159
|
+
@netcdf_elmt.getRank()
|
160
|
+
end
|
161
|
+
|
162
|
+
alias :rank :get_rank
|
163
|
+
|
164
|
+
#------------------------------------------------------------------------------------
|
165
|
+
# Get the shape: length of Variable in each dimension.
|
166
|
+
#------------------------------------------------------------------------------------
|
167
|
+
|
168
|
+
def get_shape(index = nil)
|
169
|
+
if (index)
|
170
|
+
@netcdf_elmt.getShape(index)
|
171
|
+
else
|
172
|
+
@netcdf_elmt.getShape().to_a
|
173
|
+
end
|
174
|
+
end
|
175
|
+
|
176
|
+
alias :shape :get_shape
|
177
|
+
|
178
|
+
#------------------------------------------------------------------------------------
|
179
|
+
# Get the total number of elements in the Variable.
|
180
|
+
#------------------------------------------------------------------------------------
|
181
|
+
|
182
|
+
def get_size
|
183
|
+
@netcdf_elmt.getSize()
|
184
|
+
end
|
185
|
+
|
186
|
+
alias :size :get_size
|
187
|
+
|
188
|
+
#------------------------------------------------------------------------------------
|
189
|
+
# Get the Unit String for the Variable.
|
190
|
+
#------------------------------------------------------------------------------------
|
191
|
+
|
192
|
+
def get_units_string
|
193
|
+
@netcdf_elmt.getUnitsString()
|
194
|
+
end
|
195
|
+
|
196
|
+
#------------------------------------------------------------------------------------
|
197
|
+
# Has data been read and cached.
|
198
|
+
#------------------------------------------------------------------------------------
|
199
|
+
|
200
|
+
def cached_data?
|
201
|
+
@netcdf_elmt.hasCachedData()
|
202
|
+
end
|
203
|
+
|
204
|
+
#------------------------------------------------------------------------------------
|
205
|
+
# Invalidate the data cache
|
206
|
+
#------------------------------------------------------------------------------------
|
207
|
+
|
208
|
+
def invalidate_cache
|
209
|
+
@netcdf_elmt.invalidateCache()
|
210
|
+
end
|
211
|
+
|
212
|
+
#------------------------------------------------------------------------------------
|
213
|
+
# Will this Variable be cached when read.
|
214
|
+
#------------------------------------------------------------------------------------
|
215
|
+
|
216
|
+
def caching?
|
217
|
+
@netcdf_elmt.isCaching()
|
218
|
+
end
|
219
|
+
|
220
|
+
#------------------------------------------------------------------------------------
|
221
|
+
# Calculate if this is a classic coordinate variable: has same name as its first
|
222
|
+
# dimension.
|
223
|
+
#------------------------------------------------------------------------------------
|
224
|
+
|
225
|
+
def coordinate_variable?
|
226
|
+
@netcdf_elmt.isCoordinateVariable()
|
227
|
+
end
|
228
|
+
|
229
|
+
#------------------------------------------------------------------------------------
|
230
|
+
# Is this Variable immutable
|
231
|
+
#------------------------------------------------------------------------------------
|
232
|
+
|
233
|
+
def immutable?
|
234
|
+
@netcdf_elmt.isImmutable()
|
235
|
+
end
|
236
|
+
|
237
|
+
#------------------------------------------------------------------------------------
|
238
|
+
# Is this variable metadata?.
|
239
|
+
#------------------------------------------------------------------------------------
|
240
|
+
|
241
|
+
def metadata?
|
242
|
+
@netcdf_elmt.isMetadata()
|
243
|
+
end
|
244
|
+
|
245
|
+
#------------------------------------------------------------------------------------
|
246
|
+
# Whether this is a scalar Variable (rank == 0).
|
247
|
+
#------------------------------------------------------------------------------------
|
248
|
+
|
249
|
+
def scalar?
|
250
|
+
@netcdf_elmt.isScalar()
|
251
|
+
end
|
252
|
+
|
253
|
+
#------------------------------------------------------------------------------------
|
254
|
+
# Can this variable's size grow?.
|
255
|
+
#------------------------------------------------------------------------------------
|
256
|
+
|
257
|
+
def unlimited?
|
258
|
+
@netcdf_elmt.isUnlimited()
|
259
|
+
end
|
260
|
+
|
261
|
+
#------------------------------------------------------------------------------------
|
262
|
+
# Is this Variable unsigned?.
|
263
|
+
#------------------------------------------------------------------------------------
|
264
|
+
|
265
|
+
def unsigned?
|
266
|
+
@netcdf_elmt.isUnsigned()
|
267
|
+
end
|
268
|
+
|
269
|
+
#------------------------------------------------------------------------------------
|
270
|
+
# Does this variable have a variable length dimension? If so, it has as one of its
|
271
|
+
# mensions Dimension.VLEN.
|
272
|
+
#------------------------------------------------------------------------------------
|
273
|
+
|
274
|
+
def variable_length?
|
275
|
+
@netcdf_elmt.isVariableLength()
|
276
|
+
end
|
277
|
+
|
278
|
+
#------------------------------------------------------------------------------------
|
279
|
+
# Reads data for this Variable and sets the variable @data to the memory resident
|
280
|
+
# array.
|
281
|
+
# <tt>:origin</tt> int array with the origin of data to be read
|
282
|
+
# <tt>:shape</tt> int array with the shape of the data to be read. If origin or
|
283
|
+
#------------------------------------------------------------------------------------
|
284
|
+
|
285
|
+
def read(*args)
|
286
|
+
|
287
|
+
opts = Map.options(args)
|
288
|
+
spec = opts.getopt(:spec)
|
289
|
+
origin = opts.getopt(:origin)
|
290
|
+
shape = opts.getopt(:shape)
|
291
|
+
|
292
|
+
if (origin || shape)
|
293
|
+
MDArray.build_from_nc_array(nil, @netcdf_elmt.read(origin.to_java(:int),
|
294
|
+
shape.to_java(:int)))
|
295
|
+
elsif (spec)
|
296
|
+
MDArray.build_from_nc_array(nil, @netcdf_elmt.read(spec))
|
297
|
+
else
|
298
|
+
MDArray.build_from_nc_array(nil, @netcdf_elmt.read())
|
299
|
+
end
|
300
|
+
|
301
|
+
end
|
302
|
+
|
303
|
+
#------------------------------------------------------------------------------------
|
304
|
+
#
|
305
|
+
#------------------------------------------------------------------------------------
|
306
|
+
|
307
|
+
def read_scalar(type = nil)
|
308
|
+
|
309
|
+
if (!type)
|
310
|
+
type = get_data_type
|
311
|
+
end
|
312
|
+
|
313
|
+
case type
|
314
|
+
when "double"
|
315
|
+
@netcdf_elmt.readScalarDouble()
|
316
|
+
when "float"
|
317
|
+
@netcdf_elmt.readScalarFloat()
|
318
|
+
when "long"
|
319
|
+
@netcdf_elmt.readScalarLong()
|
320
|
+
when "int"
|
321
|
+
@netcdf_elmt.readScalarInt()
|
322
|
+
when "short"
|
323
|
+
@netcdf_elmt.readScalarShort()
|
324
|
+
when "byte"
|
325
|
+
@netcdf_elmt.readScalarByte()
|
326
|
+
when "string"
|
327
|
+
@netcdf_elmt.readScalarString()
|
328
|
+
else
|
329
|
+
raise "Unknown type: #{type}"
|
330
|
+
end
|
331
|
+
|
332
|
+
end
|
333
|
+
|
334
|
+
#------------------------------------------------------------------------------------
|
335
|
+
# Set the data cache
|
336
|
+
#------------------------------------------------------------------------------------
|
337
|
+
|
338
|
+
def set_cached_data(array, metadata = nil)
|
339
|
+
@netcdf_elmt.setCachedData(array.nc_array, metadata)
|
340
|
+
end
|
341
|
+
|
342
|
+
#------------------------------------------------------------------------------------
|
343
|
+
#
|
344
|
+
#------------------------------------------------------------------------------------
|
345
|
+
|
346
|
+
def caching=(boolean)
|
347
|
+
@netcdf_elmt.setCaching(boolean)
|
348
|
+
end
|
349
|
+
|
350
|
+
#------------------------------------------------------------------------------------
|
351
|
+
# Create a new Variable that is a logical subsection of this Variable. The
|
352
|
+
# subsection can be specified passing the following arguments:
|
353
|
+
# shape
|
354
|
+
# origin
|
355
|
+
# size
|
356
|
+
# stride
|
357
|
+
# range
|
358
|
+
# section
|
359
|
+
# spec
|
360
|
+
#------------------------------------------------------------------------------------
|
361
|
+
|
362
|
+
def section(*args)
|
363
|
+
|
364
|
+
sec = MDArray::Section.build(*args)
|
365
|
+
NetCDF::Variable.new(@netcdf_elmt.section(sec.netcdf_elmt))
|
366
|
+
|
367
|
+
end
|
368
|
+
|
369
|
+
#------------------------------------------------------------------------------------
|
370
|
+
#
|
371
|
+
#------------------------------------------------------------------------------------
|
372
|
+
|
373
|
+
def set_cached_data(array, metadata)
|
374
|
+
@netcdf_elmt.setCachedData(array.nc_array, metadata)
|
375
|
+
end
|
376
|
+
|
377
|
+
#------------------------------------------------------------------------------------
|
378
|
+
# Prints the content of the current data slice
|
379
|
+
#------------------------------------------------------------------------------------
|
380
|
+
|
381
|
+
def to_string
|
382
|
+
@netcdf_elmt.toString()
|
383
|
+
end
|
384
|
+
|
385
|
+
alias :to_s :to_string
|
386
|
+
|
387
|
+
#------------------------------------------------------------------------------------
|
388
|
+
#
|
389
|
+
#------------------------------------------------------------------------------------
|
390
|
+
|
391
|
+
def to_string_debug
|
392
|
+
@netcdf_elmt.toSringDebug()
|
393
|
+
end
|
394
|
+
|
395
|
+
#------------------------------------------------------------------------------------
|
396
|
+
# Prints the content of the current data slice
|
397
|
+
#------------------------------------------------------------------------------------
|
398
|
+
|
399
|
+
def print
|
400
|
+
p to_string
|
401
|
+
end
|
402
|
+
|
403
|
+
end # Variable
|
404
|
+
|
405
|
+
#=======================================================================================
|
406
|
+
#
|
407
|
+
#=======================================================================================
|
408
|
+
|
409
|
+
class VariableWriter < Variable
|
410
|
+
|
411
|
+
#------------------------------------------------------------------------------------
|
412
|
+
# Remove an Attribute : uses the attribute hashCode to find it.
|
413
|
+
#------------------------------------------------------------------------------------
|
414
|
+
|
415
|
+
def remove_attribute(attribute, ignore_case = false)
|
416
|
+
|
417
|
+
if (attribute.is_a? String)
|
418
|
+
if (ignore_case)
|
419
|
+
@netcdf_elmt.removeAttributeIgnoreCase(attribute)
|
420
|
+
else
|
421
|
+
@netcdf_elmt.removeAttribute(attribute)
|
422
|
+
end
|
423
|
+
elsif (attribute.is_a? NetCDF::Attribute)
|
424
|
+
@netcdf_elmt.remove(attribute.netcdf_elmt)
|
425
|
+
else
|
426
|
+
raise "Given parameter is not an attribute: #{attribute}"
|
427
|
+
end
|
428
|
+
|
429
|
+
end
|
430
|
+
|
431
|
+
#------------------------------------------------------------------------------------
|
432
|
+
# Reset the dimension array.
|
433
|
+
#------------------------------------------------------------------------------------
|
434
|
+
|
435
|
+
def reset_dimensions
|
436
|
+
@netcdf_elmt.resetDimensions()
|
437
|
+
end
|
438
|
+
|
439
|
+
#------------------------------------------------------------------------------------
|
440
|
+
# Use when dimensions have changed, to recalculate the shape.
|
441
|
+
#------------------------------------------------------------------------------------
|
442
|
+
|
443
|
+
def reset_shape
|
444
|
+
@netcdf_elmt.resetShape()
|
445
|
+
end
|
446
|
+
|
447
|
+
#------------------------------------------------------------------------------------
|
448
|
+
#
|
449
|
+
#------------------------------------------------------------------------------------
|
450
|
+
#------------------------------------------------------------------------------------
|
451
|
+
#
|
452
|
+
#------------------------------------------------------------------------------------
|
453
|
+
#------------------------------------------------------------------------------------
|
454
|
+
#
|
455
|
+
#------------------------------------------------------------------------------------
|
456
|
+
#------------------------------------------------------------------------------------
|
457
|
+
#
|
458
|
+
#------------------------------------------------------------------------------------
|
459
|
+
#------------------------------------------------------------------------------------
|
460
|
+
#
|
461
|
+
#------------------------------------------------------------------------------------
|
462
|
+
#------------------------------------------------------------------------------------
|
463
|
+
#
|
464
|
+
#------------------------------------------------------------------------------------
|
465
|
+
|
466
|
+
end # VariableWriter
|
467
|
+
|
468
|
+
|
469
|
+
#=======================================================================================
|
470
|
+
#
|
471
|
+
#=======================================================================================
|
472
|
+
|
473
|
+
class TimeVariable < Variable
|
474
|
+
include_package "ucar.nc2.time"
|
475
|
+
|
476
|
+
attr_reader :calendar
|
477
|
+
attr_reader :units
|
478
|
+
attr_reader :base_date
|
479
|
+
|
480
|
+
#------------------------------------------------------------------------------------
|
481
|
+
# Initializes the Variable by giving a java netcdf_variable
|
482
|
+
#------------------------------------------------------------------------------------
|
483
|
+
|
484
|
+
def initialize(netcdf_variable)
|
485
|
+
|
486
|
+
super(netcdf_variable)
|
487
|
+
@calendar = @netcdf_elmt.findAttribute("calendar").getStringValue()
|
488
|
+
@units = @netcdf_elmt.findAttribute("units").getStringValue()
|
489
|
+
date_unit = CalendarDateUnit.of(@calendar, @units)
|
490
|
+
@base_date = date_unit.getBaseCalendarDate()
|
491
|
+
|
492
|
+
end
|
493
|
+
|
494
|
+
#------------------------------------------------------------------------------------
|
495
|
+
# Returns the number of milliseconds elapsed from the base_date to the given date.
|
496
|
+
# The given date should be in iso_format.
|
497
|
+
#------------------------------------------------------------------------------------
|
498
|
+
|
499
|
+
def to_msec(iso_date)
|
500
|
+
|
501
|
+
date = CalendarDate.parseISOformat(@calendar, iso_date)
|
502
|
+
date.getDifferenceInMsecs(@base_date)
|
503
|
+
|
504
|
+
end
|
505
|
+
|
506
|
+
#------------------------------------------------------------------------------------
|
507
|
+
#
|
508
|
+
#------------------------------------------------------------------------------------
|
509
|
+
|
510
|
+
def next
|
511
|
+
|
512
|
+
millisec_date = super
|
513
|
+
@base_date.add(millisec_date, CalendarPeriod.fromUnitString("Millisec")).toString()
|
514
|
+
|
515
|
+
end
|
516
|
+
|
517
|
+
end # TimeVariable
|
518
|
+
|
519
|
+
|
520
|
+
end # NetCDFInterface
|