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ncvariable.m
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ncvariable.m
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% NCVARIABLE Provide advanced access to variables and their related
% dimensions.
%
% NCVARIABLE is used to retrieve data for a given variable as well as the
% variables associated coordinate dimensions. Normally, you would retrive
% it using CFDATASET.VARIABLE
%
% Example of use:
% ds = cfdataset('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/deployments/m1/200810/OS_M1_20081008_TS.nc');
% v = ds.variable('TEMP');
%
% % Look at properties
% v.name
% v.axes
%
% % Data access example #1
% temp = v.data([1 1 1 1], [100 5 1 1]);
%
% % Data access example #2
% t_end = v.size;
% t_start = t_end ./ t_end;
% t_stride = t_start;
% t_stride(1)=10;
% t = v.data(t_start, t_end, t_stride);
%
%
% See also CFDATASET, SIZE, DATA
% NCTOOLBOX (https://github.com/nctoolbox/nctoolbox)
classdef ncvariable < handle
properties (SetAccess = private)
dataset % ncdataset instance
end
properties (Dependent = true)
name % The string variable name that this object represents
axes2 % ????
axes % the coordinate variables associated with the object
attributes % The attributes associated with the object.
end
properties (SetAccess = private, GetAccess = protected)
variable % ucar.nc2.Variable instance. Represents the data
axesVariables % ucar.nc2.Variable instance. Represents the data.
end
methods
%%
function obj = ncvariable(src, variableName, axesVariableNames)
% NCVARIABLE.NCVARIABLE Constructor.
%
% Use as:
% v = ncvariable(src, variableName)
% v = ncvariable(src, variableName, axesVariableNames)
%
if ischar(src)
obj.dataset = ncdataset(src); % src is a string URL/File
elseif isa(src, 'ncdataset')
obj.dataset = src; % src is a ncdataset
else
ex = MException('NCTOOLBOX:ncvariable', 'Invalid dataset was specified');
ex.throw;
end
obj.variable = obj.dataset.netcdf.findVariable(variableName);
if nargin == 3
obj.axesVariables = cell(size(axesVariableNames));
for i = 1:length(axesVariableNames)
obj.axesVariables{i} = obj.dataset.netcdf.findVariable(axesVariableNames{i});
end
else
obj.axesVariables = {};
end
end
function a = get.attributes(obj)
% NCVARIABLE.ATTRIBUTES returns the attributes for the variable.
a = obj.dataset.attributes(obj.name);
end
%%
function a = get.axes(obj)
% NCVARIABLE.AXES Returns the names of the coordinate axes
a = cell(size(obj.axesVariables));
for i = 1:length(obj.axesVariables)
name = char(obj.axesVariables{i}.getName());
a{i} = name;
end
end
%%
function v = get.name(obj)
% NCVARIABLE.NAME Provides dynamic access to the underlying
% netcdf datasets variable name
%
% Example:
% vname=v.name % returns the name of the variable
%
v = char(obj.variable.getName());
end
%%
function n = size(obj)
% NCVARIABLE.SIZE returns the size of the variable, including
% its singleton dimensions
n = obj.dataset.size(obj.name);
end
function val = attribute(obj, key)
% NCVARIABLE.ATTRIBUTE returns the value a global attribute specified by its key or the
% variable attribute specified by key and variable.
%
% Use as:
% a = ncvariable.attribute('title')
% a = ncvariable.attribute(key)
%
%
% Inputs:
% key = The name of the attribute field like 'title' or 'units'...
%
% Return:
% The value associated with the attribute field corresponding to key.
val = obj.dataset.attribute(obj.name, key);
end
%%
function d = data(obj, first, last, stride)
% NCVARIABLE.DATA Retrieve all or a subset of the data for the
% variable. The data is returned as a structure containing a
% variable for the data as well as for each dimension of the
% data.
%
% Usage:
% d = ncvariable.data
% d = ncvariable.data(first)
% d = ncvariable.data(first, last)
% d = ncvariable.data(first, last, stride)
%
% If no arguments are provided all the data is returned.
%
% Arguments:
% first = The first point you want to retrieve (first point idx = 1)
% last = The last point you want to retrive (default is the end of
% the data array)
% stride = The stride spacing (default is 1)
% NOTE! first, last, and stride must be matrices the same size as the
% matrix returned by NCDATASET.SIZE or SIZE
%
% Returns:
% The data is returned as a variable containing the actual data for the netcdf variable
%
% Example:
%
% ds = cfdataset('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/deployments/m1/200810/OS_M1_20081008_TS.nc');
% v = ds.variable('TEMP');
% t = v.data([1 1 1 1], [10 2 1 1]);
%
if (nargin == 1)
if isempty(obj.size) % check if variable obj is dimensionless (not cf compliant.....)
try
d = alldata(obj,1);
catch me
ex = MException('NCTOOLBOX:ncvariable:data', ['Failed to open ' url]);
ex = ex.addCause(me);
ex.throw;
end
else
d = alldata(obj, 1);
end
else
s = obj.size;
% Fill in missing arguments
% default stride is 1
if (nargin < 4)
stride = ones(1, length(s));
end
% Default last is the end
if (nargin < 3)
last = s;
end
d = somedata(obj, 1, first, last, stride);
end
end
function g = grid(obj, first, last, stride)
% NCVARIABLE.GRID Retrieve all or a subset of the coordinate
% data for the variable. The data is returned as a structure
% containing a variable for each dimension of the data.
%
% Usage:
% d = ncvariable.grid
% d = ncvariable.grid(first)
% d = ncvariable.grid(first, last)
% d = ncvariable.grid(first, last, stride)
%
% If no arguments are provided all the data is returned.
%
% Arguments:
% first = The first point you want to retrieve (first point idx = 1)
% last = The last point you want to retrive (default is the end of
% the data array)
% stride = The stride spacing (default is 1)
% NOTE! first, last, and stride must be matrices the same size as the
% matrix returned by NCDATASET.SIZE or SIZE
%
% Returns:
% The data is returned as a structure containing the actual data for the variable
% of interest as well as each coordinate variable
%
% Example:
%
% ds = cfdataset('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/deployments/m1/200810/OS_M1_20081008_TS.nc');
% v = ds.variable('TEMP');
% v.size % 9043x11x1x1
% g = v.grid
% t = v.data([1 1 1 1], [10 2 1 1]); % is not like
%
if (nargin == 1)
g = alldata(obj, 0);
else % all this stuff needs logic work to function as expected
s = obj.size;
% Fill in missing arguments
% default stride is 1
if (nargin < 4)
stride = ones(1, length(s));
end
% Default last is the end
if (nargin < 3)
last = s;
end
g = somedata(obj, 0, first, last, stride);
end
end
%%
function e = end(obj, k, n)
% NCVARIABLE.END the last index in an indexing
% expression.
% v.end(2) % returns the last index of the second dimension.
% e.g.: elevation.data(end-3:end,1,1)
n = obj.dataset.size(obj.name);
e = n(k);
end % Added to deal with end indexing functionality,
% otherwise the indexing arugment is ignored.
%%
function sref = subsref(obj,s)
% disp(s(2).subs{3})
% SUBSREF parses an object name for .name or ()
switch s(1).type
% Use the built-in subsref for dot notation
case '.'
switch s(1).subs
case 'data'
%% .data
nums = size(obj);
if ~isempty(nums)
switch length(s)
case 1
sref = obj;
case 2
idx = s(2).subs;
nidx = length(idx);
% Fill in missing arguments
% default stride is 1
if (nidx < 3)
stride = ones(1, length(nums));
else
stride = idx{3};
end
% Default last is the end
if (nidx < 2)
last = nums;
else
last = idx{2};
end
first = idx{1};
sref = obj.somedata(1, first, last, stride);
end
else
sref = obj.data;
warning('NCTOOLBOX:ncvariable:subsref', ...
['Variable "' obj.name '" has no netcdf dimension associated with it. Errors may result from non CF compliant files.'])
end
case 'grid'
%% .grid
nums = size(obj);
if ~isempty(nums)
switch length(s)
case 1
sref = obj;
case 2
idx = s(2).subs;
nidx = length(idx);
% Fill in missing arguments
% default stride is 1
if (nidx < 3)
stride = ones(1, length(nums));
else
stride = idx{3};
end
% Default last is the end
if (nidx < 2)
last = nums;
else
last = idx{2};
end
first = idx{1};
sref = obj.grid(first, last, stride);
end
else
warning('NCTOOLBOX:ncvariable:subsref', ...
['Variable "' name '" has no netcdf dimension associated with it. Errors may result from non CF compliant files.'])
end
otherwise
sref = builtin('subsref',obj,s);
end
case '()'
if length(s)<2
% Note that obj.Data is passed to subsref
sref = builtin('subsref',obj.data,s);
else
sref = builtin('subsref',obj,s);
end
% No support for indexing using '{}'
case '{}'
error('NCTOOLBOX:ncvariable:subsref', ...
'Not a supported subscripted reference, "{}" are not permitted to call variable object methods');
end
end
end
methods (Access = protected)
%%
function data = alldata(obj, withData)
% NCVARIABLE.ALLDATA -- extract the data or the axes
% v.alldata(1) % returns the data
% v.alldata() % returns a structure with the axesVariables
% % and their data
if withData == 1
name = char(obj.variable.getName());
data = obj.dataset.data(name);
end
if withData == 0
for i = 1:length(obj.axesVariables)
name = char(obj.axesVariables{i}.getName());
data.(name) = obj.dataset.data(name);
end
end
end
%%
function data = somedata(obj, withData, first, last, stride)
% NCGEOVARIABLE.SOMEDATA -- extract a hyperslab of data
% SOMEDATA can extract a subset of data from an NCVARIABLE or
% the subset of the corresponding axis variables.
%
% Example:
% first=ones(length(v.size));
% last=v.size;
% stride=first;
% vd = v.somedata(1,first,last,stride); % returns data
% vg = v.somedata(0,first,last,stride); % returns struct w/grid
%
% See also NCVARIABLE, NCVARIABLE.ALLDATA,
% NCVARIABLE.DATA, NCVARIABLE.GRID
s = obj.dataset.size(obj.name);
% Fill in missing arguments
% default stride is 1
if (nargin < 5)
stride = ones(1, length(s));
end
% Default last is the end
if (nargin < 4)
last = s;
end
% ---- Step 2: Add the data for the variable of interest
if withData == 1
name = char(obj.variable.getName());
data = obj.dataset.data(name, first, last, stride);
end
% ---- Step 3: Add the data for each axes variable
if withData == 0
for i = 1:length(obj.axesVariables)
name = char(obj.axesVariables{i}.getName());
% type = char(obj.axesVariables{i}.getAxisType());
% ---- Step 4: figure out how to subset the data properly
vs = obj.dataset.size(name);
if numel(vs) > 0 % Added to solve work around somedata calls that involve variables with
% no netcdf dim. (This will be frequent in some OOI files.)
if (length(vs) == length(s))
%% case: sizes are the same
if isequal(vs, s)
vFirst = first;
vLast = last;
vStride = stride;
else
me = MException('NCTOOLBOX:ncvariable:somedata', ...
['The data size of the coordinate variable,' ...
name ', does not fit the size of ' obj.name]);
me.throw;
end
elseif length(vs) == 1
%% case: singleton dimension. Find side of data with
% the same length
% TODO: the following line will give bogus results if
% the data has 2 dimensions of the same length
dim = find(s == vs, 1);
if ~isempty(dim)
vFirst = first(dim);
vLast = last(dim);
vStride = stride(dim);
else
me = MException('NCTOOLBOX:ncvariable:somedata', ...
['The data size of the coordinate variable,' ...
name ', does not fit the size of ' obj.name]);
me.throw;
end
else
%% case: variable is coordiantes. Look for size
% TODO this is a lame implementation.
dim = find(s == vs(1), 1);
if ~isempty(dim)
for j = 2:length(vs)
if vs(j) ~= s(dim + j - 1)
me = MException('NCTOOLBOX:ncvariable:somedata', ...
['The data size of the coordinate variable,' ...
name ', does not fit the size of ' obj.name]);
me.throw;
end
end
k = dim:dim + length(vs) - 1;
vFirst = first(k);
vLast = last(k);
vStride = stride(k);
end
end
data.(name) = obj.dataset.data(name, vFirst, vLast, vStride);
else
data.(name) = obj.dataset.data(name);
end
end
end
end
end
end