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[Octave-cvsupdate] SF.net SVN: octave:[10665] trunk/octave-forge/extra/ncArray/inst
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From: <aba...@us...> - 2012-06-22 15:06:04
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Revision: 10665
http://octave.svn.sourceforge.net/octave/?rev=10665&view=rev
Author: abarth93
Date: 2012-06-22 15:05:53 +0000 (Fri, 22 Jun 2012)
Log Message:
-----------
initial import of ncArray
Added Paths:
-----------
trunk/octave-forge/extra/ncArray/inst/@BaseArray/
trunk/octave-forge/extra/ncArray/inst/@BaseArray/BaseArray.m
trunk/octave-forge/extra/ncArray/inst/@BaseArray/end.m
trunk/octave-forge/extra/ncArray/inst/@BaseArray/full.m
trunk/octave-forge/extra/ncArray/inst/@BaseArray/size.m
trunk/octave-forge/extra/ncArray/inst/@CatArray/
trunk/octave-forge/extra/ncArray/inst/@CatArray/CatArray.m
trunk/octave-forge/extra/ncArray/inst/@CatArray/display.m
trunk/octave-forge/extra/ncArray/inst/@CatArray/idx_global_local_.m
trunk/octave-forge/extra/ncArray/inst/@CatArray/subsasgn.m
trunk/octave-forge/extra/ncArray/inst/@CatArray/subsref.m
trunk/octave-forge/extra/ncArray/inst/@ncArray/
trunk/octave-forge/extra/ncArray/inst/@ncArray/display.m
trunk/octave-forge/extra/ncArray/inst/@ncArray/ncArray.m
trunk/octave-forge/extra/ncArray/inst/@ncArray/ncsub.m
trunk/octave-forge/extra/ncArray/inst/@ncArray/subsasgn.m
trunk/octave-forge/extra/ncArray/inst/@ncArray/subsref.m
trunk/octave-forge/extra/ncArray/inst/@ncData/
trunk/octave-forge/extra/ncArray/inst/@ncData/coord.m
trunk/octave-forge/extra/ncArray/inst/@ncData/ncData.m
trunk/octave-forge/extra/ncArray/inst/@ncData/subsasgn.m
trunk/octave-forge/extra/ncArray/inst/@ncData/subsref.m
Added: trunk/octave-forge/extra/ncArray/inst/@BaseArray/BaseArray.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@BaseArray/BaseArray.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@BaseArray/BaseArray.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,7 @@
+% sz size of the array (with at least two elements)
+
+function retval = BaseArray(sz)
+
+self.sz = sz;
+
+retval = class(self,'BaseArray');
\ No newline at end of file
Added: trunk/octave-forge/extra/ncArray/inst/@BaseArray/end.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@BaseArray/end.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@BaseArray/end.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,3 @@
+function e = end(self,k,n)
+
+e = size(self,k);
Added: trunk/octave-forge/extra/ncArray/inst/@BaseArray/full.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@BaseArray/full.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@BaseArray/full.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,10 @@
+function F = full(self);
+
+n = length(self.sz);
+idx.type = '()';
+
+for i=1:n
+ idx.subs{i} = ':';
+end
+
+F = subsref(self,idx);
\ No newline at end of file
Added: trunk/octave-forge/extra/ncArray/inst/@BaseArray/size.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@BaseArray/size.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@BaseArray/size.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,8 @@
+function sz = size(self,dim)
+
+sz = self.sz;
+
+if nargin == 2
+ sz = sz(dim);
+end
+
Added: trunk/octave-forge/extra/ncArray/inst/@CatArray/CatArray.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@CatArray/CatArray.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@CatArray/CatArray.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,70 @@
+% C = CatArray(dim,{array1,array2,...})
+%
+% Create a concatenated array from a cell-list of arrays. Individual
+% elements can be accessed by subscribs, e.g.:
+% C(2,3)
+
+
+function retval = CatArray(dim,arrays)
+
+self.dim = dim;
+self.arrays = arrays;
+self.na = length(arrays);
+
+% number of dimensions
+self.nd = length(size(arrays{1}));
+if dim > self.nd
+ self.nd = dim;
+end
+
+self.size = ones(self.na,self.nd);
+self.start = ones(self.na,self.nd);
+
+% get size of all arrays
+for i=1:self.na
+ tmp = size(arrays{i});
+ self.size(i,1:length(tmp)) = tmp;
+end
+
+% check if dimensions are consistent
+ncd = 1:self.nd ~= dim;
+for i=2:self.na
+ if ~all(self.size(i,ncd) == self.size(1,ncd))
+ error('Array number %d has inconsistent dimension',i);
+ end
+end
+
+% start index of each sub-array
+
+for i=2:self.na
+ self.start(i,:) = self.start(i-1,:);
+ self.start(i,dim) = self.start(i,dim) + self.size(i-1,dim);
+end
+
+self.end = self.start + self.size - 1;
+
+self.sz = self.size(1,:);
+self.sz(dim) = sum(self.size(:,dim));
+self.overlap = false;
+self.bounds = [0; cumsum(prod(self.size,2))];
+
+retval = class(self,'CatArray',BaseArray(self.sz));
+
+
+% Copyright (C) 2012 Alexander Barth <bar...@gm...>
+%
+% This program is free software; you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation; either version 2 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program; If not, see <http://www.gnu.org/licenses/>.
+
+
+
Added: trunk/octave-forge/extra/ncArray/inst/@CatArray/display.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@CatArray/display.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@CatArray/display.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,6 @@
+function display(self)
+
+for i=1:self.na
+ display(self.arrays{i})
+end
+
\ No newline at end of file
Added: trunk/octave-forge/extra/ncArray/inst/@CatArray/idx_global_local_.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@CatArray/idx_global_local_.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@CatArray/idx_global_local_.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,58 @@
+% private method
+
+function [idx_global,idx_local,sz] = idx_global_local_(self,idx)
+
+assert(strcmp(idx.type,'()'))
+
+n = length(size(self));
+
+% number of indices must be equal to dimension
+assert(length(idx.subs) == n)
+
+lb = ones(1,n); % lower bound
+ub = ones(1,n); % upper bound
+sz = ones(1,n); % size
+
+% transform all colons to index range
+for i=1:n
+ if strcmp(idx.subs{i},':')
+ idx.subs{i} = 1:self.sz(i);
+ end
+
+ lb(i) = min(idx.subs{i});
+ ub(i) = max(idx.subs{i});
+ sz(i) = length(idx.subs{i});
+end
+
+%sz = ub-lb+1;
+
+idx_local = cell(1,self.na);
+idx_global = cell(1,self.na);
+
+% loop over all arrays
+for j=1:self.na
+ idx_local{j} = idx;
+ idx_global{j} = idx;
+
+ % loop over all dimensions
+ for i=1:n
+ % rebase subscribt at self.start(j,i)
+ tmp = idx.subs{i} - self.start(j,i) + 1;
+
+ % only indeces within bounds of the j-th array
+ sel = 1 <= tmp & tmp <= self.size(j,i);
+
+ % index for getting the data from the local j-th array
+ idx_local{j}.subs{i} = tmp(sel);
+
+ % index for setting the data in the global B array
+ %idx_global{j}.subs{i} = idx.subs{i}(sel) - lb(i)+1;
+
+ if sum(sel) == 0
+ idx_global{j}.subs{i} = [];
+ else
+ idx_global{j}.subs{i} = (1:sum(sel)) + find(sel,1,'first') - 1;
+ end
+ end
+
+end
Added: trunk/octave-forge/extra/ncArray/inst/@CatArray/subsasgn.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@CatArray/subsasgn.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@CatArray/subsasgn.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,14 @@
+function self = subsasgn(self,idx,x)
+
+[idx_global,idx_local,sz] = idx_global_local_(self,idx);
+
+
+
+
+for j=1:self.na
+ % get subset from global array x
+ subset = subsref(x,idx_global{j});
+
+ % set subset in j-th array
+ subsasgn(self.arrays{j},idx_local{j},subset);
+end
\ No newline at end of file
Added: trunk/octave-forge/extra/ncArray/inst/@CatArray/subsref.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@CatArray/subsref.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@CatArray/subsref.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,79 @@
+function B = subsref(self,idx)
+
+% handle case with a single subscript
+% for example CA(234)
+
+if strcmp(idx.type,'()') && length(idx.subs) == 1
+ % indices of elements in B
+ ind = idx.subs{1};
+
+ % output array
+ B = zeros(size(ind));
+ B(:) = NaN;
+
+ if self.overlap
+ % transform index to subscript
+ subs = cell(1,self.nd);
+ [subs{:}] = ind2sub(size(self),ind);
+
+ % make a nice array length(ind) by self.nd
+ subs = cell2mat(subs);
+
+
+ % get every element
+ idxe.type = '()';
+ idxe.subs = cell(1,self.nd);
+
+ for i=1:length(ind)
+ idxe.subs = mat2cell(subs(i,:),1,ones(1,self.nd));
+ %B(i) = subsref_canonical(self,idxe);
+
+ [idx_global,idx_local,sz] = idx_global_local_(self,idxe);
+ tmp = zeros(sz);
+ tmp(:) = NaN;
+
+
+ for j=1:self.na
+ % get subset from j-th array
+ subset = subsref(self.arrays{j},idx_local{j});
+
+ % set subset in global array B
+ tmp = subsasgn(tmp,idx_global{j},subset);
+ end
+ B(i) = tmp;
+
+ end
+ else
+ % assume all arrays does not overlap
+
+ for j=1:self.na
+ sel = self.bounds(j) < ind & ind <= self.bounds(j+1);
+ B(sel) = self.arrays{j}(ind(sel) - self.bounds(j));
+ end
+
+ end
+
+else
+ B = subsref_canonical(self,idx);
+end
+
+end
+
+% for this function we assume that idx.subs has the same dimension than
+% the array
+
+function B = subsref_canonical(self,idx)
+[idx_global,idx_local,sz] = idx_global_local_(self,idx);
+
+B = zeros(sz);
+B(:) = NaN;
+
+for j=1:self.na
+ % get subset from j-th array
+ subset = subsref(self.arrays{j},idx_local{j});
+
+ % set subset in global array B
+ B = subsasgn(B,idx_global{j},subset);
+end
+
+end
\ No newline at end of file
Added: trunk/octave-forge/extra/ncArray/inst/@ncArray/display.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncArray/display.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncArray/display.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,4 @@
+function display(self)
+disp([self.varname ' from ' self.filename]);
+%self.vinfo
+%self.dims
Added: trunk/octave-forge/extra/ncArray/inst/@ncArray/ncArray.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncArray/ncArray.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncArray/ncArray.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,61 @@
+% V = ncArray(filename,varname)
+% V = ncArray(filename,varname,'property',value,...)
+% create a ncArray that can be accessed as a normal matlab array.
+%
+% For read access filename can be compressed if it has the extensions
+% ".gz" or ".bz2". It use the function cache_decompress to cache to
+% decompressed files.
+%
+% Data is loaded by ncread and saved by ncwrite. Values equal to _FillValue
+% are thus replaced by NaN and the scaling (add_offset and
+% scale_factor) is applied during loading and saving.
+%
+% Properties:
+% 'tooBigToLoad': if tooBigToLoad is set to true, then only the minimum
+% data will be loaded. However this can be quite slow.
+%
+% Example:
+%
+% Loading the variable (assuming V is 3 dimensional):
+%
+% x = V(1,1,1); % load element 1,1,1
+% x = V(:,:,:); % load the complete array
+% x = V(); x = full(V) % loads also the complete array
+%
+% Saving data in the netcdf file:
+% V(1,1,1) = x; % save x in element 1,1,1
+% V(:,:,:) = x;
+%
+% Attributes
+% units = V.units; % get attribute called "units"
+% V.units = 'degree C'; % set attributes;
+%
+% Note: use the '.()' notation if the attribute has a leading underscore
+% (due to a limitation in the matlab parser):
+%
+% V.('_someStrangeAttribute') = 123;
+%
+% see also cache_decompress
+
+function retval = ncArray(filename,varname,varargin)
+
+self.tooBigToLoad = false;
+prop = varargin;
+
+for i=1:2:length(prop)
+ if strcmp(prop{i},'tooBigToLoad ')
+ self.tooBigToLoad = prop{i+1};
+ end
+end
+
+self.filename = filename;
+self.varname = varname;
+
+self.vinfo = ncinfo(cached_decompress(filename),varname);
+self.sz = self.vinfo.Size;
+
+self.dims = self.vinfo.Dimensions;
+self.nd = length(self.dims);
+
+retval = class(self,'ncArray',BaseArray(self.sz));
+end
Added: trunk/octave-forge/extra/ncArray/inst/@ncArray/ncsub.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncArray/ncsub.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncArray/ncsub.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,61 @@
+function [start, count, stride] = ncsub(self,idx)
+
+assert(strcmp(idx.type,'()'))
+
+% number of dimension (including singleton dimensions)
+%n = length(size(self));
+n = self.nd;
+
+% number of subscripts
+ns = length(idx.subs);
+
+if ns == 0
+ % load all
+ start = ones(1,n);
+ count = self.sz;
+ stride = ones(1,n);
+else
+
+ start = ones(1,ns);
+ count = ones(1,ns);
+ stride = ones(1,ns);
+
+ % sz is the size padded by 1 if more indices are given than n
+ sz = ones(1,ns);
+ sz(1:length(self.sz)) = self.sz;
+
+ for i=1:ns
+ if isempty(idx.subs{i})
+ count(i) = 0;
+
+ elseif strcmp(idx.subs{i},':')
+ count(i) = sz(i);
+
+ else
+ tmp = idx.subs{i};
+
+ if length(tmp) == 1
+ start(i) = tmp;
+ else
+ test = tmp(1):tmp(2)-tmp(1):tmp(end);
+
+ if all(tmp == test)
+ start(i) = tmp(1);
+ stride(i) = tmp(2)-tmp(1);
+ count(i) = (tmp(end)-tmp(1))/stride(i) +1;
+ else
+ error('indeces');
+ end
+ end
+ end
+ end
+
+ assert(all(count(n+1:end) == 1 | count(n+1:end) == 0))
+ assert(all(start(n+1:end) == 1))
+
+ if ~any(count == 0)
+ count = count(1:n);
+ start = start(1:n);
+ stride = stride(1:n);
+ end
+end
\ No newline at end of file
Added: trunk/octave-forge/extra/ncArray/inst/@ncArray/subsasgn.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncArray/subsasgn.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncArray/subsasgn.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,10 @@
+function self = subsasgn(self,idxs,x)
+%idx
+
+idx = idxs(1);
+assert(strcmp(idx.type,'()'))
+[start, count, stride] = ncsub(self,idx);
+
+if all(count ~= 0)
+ ncwrite(self.filename,self.varname,x,start,stride);
+end
Added: trunk/octave-forge/extra/ncArray/inst/@ncArray/subsref.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncArray/subsref.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncArray/subsref.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,65 @@
+function x = subsref(self,idx)
+
+assert(length(idx) == 1)
+
+if strcmp(idx.type,'()')
+ % load data
+
+ if strcmp(idx.type,'()') && length(idx.subs) == 1 ...
+ && length(idx.subs) < self.nd
+ % reference like A([2 3 1 5])
+
+ if self.tooBigToLoad
+ % number of elements in x
+ ind = idx.subs{1};
+
+ % transform index to subscript
+ subs = cell(1,self.nd);
+ [subs{:}] = ind2sub(size(self),ind);
+
+ % make a nice array length(ind) by self.nd
+ subs = cell2mat(subs);
+
+ % output array
+ x = zeros(size(ind));
+ x(:) = NaN;
+
+
+ % get every element
+ % can be quite slow
+ idxe.type = '()';
+ idxe.subs = cell(1,self.nd);
+
+ for i=1:length(ind)
+ idxe.subs = mat2cell(subs(i,:),1,ones(1,self.nd));
+ x(i) = subsref(self,idxe);
+ end
+ else
+ % load full array
+ tmp = full(self);
+ x = subsref(tmp,idx);
+ end
+ else
+ [start, count, stride] = ncsub(self,idx);
+
+ if any(count == 0)
+ x = zeros(count);
+ else
+ x = ncread(cached_decompress(self.filename),self.varname,...
+ start,count,stride);
+ end
+ end
+elseif strcmp(idx.type,'.')
+ % load attribute
+ name = idx.subs;
+ index = strmatch(name,{self.vinfo.Attributes(:).Name});
+
+ if isempty(index)
+ error('variable %s has no attribute called %s',self.varname,name);
+ else
+ x = self.vinfo.Attributes(index).Value;
+ end
+else
+ error('not supported');
+
+end
\ No newline at end of file
Added: trunk/octave-forge/extra/ncArray/inst/@ncData/coord.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncData/coord.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncData/coord.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,3 @@
+function c = coord(self)
+c = self.coord;
+%'her'
\ No newline at end of file
Added: trunk/octave-forge/extra/ncArray/inst/@ncData/ncData.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncData/ncData.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncData/ncData.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,30 @@
+% data = ncData(filename,varname)
+% data = ncData(var,dims,coord)
+% data with coordinate values
+
+function retval = ncData(varargin)
+
+if ischar(varargin{1})
+ filename = varargin{1};
+ varname = varargin{2};
+ var = ncArray(filename,varname);
+ [dims,coord] = nccoord(cached_decompress(filename),varname);
+
+ for i=1:length(coord)
+ coord(i).val = ncArray(filename,coord(i).name);
+ end
+else
+ var = varargin{1};
+ dims = varargin{2};
+ coord = varargin{3};
+end
+
+self.var = var;
+self.dims = dims;
+self.nd = length(self.dims);
+self.coord = coord;
+
+retval = class(self,'ncData',BaseArray(size(self.var)));
+
+
+
Added: trunk/octave-forge/extra/ncArray/inst/@ncData/subsasgn.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncData/subsasgn.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncData/subsasgn.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,3 @@
+function self = subsasgn(self,idx,x)
+
+self = subsasgn(self.var,idx,x);
Added: trunk/octave-forge/extra/ncArray/inst/@ncData/subsref.m
===================================================================
--- trunk/octave-forge/extra/ncArray/inst/@ncData/subsref.m (rev 0)
+++ trunk/octave-forge/extra/ncArray/inst/@ncData/subsref.m 2012-06-22 15:05:53 UTC (rev 10665)
@@ -0,0 +1,32 @@
+function varargout = subsref(self,idx)
+
+if strcmp(idx(1).type,'()')
+
+ % no subscripts mean that we load all () -> (:,:,...)
+ if isempty(idx(1).subs)
+ for i=1:self.nd
+ idx(1).subs{i} = ':';
+ end
+ end
+end
+
+% catch expressions like:
+% data(:,:,:).coord
+
+if length(idx) == 2 && strcmp(idx(2).type,'.') && strcmp(idx(2).subs,'coord')
+ for i=1:length(self.coord)
+ % get indeces of the dimensions of the i-th coordinate which are also
+ % coordinate of the variable
+
+ % replace dummy by ~ once older version have died
+ [dummy,j] = intersect(self.dims,self.coord(i).dims);
+ j = sort(j);
+ idx_c.type = '()';
+ idx_c.subs = idx(1).subs(j);
+
+ varargout{i} = subsref(self.coord(i).val,idx_c);
+ end
+else
+ % pass subsref to underlying ncArray
+ varargout{1} = subsref(self.var,idx);
+end
\ No newline at end of file
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