ncarray-1.0.6/ 0000755 0000000 0000000 00000000000 14606472241 010111 5 ustar 00 ncarray-1.0.6/COPYING 0000644 0000000 0000000 00000104513 14606472241 011150 0 ustar 00 GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
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How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
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Copyright (C)
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You should have received a copy of the GNU General Public License
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Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
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Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
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You should also get your employer (if you work as a programmer) or school,
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For more information on this, and how to apply and follow the GNU GPL, see
.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
.
ncarray-1.0.6/DESCRIPTION 0000644 0000000 0000000 00000000627 14606472241 011624 0 ustar 00 Name: ncarray
Version: 1.0.6
Date: 2024-04-13
Author: Alexander Barth
Maintainer: John Donoghue
Title: ncarray
Description: Access a single or a collection of NetCDF files as a multi-dimensional array
Categories: IO
Depends: octave (>= 3.4.0), netcdf (>= 1.0.2), statistics (>= 1.0.6)
License: GPLv3+
Url: https://octave.sourceforge.io/ncarray/index.html
ncarray-1.0.6/INDEX 0000644 0000000 0000000 00000000766 14606472241 010714 0 ustar 00 ncarray >> ncArray
ncArray
ncArray
ncCatArray
nccoord
nctimeunits
ncreadtime
cached_decompress
@ncArray/coord
@ncArray/subsasgn
@ncArray/subsref
ncBaseArray
@BaseArray/BaseArray
@BaseArray/end
@BaseArray/full
@BaseArray/isnumeric
@BaseArray/max
@BaseArray/mean
@BaseArray/min
@BaseArray/moment
@BaseArray/numel
@BaseArray/prod
@BaseArray/reduce
@BaseArray/size
@BaseArray/std
@BaseArray/sum
@BaseArray/sumsq
@BaseArray/var
Test script
test_ncarray
ncarray-1.0.6/Makefile 0000644 0000000 0000000 00000022547 14606472241 011563 0 ustar 00 ## Copyright 2015-2016 Carnë Draug
## Copyright 2015-2016 Oliver Heimlich
## Copyright 2017 Julien Bect
## Copyright 2017 Olaf Till
## Copyright 2019 John Donoghue
##
## Copying and distribution of this file, with or without modification,
## are permitted in any medium without royalty provided the copyright
## notice and this notice are preserved. This file is offered as-is,
## without any warranty.
## Some basic tools (can be overriden using environment variables)
SED ?= sed
TAR ?= tar
GREP ?= grep
CUT ?= cut
TR ?= tr
## Note the use of ':=' (immediate set) and not just '=' (lazy set).
## http://stackoverflow.com/a/448939/1609556
package := $(shell $(GREP) "^Name: " DESCRIPTION | $(CUT) -f2 -d" " | \
$(TR) '[:upper:]' '[:lower:]')
version := $(shell $(GREP) "^Version: " DESCRIPTION | $(CUT) -f2 -d" ")
## These are the paths that will be created for the releases.
target_dir := target
release_dir := $(target_dir)/$(package)-$(version)
release_tarball := $(target_dir)/$(package)-$(version).tar.gz
html_dir := $(target_dir)/$(package)-html
html_tarball := $(target_dir)/$(package)-html.tar.gz
## Using $(realpath ...) avoids problems with symlinks due to bug
## #50994 in Octaves scripts/pkg/private/install.m. But at least the
## release directory above is needed in the relative form, for 'git
## archive --format=tar --prefix=$(release_dir).
real_target_dir := $(realpath .)/$(target_dir)
installation_dir := $(real_target_dir)/.installation
package_list := $(installation_dir)/.octave_packages
install_stamp := $(installation_dir)/.install_stamp
## These can be set by environment variables which allow to easily
## test with different Octave versions.
ifndef OCTAVE
OCTAVE := octave
endif
OCTAVE := $(OCTAVE) --no-gui --silent --norc
MKOCTFILE ?= mkoctfile
## Command used to set permissions before creating tarballs
FIX_PERMISSIONS ?= chmod -R a+rX,u+w,go-w,ug-s
## Detect which VCS is used
vcs := $(if $(wildcard .hg),hg,$(if $(wildcard .git),git,unknown))
ifeq ($(vcs),hg)
release_dir_dep := .hg/dirstate
HG := hg
HG_CMD = $(HG) --config alias.$(1)=$(1) --config defaults.$(1)= $(1)
HG_ID := $(shell $(call HG_CMD,identify) --id | sed -e 's/+//' )
REPO_TIMESTAMP := $(firstword $(shell $(call HG_CMD,log) --rev $(HG_ID) --template '{date|hgdate}'))
endif
ifeq ($(vcs),git)
release_dir_dep := .git/index
GIT := git
REPO_TIMESTAMP := $(firstword $(shell $(GIT) log -n1 --date=unix --format="%ad"))
endif
TAR_REPRODUCIBLE_OPTIONS := --sort=name --mtime="@$(REPO_TIMESTAMP)" --owner=0 --group=0 --numeric-owner
TAR_OPTIONS := --format=ustar $(TAR_REPRODUCIBLE_OPTIONS)
## .PHONY indicates targets that are not filenames
## (https://www.gnu.org/software/make/manual/html_node/Phony-Targets.html)
.PHONY: help
## make will display the command before runnning them. Use @command
## to not display it (makes specially sense for echo).
help:
@echo "Targets:"
@echo " dist - Create $(release_tarball) for release."
@echo " html - Create $(html_tarball) for release."
@echo " release - Create both of the above and show md5sums."
@echo " install - Install the package in $(installation_dir), where it is not visible in a normal Octave session."
@echo " check - Execute package tests."
@echo " doctest - Test the help texts with the doctest package."
@echo " run - Run Octave with the package installed in $(installation_dir) in the path."
@echo " clean - Remove everything made with this Makefile."
##
## Recipes for release tarballs (package + html)
##
.PHONY: release dist html clean-tarballs clean-unpacked-release
## To make a release, build the distribution and html tarballs.
release: dist html
md5sum $(release_tarball) $(html_tarball)
@echo "Upload @ https://sourceforge.net/p/octave/package-releases/new/"
@echo " and note the changeset the release corresponds to"
## dist and html targets are only PHONY/alias targets to the release
## and html tarballs.
dist: $(release_tarball)
html: $(html_tarball)
## An implicit rule with a recipe to build the tarballs correctly.
%.tar.gz: %
$(TAR) -cf - $(TAR_OPTIONS) -C "$(target_dir)/" "$(notdir $<)" | gzip -9n > "$@"
clean-tarballs:
@echo "## Cleaning release tarballs (package + html)..."
-$(RM) $(release_tarball) $(html_tarball)
@echo
## Create the unpacked package.
##
## Notes:
## * having ".hg/dirstate" (or ".git/index") as a prerequesite means it is
## only rebuilt if we are at a different commit.
## * the variable RM usually defaults to "rm -f"
## * having this recipe separate from the one that makes the tarball
## makes it easy to have packages in alternative formats (such as zip)
## * note that if a commands needs to be run in a specific directory,
## the command to "cd" needs to be on the same line. Each line restores
## the original working directory.
$(release_dir): $(release_dir_dep)
-$(RM) -r "$@"
ifeq (${vcs},hg)
hg archive --exclude ".hg*" --type files "$@"
endif
ifeq (${vcs},git)
git archive --format=tar --prefix="$@/" HEAD | $(TAR) -x
$(RM) "$@/.gitignore"
endif
## Don't fall back to run the supposed necessary contents of
## 'bootstrap' here. Users are better off if they provide
## 'bootstrap'. Administrators, checking build reproducibility, can
## put in the missing 'bootstrap' file if they feel they know its
## necessary contents.
ifneq (,$(wildcard src/bootstrap))
cd "$@/src" && ./bootstrap && $(RM) -r "autom4te.cache"
endif
## Uncomment this if your src/Makefile.in has these targets for
## pre-building something for the release (e.g. documentation).
# cd "$@/src" && ./configure && $(MAKE) prebuild && \
# $(MAKE) distclean && $(RM) Makefile
##
${FIX_PERMISSIONS} "$@"
run_in_place = $(OCTAVE) --eval ' pkg ("local_list", "$(package_list)"); ' \
--eval ' pkg ("load", "$(package)"); '
# html_options = --eval 'options = get_html_options ("octave-forge");'
## Uncomment this for package documentation.
##html_options = --eval 'options = get_html_options ("octave-forge");' \
## --eval 'options.package_doc = "$(package).texi";'
html_options = --eval 'options = get_html_options ("octave-forge");'
$(html_dir): $(install_stamp)
$(RM) -r "$@";
$(run_in_place) \
--eval ' pkg load generate_html; ' \
$(html_options) \
--eval ' generate_package_html ("$(package)", "$@", options); ';
$(FIX_PERMISSIONS) "$@";
clean-unpacked-release:
@echo "## Cleaning unpacked release tarballs (package + html)..."
-$(RM) -r $(release_dir) $(html_dir)
@echo
##
## Recipes for installing the package.
##
.PHONY: install clean-install
octave_install_commands = \
' llist_path = pkg ("local_list"); \
mkdir ("$(installation_dir)"); \
load (llist_path); \
local_packages(cellfun (@ (x) strcmp ("$(package)", x.name), local_packages)) = []; \
save ("$(package_list)", "local_packages"); \
pkg ("local_list", "$(package_list)"); \
pkg ("prefix", "$(installation_dir)", "$(installation_dir)"); \
pkg ("install", "-local", "-verbose", "$(release_tarball)"); '
## Install unconditionally. Maybe useful for testing installation with
## different versions of Octave.
install: $(release_tarball)
@echo "Installing package under $(installation_dir) ..."
$(OCTAVE) --eval $(octave_install_commands)
touch $(install_stamp)
## Install only if installation (under target/...) is not current.
$(install_stamp): $(release_tarball)
@echo "Installing package under $(installation_dir) ..."
$(OCTAVE) --eval $(octave_install_commands)
touch $(install_stamp)
clean-install:
@echo "## Cleaning installation under $(installation_dir) ..."
-$(RM) -r $(installation_dir)
@echo
##
## Recipes for testing purposes
##
.PHONY: run doctest check
## Start an Octave session with the package directories on the path for
## interactice test of development sources.
run: $(install_stamp)
$(run_in_place) --persist
rungui: $(install_stamp)
$(run_in_place) --persist --gui
## Test example blocks in the documentation. Needs doctest package
## https://octave.sourceforge.io/doctest/index.html
doctest: $(install_stamp)
$(run_in_place) --eval 'pkg load doctest;' \
--eval "targets = '$(shell (ls inst; ls src | $(GREP) .oct) | $(CUT) -f2 -d@ | $(CUT) -f1 -d.)';" \
--eval "targets = strsplit (targets, ' '); doctest (targets);"
## Test package.
octave_test_commands = \
' pkgs = pkg("list", "$(package)"); \
cd ("$(target_dir)/"); \
dirs = {sprintf(".installation/%s-%s", pkgs{1}.name, pkgs{1}.version)}; \
__run_test_suite__ (dirs, {}); '
octave_test_commands = \
' pkgs = pkg("list", "$(package)"); \
dirs = {pkgs{1}.dir}; \
__run_test_suite__ (dirs, {}); '
## the following works, too, but provides no overall summary output as
## __run_test_suite__ does:
##
## else cellfun (@runtests, horzcat (cellfun (@ (dir) ostrsplit (([~, dirs] = system (sprintf ("find %s -type d", dir))), "\n\r", true), dirs, "UniformOutput", false){:})); endif '
check: $(install_stamp)
$(run_in_place) --eval $(octave_test_commands)
clean-check:
@echo "## Removing fntests.log..."
-$(RM) $(target_dir)/fntests.log
@echo
##
## CLEAN
##
.PHONY: clean
clean: clean-tarballs clean-unpacked-release clean-install clean-check
@echo "## Removing target directory (if empty)..."
-if [ -d $(target_dir) ]; then rmdir $(target_dir); fi
@echo
@echo "## Cleaning done"
@echo
ncarray-1.0.6/NEWS 0000644 0000000 0000000 00000003705 14606472241 010615 0 ustar 00 Summary of important user-visible changes for ncarray 1.0.6:
------------------------------------------------------------
** minor updates for octave compatibility
Summary of important user-visible changes for ncarray 1.0.5:
------------------------------------------------------------
** minor updates for octave compatibility
** update function docs for texinfo
** change license from gplv2+ to gplv3+
Summary of important user-visible changes for ncarray 1.0.4:
------------------------------------------------------------
** Avoid obsolete strmatch function
** Use a tolerance in test script (bug #49391)
Summary of important user-visible changes for ncarray 1.0.3:
------------------------------------------------------------
** use lower-case package name as upper-case letters in the package name can
cause troubles with pkg.
** new functions nctimeunits and ncreadtime for handling time variables.
Summary of important user-visible changes for ncArray 1.0.2:
------------------------------------------------------------
** new function: nansum, nanvar, nanstd: mean, variance, standard deviation
ignoring NaNs
** ncarray nows depends on package netcdf (instead of octcdf)
** Add missing dependency to statistics
** Avoid obsolete isequalwithequalnans functions
Summary of important user-visible changes for ncArray 1.0.1:
------------------------------------------------------------
** new function: nanmean: mean ignoring NaNs
** new function: load: load data based on a coordinate range or a single
value (only 1-dimensional coordinates are currently supported)
** CACHED_DECOMPRESS_DIR defaults now to a directory inside the system temporary
directory (/tmp on Linux)
** add support for xz compression
** optimization of assignement operator
** add units and standard_name in nccoord
Summary of important user-visible changes for ncArray 1.0.0:
------------------------------------------------------------
** Initial release
ncarray-1.0.6/inst/ 0000755 0000000 0000000 00000000000 14606472241 011066 5 ustar 00 ncarray-1.0.6/inst/@BaseArray/ 0000755 0000000 0000000 00000000000 14606472241 013037 5 ustar 00 ncarray-1.0.6/inst/@BaseArray/BaseArray.m 0000644 0000000 0000000 00000002376 14606472241 015076 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{BA} =} BaseArray(@var{SZ})
## Create a BaseArray of size SZ. BaseArray is an abstract class.
##
## Derived classes should implement the methods subsref and subsasgn.
## BaseArray implements several reduction methods such as sum, prod and mean.
##
## @subsubheading Inputs
## @var{SZ} - size of the array.
## SZ should have least two elements.
## @subsubheading Outputs
## @var{BA} - a BaseArray object
## @end deftypefn
function retval = BaseArray(sz)
self.sz = sz;
retval = class(self,'BaseArray');
endfunction
ncarray-1.0.6/inst/@BaseArray/end.m 0000644 0000000 0000000 00000001611 14606472241 013762 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{e} =} end(@var{A}, @var{k})
## Return last index along a dimension.
## @end deftypefn
function e = end(self,k,n)
e = size(self,k);
endfunction
ncarray-1.0.6/inst/@BaseArray/full.m 0000644 0000000 0000000 00000001717 14606472241 014165 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{F} =} full(@var{A})
## Make full (dense) array.
## @end deftypefn
function F = full(self);
n = length(self.sz);
idx.type = '()';
for i=1:n
idx.subs{i} = ':';
endfor
F = subsref(self,idx);
endfunction
ncarray-1.0.6/inst/@BaseArray/isnumeric.m 0000644 0000000 0000000 00000001571 14606472241 015217 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{isn} =} isnumeric(@var{A})
## Test if array is numeric.
## @end deftypefn
function isn = isnumeric(self)
isn = true;
endfunction
ncarray-1.0.6/inst/@BaseArray/length.m 0000644 0000000 0000000 00000001616 14606472241 014502 0 ustar 00 % len = length(A)
% Return the "length" of the object A. For matrix objects, the
% length is the number of rows or columns, whichever is greater.
function len = length(self)
len = max(size(self));
% Copyright (C) 2013 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@BaseArray/max.m 0000644 0000000 0000000 00000001761 14606472241 014007 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{s} =} max(@var{A}, [], @var{dim})
## Compute the maximum along dimension DIM.
## @end deftypefn
function s = max(self,B,varargin)
assert(isempty(B))
funred = @max;
funelem = @(x) x;
s = reduce(self,funred,funelem,varargin{:});
endfunction
ncarray-1.0.6/inst/@BaseArray/mean.m 0000644 0000000 0000000 00000002020 14606472241 014127 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{s} =} end(@var{A}, @var{dim})
## Compute the mean along dimension DIM.
## @end deftypefn
function s = mean(self,varargin)
funred = @plus;
funelem = @(x) x;
[s,n] = reduce(self,funred,funelem,varargin{:});
if isempty(s)
s = 0;
else
s = s/n;
endif
endfunction
ncarray-1.0.6/inst/@BaseArray/min.m 0000644 0000000 0000000 00000001761 14606472241 014005 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{s} =} end(@var{A}, [], @var{dim})
## Compute the minimum along dimension DIM.
## @end deftypefn
function s = min(self,B,varargin)
assert(isempty(B))
funred = @min;
funelem = @(x) x;
s = reduce(self,funred,funelem,varargin{:});
endfunction
ncarray-1.0.6/inst/@BaseArray/moment.m 0000644 0000000 0000000 00000002161 14606472241 014514 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{s} =} moment(@var{A}, @var{order}, @var{dim})
## Compute the central moment of the given order along dimension DIM.
## @end deftypefn
function s = moment(self,order,varargin)
m = mean(self,varargin{:});
funred = @plus;
funelem = @(x) (x-m).^order;
[s,n] = reduce(self,funred,funelem,varargin{:});
if isempty(s)
s = NaN;
else
s = s/n;
endif
endfunction
ncarray-1.0.6/inst/@BaseArray/nanmean.m 0000644 0000000 0000000 00000002672 14606472241 014641 0 ustar 00 % Compute the mean (ignoring NaNs).
% s = mean (X, DIM)
% Compute the mean along dimension DIM.
function [s,total,count] = nanmean(self,varargin)
% s will be a cell element containing
% {the sum, the count of elements different from NaN}
% this is necessary to avoid 2 calls to reduce
[s,n] = reduce(self,...
@(x,y) funred(x,y),...
@(x) funelem(x),...
varargin{:});
if isempty(s)
s = 0;
else
total = s{1};
count = s{2};
s = NaN*zeros(size(total));
nonz = count ~= 0;
s(nonz) = total(nonz) ./ count(nonz);
end
end
function x = funelem(x)
% make sure x is not an ncArray
x = full(x);
m = isnan(x);
x(m) = 0;
x = {x,~m};
end
function s = funred(x,y)
s = {x{1} + y{1}, x{2} + y{2}} ;
end
% Copyright (C) 2013 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@BaseArray/nanstd.m 0000644 0000000 0000000 00000001770 14606472241 014511 0 ustar 00 % Compute the standard deviation (ignoring NaNs).
% S = nanstd (X, OPT, DIM)
% Compute the standard deviation along dimension DIM. NaNs are treated as absent
% values.
% If OPT is equal to 1, then the standard deviation is bias-corrected.
function s = nanstd(self,varargin)
s = sqrt(nanvar(self,varargin{:}));
% Copyright (C) 2013 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@BaseArray/nansum.m 0000644 0000000 0000000 00000002644 14606472241 014524 0 ustar 00 % Compute the sum (ignoring NaNs).
% [s,count] = sum (X, DIM)
% Compute the sum along dimension DIM.
% The variable s is the sum and count the number of values summed.
function [total,count] = nansum(self,varargin)
% s will be a cell element containing
% {the sum, the count of elements different from NaN}
% this is necessary to avoid 2 calls to reduce
[s,n] = reduce(self,...
@(x,y) funred(x,y),...
@(x) funelem(x),...
varargin{:});
if isempty(s)
s = 0;
else
total = s{1};
count = s{2};
end
end
function x = funelem(x)
% make sure x is not an ncArray
x = full(x);
m = isnan(x);
x(m) = 0;
x = {x,~m};
end
function s = funred(x,y)
s = {x{1} + y{1}, x{2} + y{2}} ;
end
% Copyright (C) 2013 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@BaseArray/nanvar.m 0000644 0000000 0000000 00000002733 14606472241 014507 0 ustar 00 % Compute the variance (ignoring NaNs).
% V = var (X, OPT, DIM)
% Compute the variance along dimension DIM.
% If OPT is equal to 1, then the variance is bias-corrected.
function s = nanvar(self,opt,varargin)
if nargin == 1
opt = 0;
elseif isempty(opt)
opt = 0;
end
nm = nanmean(self,varargin{:});
[s,n] = reduce(self,@funred, ...
@(x) funelem(x,nm),varargin{:});
if isempty(s)
s = 0;
else
total = s{1};
count = s{2};
if opt == 0
s = total./(count-1);
else
s = total./count;
end
end
end
function x = funelem(x,nm)
% make sure x is not an ncArray
x = full(x);
mask = isnan(x) | isnan(nm);
diff = zeros(size(x));
diff(mask) = x(mask) - nm(mask);
x = {diff.^2, ~mask};
end
function s = funred(x,y)
s = {x{1} + y{1}, x{2} + y{2}} ;
end
% Copyright (C) 2013 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@BaseArray/numel.m 0000644 0000000 0000000 00000001573 14606472241 014343 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{n} =} numel(@var{A})
## Number of elements.
## @end deftypefn
function n = numel(self, varargin)
n = prod(self.sz);
endfunction
ncarray-1.0.6/inst/@BaseArray/prod.m 0000644 0000000 0000000 00000002016 14606472241 014160 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{P} =} prod(@var{A}, @var{dims})
## Compute the product of all elements along dimension DIM.
## @end deftypefn
function s = prod(self,varargin)
funred = @times;
funelem = @(x) x;
s = reduce(self,funred,funelem,varargin{:});
if isempty(s)
s = 1;
endif
endfunction
ncarray-1.0.6/inst/@BaseArray/reduce.m 0000644 0000000 0000000 00000003002 14606472241 014457 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {[@var{s}, @var{n}] =} reducce(@var{A}, @var{funred}, @var{funelem}, @var{dim})
## Reduce array using callback fundtions.
##
## Reduce array using the function FUNRED applied to all elements
## after the function FUNELEM was applied along dimension DIM.
## @end deftypefn
function [s,n] = reduce(self,funred,funelem,dim)
sz = size(self);
if nargin == 3
dim = find(sz ~= 1,1);
if isempty(dim)
dim = 1;
endif
endif
idx.type = '()';
nd = length(sz);
idx.subs = cell(1,nd);
for i=1:nd
idx.subs{i} = ':';
endfor
n = size(self,dim);
if n == 0
s = [];
else
idx.subs{dim} = 1;
s = funelem(subsref(self,idx));
for i=2:n
idx.subs{dim} = i;
s = funred(s,funelem(subsref(self,idx)));
endfor
endif
endfunction
ncarray-1.0.6/inst/@BaseArray/size.m 0000644 0000000 0000000 00000002001 14606472241 014160 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{isz} =} size(@var{A})
## Size of array
## @end deftypefn
function sz = size(self,dim)
sz = self.sz;
if length(sz) == 1
sz = [sz 1];
endif
if nargin == 2
if dim > length(sz)
sz = 1;
else
sz = sz(dim);
endif
endif
endfunction
ncarray-1.0.6/inst/@BaseArray/std.m 0000644 0000000 0000000 00000001645 14606472241 014015 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{s} =} std(@var{A}, @var{opt}, @var{dim})
## Compute the standard deviation.
## @end deftypefn
function s = std(self,varargin)
s = sqrt(var(self,varargin{:}));
endfunction
ncarray-1.0.6/inst/@BaseArray/sum.m 0000644 0000000 0000000 00000001761 14606472241 014026 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{s} =} sum(@var{A}, @var{dim})
## Compute sum along a dimension.
## @end deftypefn
function s = sum(self,varargin)
funred = @plus;
funelem = @(x) x;
s = reduce(self,funred,funelem,varargin{:});
if isempty(s)
s = 0;
endif
endfunction
ncarray-1.0.6/inst/@BaseArray/sumsq.m 0000644 0000000 0000000 00000002043 14606472241 014364 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{s} =} end(@var{A}, @var{dim})
## Compute the sum squared.
##
## Compute the sum squared along dimension DIM.
## @end deftypefn
function s = sumsq(self,varargin)
funred = @plus;
funelem = @(x) x.^2;
s = reduce(self,funred,funelem,varargin{:});
if isempty(s)
s = 1;
endif
endfunction
ncarray-1.0.6/inst/@BaseArray/var.m 0000644 0000000 0000000 00000002414 14606472241 014006 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{s} =} var(@var{A}, @var{opt}, @var{dim})
## Compute the variance along dimension DIM.
##
## If OPT is equal to 1, then the variance is bias-corrected.
## @end deftypefn
function s = var(self,opt,varargin)
if nargin == 1
opt = 0;
elseif isempty(opt)
opt = 0;
endif
m = mean(self,varargin{:});
funred = @plus;
funelem = @(x) (x-m).^2;
[s,n] = reduce(self,funred,funelem,varargin{:});
if isempty(s)
s = 0;
else
if opt == 0
s = s/(n-1);
else
s = s/n;
endif
endif
endfunction
ncarray-1.0.6/inst/@CatArray/ 0000755 0000000 0000000 00000000000 14606472241 012674 5 ustar 00 ncarray-1.0.6/inst/@CatArray/CatArray.m 0000644 0000000 0000000 00000004774 14606472241 014574 0 ustar 00 % 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
%
% 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 3 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 .
% Copyright (C) 2012 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@CatArray/display.m 0000644 0000000 0000000 00000001407 14606472241 014521 0 ustar 00 function display(self)
for i=1:self.na
display(self.arrays{i})
end
% Copyright (C) 2012 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@CatArray/idx_global_local_.m 0000644 0000000 0000000 00000004047 14606472241 016474 0 ustar 00 % 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
% Copyright (C) 2012 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@CatArray/subsasgn.m 0000644 0000000 0000000 00000001733 14606472241 014703 0 ustar 00 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
% Copyright (C) 2012 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@CatArray/subsref.m 0000644 0000000 0000000 00000004653 14606472241 014533 0 ustar 00 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};
if strcmp(ind,':')
ind = [1:numel(self)]';
end
% output array
B = zeros(size(ind));
B(:) = NaN;
if self.overlap
% transform linear index ind to subscript subs
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);
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
elseif strcmp(idx.type,'.')
% load attributes from first array
B = subsref(self.arrays{1},idx);
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
% this is slow, why?
%B = subsasgn(B,idx_global{j},subset);
% however this quite fast
idxa = idx_global{j}.subs;
B(idxa{:}) = subset;
end
end
% Copyright (C) 2012 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@ncArray/ 0000755 0000000 0000000 00000000000 14606472241 012565 5 ustar 00 ncarray-1.0.6/inst/@ncArray/coord.m 0000644 0000000 0000000 00000002007 14606472241 014050 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{c} =} coord(@var{A})
## Get a array of structures with the coordinate of ncArray A.
## @subsubheading Inputs
## @var{A} - ncArray value
## @subsubheading Outputs
## @var{c} - array of coordinates
## @end deftypefn
function c = coord(self)
c = self.coord;
endfunction
ncarray-1.0.6/inst/@ncArray/dims.m 0000644 0000000 0000000 00000001602 14606472241 013676 0 ustar 00 ## Copyright (C) 2013 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{c} =} dims(@var{A})
## Get cell-array of dimension names ncArray A.
## @end deftypefn
function c = dims(self)
c = self.dims;
endfunction
ncarray-1.0.6/inst/@ncArray/display.m 0000644 0000000 0000000 00000002351 14606472241 014411 0 ustar 00 ## Copyright (C) 2013 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {} display(@var{A})
## Display ncArray A
## @end deftypefn
function display(self)
sz = size(self);
tmp = sprintf('%dx',sz);
fprintf('Size: %s\n',tmp(1:end-1))
c = coord(self);
fprintf('Coordinates:\n')
for i = 1:length(c)
tmp = sprintf('%dx',size(c(i).val));
stdname = c(i).standard_name;
if isempty(stdname)
stdname = '';
endif
fprintf(' Name: %15s; standard name: %25s; size %10s\n',...
c(i).name,stdname,tmp(1:end-1));
endfor
endfunction
ncarray-1.0.6/inst/@ncArray/load.m 0000644 0000000 0000000 00000005455 14606472241 013673 0 ustar 00 ## Copyright (C) 2013 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {[@var{val}, @var{coord1}, @var{coord2} @dots{}] =} load(@var{A}, @var{coord_name1}, @var{range1}, @var{coord_name2}, @var{range2}, @dots{})
## Load a subset of a variable based on range of coordiante variables.
## The names of the coordinates (coord_name1, coord_name2,...) coorespond to the standard_name attribute.
## Only 1-dimensional coordinates are currently supported.
## Time units are converted to "datenum".
##
## @example
## [temp,lon,lat,depth,time] = load(self,'longitude',[0 10],'latitude',[0 10])
## @end example
## @end deftypefn
function varargout = load(self,varargin)
c = coord(self);
for i = 1:length(c)
c(i).v = full(c(i).val);
% per default take all data along a dimension
c(i).index = ':';
% convert time units
if ~isempty(strfind(c(i).units,'since'))
[t0,f] = nctimeunits(c(i).units);
c(i).v = f*double(c(i).v) + t0;
endif
% change vertical axis to positive up
if strcmp(c(i).positive,'down')
c(i).v = -double(c(i).v);
endif
c(i).sub = c(i).v;
endfor
% loop over all constraints
for i = 1:2:length(varargin)
name = varargin{i};
j = find(strcmp(name,{c.standard_name}));
if isempty(j)
warning(['no coordinate has the standard_name ' name ...
'. Try to use variable names.']);
j = find(strcmp(name,{c.name}));
if isempty(j)
error(['no coordinate has the name ' name '.']);
endif
endif
range = varargin{i+1};
if numel(range) == 1
dist = abs(c(j).v - range);
[mindist,i] = min(dist);
%i
%mindist
%c(j).v(i)
%datevec(c(j).v(i))
else
i = find(range(1) < c(j).v & c(j).v < range(end));
i = min(i):max(i);
endif
c(j).index = i;
c(j).sub = c(j).v(i);
endfor
idx = substruct('()',{c.index});
%idx
data = subsref (self,idx);
varargout = {data,c.sub};
% i = 1;
% mask = xr(1) <= x & x <= xr(2);
% l = find(mask);
% [ij{:}] = ind2sub(size(mask),l);
% for j=1:len
% mins(j) = min(ij{j});
% maxs(j) = max(ij{j});
endfunction
ncarray-1.0.6/inst/@ncArray/ncArray.m 0000644 0000000 0000000 00000005742 14606472241 014352 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{V} =} ncArray(@var{filename}, @var{varname})
## @deftypefnx {} {@var{V} =} ncArray(@var{filename}, @var{varname}, @var{propertyname}, @var{propertyvalue}, @dots{})
## Create a ncArray that can be accessed as a normal array.
##
## @subsubheading Inputs
## @var{filename} - filename to read
##
## @var{varname} - variable name to read from file
##
## @var{propertyname}, @var{propertyvalue} - property name and value pairs.
##
## @subsubheading Outputs
## @var{V} - a ncArray of the read file.
##
## 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.
##
## @subsubheading Example
##
## Loading the variable (assuming V is 3 dimensional):
## @example
## 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
## @end example
##
## Saving data in the netcdf file:
## @example
## V(1,1,1) = x; % save x in element 1,1,1
## V(:,:,:) = x;
## @end example
##
## Attributes
## @example
## units = V.units; % get attribute called "units"
## V.units = 'degree C'; % set attributes;
## @end example
##
## Note: use the '.()' notation if the attribute has a leading underscore
## (due to a limitation in the matlab parser):
##
## @example
## V.('_someStrangeAttribute') = 123;
## @end example
##
## @seealso{cache_decompress, ncCatArray}
## Web: http://modb.oce.ulg.ac.be/mediawiki/index.php/ncArray
## @end deftypefn
function retval = ncArray(varargin)
if ischar(varargin{1})
filename = varargin{1};
varname = varargin{2};
var = ncBaseArray(filename,varname);
[dims,coord] = nccoord(cached_decompress(filename),varname);
for i=1:length(coord)
coord(i).val = ncBaseArray(filename,coord(i).name);
endfor
else
var = varargin{1};
dims = varargin{2};
coord = varargin{3};
endif
self.var = var;
self.dims = dims;
self.nd = length(self.dims);
self.coord = coord;
retval = class(self,'ncArray',BaseArray(size(self.var)));
endfunction
ncarray-1.0.6/inst/@ncArray/subsasgn.m 0000644 0000000 0000000 00000002320 14606472241 014565 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {} subsasgn(@var{A}, @var{idx}, @var{rhs})
## Perform the subscripted assignment operation according to the subscript specified by idx.
##
## A slice of the NetCDF variable can be saved by using A(index1,index2,...) = rhs;
## @subsubheading Inputs
## @var{A} - ncArray value
##
## @var{idx} - idx structure
##
## @var{rhs} - value to assign
## @subsubheading Outputs
## None
## @end deftypefn
function self = subsasgn(self,idx,x)
self = subsasgn(self.var,idx,x);
endfunction
ncarray-1.0.6/inst/@ncArray/subsref.m 0000644 0000000 0000000 00000004501 14606472241 014414 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{out} =} subsref(@var{A}, @var{idx})
## Perform the subscripted element selection operation according to the subscript specified by idx.
##
## @subsubheading Inputs
## @var{A} - ncArray value
##
## @var{idx} - idx structure
##
## @subsubheading Outputs
## @var{out} - output value of operation
##
## A slice of the NetCDF variable can be load by using A(index1,index2,...) and attributes
## can be loaded by A.attribute_name or A.('attribute_name')
##
## If index selection is followed by struct selection 'coord', then the coordinates corresponding to the
## slice are loaded:
##
## For example, the coordinate of element A(4,3):
## @example
## [lon,lat] = A(4,3).coord;
## @end example
## @end deftypefn
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} = ':';
endfor
endif
endif
% 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);
endfor
else
% pass subsref to underlying ncBaseArray
varargout{1} = subsref(self.var,idx);
endif
endfunction
ncarray-1.0.6/inst/@ncBaseArray/ 0000755 0000000 0000000 00000000000 14606472241 013360 5 ustar 00 ncarray-1.0.6/inst/@ncBaseArray/display.m 0000644 0000000 0000000 00000001636 14606472241 015211 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {} display(@var{A})
## Display ncBaseArray A
## @end deftypefn
function display(self)
disp([self.varname ' from ' self.filename]);
%self.vinfo
%self.dims
endfunction
ncarray-1.0.6/inst/@ncBaseArray/ncBaseArray.m 0000644 0000000 0000000 00000006040 14606472241 015730 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{V} =} ncBaseArray(@var{filename}, @var{varname})
## @deftypefnx {} {@var{V} =} ncBaseArray(@var{filename}, @var{varname}, @var{propertyname}, @var{propertyvalue})
## create a ncBaseArray that can be accessed as a normal matlab array.
## Ths object is a helper object. Users should normally call ncArray.
##
## For read access filename can be compressed if it has the extensions
## ".gz", ".bz2" or ".xz". 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.
##
## @subsubheading Properties:
## 'tooBigToLoad': if tooBigToLoad is set to true, then only the minimum
## data will be loaded. However this can be quite slow.
## 'vinfo': result from ncinfo can be specified if it is already known.
##
## @subsubheading Examples:
##
## Loading the variable (assuming V is 3 dimensional):
## @example
## 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
## @end example
##
## Saving data in the netcdf file:
## @example
## V(1,1,1) = x; % save x in element 1,1,1
## V(:,:,:) = x;
## @end example
##
## Attributes
## @example
## units = V.units; % get attribute called "units"
## V.units = 'degree C'; % set attributes;
## @end example
##
## Note: use the '.()' notation if the attribute has a leading underscore
## (due to a limitation in the matlab parser):
##
## @example
## V.('_someStrangeAttribute') = 123;
## @end example
##
## @seealso {cache_decompress}
## @end deftypefn
function retval = ncBaseArray(filename,varname,varargin)
self.tooBigToLoad = false;
self.vinfo = [];
prop = varargin;
for i=1:2:length(prop)
if strcmp(prop{i},'tooBigToLoad')
self.tooBigToLoad = prop{i+1};
elseif strcmp(prop{i},'vinfo')
self.vinfo = prop{i+1};
endif
endfor
self.filename = filename;
self.varname = varname;
if isempty(self.vinfo)
self.vinfo = ncinfo(cached_decompress(filename),varname);
endif
self.sz = self.vinfo.Size;
self.dims = self.vinfo.Dimensions;
self.nd = length(self.dims); % number of netcdf dimensions
retval = class(self,'ncBaseArray',BaseArray(self.sz));
endfunction
ncarray-1.0.6/inst/@ncBaseArray/ncsub.m 0000644 0000000 0000000 00000004557 14606472241 014663 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {} ncsub(@var{A}, @var{idx})
## internal function of ncBaseArray
## @end deftypefn
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
% check if indexes are at regular intervals
test = tmp(1):tmp(2)-tmp(1):tmp(end);
if size(tmp,2) == 1
% tmp is a row vector, make test also a row vector
test = test';
endif
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 not at regular intervals');
endif
endif
endif
endfor
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);
endif
endif
endfunction
ncarray-1.0.6/inst/@ncBaseArray/subsasgn.m 0000644 0000000 0000000 00000001623 14606472241 015365 0 ustar 00 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
% Copyright (C) 2012 Alexander Barth
%
% 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 3 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 .
ncarray-1.0.6/inst/@ncBaseArray/subsref.m 0000644 0000000 0000000 00000005053 14606472241 015212 0 ustar 00 ## Copyright (C) 2012 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{x} =} ncsub(@var{A}, @var{idx})
## subsref function
## @end deftypefn
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);
endfor
else
% load full array
tmp = full(self);
x = subsref(tmp,idx);
endif
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);
endif
endif
elseif strcmp(idx.type,'.')
% load attribute
name = idx.subs;
% strmatch is obsolete
% index = strmatch(name,{self.vinfo.Attributes(:).Name});
index = find(strcmp(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;
endif
else
error('not supported');
endif
endfunction
ncarray-1.0.6/inst/cached_decompress.m 0000644 0000000 0000000 00000013773 14606472241 014712 0 ustar 00 ## Copyright (C) 2012-2022 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{fname} =} cached_decompress(@var{filename})
## Decompress a file using a cache.
##
## @subsubheading Inputs
## @var{filename}: name of the file which is possibly compressed
##
## @subsubheading Outputs
## @var{fname}: the filename of the uncompressed file
##
## @subsubheading Global variables
## CACHED_DECOMPRESS_DIR (default is the result of tempname)
## cache directory of decompressed files.
##
## CACHED_DECOMPRESS_LOG_FID (default 1): file id for log message
##
## CACHED_DECOMPRESS_MAX_SIZE (default 1e10): maximum size of cache in bytes.
## @end deftypefn
function fname = cached_decompress(url)
global CACHED_DECOMPRESS_DIR
global CACHED_DECOMPRESS_LOG_FID
global CACHED_DECOMPRESS_MAX_SIZE
if startswith(url,'http:') || ...
~(endswith(url,'.gz') || endswith(url,'.bz2') || endswith(url,'.xz'))
% opendap url or not compressed file
fname = url;
return
endif
cache_dir = CACHED_DECOMPRESS_DIR;
if isempty(cache_dir)
cache_dir = tempname;
CACHED_DECOMPRESS_DIR = cache_dir;
mkdir(cache_dir);
fprintf('creating directory %s for temporary files.\n',cache_dir);
endif
%if exist(cache_dir,'dir') ~= 7
% error(['cache directory for compressed files does not exist. '...
% 'Please create the directory %s or change le value of the '...
% 'global variable CACHED_DECOMPRESS_DIR'],cache_dir);
%endif
% where to print logs? default to screen
fid = CACHED_DECOMPRESS_LOG_FID;
if (isempty(fid))
fid = 1;
endif
% form filename for cache
fname = url;
fname = strrep(fname,'/','_SLASH_');
fname = strrep(fname,'*','_STAR_');
fname = strrep(fname,'\','_BSLASH_');
fname = strrep(fname,':','_COLON_');
fname = fullfile(cache_dir,fname);
% test if in cache
if exist(fname,'file') ~= 2
if ispc()
# TODO - just do for all OSs?
tmp_dir = tempname ();
[success, msg] = mkdir (tmp_dir);
if (success != 1)
error ("failed to create temporary directory: %s", msg);
endif
unwind_protect
looks_like_url = regexp (url, '^\w+://');
if looks_like_url;
[~, name, ext] = fileparts (url);
tmp_file = fullfile (tmp_dir, [name ext]);
[~, success, msg] = urlwrite (url, tmp_file);
if (success != 1)
error ("failed downloading '%s': %s", url, msg);
endif
else
[~, name, ext] = fileparts (url);
tmp_file = fullfile (tmp_dir, ["tmp_" name ext]);
success = copyfile(url, tmp_file);
if (success != 1)
error ("failed copying '%s'", url);
endif
endif
if !exist (tmp_file, "file")
error ("No local file '%s' found\n", tmp_file);
endif
if endswith(url,'.zip')
func_uncomp = @unzip;
elseif endswith(url,'.gz')
func_uncomp = @gunzip;
elseif endswith(url,'.bz2')
func_uncomp = @bunzip2;
else
func_uncomp = [];
endif
if !isempty(func_uncomp)
files = func_uncomp(tmp_file, tmp_dir);
else
files = {tmp_file};
endif
if length(files) != 1
error ("Expected single file being added");
endif
success = copyfile(files{1}, fname);
if (success != 1)
error ("Failed to copy file to cache");
endif
unwind_protect_cleanup
if (exist (tmp_dir, "file"))
confirm_recursive_rmdir (0, "local");
rmdir(tmp_dir, "s");
endif
end_unwind_protect
else
# else try via command (after checking it exists?)
if endswith(url,'.gz')
cmd = 'gunzip --stdout -';
elseif endswith(url,'.bz2')
cmd = 'bunzip2 --stdout -';
elseif endswith(url,'.xz')
cmd = 'unxz --stdout -';
else
cmd = 'cat';
endif
if startswith(url,'ftp://')
syscmd('curl --silent "%s" | %s > "%s"',url,cmd,fname);
else
syscmd('%s < "%s" > "%s"',cmd,url,fname);
endif
endif
else
% fprintf(fid,'retrieve from cache %s\n',url);
endif
% check cache size
d=dir(cache_dir);
cashe_size = sum([d.bytes]);
max_cache_size = CACHED_DECOMPRESS_MAX_SIZE;
if isempty(max_cache_size)
max_cache_size = 1e10;
endif
if (cashe_size > max_cache_size)
% look for oldest files
fdate = zeros(1,length(d));
for i=1:length(d);
fdate(i) = datenum(d(i).date);
endfor
[fdate,index] = sort(fdate,'descend');
d=d(index);
cum_size = cumsum([d(:).bytes]);
todelete = find(cum_size > max_cache_size);
for i=todelete
if (d(i).isdir == 0)
fprintf(fid,'clean cashe: delete %s\n', d(i).name);
delete(fullfile(cache_dir,d(i).name));
endif
endfor
endif
endfunction
function t = startswith(s,ext)
if length(ext) <= length(s)
t = strcmp(s(1:length(ext)),ext);
else
t = 0;
endif
endfunction
function t = endswith(s,ext)
if length(ext) <= length(s)
t = strcmp(s(end-length(ext)+1:end),ext);
else
t = 0;
endif
endfunction
function syscmd(varargin)
cmd = sprintf(varargin{:});
%disp(cmd)
status = 0;
[status, output] = system(cmd);
disp(output);
if status ~= 0
error(['command "' cmd '" failed: ' output]);
endif
endfunction
ncarray-1.0.6/inst/ncCatArray.m 0000644 0000000 0000000 00000014575 14606472241 013307 0 ustar 00 ## Copyright (C) 2012,2013 Alexander Barth
##
## 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 3 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 .
## Author: Alexander Barth (barth.alexander@gmail.com)
##
## -*- texinfo -*-
## @deftypefn {} {@var{C} =} ncCatArray(@var{dim}, @var{filenames}, @var{varname})
## @deftypefnx {} {@var{C} =} ncCatArray(@var{dim}, @var{pattern}, @var{varname})
## @deftypefnx {} {@var{C} =} ncCatArray(@var{dim}, @var{filenamefun}, @var{varname}, @var{range})
## @deftypefnx {} {@var{C} =} ncCatArray(@dots{} @var{propertyname}, @var{properyvalue})
## Create an array that represent a concatenated NetCDF variables.
##
## Create a concatenated array from variables (varname) in a list of
## netcdf files along dimension dim.Individual elements can be accessed by
## subscripts
##
## e.g. C(2,3) and the corrsponding subset of the appropriate file is loaded
##
## @subsubheading Inputs
## @var{dim} - dimensions use for variables
##
## @var{varname} - variable name to load
##
## @var{filenames} - list of filenames as a cell array
##
## @var{pattern} - shell wildcard pattern (e.g. file_*.nc)
##
## @var{filenamefunc} - a function handle where the i-th filename is
## filenamefun(range(i)).
##
## @var{propertyname}, @var{properyvalue} - propery name and value pairs.
##
## @subsubheading Properties
## 'SameAttributes': false or true (default). If SameAttribute is true,
## the variables' NetCDF attribute of all files are assumed to be the same.
## Only the attributes of the first file is loaded in this case.
##
## @subsubheading Outputs
## @var{C} - a concatenated array from the read variables of the files.
##
## @subsubheading Example
## @example
## data = ncCatArray(3,@{'file-20120708.nc','file-20120709.nc'@},'SST')
##
## data = ncCatArray(3,'file-*.nc','SST')
##
## data = ncCatArray(3,@@(t) ['file-' datestr(t,'yyyymmdd') '.nc'],'SST',...
## datenum(2012,07,08):datenum(2012,07,09));
## @end example
##
## Note: in Octave the glob function is used to determine files matching the
## shell wildcard pattern, while in Matlab rdir is used. The function rdir
## is available from Matlab exchange under BSD license
## (http://www.mathworks.com/matlabcentral/fileexchange/19550).
##
## @seealso {cache_decompress, ncArray}
## @end deftypefn
function data = ncCatArray(dim,pattern,varname,varargin)
catdimname = '_cat_dim';
SameAttributes = true;
range = [];
[reg, prop] = parseparams(varargin);
if length(reg) == 1
range = reg{1};
endif
for i = 1:2:length(prop)
if strcmp(prop{i},'SameAttributes')
SameAttributes = prop{i+1};
elseif strcmp(prop{i},'range')
range = prop{i+1};
else
error(['unknown property value ' prop{i}]);
endif
endfor
% file names
if iscell(pattern)
filenames = pattern;
elseif ischar(pattern)
try
filenames = glob(pattern);
catch
try
d = rdir(pattern);
filenames = {d(:).name};
catch
error(['The function rdir or glob (octave) is not available. '...
'rdir can be installed from '...
'http://www.mathworks.com/matlabcentral/fileexchange/19550']);
end_try_catch
end_try_catch
if isempty(filenames)
error('ncArray:nomatch','no file found matching %s',pattern);
endif
elseif isa(pattern, 'function_handle')
filenames = cell(1,length(range));
for i=1:length(range)
filenames{i} = pattern(range(i));
endfor
endif
if isempty(range)
range = 1:length(filenames);
endif
% get all file information
finfos = cell(length(filenames),1);
if SameAttributes
% assume all files have the same ncinfo as the first one
tmp = ncinfo(cached_decompress(filenames{1}));
for i=1:length(filenames)
finfos{i} = tmp;
endfor
% octave allows the following, but not matlab
%finfos(:) = tmp;
else
for i=1:length(filenames)
finfos{i} = ncinfo(cached_decompress(filenames{i}));
endfor
endif
var = arr(dim,filenames,varname,finfos);
[dims,coord] = nccoord(finfos{1},varname);
% add new dimension to coord if arrays are contatenated over a new dimension
% and if coord information already exist
if (dim > length(dims)) && ~isempty(coord)
% concatenate is new dimension
dims{dim} = catdimname;
coord(dim).dims = {catdimname};
coord(dim).val = range;
coord(dim).name = catdimname;
endif
for i=1:length(coord)
%test if value is already defined, if yes do nothing
if isfield(coord(i),'val')
if ~isempty(coord(i).val)
continue
endif
endif
% the number of the dimension might be different
% find in coord(i).dims the index of the dimension called dims{dim}
% for example we concatenate over time, then two situations can arrise
% the coordinate variable lon can dependent on time (dimc is not empty)
% or it does not depdent on time (dimc is empty)
dimc = find(strcmp(coord(i).dims,dims{dim}));
if isempty(dimc)
vinfo = varinfo(finfos{1},coord(i).name);
coord(i).val = ncBaseArray(filenames{1},coord(i).name,'vinfo',vinfo);
else
% coordinates do also depend on the dimension over which we concatenate
%i,coord(i).name,dimc,dims{dim}
coord(i).val = arr(dimc,filenames,coord(i).name,finfos);
endif
%if dim > length(coord(i).dims)
% coord(i).dims{dim} = catdimname;
%end
endfor
data = ncArray(var,dims,coord);
endfunction
function CA = arr(dim,filenames,varname,finfos)
arrays = cell(1,length(filenames));
for i=1:length(filenames)
vinfo = varinfo(finfos{i},varname);
arrays{i} = ncBaseArray(filenames{i},varname,'vinfo',vinfo);
endfor
CA = CatArray(dim,arrays);
endfunction
function vinfo = varinfo(fileinfo,varname)
index = find(strcmp({fileinfo.Variables(:).Name},varname));
vinfo = fileinfo.Variables(index);
endfunction
ncarray-1.0.6/inst/ncarray_example.m 0000644 0000000 0000000 00000002014 14606472241 014413 0 ustar 00
% Tutorial for using ncArray
% It is advised to run this script in an empty directory.
% It will delete and overwrite files named file1.nc, file2.nc and file3.nc.
% size of the example data (2x3)
n = 3;
m = 2;
% create 3 files (file1.nc, file2.nc,...) with a 2x3 variable called SST
data = zeros(n,m);
disp('create example files: file1.nc, file2.nc, file3.nc')
for i = 1:3
data(:) = i;
files{i} = sprintf('file%d.nc',i);
delete(files{i});
ncarray_example_file(files{i},data);
end
% Using ncArray
SST = ncArray('file1.nc','SST');
disp('load the entire file')
data = SST(:,:,:);
disp('get the attribute units')
units = SST.units;
disp('load a particular value');
data = SST(3,2,1);
% Using ncCatArray
disp('concatenate the files over the 3rd dimension (here time)')
SST = ncCatArray(3,{'file1.nc','file2.nc','file3.nc'},'SST');
% or just
% SST = ncCatArray(3,'file*.nc','SST');
disp('load all 3 files');
data = SST(:,:,:);
disp('load a particular value (1,2,1) of the 3rd file');
data = SST(1,2,3);
ncarray-1.0.6/inst/ncarray_example_file.m 0000644 0000000 0000000 00000003621 14606472241 015417 0 ustar 00 ## Copyright (C) 2012,2013,2015 Alexander Barth
##
## 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 3 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 .
## Create an example NetCDF file with the name filename and given data
function ncarray_example_file(filename,data)
dtype = 'double';
sz = size(data);
% Variables
nccreate(filename,'lon','Format','classic','Datatype',dtype,...
'Dimensions',{'x',sz(1), 'y',sz(2)});
ncwriteatt(filename,'lon','long_name','Longitude')
ncwriteatt(filename,'lon','units','degrees_east')
nccreate(filename,'lat','Datatype',dtype,'Dimensions',{'x',sz(1), 'y',sz(2)});
ncwriteatt(filename,'lat','long_name','Latitude')
ncwriteatt(filename,'lat','units','degrees_north')
nccreate(filename,'time','Datatype',dtype,'Dimensions',{'time',1});
ncwriteatt(filename,'time','long_name','Time')
ncwriteatt(filename,'time','units','days since 1858-11-17 00:00:00 GMT')
nccreate(filename,'SST','Datatype',dtype,'Dimensions',...
{'x',sz(1), 'y',sz(2), 'time',1});
ncwriteatt(filename,'SST','missing_value',single(9999))
ncwriteatt(filename,'SST','_FillValue',single(9999))
ncwriteatt(filename,'SST','units','degC')
ncwriteatt(filename,'SST','long_name','Sea Surface Temperature')
ncwriteatt(filename,'SST','coordinates','lat lon')
ncwrite(filename,'SST',data);
endfunction
ncarray-1.0.6/inst/nccoord.m 0000644 0000000 0000000 00000007373 14606472241 012705 0 ustar 00 ## Copyright (C) 2012, 2013, 2015 Alexander Barth
##
## 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 3 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 .
## Author: Alexander Barth (barth.alexander@gmail.com)
## -*- texinfo -*-
## @deftypefn {} {[@var{dims}, @var{coord}] =} nccoord(@var{filename}, @var{varname})
## Get coordinates of the variable varname in the
## netcdf file called filename. The netcdf is assumed to
## follow the CF convention.
##
## @subsubheading Inputs
## @var{filename} - netcdf filename
##
## @var{varname} - variable name
##
## @subsubheading Outputs
## @var{dims} - a cell-array of the dimensions of varname
##
## @var{coord} - an array of structures with the field 'name'
## for the variable name, 'dims' with a cell-array of the
## netcdf dimensions, the units and NetCDF-CF standard name.
##
## coord is an empty structure if no coordinate information have been
## found.
## @end deftypefn
## TODO: use a predictable order for coord:
## lon, lat, depth, time, ensemble,...
function [dims,coord] = nccoord(filename,varname)
if ischar(filename)
finfo = ncinfo(filename);
else
finfo = filename;
endif
% get variable info
index = find(strcmp({finfo.Variables(:).Name},varname));
vinfo = finfo.Variables(index);
% determine coordinates
% using CF convention
dims = {vinfo.Dimensions(:).Name};
% create empty coord array with the fields name and dims
coord = struct('name',{},'dims',{},'standard_name',{},...
'units',{},'positive',{});
% check the coordinate attribute
if ~isempty(vinfo.Attributes)
index = find(strcmp('coordinates',{vinfo.Attributes(:).Name}));
if ~isempty(index)
tmp = strsplit(vinfo.Attributes(index).Value,' ');
% order should not be siginficant
for i=length(tmp):-1:1
coord = addcoord(coord,tmp{i},finfo);
endfor
endif
endif
% check for coordinate dimensions
for i=1:length(dims)
% check if variable with the same name than the dimension exist
index = find(strcmp(dims{i},{finfo.Variables(:).Name}),1);
if ~isempty(index)
coord = addcoord(coord,dims{i},finfo);
endif
endfor
endfunction
function coord = addcoord(coord,name,finfo)
% check if coordinate is aleady in the list
if isempty(find(strcmp(name,{coord(:).name}),1))
% check if name is variable
index = find(strcmp(name,{finfo.Variables(:).Name}));
if ~isempty(index)
vinfo = finfo.Variables(index);
c.name = name;
d = vinfo.Dimensions;
c.dims = {d(:).Name};
c.standard_name = [];
c.units = [];
c.positive = [];
% get standard_name attribute if present
i = find(strcmp('standard_name',{vinfo.Attributes(:).Name}));
if ~isempty(i)
c.standard_name = vinfo.Attributes(i).Value;
endif
% get units attribute if present
i = find(strcmp('units',{vinfo.Attributes(:).Name}));
if ~isempty(i)
c.units = vinfo.Attributes(i).Value;
endif
% get positive attribute if present
i = find(strcmp('positive',{vinfo.Attributes(:).Name}));
if ~isempty(i)
c.positive = vinfo.Attributes(i).Value;
endif
coord(end+1) = c;
endif
endif
endfunction
ncarray-1.0.6/inst/ncreadtime.m 0000644 0000000 0000000 00000002406 14606472241 013361 0 ustar 00 ## Copyright (C) 2012-2022 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {@var{t} =} ncreadtime(@var{filename}, @var{varname})
## Read a time variable as serial day number.
##
## @subsubheading Inputs
## @var{filename} - netcdf filename
##
## @var{varname} - time variable called varname.
##
## @subsubheading Outputs
## @var{t} serial day number (days since 31 December 1 BC, as datenum).
## @end deftypefn
function t = ncreadtime(filename,varname)
t = double(ncread(filename,varname));
units = ncreadatt(filename,varname,'units');
[t0,f] = nctimeunits(units);
t = f*t + t0;
endfunction
ncarray-1.0.6/inst/nctimeunits.m 0000644 0000000 0000000 00000006014 14606472241 013607 0 ustar 00 ## Copyright (C) 2012-2022 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {[@var{t0}, @var{f}] =} nctimeunits(@var{u})
## Parse netCDF time unit.
##
## @subsubheading Inputs
## @var{u} - netCDF time unit
##
## @subsubheading Outputs
## @var{t0} - time offset (days since 31 December 1 BC, as datenum)
##
## @var{f} - scaling factor (in days)
##
## See the netCDF CF convention for the structure of the time units.
## @url{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.6/build/cf-conventions.html#time-coordinate}
## and @url{http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/CDM/CalendarDateTime.html}
## @end deftypefn
function [t0,f] = nctimeunits(u)
% years in days for udunits
% http://cfconventions.org/Data/cf-conventions/cf-conventions-1.6/build/cf-conventions.html#time-coordinate
year_in_days = 365.242198781;
l = strfind(u,'since');
if length(l) ~= 1
error(['time units sould expect one "since": "' u '"']);
endif
period = strtrim(lower(u(1:l-1)));
reference_date = strtrim(u(l+6:end));
if strcmp(period,'millisec') || strcmp(period,'msec')
f = 1/(24*60*60*1000);
elseif strcmp(period,'second') || strcmp(period,'seconds') ...
|| strcmp(period,'s') || strcmp(period,'sec')
f = 1/(24*60*60);
elseif strcmp(period,'minute') || strcmp(period,'minutes') ...
|| strcmp(period,'min')
f = 1/(24*60);
elseif strcmp(period,'hour') || strcmp(period,'hours') ...
|| strcmp(period,'hr')
f = 1/24;
elseif strcmp(period,'day') || strcmp(period,'days')
f = 1;
elseif strcmp(period,'week') || strcmp(period,'weeks')
f = 1/(24*60*60*7);
elseif strcmp(period,'year') || strcmp(period,'years') ...
strcmp(period,'yr')
f = year_in_days;
elseif strcmp(period,'month') || strcmp(period,'months') ...
strcmp(period,'mon')
f = year_in_days/12;
else
error(['unknown units "' period '"']);
endif
if strcmp(reference_date,'1900-01-01 00:00:0.0')
t0 = datenum(1900,1,1);
else
try
t0 = datenum(reference_date,'yyyy-mm-dd HH:MM:SS');
catch
try
t0 = datenum(reference_date,'yyyy-mm-ddTHH:MM:SS');
catch
try
t0 = datenum(reference_date,'yyyy-mm-dd');
catch
error(['date format is not recogized ' reference_date])
end_try_catch
end_try_catch
end_try_catch
endif
endfunction
ncarray-1.0.6/inst/private/ 0000755 0000000 0000000 00000000000 14606472241 012540 5 ustar 00 ncarray-1.0.6/inst/private/assertAlmostEqual.m 0000644 0000000 0000000 00000002446 14606472241 016375 0 ustar 00 ## Copyright (C) 2016 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {} assertAlmostEqual()
## Private function
## @end deftypefn
% this function is necessary because of the limitation of matlab
function assertAlmostEqual(observed,expected)
% tolerance for testing
tol = 1e-10;
% for compatibility with matlab which does not have
% assert (OBSERVED, EXPECTED, TOL)
assert(max(abs(observed(:) - expected(:))) < tol)
% for octave prior to 3.8.0
if isempty(which('isequaln'))
isequaln = @(x,y) isequalwithequalnans(x,y);
endif
% check also NaNS
assert(isequal(isnan(observed),isnan(expected)))
endfunction
ncarray-1.0.6/inst/private/strsplit.m 0000644 0000000 0000000 00000002373 14606472241 014607 0 ustar 00 ## Copyright (C) 2013 Alexander Barth
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {parts =} strsplit(@var{name}, @var{sep})
## A simple strsplit implementation.
##
## Once a strsplit becomes widespread in octave and Matlab,
## this file can be deleted.
##
## This file is preferred over octave's strsplit, because it is compatible
## with the Matlab interpreter.
## @end deftypefn
function parts = strsplit(name,sep);
ind = find(name == sep);
parts = cell(length(ind)+1,1);
ind = [0 ind length(name)+1];
for i=1:length(parts)
parts{i} = name(ind(i)+1:ind(i+1)-1);
endfor
endfunction
ncarray-1.0.6/inst/test_ncarray.m 0000644 0000000 0000000 00000022767 14606472241 013760 0 ustar 00 ## Copyright (C) 2012, 2015 Alexander Barth
## Copyright (C) 2019 John D
##
## 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 3 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 .
## -*- texinfo -*-
## @deftypefn {} {} test_ncarray()
## Test ncBaseArray, ncCatArray and ncArray.
## @end deftypefn
function test_ncarray()
varname = 'SST';
tmpdir = tempname;
mkdir(tmpdir);
tmpfname = tempname(tmpdir);
refdata = {};
for i = 1:3
files{i} = fullfile(tmpdir,sprintf('file%d.nc',i));
refdata{i} = randn(220,144);
ncarray_example_file(files{i},refdata{i});
endfor
filename = files{1};
% test ncread/ncwrite
copyfile(files{1},tmpfname);
SST_ref = ncread(files{1},'SST');
ncwrite(tmpfname,'SST',zeros(size(SST_ref)));
test = ncread(tmpfname,'SST');
assert(all(test(:) == 0))
ncwrite(tmpfname,'SST',SST_ref);
test = ncread(tmpfname,'SST');
assertAlmostEqual(test,SST_ref)
%%% test ncBaseArray
% reading
copyfile(files{2},tmpfname);
SST = ncBaseArray(tmpfname,varname);
test = SST(:,:,:);
SST_ref = ncread(tmpfname,varname);
assertAlmostEqual(test,SST_ref)
assert(isempty(SST(:,:,:,[])));
assertAlmostEqual(SST_ref, SST(:,:,:,1))
ind = floor(numel(SST_ref) * rand(100,1))+1;
assertAlmostEqual(SST(ind),SST_ref(ind))
% writing
r = round(randn(size(SST)));
SST(:,:,:) = r;
SST_ref = ncread(tmpfname,varname);
assertAlmostEqual(r,SST_ref);
SST(:,:,:) = 3 * r;
SST_ref = ncread(tmpfname,varname);
assertAlmostEqual(3 * r,SST_ref);
%%% test ncArray
% reading
copyfile(files{2},tmpfname);
SST = ncArray(tmpfname,varname);
test = SST(:,:,:);
SST_ref = ncread(tmpfname,varname);
assertAlmostEqual(test,SST_ref)
assert(isempty(SST(:,:,:,[])));
assertAlmostEqual(SST_ref, SST(:,:,:,1))
ind = floor(numel(SST_ref) * rand(100,1))+1;
assertAlmostEqual(SST(ind),SST_ref(ind))
assertAlmostEqual(SST_ref(1,:,:), SST(1,:,:))
% sum
nanmeanSST = nanmean(SST);
if exist ("nanmean")
nanmeanSSTref = nanmean(SST_ref);
else
nanmeanSSTref = mean(SST_ref, 'omitnan');
endif
assertAlmostEqual(nanmeanSST, nanmeanSSTref)
%momentSST = moment(SST,2,1);
%momentSSTref = moment(SST_ref,2,1);
%assertAlmostEqual(momentSST, momentSSTref)
sumSST = sum(SST,1);
sumSSTref = sum(SST_ref,1);
assertAlmostEqual(sumSST, sumSSTref)
sumSST = sum(SST,2);
sumSSTref = sum(SST_ref,2);
assertAlmostEqual(sumSST, sumSSTref)
sumSST = sum(SST,3);
sumSSTref = sum(SST_ref,3);
assertAlmostEqual(sumSST, sumSSTref)
sumSST = sum(SST);
sumSSTref = sum(SST_ref);
assertAlmostEqual(sumSST, sumSSTref)
prodSST = prod(SST);
prodSSTref = prod(SST_ref);
assertAlmostEqual(prodSST, prodSSTref)
% only for octave
%sumsqSST = sumsq(SST);
%sumsqSSTref = sumsq(SST_ref); % does not work in matlab
%assertAlmostEqual(sumsqSST, sumsqSSTref)
meanSST = mean(SST);
meanSSTref = mean(SST_ref);
assertAlmostEqual(meanSST, meanSSTref)
varSST = var(SST);
varSSTref = var(SST_ref);
assertAlmostEqual(varSST, varSSTref)
varSST = var(SST,1);
varSSTref = var(SST_ref,1);
assertAlmostEqual(varSST, varSSTref)
varSST = var(SST,[],2);
varSSTref = var(SST_ref,[],2);
assertAlmostEqual(varSST, varSSTref)
stdSST = std(SST);
stdSSTref = std(SST_ref);
assertAlmostEqual(stdSST, stdSSTref)
stdSST = std(SST,1);
stdSSTref = std(SST_ref,1);
assertAlmostEqual(stdSST, stdSSTref)
stdSST = std(SST,[],2);
stdSSTref = std(SST_ref,[],2);
assertAlmostEqual(stdSST, stdSSTref)
maxSST = max(SST,[],2);
maxSSTref = max(SST_ref,[],2);
assertAlmostEqual(maxSST, maxSSTref)
minSST = min(SST,[],2);
minSSTref = min(SST_ref,[],2);
assertAlmostEqual(minSST, minSSTref)
% writing
r = round(randn(size(SST)));
SST(:,:,:) = r;
SST_ref = ncread(tmpfname,varname);
assertAlmostEqual(r,SST_ref);
SST(:,:,:) = 3 * r;
SST_ref = ncread(tmpfname,varname);
assertAlmostEqual(3 * r,SST_ref);
%%% CatArray
% reading
CA = CatArray(3,{...
ncArray(filename,varname),...
ncArray(files{2},varname),...
ncArray(files{3},varname)...
});
assert(isequaln(size(CA),[220 144 3]))
SST_ref = ncread(filename,'SST');
tmp2 = CA(:,:,1);
assertAlmostEqual(SST_ref,tmp2)
SST_test = CA(:,:,2);
SST_ref = ncread(files{2},'SST');
assertAlmostEqual(SST_test,SST_ref)
CA2 = CatArray(4,{...
ncArray(files{1},varname),...
ncArray(files{2},varname),...
ncArray(files{3},varname)...
});
SST_test = CA2(:,:,:,2);
assertAlmostEqual(SST_test,SST_ref)
CA2 = ncCatArray(3,{...
files{1},...
files{2},...
files{3}},...
varname);
SST_test = CA2(:,:,2);
assertAlmostEqual(SST_test,SST_ref)
CA2 = ncCatArray(3,fullfile(tmpdir,'file*nc'),varname);
SST_test = CA2(:,:,2);
assertAlmostEqual(SST_test,SST_ref)
CA2 = ncCatArray(3,...
@(i) fullfile(tmpdir,sprintf('file%d.nc',i)),...
varname,...
1:3);
SST_test = CA2(:,:,2);
assertAlmostEqual(SST_test,SST_ref)
SST_ref = cat(3,...
ncread(files{1},'SST'),...
ncread(files{2},'SST'),...
ncread(files{3},'SST'));
assertAlmostEqual(CA2(:,:,:),SST_ref)
assertAlmostEqual(CA2(:,:,1),SST_ref(:,:,1))
assertAlmostEqual(CA2(3:5:50,3:5:100,1),SST_ref(3:5:50,3:5:100,1))
assertAlmostEqual(CA2(3:5:50,3:5:100,2),SST_ref(3:5:50,3:5:100,2))
assertAlmostEqual(CA2(3:5:50,3:5:100,3),SST_ref(3:5:50,3:5:100,3))
assertAlmostEqual(CA2(3:5:50,3:5:100,end),SST_ref(3:5:50,3:5:100,end))
assertAlmostEqual(CA2(50,100,1:3),SST_ref(50,100,1:3))
assertAlmostEqual(CA2(3:5:50,3:5:100,1:2:3),SST_ref(3:5:50,3:5:100,1:2:3))
assertAlmostEqual(CA2(3:5:50,3:5:end,1:2:3),SST_ref(3:5:50,3:5:end,1:2:3))
assertAlmostEqual(CA2(3:5:50,3:5:end,:),SST_ref(3:5:50,3:5:end,:))
% access with linear index
assertAlmostEqual(CA2(:),SST_ref(:))
assertAlmostEqual(CA2(1:10),SST_ref(1:10))
assertAlmostEqual(CA2(1:2:10),SST_ref(1:2:10))
ind = floor(numel(SST_ref) * rand(100,1))+1;
assertAlmostEqual(CA2(ind),SST_ref(ind))
meanSST = mean(CA2,3);
meanSSTref = mean(SST_ref,3);
%assertAlmostEqual(meanSST, meanSSTref)
diff = meanSST -meanSSTref;
assert(max(diff(:)) < 1e-6)
% writing
for i=1:3
list{i} = tempname;
copyfile(filename,list{i});
endfor
CA2 = ncCatArray(3,list,varname);
r = round(randn(size(CA2)));
CA2(:,:,:) = r;
check = ncread(list{2},varname);
assertAlmostEqual(check,r(:,:,2))
r2 = round(randn(size(CA2)));
r(3:5:50,3:5:end,:) = r2(3:5:50,3:5:end,:);
CA2(3:5:50,3:5:end,:) = r2(3:5:50,3:5:end,:);
assertAlmostEqual(CA2(:,:,:),r)
r(end-1,3:5:end,1:2:3) = 2*r2(end-1,3:5:end,1:2:3);
CA2(end-1,3:5:end,1:2:3) = 2*r2(end-1,3:5:end,1:2:3);
assertAlmostEqual(CA2(:,:,:),r)
if 1
% test ncArray (constructor: ncArray(var,dims,coord)
SST = ncBaseArray(filename,varname);
SST_ref = ncread(filename,varname);
lon_ref = ncread(filename,'lon');
coord(1).val = ncBaseArray(filename,'lon');
coord(1).dims = {'x','y'};
coord(2).val = ncBaseArray(filename,'lat');
coord(2).dims = {'x','y'};
coord(3).val = ncBaseArray(filename,'time');
coord(3).dims = {'time'};
data = ncArray(SST,{'x','y','time'},coord);
[x,y,t] = data(:,:,:).coord;
assertAlmostEqual(data(:,:,:),SST_ref)
assertAlmostEqual(x,lon_ref)
assertAlmostEqual(data(),SST_ref)
[x,y,t] = data().coord;
assertAlmostEqual(x,lon_ref)
assertAlmostEqual(data(1:3:end,:,:),SST_ref(1:3:end,:,:))
[x,y,t] = data(1:3:end,:,:).coord;
assertAlmostEqual(x,lon_ref(1:3:end,:))
% test ncArray (constructor: ncData(filename,varname)
SST = ncArray(filename,varname);
[x,y,t] = data(:,:,:).coord;
assertAlmostEqual(data(:,:,:),SST_ref)
assertAlmostEqual(x,lon_ref)
assertAlmostEqual(data(),SST_ref)
[x,y,t] = data().coord;
assertAlmostEqual(x,lon_ref)
assertAlmostEqual(data(1:3:end,:,:),SST_ref(1:3:end,:,:))
[x,y,t] = data(1:3:end,:,:).coord;
assertAlmostEqual(x,lon_ref(1:3:end,:))
%assert(strcmp(SST.units,'degC'))
assert(strcmp(SST.('units'),'degC'))
endif
% read compressed data
zname = [tmpfname '.gz'];
system(['gzip --stdout ' tmpfname ' > ' zname]);
%zname = [tmpfname '.xz'];
%system(['xz --stdout ' tmpfname ' > ' zname]);
SST = ncArray(zname,'SST');
SST_ref = ncread(tmpfname,'SST');
assertAlmostEqual(SST(),SST_ref)
CA2 = ncCatArray(3,fullfile(tmpdir,'file*nc'),varname);
SST_test = CA2(:,:,2);
SST_ref = ncread(files{2},'SST');
assertAlmostEqual(SST_test,SST_ref)
assert(strcmp(CA2.('units'),'degC'));
test_ncarray_nan
% clean-up
d = dir(tmpdir);
for i = 1:length(d)
if ~strcmp(d(i).name,'.') && ~strcmp(d(i).name,'..')
delete(fullfile(tmpdir,d(i).name));
endif
endfor
rmdir(tmpdir);
[t0,f] = nctimeunits('days since 1770-01-01 00:00:00');
assert(t0 == datenum(1770,01,01));
assert(f == 1);
disp('All tests passed.')
endfunction
%!test
%! test_ncarray()
ncarray-1.0.6/inst/test_ncarray_nan.m 0000644 0000000 0000000 00000004020 14606472241 014572 0 ustar 00 % Copyright (C) 2013 Alexander Barth
% Copyright (C) 2019 John D
%
% 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 3 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 .
% Test ncBaseArray, ncCatArray and ncArray.
function test_ncarray_nan()
% for octave prior to 3.8.0
if isempty(which('isequaln'))
isequaln = @(x,y) isequalwithequalnans(x,y);
end
varname = 'SST';
tmpdir = tempname;
mkdir(tmpdir);
tmpfname = tempname(tmpdir);
dataref = randn(220,144,3);
%dataref(rand(size(dataref)) > 0.7) = NaN;
dataref(50:80,30:90,1:2) = NaN;
for i = 1:3
files{i} = fullfile(tmpdir,sprintf('file%d.nc',i));
ncarray_example_file(files{i},dataref(:,:,i));
end
data = ncCatArray(3,files,varname);
reddata = nanmean(data,3);
if exist ("nanmean")
reddataref = nanmean(dataref,3);
else
reddataref = mean(dataref,3, 'omitnan');
endif
assertAlmostEqual(reddata, reddataref)
reddata = nansum(data,3);
reddataref = nansum(dataref,3);
assertAlmostEqual(reddata, reddataref)
reddata = nanvar(data,[],3);
if exist ("nanvar")
reddataref = nanvar(dataref,[],3);
else
reddataref = var(dataref,[],3, 'omitnan');
endif
diff = reddata - reddataref;
assert(max(diff(:)) < 1e-6)
reddata = nanstd(data,[],3);
if exist ("nanstd")
reddataref = nanstd(dataref,[],3);
else
reddataref = std(dataref,[],3, 'omitnan');
endif
diff = reddata - reddataref;
assert(max(diff(:)) < 1e-6)
% clean-up
for i = 1:3
delete(files{i});
end
rmdir(tmpdir);
endfunction
%!test
%! test_ncarray_nan ()