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% SAVEFAST fast saves of large arrays to .mat files
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%
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% savefast_safe(filename, varargin)
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%
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%
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% Matlab's 'save' command can be very slow when saving large arrays,
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% because by default Matlab attempts to use compression. This function
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% provides a much faster alternative, at the cost of larger files.
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%
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% The syntax is identical to that of the Matlab save command.
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%
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% Example:
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% >> ops = struct('algorithm', 'greedy');
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% >> A = int32(randi(20, 1000, 1200, 40));
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% >> B = randn(500, 1800, 60);
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% >> tic; save /tmp/test ops A B; toc
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% Elapsed time is 22.980294 seconds.
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% >> tic; savefast /tmp/test ops A B; toc
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% Elapsed time is 0.571098 seconds.
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% Copyright 2013 by Timothy E. Holy
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% Modified to safe version - Michal Odstrcil, 2017
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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%
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% Copyright (c) 2013, Timothy Holy
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% All rights reserved.
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%
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% Redistribution and use in source and binary forms, with or without
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% modification, are permitted provided that the following conditions are
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% met:
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%
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% * Redistributions of source code must retain the above copyright
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% notice, this list of conditions and the following disclaimer.
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% * Redistributions in binary form must reproduce the above copyright
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% notice, this list of conditions and the following disclaimer in
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% the documentation and/or other materials provided with the distribution
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%
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% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
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% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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% POSSIBILITY OF SUCH DAMAGE.
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function savefast_safe(filename, varargin)
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% Append .mat if necessary
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[filepath, filebase, ext] = fileparts(filename);
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if isempty(ext)
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filename = fullfile(filepath, [filebase '.mat']);
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end
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if ~islogical(varargin{end}) || varargin{end} == false
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% ask before overwritting
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if exist(filename,'file')
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utils.verbose(0,['File ' filename ' exists,' ])
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userans = input(['Do you want to overwrite (y/N)? '],'s');
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if strcmpi(userans,'y')
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utils.verbose(1,['Saving to ' filename]);
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else
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utils.verbose(1,['Did not save ' filename])
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return
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end
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else
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utils.verbose(1,['Saving to ' filename]);
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end
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end
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if islogical(varargin{end})
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varargin = varargin(1:end-1);
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end
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%% ask before rewritting the current file
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if ~exist(filepath,'dir') && ~isempty(filepath)
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mkdir(filepath);
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end
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varargin = unique(varargin);
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% Extract the variable values
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vars = cell(size(varargin));
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for i = 1:numel(vars)
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vars{i} = evalin('caller', varargin{i});
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end
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% Separate numeric arrays from the rest
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isnum = cellfun(@(x) isa(x, 'numeric'), vars);
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% remove -struct and -v7 options from the string
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isopt = cellfun(@(x)strcmp(x(1),'-'), varargin);
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create_dummy = false;
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if all(isnum)
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% Save a dummy variable, just to create the file
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dummy = 0; %#ok<NASGU>
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save(filename, '-v7.3', 'dummy');
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create_dummy = true;
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else
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s = struct;
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for i = 1:numel(isnum)
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if ~isnum(i) && ~isopt(i)
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s.(varargin{i}) = vars{i};
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end
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end
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save(filename, '-v7.3', '-struct', 's');
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end
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% Delete the dummy, if necessary, just in case the user supplied a
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% variable called dummy
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if create_dummy
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fid = H5F.open(filename,'H5F_ACC_RDWR','H5P_DEFAULT');
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H5L.delete(fid,'dummy','H5P_DEFAULT');
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H5F.close(fid);
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end
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% Save all numeric variables
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for i = 1:numel(isnum)
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if ~isnum(i) || isopt(i)
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continue
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end
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% always assume that single precision is enough for data saving
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if isa(vars{i}, 'double')
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vars{i} = single(vars{i});
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end
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varname = ['/' varargin{i}];
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if numel(vars{i}) == 0
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warning('Skipping empty variable %s', varname)
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continue
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else
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if isreal(vars{i})
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h5create(filename, varname, size(vars{i}), 'DataType', class(vars{i}));
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h5write(filename, varname, vars{i});
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else
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h5create(filename, [varname,'_r'], size(vars{i}), 'DataType', class(vars{i}));
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h5create(filename, [varname,'_i'], size(vars{i}), 'DataType', class(vars{i}));
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h5write(filename, [varname,'_r'], real(vars{i}));
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h5write(filename, [varname,'_i'], imag(vars{i}));
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end
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end
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end
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end
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