%SAVEDATAFILE Save datafile
%
% B = SAVEDATAFILE(A,FEATSIZE,NAME,NBITS,FILESIZE)
%
% INPUT
% A Datafile, or cell array with datafiles and/or datasets
% FEATSIZE Feature size, i.e. image size of a single object in B
% Default: as it is.
% NAME Desired name of directory
% NBITS # of bits in case of rescaling (8,16 or 32)
% Default: no rescaling
% FILESIZE # of elements stored in a single file
% Default 10000000.
%
% OUTPUT
% B New datafile
%
% DESCRIPTION
% The datafile A is completed by desired preprocessing and postprocessing.
% It should therefore be convertable to a dataset. It is saved in the
% directory NAME and B refers to it. If desired the data and target fields
% are compressed (after appropriate rescaling) to NBITS unsigned integers.
% The stored datafile can be retrieved by
%
% B = PRDATAFILE(NAME)
%
% B is a 'mature' datafile, i.e. a dataset distributed over a number of
% files with maximum size FILESIZE. This has only advantages over a 'raw'
% datafile defined for a directory of images in case of substantial pre-
% and postprocessing, due to the overhead of the dataset construct of B.
% FEATSIZE can be used to reshape the size of object (e.g. from 256 to
% [16 16])
%
% If A is cell array with datafiles and/or datasets, they are first
% horizontally concatenated before the datafile is written. The first
% element in A should be a datafile.
%
% The difference with CREATEDATAFILE is that SAVEDATAFILE assumes that
% the datafile after completion by preprocessing can be converted into a
% dataset and the data is stored as such and a sompact as possible.
% CREATEDATAFILE saves every object in a separate file and is thereby
% useful in case preprocessing does not yield a proper dataset with the
% same number of features for every object.
%
% SEE ALSO (<a href="http://37steps.com/prtools">PRTools Guide</a>)
% DATAFILES, DATASETS, CREATEDATAFILE
% Copyright: R.P.W. Duin, r.p.w.duin@37steps.com
% Faculty EWI, Delft University of Technology
% P.O. Box 5031, 2600 GA Delft, The Netherlands
function c = savedatafile(dfile_in,featsize,dirr,nbits,filesize)
if iscell(dfile_in)
b = dfile_in{1};
k = getsize(prdataset(b(1,:)),2);
m = getsize(b,1);
for j=2:length(dfile_in(:))
if size(dfile_in{j},1) ~= m
error('Datafiles or datasets to be combined should have equal number of objects')
end
k = k+size(dfile_in{j},2);
end
else
b = dfile_in;
k = getsize(prdataset(b(1,:)),2);
m = getsize(b,1);
end
isvaldfile(b);
c = b;
if nargin < 5 % maximum nr of elements in datafile
filesize = 1000000;
end
if nargin < 4 | isempty(nbits) % default: no conversion
nbits = 0;
end
if nargin < 3 | isempty(dirr) % invent name if not supplied
name = getname(b);
if ~isempty(name) & length(name) > 10
name = [deblank(name(1:10)) '_'];
else
name = 'PRDatafile_';
end
dirr = [name num2str(round(rand*100000))]; % make it unique
dirr = fullfile(pwd,dirr); %DXD store it in the working dir
end
if all(nbits ~= [0 1 8 16 32])
error('Illegal number of bits supplied for conversion')
end
if nargin < 2, featsize = []; end
% reorder datafile for faster retrieval
if isdatafile(b) & ~iscell(dfile_in)
file_index = getident(b.prdataset,'file_index');
[jj,R] = sort(file_index(:,1)+file_index(:,2)/(max(file_index(:,2),[],1)+1));
b = b(R,:);
end
%[m,k] = size(b);
nobj= floor(filesize/k); % # of objects per file
if nobj<1
error('Filesize is too small. A single object does not even fit in!');
end
nfiles = ceil(m/nobj); % # of files needed
if exist(dirr) == 7 % if datafile already exists
act_dir = pwd;
cd(dirr); % go to it
fclose('all');
delete *.mat % make it empty
delete file*
cd(act_dir) % return to original directory
else % otherwise create it
[pp,ff] = fileparts(dirr);
if isempty(pp)
pp = pwd;
end
mkdir(pp,ff)
end
obj1 = 1; % initialise start object
obj2 = min(obj1+nobj-1,m); % initialise end object
file_index = zeros(m,2);
s = sprintf('Saving %4i datafiles: ',nfiles);
prwaitbar(nfiles,s);
spaces = ' ';
% initialise structure with file information
cfiles = struct('name',cell(1,nfiles),'nbits',[], ...
'offsetd',[],'scaled',[],'offsett',[],'scalet',[]);
for j=1:nfiles % run over all files to be created
prwaitbar(nfiles,j,[s int2str(j)]);
a = prdataset(b(obj1:obj2,:)); % convert objects for a single file into dataset
if iscell(dfile_in)
for i=2:length(dfile_in(:))
a = [a prdataset(dfile_in{i}(obj1:obj2,:))];
end
end
if ~isempty(featsize)
if prod(featsize) ~= prod(getfeatsize(a))
error('Desired feature size does not match size of data')
else
a = setfeatsize(a,featsize);
end
end
lendata = size(a,2);
[a,scaled,offsetd,scalet,offsett,prec] = convert(a,nbits); % convert precision
filej = ['file',num2str(j)];
fname = fullfile(dirr,filej);
fid = fopen(fname,'w');
if fid<0
error('Unable to write file %s.',fname);
end
fwrite(fid,[a.data a.targets]',prec); % store
fclose(fid);
cfiles(j).name = filej; % name of the file
cfiles(j).prec = prec; % precision
cfiles(j).scaled = scaled; % scaling for datafield
cfiles(j).offsetd = offsetd; % offset for datafield
cfiles(j).scalet = scalet; % scaling for target field
cfiles(j).offsett = offsett; % offset for target field
cfiles(j).sized = a.featsize; % feature (image) size
cfiles(j).sizet = size(a.targets,2); % size target field
% create file_index
file_index(obj1:obj2,1) = repmat(j,obj2-obj1+1,1);
file_index(obj1:obj2,2) = [1:obj2-obj1+1]';
obj1 = obj2+1; % update start object
obj2 = min(obj1+nobj-1,m); % update end object
end
prwaitbar(0);
% finalise datafile definition
c.files = cfiles; % file information
c.type = 'mature'; % mature datafile
preproc.preproc = [];
preproc.pars = {};
c.preproc = preproc; % no preprocessing
c.postproc = prmapping([]); % default postprocessing
featsize = getfeatsize(c); % copy feature (image) size
c.postproc = setsize_in(c.postproc,featsize); % set input and ...
c.postproc = setsize_out(c.postproc,featsize); % output size postprocessing
c.prdataset = setfeatsize(c.prdataset,getfeatsize(c)); % set size datafile
c.prdataset = setident(c.prdataset,file_index,'file_index'); % store file_index
%DXD give it the name of the directory, not the complete path:
%c.prdataset = setname(c.prdataset,dirr);
[pname,dname] = fileparts(dirr);
c.prdataset = setname(c.prdataset,dname);
if isempty(pname), pname = pwd; end
c.rootpath = fullfile(pname,dname);
%DXD this path/filename is *very* strange!
%save(fullfile(pwd,dirr,dirr),'c'); % store the datafile as mat-file for fast retrieval
%DXD I changed it into this:
%save(fullfile(dirr,filej),'c'); % store the datafile as mat-file for
%fast retrieval
save(fullfile(dirr,dname),'c'); % store the datafile as mat-file for fast retrieval
%closemess([],len1+len2);
return
function [a,scaled,offsetd,scalet,offsett,prec] = convert(a,nbits)
% handle precision data and target fields
if nbits == 0 % no conversion
scaled = [];
offsetd = [];
scalet = [];
offsett = [];
prec = 'double';
return;
end
% compute data field conversion pars
data = +a;
maxd = max(max(data));
mind = min(min(data));
scaled = (2^nbits)/(maxd-mind);
offsetd = -mind;
data = (data+offsetd)*scaled;
% compute target field conversion pars
targ = gettargets(a);
if isempty(targ) % no targets set
scalet = [];
offsett = [];
else
maxt = max(max(targ));
mint = min(min(targ));
scalet = (2^nbits)/(maxt-mint);
offsett = -mint;
targ = (targ+offsett)*scalet;
end
% execute conversion
switch nbits
case 8
data = uint8(data);
targ = uint8(targ);
prec = 'uint8';
case 16
data = uint16(data);
targ = uint16(targ);
prec = 'uint16';
case 32
data = uint32(data);
targ = uint32(targ);
prec = 'uint32';
otherwise
error('Desired conversion type not found')
end
% store results
a.data = data;
a.targets = targ;
return