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% Call function without arguments for a detailed explanation of its use
% Filename: $RCSfile: cbfwrite.m,v $
%
% $Revision: 1.2 $ $Date: 2014/04/17 16:49:22 $
% $Author: $
% $Tag: $
%
% Description:
% Macro for writing data to a Crystallographic Binary File (CBF) file.
% Assumes that the data have been read from such a file beforehand, i.e.,
% that the header exists already.
%
%
% history:
%
% April 10th 2014: 1st version
%*-----------------------------------------------------------------------*
%|                                                                       |
%|  Except where otherwise noted, this work is licensed under a          |
%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
%|  International (CC BY-NC-SA 4.0) license.                             |
%|                                                                       |
%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
%|                                                                       |
%|      Author: CXS group, PSI  |
%*-----------------------------------------------------------------------*
% You may use this code with the following provisions:
%
% If the code is fully or partially redistributed, or rewritten in another
% computing language this notice should be included in the redistribution.
%
% If this code, or subfunctions or parts of it, is used for research in a
% publication or if it is fully or partially rewritten for another
% computing language the authors and institution should be acknowledged
% in written form in the publication: “Data processing was carried out
% using the “cSAXS matlab package” developed by the CXS group,
% Paul Scherrer Institut, Switzerland.”
% Variations on the latter text can be incorporated upon discussion with
% the CXS group if needed to more specifically reflect the use of the package
% for the published work.
%
% A publication that focuses on describing features, or parameters, that
% are already existing in the code should be first discussed with the
% authors.
%
% This code and subroutines are part of a continuous development, they
% are provided “as they are” without guarantees or liability on part
% of PSI or the authors. It is the user responsibility to ensure its
% proper use and the correctness of the results.
function [fcount_total] = cbfwrite(filename,frame,varargin)
import io.CBF.*
import io.*
import utils.default_parameter_value
import utils.fopen_until_exists
import utils.get_hdr_val
% 0: no debug information
% 1: some feedback
% 2: a lot of information
debug_level = 0;
% determine default orientation based on the file name extension
orient_by_extension = default_parameter_value('image_read','OrientByExtension');
fcount_total = -1;
% check minimum number of input arguments
if (nargin < 2)
fprintf('\nUsage:\n');
fprintf('[bytes_written]=%s( filename, frame-structure [[,<name>,<value>]...]);\n',mfilename);
fprintf('Write a CBF file from data that have been read via cbfread.m before.\n');
fprintf('Conventions are likely to be specific for the PILATUS detector.\n')
fprintf('\n');
fprintf('The optional <name>,<value> pairs are:\n');
image_orient_help(mfilename,'ParametersOnly',1);
fprintf('\n');
fprintf('The file name should be the name of a single file without wildcards.\n');
error('At least the filename and the data-structure have to be specified as input parameter.');
end
% check frame structure
if (~isstruct(frame))
error('The 2nd parameter needs to be a structure as read by cbfread.m');
end
if (~isfield(frame,'header'))
error('The 2nd parameter needs to be a structure with a field ''header'', as read by cbfread.m');
end
if (~isfield(frame,'data'))
error('The 2nd parameter needs to be a structure with a field ''data'', as read by cbfread.m');
end
if (size(frame.header,2) ~= 1)
error('The header has the wrong dimensions. Only single-frame structures are suppoerted.\n');
end
% check minimum number of input arguments
if (nargin < 2)
error('At least the filename and the frame have to be specified as input parameter.');
end
% accept cell array with name/value pairs as well
no_of_in_arg = nargin;
if (nargin == 3)
if (isempty(varargin))
% ignore empty cell array
no_of_in_arg = no_of_in_arg -1;
else
if (iscell(varargin{1}))
% use a filled one given as first and only variable parameter
varargin = varargin{1};
no_of_in_arg = 2 + length(varargin);
end
end
end
% check number of input arguments
if (rem(no_of_in_arg,2) ~= 0)
error('The optional parameters have to be specified as ''name'',value pairs');
end
% set default values for the variable input arguments and parse the named
% parameters:
vararg_remain = cell(4,1);
for ind = 1:2:length(varargin)
name = varargin{ind};
value = varargin{ind+1};
switch name
case 'OrientByExtension'
orient_by_extension = value;
otherwise
% pass further arguments on to fopen_until_exists
vararg_remain{end+1} = name; %#ok<AGROW>
vararg_remain{end+1} = value; %#ok<AGROW>
end
end
vararg_remain{1} = 'OrientByExtension';
vararg_remain{2} = orient_by_extension;
vararg_remain{3} = 'InvertOrientation';
vararg_remain{4} = 1;
% get the length of the zero-padding at the end of the file
padding_length = get_hdr_val(frame.header{1},'X-Binary-Size-Padding:','%d',1);
% end of header signature
eoh_signature = char([ 12 26 4 213 ]);
% orient image
[frame,vararg_remain] = image_orient(frame,vararg_remain);
% open file for write-access, overwrite in case of an existing file
[fid] = fopen(filename,'w');
if (fid < 0)
return;
end
% In byte-offset compression the difference to the previous pixel value is
% stored as a byte, 16-bit integer or 32-bit integer, depending on its
% size.
% The sizes above one byte are indicated by the escape sequence -1 in the
% previous data format, i.e, a 32-bit integer is preceded by the sequence %
% 0x80 (too large for a byte)
% 0x8000 (too large for a 16-bit integer).
ind_out = 1;
no_of_pixels = size(frame.data,1) * size(frame.data,2);
% initialize output array at maximum size
frame_out = zeros(no_of_pixels*4 + padding_length,1,'uint8');
val_prev = 0;
for ind_in = 1:no_of_pixels
val_diff = frame.data(ind_in) - val_prev;
if (abs(val_diff) < 128)
% write differences in the range from -127 to 127 directly as 8bit
% signed integer:
% manual complement to emulate the sign
if (val_diff < 0)
val_diff = 256 + val_diff;
end
frame_out(ind_out) = val_diff;
ind_out = ind_out +1;
else
% escape with 0x80
frame_out(ind_out) = 128;
% check for 16-bit integer value
if (abs(val_diff) < 32768)
% write signed 16bit integer value:
% manual complement to emulate the sign
if (val_diff < 0)
val_diff = 65536 + val_diff;
end
frame_out(ind_out+1) = bitand(val_diff,255);
frame_out(ind_out+2) = bitand(val_diff,65280)/256;
ind_out = ind_out +3;
else
% escape with 0x8000
frame_out(ind_out+1) = 0;
frame_out(ind_out+2) = 128;
% write signed 32bit integer value:
% manual complement to emulate the sign
if (val_diff < 0)
val_diff = 4294967296 + val_diff;
end
frame_out(ind_out+3) = bitand(val_diff,255);
frame_out(ind_out+4) = bitand(val_diff,65280)/256;
frame_out(ind_out+5) = bitand(val_diff,16711680)/65536;
frame_out(ind_out+6) = bitand(val_diff,4278190080)/16777216;
ind_out = ind_out +7;
end
end
% the current intensity value becomes the previous value
val_prev = frame.data(ind_in);
end
% calculate length of binary data including zero-padding at the end
binary_length = ind_out -1 + padding_length;
% update this value in the file-header
[~, line_no] = get_hdr_val(frame.header{1},'X-Binary-Size:','%f',1);
frame.header{1}{line_no} = sprintf('X-Binary-Size: %d',binary_length-padding_length);
% write header
[fcount_total] = fprintf(fid,'%s\r\n',frame.header{1}{:});
if (fcount_total == 0)
error('Could not write any header data.\n');
end
% write end-of-header signature
[fcount] = fwrite(fid,eoh_signature,'uint8');
fcount_total = fcount_total + fcount;
if (fcount == 0)
error('Could not write end-of-header signature.\n');
end
% write binary data
[fcount] = fwrite(fid,frame_out(1:(binary_length)));
fcount_total = fcount_total + fcount;
if (fcount ~= binary_length)
error('Could not write CBF image-data.');
end
% write binary-end signature
[fcount] = fprintf(fid,'\r\n--CIF-BINARY-FORMAT-SECTION----\r\n;\r\n\r\n');
fcount_total = fcount_total + fcount;
if (fcount < 1)
error('Could not write CBF binary-end signature');
end
% close output data file
fclose(fid);
if (debug_level >= 2)
fprintf('%d data bytes written\n',fcount_total);
end
return;