mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 18:29:08 +09:00
222 lines
7.3 KiB
Matlab
222 lines
7.3 KiB
Matlab
% Call function without arguments for instructions on how to use it
|
||
|
||
% Filename: $RCSfile: speread.m,v $
|
||
%
|
||
% $Revision: 1.1 $ $Date: 2008/06/10 17:05:14 $
|
||
% $Author: $
|
||
% $Tag: $
|
||
%
|
||
% Description:
|
||
% Macro for reading SPE CCD data files written by WinView from
|
||
% Roper Scientific / PI Acton
|
||
%
|
||
% Note:
|
||
% Call without arguments for a brief help text.
|
||
%
|
||
% Dependencies:
|
||
% - image_read_set_default
|
||
% - fopen_until_exists
|
||
% - get_hdr_val
|
||
%
|
||
%
|
||
% history:
|
||
%
|
||
% May 9th 2008: 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 [frame,vararg_remain] = speread(filename,varargin)
|
||
import io.*
|
||
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;
|
||
|
||
% initialize return argument
|
||
frame = struct('header',[], 'data',[]);
|
||
|
||
% check minimum number of input arguments
|
||
if (nargin < 1)
|
||
image_read_sub_help(mfilename,'SPE');
|
||
error('At least the filename has to be specified as input parameter.');
|
||
end
|
||
|
||
% accept cell array with name/value pairs as well
|
||
no_of_in_arg = nargin;
|
||
if (nargin == 2)
|
||
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 = 1 + length(varargin);
|
||
end
|
||
end
|
||
end
|
||
|
||
% check number of input arguments
|
||
if (rem(no_of_in_arg,2) ~= 1)
|
||
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 = cell(0,0);
|
||
for ind = 1:2:length(varargin)
|
||
name = varargin{ind};
|
||
value = varargin{ind+1};
|
||
switch name
|
||
otherwise
|
||
% pass further arguments on to fopen_until_exists
|
||
vararg{end+1} = name;
|
||
vararg{end+1} = value;
|
||
end
|
||
end
|
||
|
||
|
||
% expected maximum length for the text header
|
||
max_header_length = 4100;
|
||
|
||
% try to open the data file
|
||
if (debug_level >= 1)
|
||
fprintf('Opening %s.\n',filename);
|
||
end
|
||
[fid,vararg_remain] = fopen_until_exists(filename,vararg);
|
||
if (fid < 0)
|
||
return;
|
||
end
|
||
|
||
% read all data at once
|
||
[fdat,fcount] = fread(fid,'uint8=>uint8');
|
||
|
||
% close input data file
|
||
fclose(fid);
|
||
if (debug_level >= 2)
|
||
fprintf('%d data bytes read\n',fcount);
|
||
end
|
||
|
||
% some sanity checks
|
||
if (fdat(4099:4100) ~= [ 85; 85 ])
|
||
error('%s: no header end signature found',filename);
|
||
return;
|
||
end
|
||
|
||
|
||
% return some selected information from the header as lines of a cell array
|
||
% and extract some variables needed for the data extraction
|
||
% version 2.5 is assumed, otherwise some values may be wrong
|
||
frame.header = cell(0,0);
|
||
xdim = double(typecast(fdat(43:44),'uint16'));
|
||
frame.header{end+1} = sprintf('xdim %.0f',xdim);
|
||
|
||
ydim = double(typecast(fdat(657:658),'uint16'));
|
||
frame.header{end+1} = sprintf('ydim %.0f',ydim);
|
||
|
||
exposure_sec = double(typecast(fdat(11:14),'single'));
|
||
frame.header{end+1} = sprintf('exposure %.3f',exposure_sec);
|
||
|
||
frame.header{end+1} = sprintf('xDimDet %d',typecast(fdat(7:8),'uint16'));
|
||
frame.header{end+1} = sprintf('yDimDet %d',typecast(fdat(19:20),'uint16'));
|
||
|
||
frame.header{end+1} = sprintf('date %s',char(fdat(21:30)'));
|
||
frame.header{end+1} = sprintf('ExperimentTimeLocal %s:%s:%s',...
|
||
char(fdat(173:174)'),char(fdat(175:176)'),char(fdat(177:178)'));
|
||
|
||
data_type = fdat(109);
|
||
frame.header{end+1} = sprintf('datatype %d',data_type);
|
||
switch (data_type)
|
||
case 0
|
||
bytes_per_pixel = 4;
|
||
cast_type = 'single';
|
||
case 1
|
||
bytes_per_pixel = 4;
|
||
cast_type = 'int32';
|
||
case 2
|
||
bytes_per_pixel = 2;
|
||
cast_type = 'int16';
|
||
case 3
|
||
bytes_per_pixel = 2;
|
||
cast_type = 'uint16';
|
||
otherwise
|
||
error('unknown data type %d',data_type);
|
||
end
|
||
|
||
frame.header{end+1} = sprintf('BackGrndApplied %d',typecast(fdat(151:152),'uint16'));
|
||
|
||
frame.header{end+1} = sprintf('gain %d',typecast(fdat(199:200),'uint16'));
|
||
|
||
% frame.header{end+1} = sprintf('comments %s',char(fdat(201:600)'));
|
||
|
||
% number of accumulations
|
||
frame.header{end+1} = sprintf('lavgexp %ld',typecast(fdat(669:672),'uint32'));
|
||
|
||
frame.header{end+1} = sprintf('ReadoutTime %f',typecast(fdat(673:676),'single'));
|
||
|
||
frame.header{end+1} = sprintf('sw_version %s',char(fdat(689:703)'));
|
||
|
||
frame.header{end+1} = sprintf('type %d',typecast(fdat(705:706),'uint16'));
|
||
|
||
frame.header{end+1} = sprintf('flatFieldApplied %d',typecast(fdat(707:708),'uint16'));
|
||
|
||
num_frames = double(typecast(fdat(1447:1450),'uint32'));
|
||
frame.header{end+1} = sprintf('NumFrames %.0f',num_frames);
|
||
|
||
file_header_ver = double(typecast(fdat(1993:1996),'single'));
|
||
frame.header{end+1} = sprintf('file_header_ver %.2f',file_header_ver);
|
||
|
||
|
||
% extract the data frames
|
||
data_bytes = bytes_per_pixel * xdim * ydim * num_frames;
|
||
if (fcount-4100 ~= data_bytes)
|
||
error('%d bytes expected, %d found',data_bytes,fcount-4100);
|
||
end
|
||
frame.data = reshape(typecast(fdat(4101:end),cast_type),...
|
||
xdim, ydim, num_frames );
|
||
|
||
% conversion to standard view on PI-SCX4300 data at the SLS/cSAXS beamline
|
||
% if (~original_orientation)
|
||
% frame.data = permute(frame.data,[2 1 3]);
|
||
% end
|
||
|
||
% return as double precision floating point
|
||
frame.data = double(frame.data);
|
||
|
||
|