mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 21:49:08 +09:00
initial commit
This commit is contained in:
@@ -0,0 +1,339 @@
|
||||
% Call function without arguments for a detailed explanation of its use
|
||||
|
||||
% Filename: $RCSfile: cbfread.m,v $
|
||||
%
|
||||
% $Revision: 1.2 $ $Date: 2011/05/09 13:03:07 $
|
||||
% $Author: $
|
||||
% $Tag: $
|
||||
%
|
||||
% Description:
|
||||
% Macro for reading Crystallographic Binary File (CBF) files written by the
|
||||
% Pilatus detector control program camserver.
|
||||
%
|
||||
% Note:
|
||||
% Compile the C-program cbf_uncompress using mex (see header of
|
||||
% cbf_uncompress.c) to use it for uncompression instead of the slower
|
||||
% Matlab code.
|
||||
% Currently this routine supports only the subset of CBF features needed to
|
||||
% read the Pilatus detector data.
|
||||
% Call without arguments for a brief help text.
|
||||
%
|
||||
% Dependencies:
|
||||
% - image_read_set_default
|
||||
% - fopen_until_exists
|
||||
% - get_hdr_val
|
||||
% - compiling cbf_uncompress.c increases speed but is not mandatory
|
||||
%
|
||||
%
|
||||
% 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] = cbfread(filename,varargin)
|
||||
import io.*
|
||||
import io.CBF.*
|
||||
import utils.char_to_cellstr
|
||||
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,'cbf');
|
||||
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 = 4096;
|
||||
|
||||
% end of header signature
|
||||
eoh_signature = char([ 12 26 4 213 ]);
|
||||
|
||||
% CBF file signature
|
||||
cbf_signature = '###CBF: VERSION';
|
||||
|
||||
% Calling an external C routine for uncompressing the data did save about
|
||||
% 30% time on a specific machine.
|
||||
% The C-routine is used if a compiled version of it exists.
|
||||
% See the header of cbf_uncompress.c for information on how to compile the
|
||||
% C file using mex in Matlab.
|
||||
|
||||
c_routine = exist('+io/+CBF/cbf_uncompress.mexa64', 'file') || ...
|
||||
~isempty(which('cbf_uncompress')) ; % faster than which('cbf_uncompress')
|
||||
|
||||
|
||||
% 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
|
||||
|
||||
% search for end of header signature within the expected maximum length of
|
||||
% a header
|
||||
end_of_header_pos = ...
|
||||
strfind( fdat(1:min(max_header_length,length(fdat)))',...
|
||||
eoh_signature );
|
||||
if (length(end_of_header_pos) < 1)
|
||||
cbf_error(filename,'no header end signature found');
|
||||
return;
|
||||
end
|
||||
if (debug_level >= 2)
|
||||
fprintf('Header length is %d bytes.\n',end_of_header_pos -1);
|
||||
end
|
||||
|
||||
% return the complete header as lines of a cell array
|
||||
frame.header = char_to_cellstr( char(fdat(1:(end_of_header_pos-1))') );
|
||||
|
||||
% check for CBF signature
|
||||
if (~strncmp(cbf_signature,frame.header{1},length(cbf_signature)))
|
||||
cbf_error(filename,[ 'CBF signature ''' cbf_signature ...
|
||||
''' not found in first line ''' frame.header{1} '''' ]);
|
||||
end
|
||||
|
||||
% extract the mandatory information for decompression from the header
|
||||
no_of_bin_bytes = get_hdr_val(frame.header,'X-Binary-Size:','%f',1);
|
||||
dim1 = get_hdr_val(frame.header,'X-Binary-Size-Fastest-Dimension:','%f',1);
|
||||
dim2 = get_hdr_val(frame.header,'X-Binary-Size-Second-Dimension:','%f',1);
|
||||
el_type = get_hdr_val(frame.header,'X-Binary-Element-Type: "','%[^"]',1);
|
||||
switch (el_type)
|
||||
case 'signed 32-bit integer'
|
||||
bytes_per_pixel = 4;
|
||||
otherwise
|
||||
cbf_error(filename,[ 'unknown element type ' el_type ]);
|
||||
end
|
||||
compr_type = get_hdr_val(frame.header,'conversions="','%[^"]',1);
|
||||
switch (compr_type)
|
||||
case 'x-CBF_BYTE_OFFSET'
|
||||
compression_type = 1;
|
||||
case 'x-CBF_NONE'
|
||||
compression_type = 2;
|
||||
otherwise
|
||||
cbf_error(filename,[ 'unknown compression type ' compr_type ]);
|
||||
end
|
||||
if (debug_level >= 2)
|
||||
fprintf('Frame dimensions are %d x %d.\n',dim2,dim1);
|
||||
end
|
||||
|
||||
% uncompress the binary data
|
||||
[frame.data] = ...
|
||||
extract_frame(fdat((end_of_header_pos+length(eoh_signature)):end),...
|
||||
dim1,dim2,no_of_bin_bytes,compression_type,...
|
||||
filename,...
|
||||
c_routine,debug_level);
|
||||
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
function [] = cbf_error(filename,text)
|
||||
|
||||
fprintf('cbfread of %s:\n %s\n',filename,text);
|
||||
return;
|
||||
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
function [frame] = ...
|
||||
extract_frame(dat_in,...
|
||||
dim1,dim2,no_of_in_bytes,compression_type,...
|
||||
filename,...
|
||||
c_routine,debug_level)
|
||||
|
||||
import io.*
|
||||
import io.CBF.*
|
||||
import utils.char_to_cellstr
|
||||
import utils.fopen_until_exists
|
||||
import utils.get_hdr_val
|
||||
|
||||
|
||||
% uncompressed data are copied directly
|
||||
if (compression_type == 2)
|
||||
% initialize return array
|
||||
frame = zeros(dim1,dim2);
|
||||
% copy uncompressed data
|
||||
for (ind_out = 1:(dim1*dim2))
|
||||
ind_in = ind_out *4 -3;
|
||||
frame(ind_out) = double(dat_in(ind_in)) + ...
|
||||
256 * double(dat_in(ind_in+1)) + ...
|
||||
65536 * double(dat_in(ind_in+2)) + ...
|
||||
16777216 * double(dat_in(ind_in+3));
|
||||
end
|
||||
return;
|
||||
end
|
||||
|
||||
|
||||
if (c_routine)
|
||||
if (debug_level >= 2)
|
||||
fprintf('C routine called.\n');
|
||||
end
|
||||
[frame] = ...
|
||||
cbf_uncompress(dat_in,dim1,dim2,no_of_in_bytes,compression_type);
|
||||
return;
|
||||
end
|
||||
|
||||
if (debug_level >= 2)
|
||||
fprintf('Matlab routine called.\n');
|
||||
end
|
||||
|
||||
|
||||
% initialize return array
|
||||
frame = zeros(dim1,dim2);
|
||||
|
||||
% only byte-offset compression is supported
|
||||
if (compression_type ~= 1)
|
||||
cbf_error(filename,...
|
||||
['extract_frame does not support compression type no. ' ...
|
||||
num2str(compression_type)]);
|
||||
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;
|
||||
ind_in = 1;
|
||||
val_curr = 0;
|
||||
val_diff = 0;
|
||||
while (ind_in <= no_of_in_bytes)
|
||||
val_diff = double(dat_in(ind_in));
|
||||
ind_in = ind_in +1;
|
||||
if (val_diff ~= 128)
|
||||
% if not escaped as -128 (0x80=128) use the current byte as
|
||||
% difference, with manual complement to emulate the sign
|
||||
if (val_diff >= 128)
|
||||
val_diff = val_diff - 256;
|
||||
end
|
||||
else
|
||||
% otherwise check for 16-bit integer value
|
||||
if ((dat_in(ind_in) ~= 0) || (dat_in(ind_in+1) ~= 128))
|
||||
% if not escaped as -32768 (0x8000) use the current 16-bit integer
|
||||
% as difference
|
||||
val_diff = double(dat_in(ind_in)) + ...
|
||||
256 * double(dat_in(ind_in+1));
|
||||
% manual complement to emulate the sign
|
||||
if (val_diff >= 32768)
|
||||
val_diff = val_diff - 65536;
|
||||
end
|
||||
ind_in = ind_in +2;
|
||||
else
|
||||
ind_in = ind_in +2;
|
||||
% if everything else failed use the current 32-bit value as
|
||||
% difference
|
||||
val_diff = double(dat_in(ind_in)) + ...
|
||||
256 * double(dat_in(ind_in+1)) + ...
|
||||
65536 * double(dat_in(ind_in+2)) + ...
|
||||
16777216 * double(dat_in(ind_in+3));
|
||||
% manual complement to emulate the sign
|
||||
if (val_diff >= 2147483648)
|
||||
val_diff = val_diff - 4294967296;
|
||||
end
|
||||
ind_in = ind_in +4;
|
||||
end
|
||||
end
|
||||
val_curr = val_curr + val_diff;
|
||||
frame(ind_out) = val_curr;
|
||||
ind_out = ind_out +1;
|
||||
end
|
||||
|
||||
if (ind_out-1 ~= dim1*dim2)
|
||||
cbf_error(filename,[ 'mismatch between ' num2str(ind_out-1) ...
|
||||
' bytes after decompression with ' num2str(dim1*dim2) ...
|
||||
' expected ones' ]);
|
||||
end
|
||||
|
||||
|
||||
% if (~original_orientation)
|
||||
% frame.data = frame.data(end:-1:1,end:-1:1)';
|
||||
% end
|
||||
Reference in New Issue
Block a user