| GSSpcWrite (filename, spectra, axis, logtxt, logbin, options)
|
function GSSpcWrite (filename, spectra, axis, logtxt, logbin, options)
%GSSpcWrite v0.4.3
%
%This function will export a spectrum from data MATLAB-environment into an
%spc-file. The universal design of the spc-file format permits
%the use of spectra from different spectroscopic sources containing a wide
%range of spectra and information. The current function is able to export
%single-spectra spc-files. Currently multi-spectra spc-files aren't
%supported because of a lack of them during test-fase of GSSpcRead.
%
%Syntax:
% GSSpcWrite (filename, spectra, axis, logtxt, logbin, options)
% GSSpcWrite (filename, spectra, axis, logtxt, logbin)
% GSSpcWrite (filename, spectra, axis, logtxt)
% GSSpcWrite (filename, spectra, axis)
%
%Input parameters:
% - filename: the name of the file in which the spectrum will be
% written, path included
% - spectra: (double array) the spectral data itself. Spectral data are in
% a matrix, where one row represents one spectrum.
% - axis: (cell array), the xaxis of the spectra.
% - logtxt: (char array or cellstring array) logtext to save with the spectra
% - logbin: (uint8 data) binary data to save with the data
% - options: optional parameter: structure: possible fields:
% fcmnt: string: file comment
% fexper: integer: experimental technique: see SPC file format
% description (0 = general)
% fsource: string: instrument source
% fmethod: string: used methods, instrumental techniques, ...
% xunit: integer: type of x-units: see SPC file format
% description (0 = general)
% yunit: integer: type of y-units: see SPC file format
% description (0 = general)
% SaveHighPrecision: spectra are stored in float32 format as
% standard (as should be the case). When higher precision is
% needed, however, the spectra will be processed and stored as
% integer values. To use the highest precision, set this value
% to 1.
%
%Syntax 2:
% GSSpcWrite (filename, spectrum)
%
%Input parameters:
% - filename: same as above
% - spectrum: structure that either contains the fields
% spectra, axis and options (see above) or is equal to a structure
% as produced by GSSpcRead
%
%Example:
% (with X a structure containing a spectrum and the xaxis)
% GSSpcWrite ('d:\test.spc', test.spectrum, test.xaxis)
%
%Example 2:
% (with X a matrix that contains two spectra)
% axis{1} = xaxis;
% axis{2} = 1:2;
% GSSpcWrite ('d:\test.spc', X, axis)
%Technical data about the SPC-fileformat is freely avaiable and obtained
%from Galactic Industries Corp: see gspc_udf.pdf available at:
% https://ftirsearch.com/features/converters/SPCFileFormat.htm
%
%This software package is dual licensed. You can use it according to the term
%of either the GPLv3 or the BSD license.
%
%GSTools: a set of MATLAB functions to read, write and work with SPC spectra in MATLAB
%
%C 2005-2008, Kris De Gussem, Raman Spectroscopy Research Group, Department
%of analytical chemistry, Ghent University
%C2009 Kris De Gussem
%
%This file is part of GSTools.
%
%GSTools is free software: you can redistribute it and/or modify
%it under the terms of the GNU General Public License as published by
%the Free Software Foundation, either version 3 of the License, or
%(at your option) any later version.
%
%GSTools is distributed in the hope that it will be useful,
%but WITHOUT ANY WARRANTY; without even the implied warranty of
%MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
%GNU General Public License for more details.
%
%You should have received a copy of the GNU General Public License
%along with GSTools. If not, see <http://www.gnu.org/licenses/>.
%Copyright (c) 2004-2009, Kris De Gussem
%All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, are permitted provided that the following conditions are
%met:
%
% * Redistributions of source code must retain the above copyright
% notice, this list of conditions and the following disclaimer.
% * Redistributions in binary form must reproduce the above copyright
% notice, this list of conditions and the following disclaimer in
% the documentation and/or other materials provided with the distribution
% * Neither the name of Raman Spectroscopy Research Group, Department of
% analytical chemistry, Ghent University nor the names
% of its contributors may be used to endorse or promote products derived
% from this software without specific prior written permission.
%
%THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
%AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
%IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
%ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
%LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
%CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
%SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
%INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
%CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
%ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
%POSSIBILITY OF SUCH DAMAGE.
%History:
% v0.1:
% - initial release
% v0.2:
% - now correctly interpretes flags in SPC-header, which previously
% lead to negative peaks, ...
% - corrected determination whether data are evenly spaced
% v0.3:
% - small bugfixes
% - custom information about the spectrum given by the user, can now
% be written using a new options parameter
% - logtxt now supports a cellstring array
% v0.4:
% - support for multi-file spc-spectra: due to the nature of MATLAB
% (more precisely working sith matrices in which each column has a
% fixed x-value) only multi-dimensional spectra for which the x-axis
% is the same for all spectra can be written to an SPC-file
% - spectra in a GSSpcRead structure can be saved
% v0.4.1:
% - some bugfixes related to saving spectra as integers
% - spectra are now save in float32 format as standard (as is
% recommended for conversion routines). An extra option is added now
% to alter this behaviour (only syntax 1).
%Note to the developer:
%This routine is very complex, because of the different input formats that
%are to be considered. The routine is therefore split in different
%subroutines that create and write the different data blocks in the spc
%file (cfr. SPC file format description). Also, some of these subroutines
%are doubled: once for the case that the data are supplied in matrices
%(syntax 1) and once for the case when the data are supplied in structures
%(see also the name of the subroutines).
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%check input
switch nargin
case 2
logtxt = [];
logbin = [];
options = [];
case 3
logtxt = [];
logbin = [];
options = [];
case 4
logbin = [];
options = [];
case 5
options = [];
case 6
otherwise
error ('GSTools:msg', 'Wrong number of input parameters. See help GSSpcWrite.');
end
if iscellstr(filename)
filename = filename{1};
end
if ischar (filename) == false
error ('GSTools:msg', 'GSSpcWrite requires a string containing the spectral filename...');
end
%open the spc-file
[f,msg] = fopen(filename, 'wb', 'l'); %create and open the file for write access, overwrite file if it is present
if f==-1
disp(msg);
disp(filename);
error('GSTools:msg', 'Error creating file...');
end
clear msg;
if nargin > 2
CreateSPCFileFromMatrices (f, spectra, axis, logtxt, logbin, options);
else
%we have a structure that contains the spectrum
CreateSPCFileFromStructure (f, spectra, options);
end
fclose (f);
GSToolsAbout
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function CreateSPCFileFromMatrices (f, spectra, axis, logtxt, logbin, options)
%check whether the axis parameter is correctly entered
if iscell (axis) == false
if isnumeric (axis)
axis = MakeVector (axis, 'The axis should be a cell-vector...')';
tmp = axis; clear axis;
axis{1} = tmp;
clear tmp
else
error ('GSTools:msg', 'The axis parameter must be a cell containing a vector with the axis'' values');
end
else
axis{1} = MakeVector (axis{1}, 'Axis should be a cell-vector. The first element contains a row vector with the x-axis values, whereas the second element is the z-axis.')';
end
%check length of axis and spectra
if size (spectra,2) ~= size (axis{1},2)
error ('GSTools:msg', 'Length of axis and number of spectral channels do not correspond.');
end
if numel(spectra) ~= (sum(size(spectra))-1) %single spectrum?
if size (spectra,1) ~= size (axis{2},2)
error ('GSTools:msg', 'Length of axis and number of spectral channels do not correspond.');
end
end
%now the input parameters should be OK, start with the real work...
%write the spc-header of the spectrum
ThisSpcHdr = CreateSpcHeader (spectra, axis{1}, logtxt, logbin, options);
WriteSpcHeader (f, ThisSpcHdr);
WriteSpectraAndAxis (f, ThisSpcHdr, spectra, axis, options);
%log
if ThisSpcHdr.flogoff
%if not NULL: then there's a log
if isempty(logtxt) == false
if iscellstr (logtxt)
tmp = [];
for i=1:length(logtxt)
tmp = [tmp logtxt{i} '\n'];
end
logtxt = tmp;
clear tmp;
end
end
ThisLogstcHdr = CreateLogstcHeader (logtxt, logbin);
WriteLogstcHeader (f, ThisLogstcHdr);
fwrite(f,logbin,'uint8');
fwrite(f,logtxt,'char');
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function CreateSPCFileFromStructure (f, spectra, options)
%write the spc-header of the spectrum
[ThisSpcHdr, data, axis] = CreateSpcHeaderFromStructure (spectra, options);
WriteSpcHeader (f, ThisSpcHdr);
WriteSpectraAndAxis (f, ThisSpcHdr, data, axis, options);
logtxt = spectra.log.txt;
if ThisSpcHdr.flogoff
%if not NULL: then there's a log
if isempty(logtxt) == false
if iscellstr (logtxt)
tmp = [];
for i=1:length(logtxt)
tmp = [tmp logtxt{i} '\n']; %sprintf('%s%s\n', tmp, logtxt{i});
end
logtxt = tmp;
clear tmp;
end
end
ThisLogstcHdr = CreateLogstcHeader (logtxt, spectra.log.bin);
WriteLogstcHeader (f, ThisLogstcHdr);
fwrite(f,spectra.log.bin,'uint8');
fwrite(f,logtxt,'char');
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ThisSpcHdr = CreateSpcHeader (spectra, axis, logtxt, logbin, options)
%This subfunction will create an spc-header
%f is the file-pointer to the spc-file.
%
%An spc-header has the following structure (extract of the Cpp header file
%of Galactic Industries Corp.): see gspc_udf.pdf for more
%information and technical data.
[dummy1,dummy2,endian] = computer; %#ok<ASGLU>
clear dummy1 dummy2;
ftflgs = false(1,8); %BYTE: flags about type of spc-file (see main-function): single-spectrum, multi-spectrum, nr. of bits for an integer, ...
ftflgs(1) = false; %TSPREC: we want 32 bit precision %Y data blocks are 16 bit integer (only if fexp is NOT 0x80h): 1 = 16 bit integer
ftflgs2.TSPREC = ftflgs(1);
ftflgs(2) = false; %TCGRAM: normally this flag is not used %Enables fexper in older software (not used)
ftflgs2.TCGRAM = ftflgs(2);
if size (spectra, 1) > 1
ftflgs(3) = true; %TMULTI: Multifile data format (more than one subfile)
else
ftflgs(3) = false; %TMULTI: Multifile data format (more than one subfile)
end
ftflgs2.TMULTI = ftflgs(3);
ftflgs(4) = false; %TRANDM: If TMULTI and TRANDM then Z values in SUBHDR structures are in random order (not used)
ftflgs2.TRANDM = ftflgs(4);
ftflgs(5) = true; %TORDRD: If TMULTI and TORDRD then Z values are in ascending or descending ordered but not evenly spaced. Z values readv from individual SUBHDR structures.
ftflgs2.TORDRD = ftflgs(5);
ftflgs(6) = false; %%std%% %TALABS: Axis label text stored in fcatxt separated by nulls. Ignore fxtype, fytype, fztype corresponding to non-null text in fcatxt.
ftflgs2.TALABS = ftflgs(6);
ftflgs(7) = false; %TXYXYS: Each subfile has unique X array; can only be used if TXVALS is also used. Used exclusively to flag as MS data for drawing as sticks rather than connected lines.
ftflgs2.TXYXYS = ftflgs(7);
%check whether data are evenly spaced
nr = length (axis);
ind = 2:1:nr;
ind2 = 1:1:nr-1;
diff = axis(ind) - axis(ind2);
if range(diff) > 1E-8 %if not evenly spaced then intervals will be higher than 0 (or higher than a very low number due to CPU-precision)
ftflgs(8) = 1; %TXVALS: Non-evenly spaced X data. File has X value array preceding Y data block(s).
else
ftflgs(8) = 0;
end
ftflgs2.TXVALS = ftflgs(8);
clear diff EvenlySpaced;
if endian == 'B' %needs to be checked!
ftflgs = flipud(ftflgs);
end
ThisSpcHdr.ftflgs = ftflgs; clear ftflgs
ThisSpcHdr.ftflgs2 = ftflgs2; clear ftflgs2
ThisSpcHdr.fversn = 75; % BYTE: version of the spc file: currently two versions exists, only the newer is supported
if isfield (options, 'fexper')
ThisSpcHdr.fexper = options.fexper;
else
ThisSpcHdr.fexper = 11; %%std%% %type of experiment: 11: Raman spectrum: see SPC-file formate description for meanings.
end
if isfield (options,'SaveHighPrecision')
if options.SaveHighPrecision == 1
SaveAsFloats = 0;
else
SaveAsFloats = 1;
end
else
SaveAsFloats = 1;
end
if SaveAsFloats
ThisSpcHdr.fexp = 128;
else
ThisSpcHdr.fexp = OptimalPower (spectra(1,:)); % char: Fraction scaling exponent integer (80h = 128 decimal => spec values are float variables)
end
ThisSpcHdr.fnpts = nr; % DWORD: number of points
ThisSpcHdr.ffirst = axis(1); % double: Floating X coordinate of first point
ThisSpcHdr.flast = axis(nr); % double: Floating X coordinate of last point
ThisSpcHdr.fnsub = size(spectra, 1); % DWORD: Integer number of subfiles (1 if not TMULTI)
if isfield (options, 'xunit')
ThisSpcHdr.fxtype = options.xunit; %%std%%%BYTE: Type of X units
else
ThisSpcHdr.fxtype = 13; %%std%%%BYTE: Type of X units
end
if isfield (options, 'yunit')
ThisSpcHdr.fytype = options.yunit; %%std%%%BYTE: Type of Y units
else
ThisSpcHdr.fytype = 0; %%std%%%BYTE: Type of Y units
end
if isfield (options, 'zunit')
ThisSpcHdr.fztype = options.zunit; %%std%%%BYTE: Type of z units
else
ThisSpcHdr.fztype = 0; %%std%%%BYTE: Type of Z units
end
ThisSpcHdr.fpost = 0; % BYTE fpost; /* Posting disposition (see GRAMSDDE.H) */
ThisSpcHdr.fdate = CalcSpecDateTime; % DWORD fdate; /* Date/Time LSB: min=6b,hour=5b,day=5b,month=4b,year=12b */
tmp = zeros(1,9);
tmp(1:8) = uint8('Math det');
ThisSpcHdr.fres = tmp; % char fres[9]; /* Resolution description text (null terminated) */
clear tmp;
tmp = zeros(1,9);
if isfield(options, 'fsource')
le = length(options.fsource);
if le > 9
warning ('GSTools:msg', 'instrument source string is to long, it will be cut...')
options.fsource = options.fsource(1:9);
le = 9;
end
tmp(1:le) = uint8(options.fsource);
else
tmp(1:5) = uint8('GSSpc');
end
ThisSpcHdr.fsource = tmp; % char fsource[9]; /* Source instrument description text (null terminated) */
clear tmp;
ThisSpcHdr.fpeakpt = 0; % WORD fpeakpt; /* Peak point number for interferograms (0=not known) */
ThisSpcHdr.fspare = zeros (1,8); % float fspare[8]; /* Used for Array Basic storage */
tmp = zeros (1,130); % char fcmnt[130]; /* Null terminated comment ASCII text string */
if isfield (options, 'fcmnt')
le = length(options.fcmnt);
if le > 130
warning ('GSTools:msg', 'file comment string is to long, it will be cut...')
options.fcmnt = options.fcmnt(1:130);
le = 130;
end
tmp(1:le) = options.fcmnt;
else
tmp(1:28) = uint8('Created by GSSpcWrite v0.4.1') ;
end
ThisSpcHdr.fcmnt = tmp;
ThisSpcHdr.fcatxt = zeros (1,30);
if isempty (logtxt) && isempty (logbin)
ThisSpcHdr.flogoff = 0; % DWORD flogoff; /* File offset to log block or 0 (see above) */
else
%offset= size (SPC-header) + size (xaxis) + nr_spec (size(sub-header) + size(spectrum)
offset = 512 + (ThisSpcHdr.ftflgs2.TXVALS * 4 * length (axis)) + size (spectra, 1) * (32 + 4 * length (axis));
ThisSpcHdr.flogoff = offset;
end
ThisSpcHdr.fmods = 0; % DWORD fmods; /* File Modification Flags (see below: 1=A,2=B,4=C,8=D..) */
ThisSpcHdr.fprocs = 0; % BYTE fprocs; /* Processing code (see GRAMSDDE.H) */
ThisSpcHdr.flevel = 1; % BYTE flevel; /* Calibration level plus one (1 = not calibration data) */
ThisSpcHdr.fsampin = 1; % WORD fsampin; /* Sub-method sample injection number (1 = first or only ) */
ThisSpcHdr.ffactor = 1; % float ffactor; /* Floating data multiplier concentration factor (IEEE-32) */
tmp = zeros(1,48); % char fmethod[48]; /* Method/program/data filename w/extensions comma list */
if isfield (options, 'fmethod')
le = length(options.fmethod);
if le > 48
warning ('GSTools:msg', 'Program string is to long, it will be cut...')
options.fmethod = options.fmethod(1:48);
le = 48;
end
tmp(1:le) = options.fmethod;
else
tmp(1:28) = uint8('Created by GSSpcWrite v0.4.1') ;
end
ThisSpcHdr.fmethod = tmp;
clear tmp;
ThisSpcHdr.fzinc = 0; % float fzinc; /* Z subfile increment (0 = use 1st subnext-subfirst) */
ThisSpcHdr.fwplanes = 0;% DWORD fwplanes; /* Number of planes for 4D with W dimension (0=normal) */
ThisSpcHdr.fwinc = 0; % float fwinc; /* W plane increment (only if fwplanes is not 0) */
ThisSpcHdr.fwtype = 0; % BYTE fwtype; /* Type of W axis units (see definitions below) */
ThisSpcHdr.freserv = zeros(1,187); % char freserv[187]; /* Reserved (must be set to zero) */
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ThisSpcHdr, data, axis2] = CreateSpcHeaderFromStructure (spectra, options)
%This subfunction will create an spc-header
%f is the file-pointer to the spc-file.
%
%An spc-header has the following structure (extract of the Cpp header file
%of Galactic Industries Corp.): see gspc_udf.pdf for more
%information and technical data.
[dummy1,dummy2,endian] = computer; %#ok<ASGLU>
clear dummy1 dummy2;
ftflgs = false(1,8); %BYTE: flags about type of spc-file (see main-function): single-spectrum, multi-spectrum, nr. of bits for an integer, ...
ftflgs(1) = false; %TSPREC: we want 32 bit precision %Y data blocks are 16 bit integer (only if fexp is NOT 0x80h): 1 = 16 bit integer
ftflgs2.TSPREC = ftflgs(1);
ftflgs(2) = false; %TCGRAM: normally this flag is not used %Enables fexper in older software (not used)
ftflgs2.TCGRAM = ftflgs(2);
%determine the xaxis
axis = [];
if isfield(spectra, 'xaxis')
if isempty(spectra.xaxis) == false
axis{1} = spectra.xaxis;
end
end
if isempty (axis)
if isfield(spectra, 'axis')
if isempty(spectra.axis) == false
axis{1} = spectra.axis;
end
end
end
%determine where we can find the spectrum/spectra
data = [];
if isfield(spectra, 'data')
if isempty(spectra.data) == false
data = spectra.data;
end
end
if isempty (data)
if isfield(spectra, 'spectra')
if isempty(spectra.spectra) == false
if isnumeric (spectra.spectra)
data = spectra.spectra;
else
%Note to the developer: this can generate a bug: we only
%consider data with the same xaxis
le = length (spectra.spectra);
data = zeros (le, size (spectra.spectra(1).data));
zvalues = zeros (1,le);
axis{1} = spectra.spectra(1).xaxis;
for i=1:le
data(1,:) = spectra.spectra(i).data;
zvalues(i) = spectra.spectra(i).zvalue;
end
axis{2} = zvalues;
end
else
error ('GSTools:msg', 'Error: can not interprete the structure that contains the spectrum/spectra. Can not find a field data or spectra with appropriate data.');
end
end
end
axis2 = axis;
axis = axis{1};
if size (data, 1) > 1
ftflgs(3) = true; %TMULTI: Multifile data format (more than one subfile)
else
ftflgs(3) = false; %TMULTI: Multifile data format (more than one subfile)
end
ftflgs2.TMULTI = ftflgs(3);
ftflgs(4) = false; %TRANDM: If TMULTI and TRANDM then Z values in SUBHDR structures are in random order (not used)
ftflgs2.TRANDM = ftflgs(4);
ftflgs(5) = true; %TORDRD: If TMULTI and TORDRD then Z values are in ascending or descending ordered but not evenly spaced. Z values readv from individual SUBHDR structures.
ftflgs2.TORDRD = ftflgs(5);
ftflgs(6) = false; %%std%% %TALABS: Axis label text stored in fcatxt separated by nulls. Ignore fxtype, fytype, fztype corresponding to non-null text in fcatxt.
ftflgs2.TALABS = ftflgs(6);
ftflgs(7) = false; %TXYXYS: Each subfile has unique X array; can only be used if TXVALS is also used. Used exclusively to flag as MS data for drawing as sticks rather than connected lines.
ftflgs2.TXYXYS = ftflgs(7);
%check whether data are evenly spaced
nr = length (axis);
ind = 2:1:nr;
ind2 = 1:1:nr-1;
diff = axis(ind) - axis(ind2);
if range (diff) > 1E-8 %if not evenly spaced then intervals will be higher than 0 (or higher than a very low number due to CPU-precision)
ftflgs(8) = 1; %TXVALS: Non-evenly spaced X data. File has X value array preceding Y data block(s).
else
ftflgs(8) = 0;
end
ftflgs2.TXVALS = ftflgs(8);
clear diff EvenlySpaced;
if endian == 'B'
ftflgs = flipud(ftflgs);
end
ThisSpcHdr.ftflgs = ftflgs; clear ftflgs
ThisSpcHdr.ftflgs2 = ftflgs2; clear ftflgs2
ThisSpcHdr.fversn = 75; % BYTE: version of the spc file: currently two versions exists, only the newer is supported
if isfield (spectra, 'TechniqueNr')
ThisSpcHdr.fexper = spectra.TechniqueNr;
else
ThisSpcHdr.fexper = 11; %%std%% %type of experiment: 11: Raman spectrum: see SPC-file formate description for meanings.
end
if isfield (options,'SaveHighPrecision')
if options.SaveHighPrecision == 1
SaveAsFloats = 0;
else
SaveAsFloats = 1;
end
else
SaveAsFloats = 1;
end
if SaveAsFloats
ThisSpcHdr.fexp = 128;
else
ThisSpcHdr.fexp = OptimalPower (data(1,:)); % char: Fraction scaling exponent integer (80h = 128 decimal => spec values are float variables)
end
ThisSpcHdr.fnpts = nr; % DWORD: number of points
ThisSpcHdr.ffirst = axis(1); % double: Floating X coordinate of first point
ThisSpcHdr.flast = axis(nr); % double: Floating X coordinate of last point
ThisSpcHdr.fnsub = size(spectra, 1); % DWORD: Integer number of subfiles (1 if not TMULTI)
Types = GetSPCAxisTypes(1);
if isfield (spectra, 'xtype')
ThisSpcHdr.fxtype = LocateItem (spectra.xtype, Types.X, 2); %%std%%%BYTE: Type of X units
else
ThisSpcHdr.fxtype = 13; %%std%%%BYTE: Type of X units
end
if isfield (spectra, 'ytype')
ThisSpcHdr.fytype = LocateItem (spectra.ytype, Types.Y, 2); %%std%%%BYTE: Type of Y units
else
ThisSpcHdr.fytype = 0; %%std%%%BYTE: Type of Y units
end
if isfield (spectra, 'ztype')
ThisSpcHdr.fztype = LocateItem (spectra.ztype, Types.X, 2); %%std%%%BYTE: Type of z units
else
ThisSpcHdr.fztype = 0; %%std%%%BYTE: Type of Z units
end
ThisSpcHdr.fpost = 0; % BYTE fpost; /* Posting disposition (see GRAMSDDE.H) */
ThisSpcHdr.fdate = CalcSpecDateTime; % DWORD fdate; /* Date/Time LSB: min=6b,hour=5b,day=5b,month=4b,year=12b */
if isfield (spectra, 'Resolution')
tmp = spectra.Resolution;
ThisSpcHdr.fres = zeros(1,9);
if length (tmp) > 8
tmp = tmp(1:8);
end
ThisSpcHdr.fres(1:length(tmp)) = tmp;
else
tmp = zeros(1,9);
tmp(1:8) = uint8('Math det');
ThisSpcHdr.fres = tmp; % char fres[9]; /* Resolution description text (null terminated) */
clear tmp;
end
tmp = zeros(1,9);
if isfield (spectra, 'InstrumentSource')
le = length(spectra.InstrumentSource);
if le > 9
warning ('GSTools:msg', 'instrument source string is to long, it will be shortened...')
spectra.InstrumentSource = spectra.InstrumentSource(1:9);
le = 9;
end
tmp(1:le) = uint8(spectra.InstrumentSource);
else
tmp(1:5) = uint8('GSSpc');
end
ThisSpcHdr.fsource = tmp; % char fsource[9]; /* Source instrument description text (null terminated) */
clear tmp;
ThisSpcHdr.fpeakpt = 0; % WORD fpeakpt; /* Peak point number for interferograms (0=not known) */
ThisSpcHdr.fspare = zeros (1,8); % float fspare[8]; /* Used for Array Basic storage */
tmp = zeros(1,130); % char fcmnt[130]; /* Null terminated comment ASCII text string */
if isfield (spectra, 'Comment')
le = length(spectra.Comment);
if le > 130
warning ('GSTools:msg', 'file comment string is to long, it will be cut...')
spectra.Comment = spectra.Comment(1:130);
le = 130;
end
tmp(1:le) = spectra.Comment;
else
tmp(1:26) = uint8('Created by GSSpcWrite v0.4') ;
end
ThisSpcHdr.fcmnt = tmp;
ThisSpcHdr.fcatxt = zeros (1,30);
if isempty (spectra.log.txt) && isempty (spectra.log.bin)
ThisSpcHdr.flogoff = 0; % DWORD flogoff; /* File offset to log block or 0 (see above) */
else
%offset= size (SPC-header) + size (xaxis) + nr_spec (size(sub-header) + size(spectrum)
offset = 512 + (ThisSpcHdr.ftflgs2.TXVALS * 4 * length (axis)) + size (data, 1) * (32 + 4 * length (axis));
ThisSpcHdr.flogoff = offset;
end
ThisSpcHdr.fmods = 0; % DWORD fmods; /* File Modification Flags */
ThisSpcHdr.fprocs = 0; % BYTE fprocs; /* Processing code (see GRAMSDDE.H) */
ThisSpcHdr.flevel = 1; % BYTE flevel; /* Calibration level plus one (1 = not calibration data) */
if isfield(spectra, 'Injection')
ThisSpcHdr.fsampin = spectra.Injection; % WORD fsampin; /* Sub-method sample injection number (1 = first or only ) */
end
if isfield(spectra, 'ConcentrationFactor')
ThisSpcHdr.ffactor = spectra.ConcentrationFactor; % float ffactor; /* Floating data multiplier concentration factor (IEEE-32) */
end
tmp = zeros(1,48); % char fmethod[48]; /* Method/program/data filename w/extensions comma list */
if isfield (spectra, 'Program')
le = length(spectra.Program);
if le > 48
warning ('GSTools:msg', 'Program string is to long, it will be cut...')
spectra.Program = spectra.Program(1:48);
le = 48;
end
tmp(1:le) = spectra.Program;
else
tmp(1:26) = uint8('Created by GSSpcWrite v0.4') ;
end
ThisSpcHdr.fmethod = tmp;
clear tmp;
ThisSpcHdr.fzinc = 0; % float fzinc; /* Z subfile increment (0 = use 1st subnext-subfirst) */
ThisSpcHdr.fwplanes = 0;% DWORD fwplanes; /* Number of planes for 4D with W dimension (0=normal) */
ThisSpcHdr.fwinc = 0; % float fwinc; /* W plane increment (only if fwplanes is not 0) */
ThisSpcHdr.fwtype = 0; % BYTE fwtype; /* Type of W axis units (see definitions below) */
ThisSpcHdr.freserv = zeros(1,187); % char freserv[187]; /* Reserved (must be set to zero) */
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function fdate = CalcSpecDateTime
% fdate is the date and time the data in the file was collected/stored. This
% is not the same as the date and time stamp put on the SPC file by the
% operating system when it is stored. The information is encoded as
% unsigned integers into a 32-bit value for compactness as follows (most
% significant bit is on the left):
% Minute (6bits) Hour (5 bits) Day (5 bits) Month (4 bits) Year (12 bits)
%it's the reverse way!
fdate = false (1, 32); %predefine 32bit array
date = clock;
Year = Transform2Bits (date(1), 12);
Month = Transform2Bits (date(2), 4);
Day = Transform2Bits (date(3), 5);
Hour = Transform2Bits (date(4), 5);
Minute = Transform2Bits (date(5), 6);
fdate (1:6) = Minute;
fdate (7:11) = Hour;
fdate (12:16) = Day;
fdate (17:20) = Month;
fdate (21:32) = Year;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function nrb = Transform2Bits (number, nrbits)
factor = 1;
nrb = false (1,nrbits); %predefine matrix to store the right amount of bits
for i = 1:nrbits
factor = factor * 2; % to calculate the remainder of respectively 2, 4, 8, ...
bit = rem (number, factor); %the value of the bit i
nrb (1,i) = (bit > 0);
number = number - bit;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function WriteSpcHeader (f, ThisSpcHdr)
fwrite(f, ThisSpcHdr.ftflgs, 'ubit1');
fwrite(f, char(ThisSpcHdr.fversn), 'char');
fwrite(f, uint8(ThisSpcHdr.fexper), 'uint8');
fwrite(f, uint8(ThisSpcHdr.fexp), 'uint8');
fwrite(f, uint32(ThisSpcHdr.fnpts), 'uint32');
fwrite(f, (ThisSpcHdr.ffirst), 'float64');
fwrite(f, (ThisSpcHdr.flast), 'float64');
fwrite(f, uint32(ThisSpcHdr.fnsub), 'uint32');
fwrite(f, uint8(ThisSpcHdr.fxtype), 'uint8');
fwrite(f, uint8(ThisSpcHdr.fytype), 'uint8');
fwrite(f, uint8(ThisSpcHdr.fztype), 'uint8');
fwrite(f, uint8(ThisSpcHdr.fpost), 'uint8');
fwrite(f, ThisSpcHdr.fdate, 'ubit1');
fwrite(f, char(ThisSpcHdr.fres), 'char');
fwrite(f, char(ThisSpcHdr.fsource), 'char');
fwrite(f, uint16(ThisSpcHdr.fpeakpt), 'uint16');
fwrite(f, (ThisSpcHdr.fspare), 'float32');
fwrite(f, char(ThisSpcHdr.fcmnt), 'char');
fwrite(f, char(ThisSpcHdr.fcatxt), 'char');
fwrite(f, uint32(ThisSpcHdr.flogoff), 'uint32');
fwrite(f, uint32(ThisSpcHdr.fmods), 'uint32');
fwrite(f, char(ThisSpcHdr.fprocs), 'char');
fwrite(f, char(ThisSpcHdr.flevel), 'char');
fwrite(f, uint16(ThisSpcHdr.fsampin), 'uint16');
fwrite(f, (ThisSpcHdr.ffactor), 'float32');
fwrite(f, char(ThisSpcHdr.fmethod), 'char');
fwrite(f, (ThisSpcHdr.fzinc), 'float32');
fwrite(f, uint32(ThisSpcHdr.fwplanes), 'uint32');
fwrite(f, (ThisSpcHdr.fwinc), 'float32');
fwrite(f, char(ThisSpcHdr.fwtype), 'char');
fwrite(f, char(ThisSpcHdr.freserv), 'char');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ThisSubHdr = CreateSubHeader(data, axis, nr, SaveAsFloats)
%This subfunction will write a sub-header for each spectrum in the
%spc-file. f is the file-pointer to the spc-file.
%
%An sub-header has the following structure (extract of the Cpp header file
%of Galactic Industries Corp.): see gspc_udf.pdf for more
%information and technical data.
ThisSubHdr.subflgs = 0; %standard value for conversion routines BYTE subflgs; /* Flags as defined below */
if SaveAsFloats
ThisSubHdr.subexp = 128;
else
ThisSubHdr.subexp = OptimalPower (data(nr+1,:)); % char subexp; /* Exponent for sub-file's Y values (80h=>float) */
end
ThisSubHdr.subindx = nr; % WORD subindx; /* Integer index number of trace subfile (0=first) */
if size(data,1) == 1
ThisSubHdr.subtime = 0; %float subtime; /* Floating time for trace (Z axis corrdinate) */
else
tmp = axis{2};
ThisSubHdr.subtime = tmp(nr+1);
end
ThisSubHdr.subnext = 0; %Z not yet implemented. float subnext; /* Floating time for next trace (May be same as beg) */
ThisSubHdr.subnois = 0; %not yet implemented float subnois; /* Floating peak pick noise level if high byte nonzero*/
ThisSubHdr.subnpts = 0; % DWORD subnpts; /* Integer number of subfile points for TXYXYS type*/
ThisSubHdr.subscan = 0; %This is just or standard Raman collection! DWORD subscan; /*Integer number of co-added scans or 0 (for collect)*/
ThisSubHdr.subwlevel = 0;
ThisSubHdr.subresv = repmat (char(0), 1, 4); % char subresv[8]; /* Reserved area (must be set to zero) */
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function WriteSubHeader(f, ThisSubHdr)
fwrite(f,ThisSubHdr.subflgs,'uint8');
fwrite(f,ThisSubHdr.subexp,'uint8');
fwrite(f,ThisSubHdr.subindx,'uint16');
fwrite(f,ThisSubHdr.subtime,'float32');
fwrite(f,ThisSubHdr.subnext,'float32');
fwrite(f,ThisSubHdr.subnois,'float32');
fwrite(f,ThisSubHdr.subnpts,'uint32');
fwrite(f,ThisSubHdr.subscan,'uint32');
fwrite(f,ThisSubHdr.subwlevel,'float32');
fwrite(f,ThisSubHdr.subresv,'uchar');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function WriteSpectraAndAxis (f, ThisSpcHdr, data, axis, options)
if ThisSpcHdr.ftflgs2.TXVALS == false
%Evenly spaced X-data: the most common form of spc-files.
%It is typically used to store data for a single spectrum or
%chromatogram where the X axis data point spacing is evenly
%throughout the data array.
else
% Non-evenly spaced X data. File has X value array preceding Y data block(s).
fwrite (f, axis{1}, 'float32');
end
%for all spectra in the matrix: write one subfile (header + values)
for i=1:size (data,1)
%Write sub header of the current spectrum
if isfield (options, 'SaveHighPrecision')
if options.SaveHighPrecision
ThisSubHdr = CreateSubHeader(data, axis, i-1, 0);
else
ThisSubHdr = CreateSubHeader(data, axis, i-1, 1);
end
else
ThisSubHdr = CreateSubHeader(data, axis, i-1, 1);
end
WriteSubHeader(f, ThisSubHdr);
%write spectrum
if ThisSubHdr.subexp == 128
%means spectral values are floating point variables instead of the
%standard integers
fwrite (f, data(i,:), 'float32');
else
if ThisSpcHdr.ftflgs2.TSPREC
%Y data blocks are 16 bit integer (only if fexp is NOT 0x80h)
tmp = data (i,:) .* (2^(16 - (ThisSubHdr.subexp)));
fwrite (f, int16(tmp), 'int16');
else
tmp = data (i,:) .* (2^(32 - (ThisSubHdr.subexp)));
fwrite (f, int32(tmp), 'int32');
end
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ThisLogstcHdr = CreateLogstcHeader (logtxt, logbin)
%This subfunction will load a LOGSTC-header in the spc-file.
%f is the file-pointer to the spc-file.
%
%An LOGSTC-header has the following structure (extract of the Cpp header file
%of Galactic Industries Corp.): see gspc_udf.pdf for more
%information and technical data.
ThisLogstcHdr.logsizd = 64 + length (logtxt) + length (logbin); % byte size of disk block
ThisLogstcHdr.logsizm = ceil (ThisLogstcHdr.logsizd /4096)*4096; % byte size of memory block
ThisLogstcHdr.logtxto = 64 + length (logbin); % byte offset to text
ThisLogstcHdr.logbins = length (logbin); % byte size of binary area (after logstc
ThisLogstcHdr.logdsks = 0; % byte size of disk area (after logbins)
ThisLogstcHdr.logspar = repmat(0,1,44); % reserved (must be zero)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function WriteLogstcHeader (f, ThisLogstcHdr)
fwrite(f,ThisLogstcHdr.logsizd,'uint32'); % byte size of disk block
fwrite(f,ThisLogstcHdr.logsizm,'uint32'); % byte size of memory block
fwrite(f,ThisLogstcHdr.logtxto,'uint32'); % byte offset to text
fwrite(f,ThisLogstcHdr.logbins,'uint32'); % byte size of binary area (after logstc
fwrite(f,ThisLogstcHdr.logdsks,'uint32'); % byte size of disk area (after logbins)
fwrite(f,ThisLogstcHdr.logspar,'char'); % reserved (must be zero)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function opw = OptimalPower (spectrum)
%opw = 32 - double(int8(log2(2^32 / max(abs(spectrum (1,:))))))-1; %+1 for sign of integer: intensity values are signed integers
%---> incorrect
%for example if max = 0.1780, then according to the following formule, opw=-2
%thus, we need to make it an uint8 number (as defined by the spc header: char
%opw = 32 - floor(log2(2^32 / max(abs(spectrum (1,:)))))+1; %+1 for sign of integer: intensity values are signed integers
opw = 32 - floor(log2(2^31 / max(abs(spectrum (1,:))))); %equal formula: we should obtain 31 bits for the intensity, while bit 32 is for the sign of the integer
opw = uint8(opw);
opw = double (opw); %MATLAB requires doubles for subtracting values (is used in the functions that call OptimalPower)
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