Eriks at 20:24, 17 March 2011

2011-03-17T20:24:13Z

Eriks: Created page with '

 % Title:        CALSPEC.M % Date:         02/2000 % Author:       EB/SRW % Input:        list_file:string % Output:       [returns:dimension] % Files:        list_file(qcal…'

2011-03-17T20:23:49Z

Created page with '<pre> % Title: CALSPEC.M % Date: 02/2000 % Author: EB/SRW % Input: list_file:string % Output: [returns:dimension] % Files: list_file(qcal…'

New page

<pre>
% Title: CALSPEC.M
% Date: 02/2000
% Author: EB/SRW
% Input: list_file:string
% Output: [returns:dimension]
% Files: list_file(qcal.txt), calfile.txt
% Assumes: list_file in local dir with file names and intervals,
% calibration files are in the local directory,
% header of ac9.dat files end with 'aquisition binsize',
% Purpose: calculate spectral average of calibration file
% Calls:
% Uses: ac9 calibration
% Example: calsec('qcal.txt')
% NOTES:
% 02/2000
% Wetlabs recommends calibrating a,c separately therefore this needs
% to be modified to accomodate ac9.dat files that don't have a or c.
% Need a channel flag and then place error flags in the unused signal.

%function fig=calspec(list_file,autorun,filetype,prop)
function fig=calspec(varargin)
[ac9calfig,ac9]=ac9cal;
%assign command line parameters to local variables
narg=length(varargin);
nrow=narg/2;
if nrow==round(nrow),
for iarg=1:2:length(varargin),
eval(['ac9.par.' varargin{iarg} '= varargin{iarg+1};']);
end
else
display('calspec: command line pairs not correctly formed');
return
end
if isempty(ac9.par.prop),
msgbox('Select an IOP, rerun calspec');
return
end
if isempty(ac9.par.fluid),
msgbox('Select a fluid, rerun calspec');
return
end
if ac9.par.fluid, % 1 for water
if ~isfield(ac9.par,'instr_num'),
msgbox('Select an AC9, rerun calspec');
return
end
if ~isfield(ac9.par,'Tref'),
msgbox('Select a factory cal, rerun calspec');
return
end
Tref=ac9.par.Tref;
if isempty(Tref),
msgbox('Tref is empty, check factory cal, rerun calspec');
return
end
end
qcal=qcaled_cb('list_load','list_file',ac9.par.list_file)

fig=calspecplot(0);
set(fig,'Userdata',ac9);
calspecplot(1);

filetext=qcal.FileText.str
fileval=qcal.FileText.val
channels=ac9.sort_channels;
I=ac9.I; %index of channels from .dat file is sorted alphabetically
ichannels=ac9.isort_channels; %index of channels in sorted array
for ifile=1:length(fileval), %size(udata.list.fname,1),
if(fileval(ifile)>0),
ival=fileval(ifile);
file=deblank(qcal.list.fname(ifile,:))
if filetext(ival,1)=='#',
display('uncomment this file, save and rerun');
break;
end
set(findobj('Tag','FileText'),'Value',ival);
if ac9.par.filetype==1
temp=read_ac9([file '.dat']);
%temp=read_ac9(file);
%eval(['temp=read_ac9(''' shrink(file) '.dat'');']);
temp=exciseit(temp,20);
else
temp=read_strip([file '.da2']);
%eval(['temp=readstr(''' shrink(file) '.da2'');']);
end;
minmin=str2num(qcal.list.t1(ifile,:)); % in decimal minutes
maxmin=str2num(qcal.list.t2(ifile,:));
if maxmin==0,
maxmin=temp(end,1);
end
time=temp(:,1)/60000;
range=find(time>minmin & time<maxmin);
temp2=medfilt1(temp,15);
if ac9.par.filetype==1
chan2=temp2(range,2:19);
ref2=temp2(range,24:41);
itemp2=temp2(range,20);
else
chan2=temp2(range,3:20);
ref2=temp2(range,24:41);
itemp2=temp2(range,21);
end;
if ac9.par.fluid,
%add wetlabs temperature correction
%get Tcal from a list file
Tcaldate=qcal.list.date(ifile,:)
%Tcalfile=['watertemp_' ac9.par.instr_num '.txt'];
Tcalfile=[ac9.par.instr_num ac9.par.Tcalfile];
Tcalfile=fullfile(ac9.par.calroot_dir, ac9.par.instr_num, ...
ac9.par.Tcaldir, Tcalfile);
qcal.list.tcal=read_text(Tcalfile);
find( datenum(Tcaldate)==datenum(parse(qcal.list.tcal,1)) );
Tcal=0;
if ~isempty(ans),
Tcal=parse(qcal.list.tcal(ans(1),:),2);
%add cal check
if ~strcmp(Tcal,'Reserved');
Tcal=str2num(Tcal)
else
msgbox('Enter Tcal into line 5 of the qcal.txt and rerun');
close(fig);
return
end
else
qcal.list.tcal
disp(['Tcaldate is not in this list, check ' Tcalfile]);
return
end
if Tcal>0,
del_ts=ac9.par.sit*(Tcal-ac9.par.Tref);
del_ts=[del_ts del_ts];
for irow=1:size(chan2,1),
chan2(irow,:)=chan2(irow,:)-del_ts(I);
end
end
end
chan3=mean(chan2);
specdata=mean(chan2);
stddata=std(chan2);
ndata=size(chan2,1);
udata=get(fig,'Userdata');
udata.data(ifile).file=file;
udata.data(ifile).specdata=specdata(I(ichannels));
udata.data(ifile).specdata;
udata.data(ifile).nspecdata=udata.data(ifile).specdata - ...
udata.data(ifile).specdata(6);
udata.data(ifile).stddata=stddata(I(ichannels));
udata.data(ifile).inttemp=mean(exciseit(itemp2,0,-1000,1000));
udata.data(ifile).ndata=ndata*ones(1,9);
set(fig,'Userdata',udata);
udata.han=calspecplot(2)
set(fig,'Userdata',udata);
calspecplot(3)
calspecplot(4)
leg_names =('');
leg_names=strvcat(leg_names,strrep(udata.data(ifile).file,'_','\_'))

if ~ac9.par.autorun
disp('press return key or go button for next plot');
uiwait(fig);
if isempty(get(findall(0,'Tag','goBut'),'Userdata')),
break
end
end;
end
end %ifile
figure(fig);
udata.leg_names=leg_names;
a=legend(udata.han,udata.leg_names,-1);
udata.legend=a;
set(fig,'Userdata',udata);
%Query list_file save and write mean value files
ButtonName=questdlg('Save list_file and write mean value files?');
switch ButtonName,
case 'Yes',
qcaled_cb('save');
for ifile=1:size(udata.data,2),
ispec=[udata.par.wave;
udata.data(ifile).specdata;
udata.data(ifile).stddata;
udata.data(ifile).ndata];
save([udata.data(ifile).file '.txt'],'ispec','-ascii')
end
end

%TODO

%add legends
<\pre>

[[calspec]]

Calspec.m - Revision history

Eriks at 20:24, 17 March 2011

Eriks: Created page with '
% Title: CALSPEC.M % Date: 02/2000 % Author: EB/SRW % Input: list_file:string % Output: [returns:dimension] % Files: list_file(qcal…'

@@ Line 188: / Line 188: @@
 %add legends
-<\pre>
+</pre>
 [[calspec]]