spec file reader: monitorscan - File Exchange

Code covered by the BSD License

Highlights from
spec file reader

curvesave(varargin) CURVESAVE Called by specr and trueref to save current curves to files.
engwave ENGWAVE GUI to convert between energy and wavelength (X-ray)
foldxaxis FOLDXAXIS Fold the x axis along a user-defined center line. Called by
georocking Perform geometric correction for rocking scans. Called by specr
print2figure(varargin) PRINT2FIGURE Called by specr and trueref to print current plot to another
showmotorposition SHOWMOTORPOSITION Called by specr to show the current motor positions
showscan SHOWSCAN Called by specr to show the current scan data.
specr(varargin) SPECR Program to read spec files
specrsetting(varargin) GUI for specr settings
timebar(message,name,update_r... TIMEBAR Progress bar with estimated time remaining
truerefimport(varargin) TRUEREFIMPORT Called by trueref to import data.
ColorSet=varycolor(NumberOfPl... VARYCOLOR Produces colors with maximum variation on plots with multiple
convert2theta2qz(varargin)
curvederivative CURVEDERIVATIVE Called by specr to calculate curve gradient
curvelegend(hCurrentFig) CURVELENGEND Called by specr and trueref
curvenormalize(varargin) CURVENORMALIZE Called by specr and trueref
curvesmooth(varargin) CURVESMOOTH Called by specr to smooth current scans
footprint(varargin) FOOTPRINTGUI Called by specr and trueref.
invertxaxis(varargin)
litcount(filename, literal) Search for number of string matches per line.
mergescan(varargin) MERGESCAN Merge and plot scans from the same spec file.
monitorscan OPENSPEC Called by specr to load fids of scans in a selected spec file
mrgker(varargin) MRGKER Merge kernel function.
norm2maxi(varargin) NORM2MAXI Normalize reflectivity to maximum intensity
openspec(varargin) OPENSPEC Called by specr to load fids of scans in a selected spec file
params(scan) PARAMS Calculate peak,COM and FWHM of a scan
plotstyle(varargin)
rdspec(varargin) RDSPEC Non-interactive function to load a single scan from spec file.
refreshscanplot(varargin) REFRESHSCANPLOT Called by specr to reload scan(s) and plot.
resetfigspecr(varargin) Reset all the plots in specr
resettoolbar(hCurrentFig)
resettrueref(varargin)
save2workspace(varargin) SAVE2WORKSPACE Called by specr and trueref to save current plot data to
scanmerge(varargin) SCANMERGE Called by specr to read scans from current plot to call mrgker
scanplot(varargin) SCANPLOT Called by specr to plot scans.
selectscan(varargin) SELECTSCAN Called by specr to open scan listbox and load scans to plot.
smooth(varargin) SMOOTH Smooth data.
subtractbkg(varargin) SUBTRACTBKG GUI to subtract constant background; called by specr.
titlestr(a) TITLESTR Convert a string with underscores to a string that can be
trueref(varargin) TRUEREF GUI to calculate true reflectivity by subtracting longitudinal
truerefcal(varargin) TRUEREFCAL Called by trueref to calculate true reflectivity.
truerefmerge(varargin) TRUEREFMERGE Called by trueref to load current plots and call mrgker to
truerefplot(varargin) TRUEREFPLOT Called by trueref to plot data
View all files

from spec file reader by Zhang Jiang
Monitor, read, save scans from SPEC files and calculate true reflectivity.

monitorscan

function monitorscan
% OPENSPEC Called by specr to load fids of scans in a selected spec file
%
% Copyright 2005, Zhang Jiang

hFigSpecr = findall(0,'Tag','specr_Fig');
hToolbarMonitor = findall(hFigSpecr,'Tag','toolbarMonitor');
hTimerMonitor   = timerfindall('Tag','timerMonitor');

% --- get setttings
settings = getappdata(hFigSpecr,'settings');
settings.monitorAutoPeriod = settings.monitorPeriod;
setappdata(hFigSpecr,'settings',settings);
file = settings.file;
scan = settings.scan;

% --- get initial 'enable' property of menus,toolbars and pushbuttons
hEnableGroup  = [...
    findall(hFigSpecr,'Tag','specr_MenuTools');...
    findall(hFigSpecr,'Tag','specr_MenuFile');...
    findall(hFigSpecr,'Tag','toolbarOpen');...
    findall(hFigSpecr,'Tag','toolbarSave');...
    findall(hFigSpecr,'Tag','toolbarPrint');...
    findall(hFigSpecr,'Tag','toolbarEditPlot');...
    findall(hFigSpecr,'Tag','toolbarZoom');...
    findall(hFigSpecr,'Tag','toolbarDataCursor');...
    findall(hFigSpecr,'Tag','toolbarLegend');...
    findall(hFigSpecr,'Tag','toolbarPlottoolsOff');...
    findall(hFigSpecr,'Tag','toolbarPlottoolsOn');...
    findall(hFigSpecr,'Tag','toolbarInvert');...
    findall(hFigSpecr,'Tag','toolbarSubtractbkg');...
    findall(hFigSpecr,'Tag','toolbarSmooth');...
    findall(hFigSpecr,'Tag','toolbarDev');...
    findall(hFigSpecr,'Tag','toolbarShowScan');...
    findall(hFigSpecr,'Tag','toolbarShowMotor');...
    findall(hFigSpecr,'Tag','toolbarMerge');...
    findall(hFigSpecr,'Tag','toolbarConvert');...
    findall(hFigSpecr,'Tag','toolbarFootprint');...
    findall(hFigSpecr,'Tag','specr_PushbuttonSelectScan');...
    ];
initEnable = get(hEnableGroup,'Enable');

if isempty(file) | isempty(scan.fidPos)
    set(hToolbarMonitor,'state','off');
    return;
end

icons = load('icons.mat');
if strcmp(get(hToolbarMonitor,'state'),'on');
    set(hToolbarMonitor,'CData',icons.iconmonitor.pause);
else
    set(hToolbarMonitor,'CData',icons.iconmonitor.play);
    if ~isempty(hTimerMonitor)
        if isvalid(hTimerMonitor)
            stop(hTimerMonitor);
        end
        delete(hTimerMonitor);
    end
    return;
end
hTimerMonitor=timer(...
    'Tag','timerMonitor',...
    'StartDelay', 1,...
    'TimerFcn', @timerMonitorFcn,...
    'StartFcn', {@timerMonitorStartFcn,hEnableGroup,initEnable},...
    'StopFcn',  {@timerMonitorStopFcn,hEnableGroup,initEnable},...
    'ExecutionMode','fixedRate',...
    'BusyMode','drop',...
    'TasksToExecute',inf,...
    'Period',settings.monitorPeriod,...
    'userdata',{hEnableGroup,initEnable});
start(hTimerMonitor);

%================================================================
% --- callback function of monitor timer
%================================================================
function timerMonitorFcn(hObject,eventdata)
tStart=tic;
hFigSpecr = findall(0,'Tag','specr_Fig');
hTimerMonitor   = timerfind('Tag','timerMonitor');
hPopupmenuX = findall(hFigSpecr,'Tag','specr_PopupmenuX');
hPopupmenuY = findall(hFigSpecr,'Tag','specr_PopupmenuY');
settings = getappdata(hFigSpecr,'settings');

file = settings.file;
scan = settings.scan;
% --- check dynamically if there are more scans added to spec file
[fid,message] = fopen(file);
fseek(fid,scan.fidPos(end),'bof');  % move fid to end of the last stored scan
scanline = fgetl(fid);      % skip the currentline (head of the last stored scan);
flagNewScan = 0;
while feof(fid) == 0
    tempfid = ftell(fid);
    scanline = fgetl(fid);
    if length(scanline) >= 3 && strcmp(scanline(1:3),'#S ')
        scan.fidPos = [scan.fidPos,tempfid];
        scan.head{length(scan.fidPos)} = scanline;
        flagNewScan = 1;
    end
end
fclose(fid);
settings.scan = scan;
setappdata(hFigSpecr,'settings',settings);
settings = getappdata(hFigSpecr,'settings');
selection = length(scan.fidPos);

if settings.monitorErasemode == 1 | ~isfield(scan,'selection')
    scan.selection = cell(length(selection),1);
    scan.selection{1,1}.time = '';               % initialize scan.selection
    scan.selectionIndex = selection;        % store the selected scan index
    scan.selectionNumber = [];
else
    if scan.selectionIndex(end) ~= selection
        scan.selection(end+1,1) = cell(1,1);
        scan.selectionIndex = [scan.selectionIndex,selection];
    end
end
tmp_selectionNumber = [];

[fid,message] = fopen(file);
try
    fseek(fid,scan.fidPos(selection),'bof');
    % --- read the scan number      PS: scan number sometimes is not the
    % same of scan index.
    scanline = fgetl(fid);
    while ~strcmp(scanline(1:3),'#S ')
        scanline = fgetl(fid);
    end
    space_pos = findstr(scanline,' ');
    tmp_selectionNumber = str2num(scanline(space_pos(1)+1:space_pos(2)-1));
    if isempty(scan.selectionNumber) | scan.selectionNumber(end) ~= tmp_selectionNumber
        scan.selectionNumber = [scan.selectionNumber, tmp_selectionNumber];
    end
    % --- read time of scan #D
    while ~strcmp(scanline(1:2),'#D')
        scanline = fgetl(fid);
    end
    scan.selection{end,1}.time = scanline(4:end);
    % --- read current motor positions
    scan.selection{end,1}.motorPos = [];
    while ~strcmp(scanline(1:2),'#P')
        scanline = fgetl(fid);
    end
    while length(scan.selection{end,1}.motorPos) < length(scan.motorName)
        tmpspace = findstr(scanline,' ');
        scanline = scanline(tmpspace(1):end);
        scan.selection{end,1}.motorPos = [scan.selection{end,1}.motorPos, str2num(scanline)];
        scanline = fgetl(fid);
    end
    % --- read number of scan columns #N ...
    while ~strcmp(scanline(1:2),'#N')
        scanline = fgetl(fid);
    end
    scan.selection{end,1}.length = str2num(scanline(3:end));
    % --- read head of scan columns #L ...
    while ~strcmp(scanline(1:2),'#L')
        scanline = fgetl(fid);
    end
    scanline = scanline(4:end);
    space = findstr(scanline,'  ');
    lengthSpace = length(space);
    for iSpace = lengthSpace:-1:2
        if space(iSpace) == space(iSpace-1)+1
            space(iSpace) = [];
        end
    end
    space = [-1 space length(scanline)+1];
    scan.selection{end,1}.colHead = ...
        cell(1,scan.selection{end,1}.length);
    for iCol = 1:scan.selection{end,1}.length
        colHead = scanline(space(iCol)+2:space(iCol+1)-1);
        while colHead(1) == ' '
            colHead(1) = '';
        end
        scan.selection{end,1}.colHead{iCol} = colHead;
    end

    % --- read scan data
    colData = [];
    str_scanline = num2str(scanline);
    while ~strcmp(str_scanline,'') & ~strcmp(str_scanline,'-1')
        fidPos = ftell(fid);
        scanline = fgetl(fid);
        str_scanline = num2str(scanline);
        while ~strcmp(str_scanline,'') & ~strcmp(str_scanline,'-1')...
                & ~strcmp(str_scanline(1:1),'#')
            fseek(fid,fidPos,'bof');
            colData = [colData fscanf(fid,'%g',[scan.selection{end,1}.length,1])];
            scanline = fgetl(fid);
            fidPos = ftell(fid);
            scanline = fgetl(fid);
            str_scanline = num2str(scanline);
        end
    end
    scan.selection{end,1}.colData = colData';
catch
    return;
end
fclose(fid);
% --- if not the same type scan selected, switch back to erase mode
if length(scan.selection) >= 2
    for iSelection = 2:length(scan.selection)
        if scan.selection{iSelection}.length == scan.selection{iSelection-1}.length
            colHeadCmp = strcmp(scan.selection{iSelection}.colHead,...
                scan.selection{iSelection-1}.colHead);
        else
            colHeadCmp = 0;
        end
        if ~isempty(find(colHeadCmp == 0))
            scan.selection(1:end-1) = '';
            scan.selectionIndex(1:end-1) = '';
            scan.selectionNumber(1:end-1) = '';
            break;
        end
    end
end
settings.scan = scan;
setappdata(hFigSpecr,'settings',settings);

if get(hTimerMonitor,'TasksExecuted') == 1 | flagNewScan == 1;
    set(hPopupmenuX,...
        'String',scan.selection{end}.colHead,...
        'Value',1);
    ihklscan = findstr(lower(scan.head{end}),' hklscan');    % check if it is hklscan
    if ihklscan
        a = scan.head{end};
        b = str2num(a(ihklscan+8:end));
        c = find(abs(b([1,3,5])-b([2,4,6]))>eps);
        if c
            set(hPopupmenuX,...
                'String',scan.selection{end}.colHead,...
                'Value',c(1));
        end
    end
    set(hPopupmenuY,...
        'String',scan.selection{end}.colHead,...
        'Value',scan.selection{end}.length);
end
try
    scanplot;
catch
end
tElapsed = ceil(toc(tStart)*1000)/1000;
% --- set checking period
if settings.monitorAutoPeriodMode ~= 1 & tElapsed > settings.monitorPeriod
    settings.monitorAutoPeriodMode = 1;
    settings.monitorAutoPeriod = settings.monitorPeriod;
end
if settings.monitorAutoPeriodMode == 1;
    if tElapsed > settings.monitorAutoPeriod
        settings.monitorAutoPeriod = tElapsed+0.1;
        setappdata(hFigSpecr,'settings',settings);
        userData = get(hTimerMonitor,'userdata');
        hEnableGroup = userData{1};
        initEnable = userData{2};
        stop(hTimerMonitor);
        delete(hTimerMonitor);
        hTimerMonitor=timer(...
            'Tag','timerMonitor',...
            'StartDelay', 1,...
            'TimerFcn', @timerMonitorFcn,...
            'StartFcn', {@timerMonitorStartFcn,hEnableGroup,initEnable},...
            'StopFcn',  {@timerMonitorStopFcn,hEnableGroup,initEnable},...
            'ExecutionMode','fixedRate',...
            'BusyMode','drop',...
            'TasksToExecute',inf,...
            'Period',max(settings.monitorAutoPeriod,settings.monitorPeriod),...
            'userdata',{hEnableGroup,initEnable});
         start(hTimerMonitor);
    end
end


%================================================================
% --- start callback function of monitor timer
%================================================================
function timerMonitorStartFcn(hObject,eventdata,hEnableGroup,initEnable)
hFigSpecr = findall(0,'Tag','specr_Fig');
resettoolbar(hFigSpecr);
set(hEnableGroup,'Enable','off');


%================================================================
% --- stop callback function of monitor timer
%================================================================
function timerMonitorStopFcn(hObject,eventdata,hEnableGroup,initEnable)
for i=1:length(hEnableGroup)
    set(hEnableGroup(i),'Enable',initEnable{i});
end

Highlights from spec file reader

Highlights from
spec file reader