Ocean Optics *.ProcSpec Spectrum Extrator/Plotter Script

%Gets the processed spectrum of a ProcSpec file.

files=ls('*.ProcSpec'); %Lists every *.ProcSpec file

if size(files,1) == 0
    error('No *.ProcSpec file found!')
end

numOfFiles=size(files,1);

specx=cell(numOfFiles,1); %Cells array with the x/y data for every file.
specy=cell(numOfFiles,1);

for fnum = 1:numOfFiles

% ####################################################################################
% Unzipping, converting and reading files:

unzip(files(fnum,:),'temp'); %Unzips the ProcSpec file.

oldEncoding=slCharacterEncoding(); %Converting the file to UTF-8.
slCharacterEncoding('UTF-8');
fname_raw=ls('temp\ps_*.xml');
fid=fopen(['temp\' fname_raw]);
nfid=fopen('temp\rawxml.xml','a','n','UTF-8');
rawXML=fscanf(fid,'%c');
fprintf(nfid,'%c',rawXML);
fclose(fid);
fclose(nfid);
slCharacterEncoding(oldEncoding);

xfile=xmlread('temp\rawxml.xml'); %Loads the XML file.

try %Deletes temporary files, remove the folder if possible.
    delete('temp\OOIVersion.txt','temp\OOISignatures.xml',['temp\' fname_raw],'temp\rawxml.xml');
    rmdir('temp');
end


% ####################################################################################
%Obtaining the spectrum channels (X axis):

x_xmlval=xfile.getElementsByTagName('channelWavelengths');

for n = 0:x_xmlval.getLength-1 %Detecting corrrect element for channelWavelenths
    if x_xmlval.item(n).getLength/2-1/2 > 100
        specx{fnum}=zeros(1,x_xmlval.item(n).getLength/2-1/2);
        break
    end
end
if x_xmlval.item(n).getLength/2-1/2 < 100
    error('XML File doesn''t seems ok... channelWavelengths size doesn''t fits!')
end

specx{fnum}=str2num(x_xmlval.item(n).getTextContent)'; %Gets the data

% ####################################################################################
%Obtaining the absorvance data (Y axis):

y_xmlval=xfile.getElementsByTagName('processedPixels');

for n = 0:y_xmlval.getLength-1 %Detecting corrrect item for processedPixels
    if y_xmlval.item(n).getLength/2-1/2 > 100
        specy{fnum}=zeros(1,y_xmlval.item(n).getLength/2-1/2);
        break
    end
end
if y_xmlval.item(n).getLength/2-1/2 < 100
    error('XML File doesn''t seems ok... processedPixels size doesn''t fits!')
end

if size(specy{fnum},2) ~= size(specx{fnum},2) %Checks if both sizes are equal.
    error('channelWavelengths and processedPixels sizes doesn''t match!')
end

specy{fnum}=str2num(y_xmlval.item(n).getTextContent)'; %Gets the data

% ####################################################################################

disp([ num2str(fnum) '/' num2str(numOfFiles) ' - ' deblank(files(fnum,:)) ' done...' ]);

end

clear fid fname_raw fnum i k n nfid numOfFiles rawXML x_xmlval xfile y_xmlval ans oldEncoding

pHandle=plot(cell2mat(specx)',cell2mat(specy)'); %Plotting