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added load function for Thorlabs *.oct files
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- does not need to extract / unzip files
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Micha authored and Micha committed Aug 12, 2020
1 parent ef46b1a commit 12e9ef3
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6 changes: 6 additions & 0 deletions resources/project/Root.type.Files/thorlabs_oct.m.type.File.xml
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<?xml version='1.0' encoding='UTF-8'?>
<Info>
<Category UUID="FileClassCategory">
<Label UUID="design" />
</Category>
</Info>
251 changes: 251 additions & 0 deletions thorlabs_oct.m
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function [inf,raw] = thorlabs_oct(inf)
clc; clearvars -except inf
if strcmp(inf.disp,'special')
[inf,~] = thorlabs_oct_special(inf);
disp('special_mode_active')
raw = 0;
inf.disp = 'special';
return
end
%profile on
tic
try
fclose(fileID);
catch
end
try
fileID = fopen(fullfile(inf.path,string(inf.file{inf.i})),'r');
catch
fileID = fopen(fullfile(inf.path,inf.file{1,1}),'r');
end
%%%% read zip file
File_name = 'Start';
spectrometer ='Thorlabs';
i = 1;
fseek(fileID,0,'bof');
% profile on
% tic
while contains(File_name,"Header.xml")~=1
%fseek(fileID,4,'cof'); %Local_file_inf.Header = typecast(fread(fileID,4,'uint8=>uint8'),'uint32');
%fseek(fileID,2,'cof'); %Version_needed = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
%fseek(fileID,2,'cof'); %Gpbf = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
%fseek(fileID,2,'cof'); %Compression_method = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
%fseek(fileID,2,'cof'); %Flmt = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
%fseek(fileID,2,'cof'); %Flmd = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
%fseek(fileID,4,'cof'); %CRC32 = typecast(fread(fileID,4,'uint8=>uint8'),'uint32');
fseek(fileID,18,'cof');
%Cs = typecast(fread(fileID,4,'uint8=>uint8'),'uint32');
Cs = fread(fileID,1,'uint32');
fseek(fileID,4,'cof'); %Us = typecast(fread(fileID,4,'uint8=>uint8'),'uint32');
Fnl = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
Efl = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
File_name = string(fread(fileID,Fnl,'*char')'); % read File Name
fseek(fileID,Efl,'cof'); %index = find(contains(raw(:,1),File_name));
pointer = ftell(fileID);
List{i,1} = string(File_name');
List{i,2} = pointer; % offset
List{i,3} = Cs;
fseek(fileID, Cs,'cof');
i = i+1;
end
% toc
% profile viewer

%%% extract special important parts
index = contains(string(List(:,1)),"Chirp"); % Extract Chirp
fseek(fileID,List{index,2},'bof');
Chirp = (typecast(fread(fileID,List{index,3},'uint8=>uint8'),'single'));

index = contains(string(List(:,1)),"Offset"); % Extract Offset
fseek(fileID,List{index,2},'bof');
Offset = single((typecast(fread(fileID,List{index,3},'uint8=>uint8'),'single')));

index = contains(string(List(:,1)),"Probe"); % Extract Probe
fseek(fileID,List{index,2},'bof');
inf.Probe = convertCharsToStrings(fread(fileID,List{index,3},'*char'));

index = contains(string(List(:,1)),"Header"); % Extract Header
fseek(fileID,List{index,2},'bof');
inf.Header = convertCharsToStrings(fread(fileID,List{index,3},'*char'));

% Sort used Dispersion and preallocate some stuff
try % Set dispersion
if strcmp(inf.disp,'off')
Dispersion_index = strfind(inf.Probe,'Dispersion');
Dispersion_hlp = extractAfter(inf.Probe,Dispersion_index(1)-1);
Dispersion_used = extractBefore(extractAfter(inf.Header,'<DispersionPreset>'),'</DispersionPreset>');
inf.Dispersion = str2num(replace(erase(extractBefore(extractAfter(Dispersion_hlp,Dispersion_used),'Dispersion'),' ='),',',' '));
elseif strcmp(inf.disp,'Put dispersion here')
inf.Dispersion = inf.disp;
else
inf.Dispersion = str2num(inf.disp);
end
catch
disp(['Dispersion load failed or wrong input, tried to laod',Dispersion_Used])
disp(inf.Probe)
return
end

BytesPerPixel = str2double(extractBefore(extractAfter(inf.Header,'<BytesPerPixel>'),'</BytesPerPixel>'));
if BytesPerPixel == 1
ltypespectral = 'uint8';
elseif BytesPerPixel == 2
ltypespectral = 'uint16';
end
ChirpN = single(linspace(0,round(size(Chirp,1))-1,round(size(Chirp,1))));
SE = str2double(extractBefore(extractAfter(inf.Header,'<SpectrometerElements>'),'</SpectrometerElements>'));
BtECS = str2double(extractBefore(extractAfter(inf.Header,'<BinaryToElectronCountScaling>'),'</BinaryToElectronCountScaling>'));
inf.Comment = extractBefore(extractAfter(inf.Header,'<Comment>'),'</Comment>');
File = string(inf.file{inf.i});
File = erase(File,'.oct');
Path = string(inf.path);

Model = extractBefore(extractAfter(inf.Header,'<Model>'),'</Model>');
if contains(Model,'GAN600')
Size = extractBefore(extractAfter(inf.Header,'<SizePixel Unit="px">'),'</SizePixel>');
inf.SizeZ = str2double(extractBefore(extractAfter(Size,'<SizeZ>'),'</SizeZ>'));
inf.SizeX = str2double(extractBefore(extractAfter(Size,'<SizeX>'),'</SizeX>'));
inf.SizeY = str2double(extractBefore(extractAfter(Size,'<SizeY>'),'</SizeY>'));
if isnan(inf.SizeY)
inf.SizeY = 1;
end
inf.SizeZ_real = str2double(extractBefore(extractAfter(inf.Header,'RangeZ="'),'"'));
inf.SizeX_real = str2double(extractBefore(extractAfter(inf.Header,'RangeX="'),'"'));
inf.SizeY_real = str2double(extractBefore(extractAfter(inf.Header,'RangeY="'),'"'));
elseif contains(Model,'Hyperion_V1') || contains(Model,'Ganymed-III_V1')
Size = extractBefore(extractAfter(inf.Header,'<SizePixel Unit="mm">'),'</SizePixel>');
inf.SizeZ = str2num(extractBefore(extractAfter(Size,'<SizeZ>'),'</SizeZ>'));
inf.SizeX = str2num(extractBefore(extractAfter(Size,'<SizeX>'),'</SizeX>'));
inf.SizeY = str2num(extractBefore(extractAfter(Size,'<SizeY>'),'</SizeY>'));
inf.SizeZ_real = inf.SizeZ ;
inf.SizeX_real = inf.SizeX ;
inf.SizeY_real = inf.SizeY;
if isnan(inf.SizeY)
inf.SizeY = 1;
end
end

inf.SpeckleAveraging = extractBefore(extractAfter(inf.Header,'<SpeckleAveraging>'),'</SpeckleAveraging>');
inf.SaSA = str2double(extractBefore(extractAfter(inf.SpeckleAveraging,'<SlowAxis>'),'</SlowAxis>')); % Averaging Slow Axis
inf.SaFA = str2double(extractBefore(extractAfter(inf.SpeckleAveraging,'<FastAxis>'),'</FastAxis>')); % Averaging Slow Axis
if isnan(inf.SaSA)
inf.SaSA = 1;
end
Apo(1) = str2double(extractBefore(extractAfter(inf.Header,'ApoRegionStart0="'),'"'))+1; % Averaging Slow Axis
Apo(2) = str2double(extractBefore(extractAfter(inf.Header,'ApoRegionEnd0="'),'"'))+1; % Averaging Slow Axis

inf.CameraLineRate = str2num(extractBefore(extractAfter(inf.Header,'<CameraLineRate>'),'</CameraLineRate>'));

inf.CenterX = str2num(extractBefore(extractAfter(inf.Header,'<CenterX>'),'</CenterX>'));
inf.CenterY = str2num(extractBefore(extractAfter(inf.Header,'<CenterY>'),'</CenterY>'));

inf.MetaInfo = extractBefore(extractAfter(inf.Header,'<MetaInfo>'),'</MetaInfo>');
inf.MetaInfoAcquisitionMode = extractBefore(extractAfter(inf.MetaInfo,'<AcquisitionMode>'),'</AcquisitionMode>');


% inf.CenterX = str2num(extractBefore(extractAfter(inf.Header,'<CenterX>'),'</CenterX>'));

if strcmp(inf.extract_info,'on')
fclose(fileID);
raw = 0;
return;
end

try
p = gcp();
catch
p = parpool();
end

% Processing Start
fseek(fileID,0,'bof'); % go back to init of file

% Check for horror
if ~isequal(size(Chirp), [SE,1])
Chirp = Chirp';
end
if ~isequal(size(ChirpN), [SE,1])
ChirpN = ChirpN';
end
if ~isequal(size(Offset), [SE,1])
Offset = Offset';
end

try
mkdir(fullfile(Path,File))
catch
end

k=1;

fseek(fileID,0,'bof'); % go back to init of file
try
for i=1:size(List,1)
fseek(fileID,4,'cof'); %Local_file_inf.Header = typecast(fread(fileID,4,'uint8=>uint8'),'uint32');
fseek(fileID,2,'cof'); %Version_needed = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
fseek(fileID,2,'cof'); %Gpbf = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
fseek(fileID,2,'cof'); %Compression_method = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
fseek(fileID,2,'cof'); %Flmt = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
fseek(fileID,2,'cof'); %Flmd = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
fseek(fileID,4,'cof'); %CRC32 = typecast(fread(fileID,4,'uint8=>uint8'),'uint32');
Cs = typecast(fread(fileID,4,'uint8=>uint8'),'uint32');
Us = typecast(fread(fileID,4,'uint8=>uint8'),'uint32');
Fnl = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
Efl = typecast(fread(fileID,2,'uint8=>uint8'),'uint16');
File_name = strcat(fread(fileID,Fnl,'*char'))'; % read File Name
Extra_field = typecast(fread(fileID,Efl,'uint8=>uint8'),'uint8');

inf.interp_par = 'linear';

if contains(File_name,'Spectral') && k<=inf.SizeY*inf.SaSA
bscan= typecast(fread(fileID,Cs,'uint8=>uint8'),ltypespectral);
if strcmp(inf.disp,'Calc or put dispersion here') && k==1 % only correct first Bscan
inf.Dispersion = dispersion_correction_image(inf,bscan,Offset,Chirp,ChirpN,inf.Dispersion,SE,inf.b_a,inf.b_b,inf.interp_par,BtECS,File_name,File,Path,Apo,inf.process_complex,spectrometer,inf.proc.half);
if strcmp(inf.Dispersion,'Dispersion return');
return
end
elseif strcmp(inf.disp,'Experimental')
rec1(k,bscan,Offset,Chirp,ChirpN,inf.Dispersion,SE,inf.b_a,inf.b_b,inf.interp_par,BtECS,File_name,File,Path,Apo,inf.process_complex,spectrometer,inf.proc.half);
% rec2(i,bscan,Offset,Chirp,inf.Dispersion,inf.b_a,inf.b_b,BtECS,File_name,File,Path,Apo,inf.process_complex,spectrometer);
elseif strcmp(inf.disp,'GUI')
dispersion_correction_image_gui(inf,bscan,Offset,Chirp,ChirpN,inf.Dispersion,SE,inf.b_a,inf.b_b,inf.interp_par,BtECS,File_name,File,Path,Apo,inf.process_complex,spectrometer,inf.proc.half)
return
end
if strcmp(inf.rec,'1')
f(k) = parfeval(p,@rec1,0,k,bscan,Offset,Chirp,ChirpN,inf.Dispersion,SE,inf.b_a,inf.b_b,inf.interp_par,BtECS,File_name,File,Path,Apo,inf.process_complex,spectrometer,inf.proc.half); % Square size determined by idx
elseif strcmp(inf.rec,'2')
f(k) = parfeval(p,@rec2,0,k,bscan,Offset,Chirp,inf.Dispersion,inf.b_a,inf.b_b,BtECS,File_name,File,Path,Apo,inf.process_complex,spectrometer,inf.proc.half); % Square size determined by idx
end
k =k+1;
else
if contains(File_name,'Apodization') || contains(File_name,'Chirp') ||contains(File_name,'OffsetErrors.data')
ltype = 'single';
raw{i,2} = (typecast(fread(fileID,Cs,'uint8=>uint8'),ltype));
elseif contains(File_name,'Probe.ini') || contains(File_name,'Header.xml')
ltype = '*char';
raw{i,2} = convertCharsToStrings(fread(fileID,Cs,ltype));
elseif contains(File_name,'Video') || contains(File_name,'PreviewImage')
ltype = 'uint8';
fread(fileID,Cs,ltype);
end
end
end
catch
disp('Could not process all files')
end
raw = 0;
wb = waitbar(0,'Start Processing...');
clearvars m;
for i = 1:k-1
[~] = fetchNext(f);
waitbar(i/k,wb,'Processing your data');
end
close(wb)
fclose(fileID);
if size(inf.file,1) == 1
%delete(p)
end
%profile viewer
save(fullfile(inf.path,[inf.file{inf.i}(1:end-4),'_inf.mat']),'inf');
toc
end

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