Can somebody please help me how to convert *.bil files to *.cyt file formats ?

Hi I have a hyperspectral datacube in *.bil format and I need to convert it to *.cyt file format. Can you please help me with this code? Appreciate for the great help.

[Rik]

If you can provide the file type descriptions, we can help you with implementation. Have you already tried your favorite internet search engine for a converter?

[Rik]

OK, so now we have a function to read the .bil files, we need a description of how a .cyt file works. Also, can you select the code and then click the {}Code button? Currently your function is unreadable.

[Guillaume]

Surya Gnyawali's comment mistakenly posted as an Answer moved here:

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Loading a Hyperspectral Cube into Matlab  %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Import the header file
[FileName,PathName,FilterIndex] =...
    uigetfile({'*.hdr','Hyperspec Header File'},...
    'Open Hyperspec Header File'); 
%%Gets the data from the Header File
fid = fopen([PathName,FileName]);  
% fid is file ID
% fgetl gets one line
% char changes cell array to character array
% textscan helps parse around ' ' spaces
% char(Camera.Gain{3}) makes the third cell in Gain into a char array
% str2double converst the string of characters to a double number.
Data.Format = fgetl(fid);
DateStamp               = fgetl(fid);
DateStamp             = textscan(char(DateStamp),'%s%s%s%s%s%s%s%s',1);
Temp1 = char(DateStamp{3});
Temp2 = char(DateStamp{4});
Temp3 = char(DateStamp{5});
Temp4 = char(DateStamp{6});
Temp5 = char(DateStamp{7});
Temp6 = char(DateStamp{8});
DateStamp = [Temp1(3:length(Temp1)),' ',Temp2,' ',Temp3,' ',Temp4,...
    ' ',Temp5,' ',Temp6(1:(length(Temp6)-2))];
DataFormat.Samples      = textscan(char(fgetl(fid)),'%s%s%s',1);
DataFormat.Samples = str2double(char((DataFormat.Samples{3})));
DataFormat.Lines      = textscan(char(fgetl(fid)),'%s%s%s',1);
DataFormat.Lines = str2double(char((DataFormat.Lines{3})));
DataFormat.Bands      = textscan(char(fgetl(fid)),'%s%s%s',1);
DataFormat.Bands = str2double(char((DataFormat.Bands{3})));
DataFormat.HeaderOffset      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.HeaderOffset = str2double(char((DataFormat.HeaderOffset{4})));
DataFormat.FileType      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.FileType = ([char((DataFormat.FileType{3})),' ',...
    char((DataFormat.FileType{4}))]);
Temp      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
Temp2 = str2double(char((Temp{4})));
switch Temp2 
    case 1
        DataFormat.DataType = 'uint8';
    case 2
        DataFormat.DataType = 'int16';
    case 3
        DataFormat.DataType = 'int32';
    case 4
        DataFormat.DataType = 'float32';
    case 5
        DataFormat.DataType = 'double';
    case 9
        DataFormat.DataType = 'complex';
    case 12
        DataFormat.DataType = 'uint16';
end
DataFormat.Interleave      = textscan(char(fgetl(fid)),'%s%s%s',1);
DataFormat.Interleave = (char((DataFormat.Interleave{3})));
DataFormat.SensorType      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.SensorType = (char((DataFormat.SensorType{4})));
DataFormat.ByteOrder      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.ByteOrder = str2double(char((DataFormat.ByteOrder{4})));
if mod(DataFormat.ByteOrder,2) == 0
    DataFormat.ByteOrder = 'ieee-le';
elseif mod(DataFormat.ByteOrder,2) == 1
    DataFormat.ByteOrder = 'ieee-be';
end
DataFormat.Units      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.Units = (char((DataFormat.Units{4})));
Junk = fgetl(fid); % We just don't need this line, but we need to read past            it.
%%Gets the wavelength data and puts it in a vector 
i = 1;
j = 0;
a = [];
while i==1
    b = fgetl(fid);
     if b == -1
         i=0;
     elseif b(length(b))=='}'
         a = cat(2,a,b(1:(length(b)-1)));
     else
         a = cat(2,a,b);
     end
  end
  Wavelengths = str2num(a);
  fclose(fid); % Closes the file.
  clear Temp Temp2 Temp3 Temp4 Temp5 Temp6 a b Junk
%%Import the data file (UI version)
[FileNameData,PathName,FilterIndex] =...
    uigetfile({'*.bil','Hyperspec Data File';'*.*','All Files'},...
    'Open Hyperspec Data File', PathName) ;
% Set the Data Size
DataSize = [ DataFormat.Lines  DataFormat.Samples  DataFormat.Bands ];
% Load data with multibandread and assign to variable
HyperDataCube = multibandread([PathName,FileNameData], DataSize,...
    DataFormat.DataType,DataFormat.HeaderOffset,...
    DataFormat.Interleave, DataFormat.ByteOrder);

Mesh Plot of Data at specific wavelength.

Lambda = 10; % One element of the Wavelength vector
figure(3);mesh(fliplr(squeeze(HyperDataCube(:,:,Lambda))));view(180,90);
title(['Hyperspectral Data: \lambda = ',num2str(Wavelengths(Lambda)),...
    ' nm'],'FontSize',14);
xlabel('Pixels','FontSize',12);
ylabel('Pixels','FontSize',12);

[Guillaume]

Surya Gnyawali's comment mistakenly posted as an Answer moved here:

File created by Cytospec - date: 17-Mar-2018 , time: 17:30:39 
please do not modify this file 
INS - IFS Vector 22 + IRscope II 
MAN - Bruker 
SRC -  MAN 
BSP - Globar 
FIL - open 
DET - MCT (microscope) 
VEL - 20 kHz 
LAS - 15799.1 
AQM - double sided fw bw 
SNG - automatic 
LWN - 397.746 
UWN - 994.8992 
WVS - 25.9632 
NOD - 24 
DAT - 09-OCT-2000 
TIM - 11:30:00 
PHC - Mertz 
PHR - 32 
PIP -  
ZFF - 4 
RES - 8 
APO - Happ-Genzel 
APT - 45 
STX - 30 
STY - 30 
TOS - absorbance 
NOS - 8 
XDI - 1192 
YDI - 1600 
SZX - 2400 
SZY - 2400 
SAM - B1760/98(Buch) 
SAF - dry on CaF2 
OPN - Peter Lasch 
AS1 - dry colon adenocarcinoma sample 
AS2 - colon sample, spectrally and spatially interpolated 
AS3 - Hunter College, New York 
BLO - 1  0  0  0 
4 ORG (original data): 
data imported as ascii files, date: 10-Oct-2000, time: 15:57:0                                    
spectral interpolation factor: 2, NOD (old): 1323, new NOD: 662, date: 14-Apr-2006, time: 16:16:19
map dimensions (old): 84 x 84, new map dimensions: 42 x 42, date: 14-Apr-2006, time: 16:17:0      
spectral interpolation factor: 16, NOD (old): 373, new NOD: 24, date: 17-Mar-2018, time: 17:14:29 
2 PRE (preprocessed data): 
spectral interpolation factor: 2, NOD (old): 1323, new NOD: 662, date: 14-Apr-2006, time: 16:16:19
map dimensions (old): 84 x 84, new map dimensions: 42 x 42, date: 14-Apr-2006, time: 16:17:0      
2 DER (derivative data): 
spectral interpolation factor: 2, NOD (old): 1323, new NOD: 662, date: 14-Apr-2006, time: 16:16:19
map dimensions (old): 84 x 84, new map dimensions: 42 x 42, date: 14-Apr-2006, time: 16:17:0      
2 DEC (deconvolution data): 
spectral interpolation factor: 2, NOD (old): 1323, new NOD: 662, date: 14-Apr-2006, time: 16:16:19
map dimensions (old): 84 x 84, new map dimensions: 42 x 42, date: 14-Apr-2006, time: 16:17:0

[Guillaume]

Surya Gnyawali's comment mistakenly posted as an Answer moved here:

The last text is taken from a .cyt file. I am not familier about this file type.

[Guillaume]

Please use Comment on this question rather than spamming your own question with Answers. If people see that the question has already 3 answers, there's less chance they'll look at it and you'll have less chances of getting an answer.

And learn about formatting your question and comments

[Surya Gnyawali]

% Import the header file
[FileName,PathName,FilterIndex] =...
    uigetfile({'*.hdr','Hyperspec Header File'},...
    'Open Hyperspec Header File'); 

%%Gets the data from the Header File
fid = fopen([PathName,FileName]);  
% fid is file ID
% fgetl gets one line
% char changes cell array to character array
% textscan helps parse around ' ' spaces
% char(Camera.Gain{3}) makes the third cell in Gain into a char array
% str2double converst the string of characters to a double number.
Data.Format = fgetl(fid);

DateStamp               = fgetl(fid);
DateStamp             = textscan(char(DateStamp),'%s%s%s%s%s%s%s%s',1);
Temp1 = char(DateStamp{3});
Temp2 = char(DateStamp{4});
Temp3 = char(DateStamp{5});
Temp4 = char(DateStamp{6});
Temp5 = char(DateStamp{7});
Temp6 = char(DateStamp{8});
DateStamp = [Temp1(3:length(Temp1)),' ',Temp2,' ',Temp3,' ',Temp4,...
    ' ',Temp5,' ',Temp6(1:(length(Temp6)-2))];

DataFormat.Samples      = textscan(char(fgetl(fid)),'%s%s%s',1);
DataFormat.Samples = str2double(char((DataFormat.Samples{3})));
DataFormat.Lines      = textscan(char(fgetl(fid)),'%s%s%s',1);
DataFormat.Lines = str2double(char((DataFormat.Lines{3})));
DataFormat.Bands      = textscan(char(fgetl(fid)),'%s%s%s',1);
DataFormat.Bands = str2double(char((DataFormat.Bands{3})));
DataFormat.HeaderOffset      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.HeaderOffset = str2double(char((DataFormat.HeaderOffset{4})));
DataFormat.FileType      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.FileType = ([char((DataFormat.FileType{3})),' ',...
    char((DataFormat.FileType{4}))]);

Temp      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
Temp2 = str2double(char((Temp{4})));
switch Temp2 
    case 1
        DataFormat.DataType = 'uint8';
    case 2
        DataFormat.DataType = 'int16';
    case 3
        DataFormat.DataType = 'int32';
    case 4
        DataFormat.DataType = 'float32';
    case 5
        DataFormat.DataType = 'double';
    case 9
        DataFormat.DataType = 'complex';
    case 12
        DataFormat.DataType = 'uint16';
end

DataFormat.Interleave      = textscan(char(fgetl(fid)),'%s%s%s',1);
DataFormat.Interleave = (char((DataFormat.Interleave{3})));
DataFormat.SensorType      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.SensorType = (char((DataFormat.SensorType{4})));

DataFormat.ByteOrder      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.ByteOrder = str2double(char((DataFormat.ByteOrder{4})));
if mod(DataFormat.ByteOrder,2) == 0
    DataFormat.ByteOrder = 'ieee-le';
elseif mod(DataFormat.ByteOrder,2) == 1
    DataFormat.ByteOrder = 'ieee-be';
end

DataFormat.Units      = textscan(char(fgetl(fid)),'%s%s%s%s',1);
DataFormat.Units = (char((DataFormat.Units{4})));

Junk = fgetl(fid); % We just don't need this line, but we need to read past            it.

%%Gets the wavelength data and puts it in a vector 
i = 1;
j = 0;
a = [];
while i==1
    b = fgetl(fid);

     if b == -1
         i=0;
     elseif b(length(b))=='}'
         a = cat(2,a,b(1:(length(b)-1)));
     else
         a = cat(2,a,b);
     end
  end
  Wavelengths = str2num(a);
  fclose(fid); % Closes the file.
  clear Temp Temp2 Temp3 Temp4 Temp5 Temp6 a b Junk

%%Import the data file (UI version)
[FileNameData,PathName,FilterIndex] =...
    uigetfile({'*.bil','Hyperspec Data File';'*.*','All Files'},...
    'Open Hyperspec Data File', PathName) ;

% Set the Data Size
DataSize = [ DataFormat.Lines  DataFormat.Samples  DataFormat.Bands ];

% Load data with multibandread and assign to variable
HyperDataCube = multibandread([PathName,FileNameData], DataSize,...
    DataFormat.DataType,DataFormat.HeaderOffset,...
    DataFormat.Interleave, DataFormat.ByteOrder);

Mesh Plot of Data at specific wavelength.

Lambda = 10; % One element of the Wavelength vector
figure(3);mesh(fliplr(squeeze(HyperDataCube(:,:,Lambda))));view(180,90);
title(['Hyperspectral Data: \lambda = ',num2str(Wavelengths(Lambda)),...
    ' nm'],'FontSize',14);
xlabel('Pixels','FontSize',12);
ylabel('Pixels','FontSize',12);

    if true
      % code
    end
%------------------------------------------------------------

http://www.cytospec.com/bin/CytoSpec.2.00.04.pcode.zip

This link has all the matlab code used on the software "CytoSpec". You may find useful info on these files. Thanks a lot