How to open .lmf file

Dear All,

I have the pointclass3.lmf file as attached. But I dont know how to open it. In manual just said like below:

"This routine saves information about the photon history in a binary list mode file. The file will have the extension *.lmf. To save disk space, each record of a history in the binary file will have nine 16-bit integer values, one 64-bit float value, and one 8-bit value in the order indicated in the table. "

Anyone can hel me?

[Walter Roberson]

.lmf files just might be related to https://amo-csd.lbl.gov/downloads/LMF2ROOT%20in%20a%20nutshell.pdf

[DGM]

I have no idea what the file is, but maybe this is a start.

% i'm assuming byte order and signedness of integer classes
% is there a header?  file length is not integer-divisible by described record length
% i'm assuming that the data is not compressed, and that the there is nothing trailing the data
% that assumption leaves _at least_ 16B that can't be data.

fid = fopen('pointclass3.lmf');
stream = fread(fid,inf,'*uint8');
fclose(fid);

recordlen = 18 + 8 + 1; % 9x16b, 1x64b, 1x8b
headerlen = mod(numel(stream),recordlen); % is there a header??
header = stream(1:headerlen);
data = reshape(stream(headerlen+1:end),recordlen,[]);

% the 16b fields
fields1 = typecast(reshape(data(1:18,:),[],1),'uint16'); 
fields1 = reshape(fields1,9,[]).';

% the double float field
fields2 = typecast(reshape(data(19:26,:),[],1),'double'); 

% the 8b field (the recasting here is redundant, but i'm just being explicit)
fields3 = typecast(reshape(data(23,:),[],1),'uint8'); 

In the case of blindly decoding physical images, there's often some discernable structure that tells us if we're decoding things grossly wrong. With tabular data, we don't really get the same insight. The results can be completely wrong, and I would have no idea.

EDIT: My blind suggestion is probably garbage. This is probably closer, since you seem to be doing a lot of medical image stuff.

https://depts.washington.edu/simset/html/simSET_resources/list_mode_library.html

That suggests though, that each LMF file should have a text file which describes its structure -- something like a header file. This is at odds with my assumption that the LMF file itself apparently must have had a header due to its length.

[Cris LaPierre]

Can you share the table the quoted text refers to?

[mohd akmal masud]

Dear @DGM@Cris LaPierre,

I think there is file image produced together. You can get the file image as link here: https://drive.google.com/drive/folders/18f_e3KljFuebeQHH6KRVXHbCyRx_0Moq?usp=sharing .

pointlmf.a00 = the image file

pointlmf.h00 = the header file image

pointlmf.lmf = saves information about the photon history in a binary list mode file.

Actually the lmf file accordingly to manual is saves information about the photon history in a binary list mode file. The manual just said like below:

[mohd akmal masud]

dear @DGM@DGM@Cris LaPierre

https://drive.google.com/drive/folders/18f_e3KljFuebeQHH6KRVXHbCyRx_0Moq?usp=sharing

[DGM]

Yee. Well, as much as that looks helpful, I'm not able to download 1.3GB in a reasonable timeframe.

The screenshot does, however tell us that there's an extra field. With that information, the file does appear to have an integer number of records.

fid = fopen('pointclass3.lmf');
stream = fread(fid,inf,'*uint8');
fclose(fid);

recordlen = 20 + 8 + 1; % 10x16b, 1x64b, 1x8b
headerlen = mod(numel(stream),recordlen) % is there a header??
header = stream(1:headerlen);
data = reshape(stream(headerlen+1:end),recordlen,[]);

% the 16b fields
xyz0 = typecast(reshape(data(1:6,:),[],1),'uint16'); 
xyz0 = reshape(xyz0,3,[]).';
xyzphantom = typecast(reshape(data(7:12,:),[],1),'uint16'); 
xyzphantom = reshape(xyzphantom,3,[]).';
xyzcrystal = typecast(reshape(data(13:18,:),[],1),'uint16'); 
xyzcrystal = reshape(xyzcrystal,3,[]).';
energy = typecast(reshape(data(19:20,:),[],1),'uint16'); 

% the double float field
photonweight = typecast(reshape(data(21:28,:),[],1),'double');

% the 8b field
scatterorder = typecast(reshape(data(29,:),[],1),'uint8'); 

[mohd akmal masud]

Dear @DGM

I was try your syntax. All is well.

But the value in workspace I dont know what is it actually?

Is it is images? is it is data? is it is graph profile?

Can you help me how to view all that valu workspace?

[mohd akmal masud]

Dear @DGM,

headerlen = mod(numel(stream),recordlen) % is there a header??

The header files is attached.

Answer 1

[Harsh Sharma]

Hi Akmal,

You can use “fread” function to read a binary file in MATLAB. Below is the code to read data in the format mentioned by you.

% Open the file in binary read mode
fileID = fopen('pointclass3.lmf', 'rb');

numRecords = 10; % As an example we read 10 records 
 
% Preallocate arrays to store data 
int16Data = zeros(numRecords, 9, 'int16'); % 9 int16 values per record 
float64Data = zeros(numRecords, 1, 'double'); % 1 float64 value per record 
int8Data = zeros(numRecords, 1, 'int8'); % 1 int8 value per record 
 
% Loop to read each record 
for i = 1:numRecords 
    int16Data(i, :) = fread(fileID, 9, 'int16'); % Read 9 int16 values 
    float64Data(i) = fread(fileID, 1, 'double'); % Read 1 float64 value 
    int8Data(i) = fread(fileID, 1, 'int8'); % Read 1 int8 value 
end 
 
% Close the file 
fclose(fileID); 
 
% Display the first record as an example 
disp('First Record:'); 
disp('Int16 Data:'); 
disp(int16Data(1, :)); 
disp('Float64 Data:'); 
disp(float64Data(1)); 
disp('Int8 Data:'); 
disp(int8Data(1)); 

Here’s the output for the above code-

You may refer to the following documentation to learn more about “fread” function - https://www.mathworks.com/help/matlab/ref/fread.html