converted vtk files are not seen

I was trying to convert my 3d mat files to .vtk format using the code showed inside the below link

http://www.mathworks.com/matlabcentral/fileexchange/23416-writetovtk

For example,i was first trying to convert one mat file to .vtk file. So before the code begins this is what i typed:

filename='P3290321.mat';
matrix=size('P3290321.mat');

Output: no errors , but nothing is written either.(i am certain this code works well when looking at the comments, but i don't know what mistake i am doing here)

I wonder what happened to my converted .vtk files? Can anyone kindly guide me to overcome this issue.

Answer 1

[Walter Roberson]

size('P3290321.mat') means to take size() of the string 'P3290321.mat' which is a 1 x 12 char array.

If you want to use data inside of P3290321.mat then you need to load() the file and access the appropriate loaded variable.

[Chathu]

Thank you very much for your response,Walter.

I came up with an error though.Let me brief what happened.

First, the segmented masked image(x,y) is saved as a .mat file. Second, i wanted to add the slice thickness to the above mentioned .Mat file(x,y,z). So i did the following:

load('P3290319.mat');

[x,y]=find(any(maskedRgbImage,3));

xyz = [x, y];

xyz(:,3) = 0.2;

save('P3290190.mat', 'xyz', '-append')

Third,now i have the appended .Mat file. I used that .Mat file to convert it to a VTK file and then run the code. i wrote the following line:

load('P3290319.mat');

Then an error comes up as following: _

Error using load
Unable to read MAT-file C:\format_img\imageArray\P3290319.mat. Not a binary MAT-file. Try
LOAD -ASCII to read as text.

Kindly correct me if i am wrong anywhere (certainly there is something wrong). Can you pls tell me how to overcome this.

[Walter Roberson]

I do not see anything obvious.

I notice that you load from 319 and save to 190. And then you load again from 319 without having saved to it??

[Chathu]

Hi Walter, thanks for replying me rapidly. And what you said is correct(actually i made a mistake).

But once again i rerun the code with the same filename (as in 'P3290319'). Still i am getting an error.

Error using load
Unable to read MAT-file C:\format_img\imageArray\3d_mat\P3290319.mat. Not a binary MAT-file. Try LOAD
-ASCII to read as text.

Can i clarify a doubt which i have.

So right after segmenting the Region of interest, i get (x,y) coordinates. Then i add a 3rd column which is the slice thickness (in mm). My doubt is, i should make x,y,z coordinates in the same unit format. Hence, shouldn't i multiply my x and y coordinates both with the calibration factor so then all are in mm. Kindly correct me if i have mistaken somewhere. Your response is highly appreciated.

[Walter Roberson]

Converting the coordinates sounds like a good idea.

With regards to the problem with load: I need to see your current code including your call to writetovtk

[Chathu]

Walter, First of all, you have been very helpful. Really admire it.

Second of all, With respect to the image P3290319.jpg: i calculated the calibration factor which is 0.0003 (mm). slice thickness is 2 (mm). Finally i did not get the above error(eg:Not a binary MAT-file) when loading the mat file because i added '-v7' to the code, as follows:

load ('P3290319.mat') % load the MAT file in the workspace

[x,y]=find(any(maskedRgbImage,3));

xyz = [x, y];

xyz(:,1) =xyz(:,1).*0.0003;

xyz(:,2) =xyz(:,2).*0.0003;

xyz(:,3) = 0.2;

save('P3290319.mat', 'xyz','-v7','-append')

Third of all, with respect to size(), you have asked to use string of 'P3290321.mat'. Did you mean,

filename=load('P3290319.mat');

str = mat2str(filename)
str=size(str);

But i am getting an error.

Error using mat2str (line 55)
Input matrix must be numeric.

Fourth of all, so let me send the full code then.

filename=load('P3290319.mat');

str = mat2str(filename);

str=size(str);

% Get the matrix dimensions.
[N M O] = size(matrix);

% Get the maximum value for the normalisation.
mx = max(matrix(:));

% Open the file.
fid = fopen(filename, 'w');
if fid == -1
    error('Cannot open file for writing.');
end

% New line.
nl = sprintf('\n'); % Stupid matlab doesn't interpret \n normally.

% Write the file header.
fwrite(fid, ['# vtk DataFile Version 2.0' nl 'Volume example' nl 'ASCII' nl ...
    'DATASET STRUCTURED_POINTS' nl 'DIMENSIONS ' ...
    num2str(N) ' ' num2str(M) ' ' num2str(O) nl 'ASPECT_RATIO 1 1 1' nl ...
    'ORIGIN 0 0 0' nl 'POINT_DATA ' ...
    num2str(N*M*O) nl 'SCALARS volume_scalars char 1' nl 'LOOKUP_TABLE default' nl]);

for z = 1:O
    % Get this layer.
    v = matrix(:, :, z);
    % Scale it. This assumes there are no negative numbers. I'm not sure
    % this is actually necessary.
    v = round(100 .* v(:) ./ mx);
    % Write the values as text numbers.
    fwrite(fid, num2str(v'));
    % Newline.
    fwrite(fid, nl);

   % Display progress.
      disp([num2str(round(100*z/O)) '%']);
  end

% Close the file.
fclose(fid);

end

Kindly, can you correct my mistakes(if any)? Thank you so much in advance.Really admire your assistance.

[Chathu]

As you said, there is a problem with my writetovtk (i am not sure what that is though). Can you kindly guide me ?

[Walter Roberson]

dataset = 'P3290319';
infile = sprintf('%s.mat', dataset);
vtkfile = sprintf('%s.vtk', dataset);

filestruct = load(infile);
matrix = filestruct.maskedRgbImage;  %double check this

[N M O] = size(matrix);
mx = max(matrix(:));

fid = fopen(vtkfile, 'wt');

fprintf(fid, ...
  '# vtk DataFile Version 2.0\n' ...
  'Volume example\n' ...
  'ASCII\n' ...
  'DATASET STRUCTURED_POINTS\n' ...
  'DIMENSIONS %d %d %d\n' ...
  'ASPECT_RATIO 1 1 1\n' ...
  'ORIGIN 0 0 0\n' ...
  'POINT_DATA %d\n' ...
  'SCALARS volume_scalars char 1\n' ...
  'LOOKUP_TABLE default\n',
  N, M, O, N*M*O);

for z = 1:O
  % Get this layer.
  v = matrix(:, :, z);
  % Scale it. This assumes there are no negative numbers. I'm not sure
  % this is actually necessary.
  v = round(100 .* v(:) ./ mx);
  % Write the values as text numbers.
  fwrite(fid, num2str(v'));
  % Newline.
  fprintf(fid, '\n');
end

fclose(fid);

Please double check that makedRGBImage is really the variable you intended to refer to as "matrix".

[Chathu]

Walter, you have been very helpful whole throughout.I do really appreciate your kindest support. Yes, you're right. 'matrix' shd be xyz. In order to obtain xyz(i converted the coordinates), i run the following code:

xyz(:,1) =xyz(:,1).*0.0003;
xyz(:,2) =xyz(:,2).*0.0003;
xyz(:,3) = 0.2;

I got an error, as follows:

Error using vertcat Dimensions of matrices being concatenated are not consistent. Error in mat_vtk_3D (line 12) fprintf(fid,['# vtk DataFile Version 2.0\n' ...

Also, i get an empty .vtk file. i wonder why though?

Walter, if it's possible just give me a clue of the error.So far also, you were so helpful. Once again, thank you very much for your kindest guidance:)

[Walter Roberson]

 fprintf(fid, [...
  '# vtk DataFile Version 2.0\n' ...
  'Volume example\n' ...
  'ASCII\n' ...
  'DATASET STRUCTURED_POINTS\n' ...
  'DIMENSIONS %d %d %d\n' ...
  'ASPECT_RATIO 1 1 1\n' ...
  'ORIGIN 0 0 0\n' ...
  'POINT_DATA %d\n' ...
  'SCALARS volume_scalars char 1\n' ...
  'LOOKUP_TABLE default\n' ], ...
  N, M, O, N*M*O);

[Chathu]

Walter,finally i was able to convert .mat to .vtk files. Thank you so much for all your assistance. I really appreciate your sincere effort in resolving this matter. Highly admire it, Walter! One last question,i was wondering whether VoLView can be used to visualize the model instead of Paraview? Finally, thanks a million for your kindest assistance.

[Walter Roberson]

VTK does seem to be mentioned for VolView, and as it is open source it appears to be worth a try.

[Chathu]

Alright Walter:) Thank you soo much for your kindest support. Really appreciate it.