My 4- D data is not supported by tiff files, what do I need to change so it does go into a .tiff file?

I am taking multiple images and tryting to save them using the code below, however the error I get when I run it is Error using writetif 4-D data not supported for TIFF files.

end; stoppreview(vid);

alpha=input('What do you want to name you file? ','s')
lambda = input('Variable ?', 's')
x = getdata(vid);
filename = alpha
RE = lambda
imwrite(x, [filename '.tif']);
clear lambda;

Answer 1

[Walter Roberson]

Is your data hyperspectral or is it multislice?

If your data is multislice then you can loop through the slices and imwrite each of them using writemode append

If your data is hyperspectral then is it geotiff? If so use geotiffwrite

If your image is hyperspectral then you have the choice of encoding it as AdditionalSamples or as subimages (but that is not what subimages are intended for) or as additional image entries (which is what writemode append will use)

Usually when there is a requirement to write beyond rgb or rgba or cmyk then it is for use with a particular post processing tool. In such a case you need to match the expectations of that tool rather than just writing whatever is convenient.

You should not expect to be able to write a 4d tiff in MATLAB and then double click on the image icon in your operating system and have it somehow displayed such as by volumetric display.

[Merrilee Thomas]

My data is coming from a hamamatsu camera, the Orca flash, I am imaging a plate of cells, taking about 30 images. I don't know if that means it is hyperspectral? or a multisplice. or neither?

I am guessing its just a multislice. not sure how to use the imwrite append, but even if I use it, will it take the full data? and how should I be able to open it once I have saved it? I usually try to use the image proccessing batch app.

[Walter Roberson]

alpha = input('What do you want to name you file? ','s');
x = getdata(vid);
filename = [alpha '.tif'];

for slnum = 1 : size(x, 4)
  if slnum == 1; mode = 'overwrite'; else mode = 'append'; end
  imwrite( x(:,:,slnum), filename, 'writemode', mode);
end

[Merrilee Thomas]

THANK YOU!!!!!! That is almost what I need, but it is still not addind the loops that I have, I only get 30 images from my file, not 60 or 90 (if I loop three times)

[Walter Roberson]

alpha = input('What do you want to name you file? ','s');
first_time = true;

for frame_count = 1 : 3

    x = getdata(vid);
    filename = [alpha '.tif'];

    for slnum = 1 : size(x, 4)
      if first_time; mode = 'overwrite'; first_time = false; else mode = 'append'; end
      imwrite( x(:,:,slnum), filename, 'writemode', mode);
    end

end

[Merrilee Thomas]

I get an error when I run this code that there is a Error using imaqdevice/getdata (line 154) OBJ is not running and no frames are available.

[Walter Roberson]

Could you explain further what you would be doing when you loop three times?

[Merrilee Thomas]

Here is the code I wrote . I am using serial commands to control the LED lights, and I put the imaging in a for loop. I want to be able to image for 10secs, pause imaging, wait for 120 seconds, and then go through that loop three times. I changed the time on those in the loop just to be able to de-bug the code faster.

I am trying to then write this image using the append mode. However, I think that something is either going wrong when I am writing the apend, or I am loosing data every time the for loop goes through the iteration.

Thank you for your time and help, Merrilee Thomas

Answer 2

[Merrilee Thomas]

%first set up channel....

obj = instrfind('Port', 'COM3')

if isempty(obj)
    obj = serial('COM3');
else
    fclose(obj);
    obj = obj(1)
end

fopen(obj);
set(obj, 'BaudRate', 115200);
set(obj, 'DataTerminalReady', 'off');
set(obj, 'FlowControl', 'hardware');
set(obj, 'Terminator', {10,10});
fprintf(obj, 'M 0');
data = query(obj, 'L? 0');

% this will set current for channel 1
% and the "L" is the limit.
fprintf(obj, 'L 0 700');
currentlimit = query(obj, 'L? 0');

% this will set current for channel 2
fprintf(obj, 'L 1 700');
currentlimit = query(obj, 'L? 1');

% to set or change "brightness Mode" also must turn off LED first before
% changing brightness if doing this in a command line.
fprintf(obj, 'BP 0 100');
brightnessvalue = query(obj, 'BP? 0');

% this will change brightness for channel 2
fprintf(obj, 'BP 0 100');
brightnessvalue = query(obj, 'BP? 0');

% this is the quickest on/off switch(470) 
fprintf(obj, 'O 0 1'); %on
fprintf(obj, 'O 0 0'); %off

% and this turns on and off channel 2(560)!!!
fprintf(obj, 'O 1 1') % on
fprintf(obj, 'O 1 0') % off

% now set up imaging....

%vid = videoinput('hamamatsu', 1, 'MONO16_BIN2x2_1024x1024_FastMode');
vid = videoinput('hamamatsu', 1, 'MONO16_BIN4x4_512x512_FastMode');
src = getselectedsource(vid);
%vid.FramesPerTrigger = 10;
% TriggerRepeat is zero based and is always one
% less than the number of triggers.

%vid.TriggerRepeat = 2;

src.ExposureTime = .3;
%when I want to take multiple images, wait awhile and then takee more
%images in the same file. 

for i = 1:2
    tic
    vid.FramesPerTrigger = 30;
    fprintf(obj, 'O 0 1'); %on
    preview(vid);
    %fprintf(obj, 'O 0 1'); %on
    start(vid),wait(vid);
    toc

       for l = 1:2
           fprintf(obj, 'O 0 0'); %off 
           pause (10);
       end;

end;
stoppreview(vid);
stop(vid);

alpha = input('What do you want to name you file? ','s');
first_time = true;

for frame_count = 1 : 3
    x = getdata(vid);
    filename = [alpha '.tif'];

      for slnum = 1 : size(x, 4)
        if first_time; mode = 'overwrite'; first_time = false; else mode = 'append'; end
        imwrite( x(:,:,slnum), filename, 'writemode', mode);
      end
  end
  closepreview(vid);
  delete(vid); 
  clear vid;

Answer 3

[Merrilee Thomas]

% now set up imaging....

%vid = videoinput('hamamatsu', 1, 'MONO16_BIN2x2_1024x1024_FastMode'); vid = videoinput('hamamatsu', 1, 'MONO16_BIN4x4_512x512_FastMode'); src = getselectedsource(vid); %vid.FramesPerTrigger = 10; % TriggerRepeat is zero based and is always one % less than the number of triggers.

%vid.TriggerRepeat = 2;

src.ExposureTime = .3; %when I want to take multiple images, wait awhile and then takee more %images in the same file.

tic vid.FramesPerTrigger = 30; fprintf(obj, 'O 0 1'); %on preview(vid); %fprintf(obj, 'O 0 1'); %on start(vid),wait(vid); toc fprintf(obj, 'O 0 0'); %off pause (10); vid.FramesPerTrigger = 30; fprintf(obj, 'O 0 1'); %on preview(vid); %fprintf(obj, 'O 0 1'); %on start(vid),wait(vid);

stoppreview(vid); stop(vid);

alpha = input('What do you want to name you file? ','s'); x = getdata(vid); filename = [alpha '.tif']; for slnum = 1 : size(x, 4) if slnum == 1; mode = 'overwrite'; else mode = 'append'; end imwrite( x(:,:,slnum), filename, 'writemode', mode); end

closepreview(vid); delete(vid); clear vid;

I took out the for loop and I still only get 30 frames... I think that when I call the trigger event it deletes the previous 30 frames. maybe