How can I save this .tiff file correctly?

The code below is the code I wrote to control our microscope and led lights using serial commands.

I am running into a problem with saving it however, the image collected is not being saved correctly. HELP!

The area with the double stars (bold) is where I wrote the code to save our image, and take user input to save the image.

best

Merrilee

    %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 = .7;
%when I want to take multiple images, wait awhile and then takee more
%images in the same file. 

for i = 1:2
    vid.FramesPerTrigger = 10;
    fprintf(obj, 'O 0 1'); %on
    preview(vid);
    %fprintf(obj, 'O 0 1'); %on
    start(vid),wait(vid);

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

end;
stoppreview(vid);
% below is where my code isn't saving the image correctly - the .tiff file that saves has no data (i think) saved to %it. it just looks like a pixel landscape. 

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

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

Answer 1

[Walter Roberson]

Use imwrite() or the tiff class to save tif files. save() is for saving as .mat files.

[Merrilee Thomas]

so, you mean ....not sure how to implement that into my code. can you show me an example using the below code? I am sorry, new to programing.

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

[Merrilee Thomas]

ok. I rewrote the code to imwrite(x, [filename '.tif']); however, now I get an error that says 4-D data not supported for TIFF files. what do i need to change. I need the images I am taking to be in a tiff format. best, Merr

[Walter Roberson]

There are a lot of examples in the imwrite documentation. Just pass in RE and then the file name.