How to plot an intensity graph?

I have obtained an average value of red pixel count as well the time involved. How do I plot an intensity graph?

Answer 1

[Walter Roberson]

plot(t, average_red_value_vector);
xlabel('time');
ylabel('Intensity');

[Gee Cheng Mun]

Thank you for the help! How can I declare the value of t? For example, t is the range between 320 and 400 seconds.

[Walter Roberson]

t = 320:400; %if consecutive integers

[Gee Cheng Mun]

Okay! How about the average red vector? I have different average values measured. How can I specify each average value in the graph?

[Walter Roberson]

average_red_value_vector should be the vector of averages, however you obtain them. This would require that you have multiple things you were averaging together at each time, which is certainly a possibility, but I wonder if what you have instead is the counts, something like

dinfo = dir('ghostkidney_*.tiff');
for K = 1 : length(dinfo)
  thisfile = dinfo(K).name;
  thisimage = imread(thisfile);
  meets_red_threshold = thisimage(:,:,1) > 180 & thisimage(:,:,2) < 60 & thisimage(:,:,3) < 60;  %strong red compared to G or B
  red_counts(K) = nnz(meets_red_threshold);
  t(K) = (K-1)/24;    %24 frames per second
end

plot(t, red_counts)

[Gee Cheng Mun]

I have different folders of images, thus I have to calculate the average of red pixels for each individual folder of images. I have calculated the average of red counts for each folder, so I need to plot a graph of red counts vs time.

[Walter Roberson]

projectdir = fullfile(pwd, 'MyProject');   %or use an absolute path

folder_info = dir(projectdir);
folder_info(~[folder_info.isdir]) = [];   %ignore non-folders
folder_info( ismember({folder_info.name}, {'.', '..'}) ) = [];  %remove . and .. directories

num_folders = length(folder_info);

avg_counts = zeros(1, num_folders);
folder_times = zeros(1, num_folders);

for fold_idx = 1 : num_folders
  this_folder = fullfile( projectdir, folder_info(fold_idx).name );

    folder_times(fold_idx) = ... you didn't say how you know the time

    file_info = dir( fullfile(this_folder, '*.tiff') );  %example image name pattern
    num_files = length(file_info);

    red_count = 0;

    for file_idx = 1 : num_files
      thisfile = fullfile(this_folder, file_info(file_idx).name );
      thisimage = imread(thisfile);

      %determine which pixels count as red
      meets_red_threshold = thisimage(:,:,1) > 180 & thisimage(:,:,2) < 60 & thisimage(:,:,3) < 60;  %strong red compared to G or B ??

      red_count = red_count + nnz(meets_red_threshold);
    end

    avg_count = red_count / num_files;
    avg_counts(fold_idx) = avg_count;
  end

plot(folder_times, avg_counts)

[Gee Cheng Mun]

The time taken was given by my collaborators. From 540 -3780 sec. How can I input that in MATLAB as the folder_times?

[Walter Roberson]

Are they equal intervals in seconds? Does the folder name include the time in it somewhere? Do the file names of the images include the time in them somewhere? Is there a text file or xls file that has the times recorded?

[Gee Cheng Mun]

The folders are named as shown below and they have an equal interval of 180 sec. Those timings below do not have a text file. How can I display those timings in the graph?

Frame 13: 540 - 720

Frame 14: 720 - 900

Frame 15: 900 - 1080

Frame 16: 1080 - 1260

Frame 17: 1260 - 1440

Frame 18: 1440 - 1620

[Walter Roberson]

In the code I give above, replace

     folder_times(fold_idx) = ... you didn't say how you know the time

with

     timestr = regexprep( folder_info(fold_idx).name, {'^[:]+:\s+', '\s+-\s+\d+$'}, {'', ''});
     folder_times(fold_idx) = str2double(timestr);