How to subtract images and get the largest blob from the subtracted image

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Warid Islam
Warid Islam 2019-10-17
评论： Warid Islam 2019-10-21
I have few images from which I want to subtract the first image from the subsequent images. The first image is used as a reference point which would be subtracted from the other images. Please find the code below:
dirpath = uigetdir(pwd);
dirList = dir(dirpath);
dirList = {dirList.name};
find_regexp=regexp(dirList,'[0-9]F+[0-9]');
find_regex_indxs=find(~cellfun(@isempty,find_regexp));
dirList=dirList(find_regex_indxs);
dirList=natsort(dirList);
num_files = length(dirList);
imgs = cell(1,num_files);
for val = 1:num_files
imgs{val} = imread(dirList{val});
end
%%
final_segments = cell(1,num_files);
for idx = 1:num_files
%% convert rgb to grayscale
L = rgb2gray(imgs{idx});
% figure, imshow(L)
%% Thresholding multi-level
thresh = multithresh(imgs{idx},2);
seg_I = imquantize(imgs{idx},thresh);
% figure, imshow(seg_I,[]);
%% Removing the background
seg_img = seg_I;
seg_img(seg_I ~= 2) = 0;
% figure, imshow(seg_img,[]);
%% filtering using imclose
struct_elem = strel('diamond',4);
seg_img_close = imclose(seg_img,struct_elem);
% figure, imshow(seg_img_close,[]);
%% Get largest object
bw_keep = bwareafilt(logical(seg_img_close),1);
% figure, imshow(bw_keep,[]);
%% fill holes within
fill_bw_keep = imfill(bw_keep,'holes');
% figure, imshow(fill_bw_keep,[]);
%% Count nnz or area
area_fill_bw_keep = nnz(fill_bw_keep);
sprintf('area of segmented region: %d', area_fill_bw_keep)
%% map the image back to original pixel values
img_class = class(imgs{1});
fill_bw_keep = cast(fill_bw_keep, img_class);
map_img = fill_bw_keep.*imgs{idx};
% figure, imshow(map_img,[]);
%% save to cell
final_segments{idx} = map_img;
end
%% disp final segments
for idx = 1:num_files
% figure(1), imshow(final_segments{idx},[]);
pause(1)
end
%% subtract 2 to n from 1st image and display
sub_final_segments = cell(1,num_files-1); % initialisation
for idx = 2:num_files
sub_final_segments{idx-1} = final_segments{idx} - final_segments{1};
figure(2), imshow(sub_final_segments{idx-1},[]);
pause(1)
end
g = cell(1,num_files);
for idx = 2:num_files
g = rgb2gray(sub_final_segments{idx-1});
% figure, imshow(g,[]);
pause(1)
end
%% subtraction areas
% areas_subtraction = [];
% for idx = 1:num_files-1
% areas_subtraction = [areas_subtraction, nnz(sub_final_segments{idx})];
% end
% sprintf('Areas after subtraction: '), disp(areas_subtraction)
% Standard Deviation
subtraction_standard_deviation = [];
for idx = 1:num_files-1
subtraction_standard_deviation = [subtraction_standard_deviation, std2(sub_final_segments{idx})];
end
sprintf('Standard Deviation after subtraction: '), disp(subtraction_standard_deviation)
g_deviation = [];
for idx = 1:num_files-1
g_deviation = [g_deviation, std2(g(idx))];
end
sprintf('Standard Deviation after subtraction: '), disp(g_deviation)
%average density
subtraction_average_denstiy = [];
for idx = 1:num_files-1
subtraction_average_denstiy = [subtraction_average_denstiy, mean2(sub_final_segments{idx})];
end
sprintf('Average Density after subtraction: '), disp(subtraction_average_denstiy)
g_denstiy = [];
for idx = 1:num_files-1
g_denstiy = [g_denstiy, mean2(g(idx))];
end
sprintf('Average Density after subtraction: '), disp(g_denstiy)
However, I get the following error message:
Error in warid_codes (line 37)
bw_keep = bwareafilt(logical(seg_img_close),1);
I am using the bwareafilt function to take the largest blob from the subtracted image. But I am getting confused about the error message. I have attached few images. Any suggestions would be very much appreciated. Thank you.
  4 个评论
显示 2更早的评论
Warid Islam
Warid Islam 2019-10-18
Hi @Matt,
I am sorry that I have missed the full error message. Please find it below:
Error using bwpropfilt
Expected input number 1, BW, to be two-dimensional.
Error in bwpropfilt>parse_inputs (line 121)
validateattributes(bw, {'logical'}, {'nonsparse', '2d'}, mfilename, 'BW', 1);
Error in bwpropfilt (line 58)
[bw, I, attrib, p, direction, conn] = parse_inputs(args{:});
Error in bwareafilt (line 34)
bw2 = bwpropfilt(bw, 'area', p, direction, conn);
Error in warid_codes (line 37)
bw_keep = bwareafilt(logical(seg_img_close),1);
Thank you.

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采纳的回答

Sid Singh
Sid Singh 2019-10-21
Hi, bwareafilt expects a 2-D logical image. In your code, you are using RGB (3-D) images for preprocessing and the input to bwareafilt is a 3-D logical image. That's why you are getting the error. Check your preprocessing steps.
%% convert rgb to grayscale
L = rgb2gray(imgs{idx});
% figure, imshow(L)
%% Thresholding multi-level
thresh = multithresh(imgs{idx},2);
seg_I = imquantize(imgs{idx},thresh);
% figure, imshow(seg_I,[]);
  1 个评论
Warid Islam
Warid Islam 2019-10-21
Hi Sid,
I changed couple of lines of code above. But I am getting the same error.
%% convert rgb to grayscale
% L = rgb2gray(imgs{idx});
% figure, imshow(L)
%% Thresholding multi-level
thresh = multithresh(imgs{idx},2);
seg_I = imquantize(imgs{idx},thresh);
% figure, imshow(seg_I,[]);
%% Removing the background
seg_img = seg_I;
seg_img(seg_I ~= 2) = 0;
% figure, imshow(seg_img,[]);
%% filtering using imclose
struct_elem = strel('diamond',4);
seg_img_close = imclose(seg_img,struct_elem);
% figure, imshow(seg_img_close,[]);
%% Get largest object
bw_keep = bwareafilt(logical(seg_img_close),1);
% figure, imshow(bw_keep,[]);
Previously, I converted the image from rgb to gray but my image here is not rgb. So I commented out that part of the code. But the error still persists.

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