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LeafProcessor.m
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LeafProcessor.m
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% This leaf processor can be used to parse any Arabidopsis plants.
% Author: Ke Gao, Najwa Nurhidayatun, Yen On Chan
% Use at your own risk.
classdef LeafProcessor < handle
properties(Access=private)
seperator
topImage = [];
topImageInDouble = [];
topImageRows = 0;
topImageColumns = 0;
topImageChannels = 0;
sideImage = [];
sideImageInDouble = [];
sideImageRows = 0;
sideImageColumns = 0;
sideImageChannels = 0;
thresh_mask = 130; % threshold for generating the foreground mask
tolerance_mask = 20; % tolerance for threshold
black_checker = [49; 48; 51];
blue_checker = [34; 63; 147];
green_checker = [67; 149; 74];
red_checker = [180; 49; 57];
colorsChecker = [];
topColorsCorrupt = [];
sideColorsCorrupt = [];
topCorrectMatrix = [];
sideCorrectMatrix = [];
topColorCorrectedImage = [];
sideColorCorrectedImage = [];
topNormalizedImage = [];
sideNormalizedImage = [];
topImgMaskGreen = [];
sideImgMaskGreen = [];
topForegroundImage = [];
sideForegroundImage = [];
topAverageColor = [0,0,0];
sideAverageColor = [0,0,0];
topForegroundImageWithCC = [];
sideForegroundImageWithCC = [];
topBWForegroundImage = [];
sideBWForegroundImage = [];
topBWForegroundImageWithCC = [];
sideBWForegroundImageWithCC = [];
topGradientMagnitudeImage = [];
sideGradientMagnitudeImage = [];
topLeavesCutImage = [];
sideLeavesCutImage = [];
topNumberOfLeaves = 0;
topLeavesDetails = {};
topLeavesLabeledImage = [];
topLeavesTextLabeledImage = [];
topTextFontSize = 30; % Text size for text on topLeavesLabeledImage
topLabelShiftX = -15; % Shift to text position on topLeavesLabeledImage
topLabelShiftY = -15;
pixelPerCM = 0;
areaPerPixel = 0;
lengthPerPixelSide = 0;
topForegroundArea = 0;
csReference_Area = [];
xArray_Area = [];
yArray_Area = [];
xCell_Area = [];
yCell_Area = [];
csReference_LeafNum = [];
xArray_LeafNum = [];
yArray_LeafNum = [];
xCell_LeafNum = [];
yCell_LeafNum = [];
end
properties(Constant, Hidden=true)
extList={'jpg'};
end
methods(Access=private)
function obj = calculateColorsChecker(obj)
obj.colorsChecker = cat(2, obj.black_checker, obj.blue_checker, obj.green_checker, obj.red_checker);
end
function img_name = getImageNameFromFilePath(obj, filePath)
dirComponents = strsplit(filePath, '\');
img_name = dirComponents(size(dirComponents,2));
img_name = img_name{1};
img_name = img_name(1:end-4);
end
end
methods
%% Constructor and Destructor
% constructor
function obj = LeafProcessor(topImage, sideImage)
if(strcmpi(computer,'PCWIN') || strcmpi(computer,'PCWIN64'))
obj.seperator='\';
elseif(strcmpi(computer,'GLNX86') || strcmpi(computer,'GLNXA86'))
obj.seperator='/';
elseif(strcmpi(computer,'MACI64'))
obj.seperator='/';
end
if(isempty(topImage) == 0)
obj.topImage = topImage;
obj.topImageInDouble = double(topImage);
[obj.topImageRows, obj.topImageColumns, obj.topImageChannels] = size(topImage);
end
if(isempty(sideImage) == 0)
obj.sideImage = sideImage;
obj.sideImageInDouble = double(sideImage);
[obj.sideImageRows, obj.sideImageColumns, obj.sideImageChannels] = size(sideImage);
end
end
% destructor
function delete(obj)
end
%% Get and Set Functions
% set top image
function obj = setTopImage(obj, img)
obj.topImage = [];
obj.topImage = img;
obj.topImageInDouble = double(img);
[obj.topImageRows, obj.topImageColumns, obj.topImageChannels] = size(img);
end
% get top image
function top_image = getTopImage(obj)
top_image = obj.topImage;
end
% set side image
function obj = setSideImage(obj, img)
obj.sideImage = [];
obj.sideImage = img;
obj.sideImageInDouble = double(img);
[obj.sideImageRows, obj.sideImageColumns, obj.sideImageChannels] = size(img);
end
% get side image
function side_image = getSideImage(obj)
side_image = obj.sideImage;
end
% set mask threshold
function obj = setMaskThreshold(obj, threshMask)
obj.thresh_mask = threshMask;
end
% get mask threshold
function threshold_mask = getMaskThreshold(obj)
threshold_mask = obj.thresh_mask;
end
% set tolerance mask
function obj = setMaskTolerance(obj, toleranceMask)
obj.tolerance_mask = toleranceMask;
end
% get tolerance mask
function tolerance_mask = getMaskTolerance(obj)
tolerance_mask = obj.tolerance_mask;
end
% set black checker
function obj = setBlackChecker(obj, blackChecker)
obj.black_checker = blackChecker;
end
% get black Checker
function black_checker = getBlackChecker(obj)
black_checker = obj.black_checker;
end
% set blue checker
function obj = setBlueChecker(obj, blueChecker)
obj.blue_checker = blueChecker;
end
% get blue Checker
function blue_checker = getBlueChecker(obj)
blue_checker = obj.blue_checker;
end
% set green checker
function obj = setGreenChecker(obj, greenChecker)
obj.green_checker = greenChecker;
end
% get green Checker
function green_checker = getGreenChecker(obj)
green_checker = obj.green_checker;
end
% set red checker
function obj = setRedChecker(obj, redChecker)
obj.red_checker = redChecker;
end
% get red Checker
function red_checker = getRedChecker(obj)
red_checker = obj.red_checker;
end
% set top image mask (green)
function obj = setTopImgMaskGreen(obj, topImgMaskGreen)
obj.topImgMaskGreen = topImgMaskGreen;
end
% get top image mask (green)
function top_img_mask_green = getTopImgMaskGreen(obj)
top_img_mask_green = obj.topImgMaskGreen;
end
% set side image mask (green)
function obj = setSideImgMaskGreen(obj, sideImgMaskGreen)
obj.sideImgMaskGreen = sideImgMaskGreen;
end
% get side image mask (green)
function side_img_mask_green = getSideImgMaskGreen(obj)
side_img_mask_green = obj.sideImgMaskGreen;
end
% set Pixel per cm and calculate cm per pixel and cm2 per pixel
function obj = setPixelPerCM(obj, pixelPerCM)
obj.pixelPerCM = pixelPerCM;
obj.lengthPerPixelSide = 1/obj.pixelPerCM;
obj.areaPerPixel = obj.lengthPerPixelSide ^ 2;
end
% get colors checker matrix
function colors_checker = getColorsChecker(obj)
colors_checker = obj.colorsChecker;
end
% get top colors corrupt matrix
function top_colors_corrupt = getTopColorsCorrupt(obj)
top_colors_corrupt = obj.topColorsCorrupt;
end
% get side colors corrupt matrix
function side_colors_corrupt = getSideColorsCorrupt(obj)
side_colors_corrupt = obj.sideColorsCorrupt;
end
%% Generate mask without color correction
% generate top normalized RGB Image without color correction
function top_img_norm = generateTopNormalizedImageWithoutCC(obj)
obj.topColorCorrectedImage = obj.topImageInDouble;
top_img_norm = obj.generateTopNormalizedImage();
end
% generate top green mask without color correction
function top_img_mask_green = generateTopGreenMaskWithoutCC(obj)
obj.topImgMaskGreen = obj.topNormalizedImage(:,:,2);
obj.topImgMaskGreen(abs(obj.topImgMaskGreen-obj.thresh_mask)<obj.tolerance_mask) = 0;
obj.topImgMaskGreen(obj.topImgMaskGreen~=0) = 1;
se1 = strel('disk', 5);
obj.topImgMaskGreen = imopen(obj.topImgMaskGreen, se1); % remove salt-and-pepper noise
obj.topImgMaskGreen = imclose(obj.topImgMaskGreen, se1); % fill the holes in the mask
img_mask2 = bwpropfilt(logical(obj.topImgMaskGreen(50:300,:,:)),'Area',[0 12100]);
obj.topImgMaskGreen(50:300,:,:) = img_mask2;
img_mask3 = bwpropfilt(logical(obj.topImgMaskGreen(1150:end,:,:)),'Area',[0 12100]);
obj.topImgMaskGreen(1150:end,:,:) = img_mask3;
for i=300:-1:1
if(sum(obj.topImgMaskGreen(:,i,:))==0) % left
obj.topImgMaskGreen(:,1:i,:)=0;
break;
end
end
for i=300:-1:1
if(sum(obj.topImgMaskGreen(i,:,:))==0) % top
obj.topImgMaskGreen(1:i,:,:)=0;
break;
end
end
for i=900:size(obj.topImgMaskGreen,1)
if(sum(obj.topImgMaskGreen(i,:,:))==0) % bottom
obj.topImgMaskGreen(i:end,:,:)=0;
break;
end
end
for i=700:size(obj.topImgMaskGreen,2)
if(sum(obj.topImgMaskGreen(:,i,:))==0) % right
obj.topImgMaskGreen(:,i:end,:)=0;
break;
end
end
top_img_mask_green = logical(obj.topImgMaskGreen);
end
%% Generate mask after doing color correction
% get sample colors from top image
function obj = collectTopSampleColors(obj, img, x, y)
tempImage = double(img);
x = round(x);
y = round(y);
black_corrupt = [tempImage(y(1),x(1),1); tempImage(y(1),x(1),2); tempImage(y(1),x(1),3)];
blue_corrupt = [tempImage(y(2),x(2),1); tempImage(y(2),x(2),2); tempImage(y(2),x(2),3)];
green_corrupt = [tempImage(y(3),x(3),1); tempImage(y(3),x(3),2); tempImage(y(3),x(3),3)];
red_corrupt = [tempImage(y(4),x(4),1); tempImage(y(4),x(4),2); tempImage(y(4),x(4),3)];
if(isempty(obj.topColorsCorrupt)==1)
obj.topColorsCorrupt = cat(2, black_corrupt, blue_corrupt, green_corrupt, red_corrupt);
else
obj.topColorsCorrupt = (obj.topColorsCorrupt + cat(2, black_corrupt, blue_corrupt, green_corrupt, red_corrupt))./2;
end
end
% get sample colors from side image
function obj = collectSideSampleColors(obj, img, x, y)
tempImage = double(img);
x = round(x);
y = round(y);
black_corrupt = [tempImage(y(1),x(1),1); tempImage(y(1),x(1),2); tempImage(y(1),x(1),3)];
blue_corrupt = [tempImage(y(2),x(2),1); tempImage(y(2),x(2),2); tempImage(y(2),x(2),3)];
green_corrupt = [tempImage(y(3),x(3),1); tempImage(y(3),x(3),2); tempImage(y(3),x(3),3)];
red_corrupt = [tempImage(y(4),x(4),1); tempImage(y(4),x(4),2); tempImage(y(4),x(4),3)];
if(isempty(obj.sideColorsCorrupt)==1)
obj.sideColorsCorrupt = cat(2, black_corrupt, blue_corrupt, green_corrupt, red_corrupt);
else
obj.sideColorsCorrupt = (obj.sideColorsCorrupt + cat(2, black_corrupt, blue_corrupt, green_corrupt, red_corrupt))./2;
end
end
% generate top correction matrix
function obj = generateTopColorCorelationalMatrix(obj)
obj.colorsChecker = [];
obj = obj.calculateColorsChecker();
obj.topCorrectMatrix = obj.colorsChecker / obj.topColorsCorrupt; % color corelation matrix
end
% generate side correction matrix
function obj = generateSideColorCorelationalMatrix(obj)
obj.colorsChecker = [];
obj = obj.calculateColorsChecker();
obj.sideCorrectMatrix = obj.colorsChecker / obj.sideColorsCorrupt; % color corelation matrix
end
% generate top color corrected image
function top_color_corrected_image = generateTopColorCorrectedImage(obj)
obj.topColorCorrectedImage = zeros(size(obj.topImageInDouble));
for i0 = 1:obj.topImageRows
for j0 = 1:obj.topImageColumns
rgb_out = obj.topCorrectMatrix * [obj.topImageInDouble(i0,j0,1); obj.topImageInDouble(i0,j0,2); obj.topImageInDouble(i0,j0,3)];
obj.topColorCorrectedImage(i0,j0,1) = rgb_out(1);
obj.topColorCorrectedImage(i0,j0,2) = rgb_out(2);
obj.topColorCorrectedImage(i0,j0,3) = rgb_out(3);
end
end
top_color_corrected_image = uint8(obj.topColorCorrectedImage);
end
% generate side color corrected image
function side_color_corrected_image = generateSideColorCorrectedImage(obj)
obj.sideColorCorrectedImage = zeros(size(obj.sideImageInDouble));
for i0 = 1:obj.sideImageRows
for j0 = 1:obj.sideImageColumns
rgb_out = obj.sideCorrectMatrix * [obj.sideImageInDouble(i0,j0,1); obj.sideImageInDouble(i0,j0,2); obj.sideImageInDouble(i0,j0,3)];
obj.sideColorCorrectedImage(i0,j0,1) = rgb_out(1);
obj.sideColorCorrectedImage(i0,j0,2) = rgb_out(2);
obj.sideColorCorrectedImage(i0,j0,3) = rgb_out(3);
end
end
side_color_corrected_image = uint8(obj.sideColorCorrectedImage);
end
% generate top normalized RGB image
function top_img_norm = generateTopNormalizedImage(obj)
img_r = obj.topColorCorrectedImage(:,:,1); % red channel
img_g = obj.topColorCorrectedImage(:,:,2); % green channel
img_b = obj.topColorCorrectedImage(:,:,3); % blue channel
img_sum = img_r + img_g + img_b;
img_r_n = 255 * img_r ./ img_sum; % normalized red channel
img_g_n = 255 * img_g ./ img_sum; % normalized green channel
img_b_n = 255 * img_b ./ img_sum; % normalized blue channel
obj.topNormalizedImage = zeros(size(obj.topImage));
obj.topNormalizedImage(:,:,1) = img_r_n;
obj.topNormalizedImage(:,:,2) = img_g_n;
obj.topNormalizedImage(:,:,3) = img_b_n;
top_img_norm = uint8(obj.topNormalizedImage);
end
% generate side normalized RGB image
function side_img_norm = generateSideNormalizedImage(obj)
img_r = obj.sideColorCorrectedImage(:,:,1); % red channel
img_g = obj.sideColorCorrectedImage(:,:,2); % green channel
img_b = obj.sideColorCorrectedImage(:,:,3); % blue channel
img_sum = img_r + img_g + img_b;
img_r_n = 255 * img_r ./ img_sum; % normalized red channel
img_g_n = 255 * img_g ./ img_sum; % normalized green channel
img_b_n = 255 * img_b ./ img_sum; % normalized blue channel
obj.sideNormalizedImage = zeros(size(obj.sideImage));
obj.sideNormalizedImage(:,:,1) = img_r_n;
obj.sideNormalizedImage(:,:,2) = img_g_n;
obj.sideNormalizedImage(:,:,3) = img_b_n;
side_img_norm = uint8(obj.sideNormalizedImage);
end
% generate top green mask
function top_img_mask_green = generateTopGreenMask(obj)
obj.topImgMaskGreen = obj.topNormalizedImage(:,:,2);
obj.topImgMaskGreen(abs(obj.topImgMaskGreen-obj.thresh_mask)<obj.tolerance_mask) = 1;
obj.topImgMaskGreen(obj.topImgMaskGreen~=1) = 0;
se1 = strel('disk', 5);
obj.topImgMaskGreen = imopen(obj.topImgMaskGreen, se1); % remove salt-and-pepper noise
obj.topImgMaskGreen = imclose(obj.topImgMaskGreen, se1); % fill the holes in the mask
% img_mask2 = bwpropfilt(logical(obj.topImgMaskGreen(50:300,:,:)),'Area',[0 12100]);
% obj.topImgMaskGreen(50:300,:,:) = img_mask2;
% img_mask3 = bwpropfilt(logical(obj.topImgMaskGreen(1150:end,:,:)),'Area',[0 12100]);
% obj.topImgMaskGreen(1150:end,:,:) = img_mask3;
for i=300:-1:1
if(sum(obj.topImgMaskGreen(:,i,:))==0) % left
obj.topImgMaskGreen(:,1:i,:)=0;
break;
end
end
for i=300:-1:1
if(sum(obj.topImgMaskGreen(i,:,:))==0) % top
obj.topImgMaskGreen(1:i,:,:)=0;
break;
end
end
for i=900:size(obj.topImgMaskGreen,1)
if(sum(obj.topImgMaskGreen(i,:,:))==0) % bottom
obj.topImgMaskGreen(i:end,:,:)=0;
break;
end
end
for i=700:size(obj.topImgMaskGreen,2)
if(sum(obj.topImgMaskGreen(:,i,:))==0) % right
obj.topImgMaskGreen(:,i:end,:)=0;
break;
end
end
top_img_mask_green = logical(obj.topImgMaskGreen);
end
% generate side green mask
function side_img_mask_green = generateSideGreenMask(obj)
obj.sideImgMaskGreen = obj.sideNormalizedImage(:,:,2);
obj.sideImgMaskGreen(abs(obj.sideImgMaskGreen-obj.thresh_mask)<obj.tolerance_mask) = 1;
obj.sideImgMaskGreen(obj.sideImgMaskGreen~=1) = 0;
se1 = strel('disk', 5);
obj.sideImgMaskGreen = imopen(obj.sideImgMaskGreen, se1); % remove salt-and-pepper noise
obj.sideImgMaskGreen = imclose(obj.sideImgMaskGreen, se1); % fill the holes in the mask
img_mask2 = bwpropfilt(logical(obj.sideImgMaskGreen(50:300,:,:)),'Area',[0 12100]);
obj.sideImgMaskGreen(50:300,:,:) = img_mask2;
img_mask3 = bwpropfilt(logical(obj.sideImgMaskGreen(1150:end,:,:)),'Area',[0 12100]);
obj.sideImgMaskGreen(1150:end,:,:) = img_mask3;
for i=300:-1:1
if(sum(obj.sideImgMaskGreen(:,i,:))==0) % left
obj.sideImgMaskGreen(:,1:i,:)=0;
break;
end
end
for i=300:-1:1
if(sum(obj.sideImgMaskGreen(i,:,:))==0) % top
obj.sideImgMaskGreen(1:i,:,:)=0;
break;
end
end
for i=900:size(obj.sideImgMaskGreen,1)
if(sum(obj.sideImgMaskGreen(i,:,:))==0) % bottom
obj.sideImgMaskGreen(i:end,:,:)=0;
break;
end
end
for i=700:size(obj.sideImgMaskGreen,2)
if(sum(obj.sideImgMaskGreen(:,i,:))==0) % right
obj.sideImgMaskGreen(:,i:end,:)=0;
break;
end
end
side_img_mask_green = logical(obj.sideImgMaskGreen);
end
%% Generate foreground images
% generate top foreground image and calculate average RGB value
function [top_foreground_image, top_foreground_image_with_cc, top_average_color] = generateTopForegroundImage(obj)
area_fg = sum(obj.topImgMaskGreen(:));
img_r_fg = obj.topImageInDouble(:,:,1);
img_g_fg = obj.topImageInDouble(:,:,2);
img_b_fg = obj.topImageInDouble(:,:,3);
img_r_fg(obj.topImgMaskGreen==0) = 0;
img_g_fg(obj.topImgMaskGreen==0) = 0;
img_b_fg(obj.topImgMaskGreen==0) = 0;
obj.topForegroundImage = zeros(size(obj.topImage));
obj.topForegroundImage(:,:,1) = img_r_fg;
obj.topForegroundImage(:,:,2) = img_g_fg;
obj.topForegroundImage(:,:,3) = img_b_fg;
if(area_fg == 0)
obj.topAverageColor(1) = 0;
obj.topAverageColor(2) = 0;
obj.topAverageColor(3) = 0;
else
obj.topAverageColor(1) = sum(img_r_fg(:))/area_fg;
obj.topAverageColor(2) = sum(img_g_fg(:))/area_fg;
obj.topAverageColor(3) = sum(img_b_fg(:))/area_fg;
end
top_average_color = obj.topAverageColor;
top_foreground_image = uint8(obj.topForegroundImage);
img_r_fg = obj.topNormalizedImage(:,:,1);
img_g_fg = obj.topNormalizedImage(:,:,2);
img_b_fg = obj.topNormalizedImage(:,:,3);
img_r_fg(obj.topImgMaskGreen==0) = 0;
img_g_fg(obj.topImgMaskGreen==0) = 0;
img_b_fg(obj.topImgMaskGreen==0) = 0;
obj.topForegroundImageWithCC = zeros(size(obj.topImage));
obj.topForegroundImageWithCC(:,:,1) = img_r_fg;
obj.topForegroundImageWithCC(:,:,2) = img_g_fg;
obj.topForegroundImageWithCC(:,:,3) = img_b_fg;
top_foreground_image_with_cc = uint8(obj.topForegroundImageWithCC);
end
% generate side foreground image
function [side_foreground_image, side_foreground_image_with_cc, side_average_color] = generateSideForegroundImage(obj)
area_fg = sum(obj.topImgMaskGreen(:));
img_r_fg = obj.sideImageInDouble(:,:,1);
img_g_fg = obj.sideImageInDouble(:,:,2);
img_b_fg = obj.sideImageInDouble(:,:,3);
img_r_fg(obj.sideImgMaskGreen==0) = 0;
img_g_fg(obj.sideImgMaskGreen==0) = 0;
img_b_fg(obj.sideImgMaskGreen==0) = 0;
obj.sideForegroundImage = zeros(size(obj.sideImage));
obj.sideForegroundImage(:,:,1) = img_r_fg;
obj.sideForegroundImage(:,:,2) = img_g_fg;
obj.sideForegroundImage(:,:,3) = img_b_fg;
if(area_fg == 0)
obj.sideAverageColor(1) = 0;
obj.sideAverageColor(2) = 0;
obj.sideAverageColor(3) = 0;
else
obj.sideAverageColor(1) = sum(img_r_fg(:))/area_fg;
obj.sideAverageColor(2) = sum(img_g_fg(:))/area_fg;
obj.sideAverageColor(3) = sum(img_b_fg(:))/area_fg;
end
side_average_color = obj.sideAverageColor;
side_foreground_image = uint8(obj.sideForegroundImage);
img_r_fg = obj.sideNormalizedImage(:,:,1);
img_g_fg = obj.sideNormalizedImage(:,:,2);
img_b_fg = obj.sideNormalizedImage(:,:,3);
img_r_fg(obj.sideImgMaskGreen==0) = 0;
img_g_fg(obj.sideImgMaskGreen==0) = 0;
img_b_fg(obj.sideImgMaskGreen==0) = 0;
obj.sideForegroundImageWithCC = zeros(size(obj.sideImage));
obj.sideForegroundImageWithCC(:,:,1) = img_r_fg;
obj.sideForegroundImageWithCC(:,:,2) = img_g_fg;
obj.sideForegroundImageWithCC(:,:,3) = img_b_fg;
side_foreground_image_with_cc = uint8(obj.sideForegroundImageWithCC);
end
% generate top black and white foreground image
function top_BW_foreground_image = generateTopBWForegroundImage(obj)
obj.topBWForegroundImage = rgb2gray(uint8(obj.topForegroundImage));
top_BW_foreground_image = obj.topBWForegroundImage;
end
% generate side black and white foreground image
function side_BW_foreground_image = generateSideBWForegroundImage(obj)
obj.sideBWForegroundImage = rgb2gray(uint8(obj.sideForegroundImage));
side_BW_foreground_image = obj.sideBWForegroundImage;
end
%% Generate gradient magnitude image
% generate top gradient magnitude image
function top_gradient_magnitude_image = generateTopGradientMagnitudeImage(obj)
hy = fspecial('sobel');
hx = hy';
Iy = imfilter(double(obj.topBWForegroundImage), hy, 'replicate');
Ix = imfilter(double(obj.topBWForegroundImage), hx, 'replicate');
obj.topGradientMagnitudeImage = sqrt(Ix.^2 + Iy.^2);
top_gradient_magnitude_image = uint8(obj.topGradientMagnitudeImage);
end
% generate side gradient magnitude image
function side_gradient_magnitude_image = generateSideGradientMagnitudeImage(obj)
hy = fspecial('sobel');
hx = hy';
Iy = imfilter(double(obj.sideBWForegroundImage), hy, 'replicate');
Ix = imfilter(double(obj.sideBWForegroundImage), hx, 'replicate');
obj.sideGradientMagnitudeImage = sqrt(Ix.^2 + Iy.^2);
side_gradient_magnitude_image = uint8(obj.sideGradientMagnitudeImage);
end
%% Leaves cutting
% generate top leaves cut image
function top_leaves_cut_image = generateTopLeavesCutImage(obj)
area_fg = sum(obj.topImgMaskGreen(:));
D = -bwdist(~obj.topBWForegroundImage);
mask = imextendedmin(D,2);
D = imimposemin(D,mask);
D = watershed(D);
obj.topLeavesCutImage = obj.topImgMaskGreen;
obj.topLeavesCutImage(D == 0) = 0;
% if(area_fg<10000)
% se = strel('disk', 5);
% Ie1 = imopen(obj.topBWForegroundImage, se);
%
% D1 = bwdist(Ie1);
% DL1 = watershed(D1);
% bgm1 = DL1 == 0;
%
% obj.topLeavesCutImage(bgm1~=0)=0;
%
% elseif(area_fg<110000)
% se = strel('disk', 10);
% Ie1 = imerode(obj.topBWForegroundImage, se);
%
% se = strel('disk', 20);
% Ie2 = imerode(obj.topBWForegroundImage, se);
%
% D1 = bwdist(Ie1);
% DL1 = watershed(D1);
% bgm1 = DL1 == 0;
%
% D2 = bwdist(Ie2);
% DL2 = watershed(D2);
% bgm2 = DL2 == 0;
%
% obj.topLeavesCutImage(bgm1~=0)=0;
% obj.topLeavesCutImage(bgm2~=0)=0;
%
% se = strel('disk', 8);
% obj.topLeavesCutImage = imopen(obj.topLeavesCutImage, se);
% else
% se = strel('disk', 10);
% Ie1 = imerode(obj.topBWForegroundImage, se);
%
% se = strel('disk', 20);
% Ie2 = imerode(obj.topBWForegroundImage, se);
%
% se = strel('disk', 30);
% Ie3 = imerode(obj.topBWForegroundImage, se);
%
% D1 = bwdist(Ie1);
% DL1 = watershed(D1);
% bgm1 = DL1 == 0;
%
% D2 = bwdist(Ie2);
% DL2 = watershed(D2);
% bgm2 = DL2 == 0;
%
% D3 = bwdist(Ie3);
% DL3 = watershed(D3);
% bgm3 = DL3 == 0;
%
% obj.topLeavesCutImage(bgm1~=0)=0;
% obj.topLeavesCutImage(bgm2~=0)=0;
% obj.topLeavesCutImage(bgm3~=0)=0;
%
% se = strel('disk', 8);
% obj.topLeavesCutImage = imopen(obj.topLeavesCutImage, se);
% end
top_leaves_cut_image = logical(obj.topLeavesCutImage);
end
%% Leaves counting
% generate top leaves counted image
function [foreground_area, number_of_leaves, top_average_color, leaves_details, top_leaves_labeled_image, top_leaves_text_labeled_image] = generateTopLeavesCountedImage(obj)
foreground_area = sum(obj.topImgMaskGreen(:)) * obj.areaPerPixel;
labeledImage = bwlabel(obj.topLeavesCutImage, 8);
obj.topLeavesLabeledImage = label2rgb (labeledImage, 'hsv', 'k', 'shuffle');
obj.topLeavesTextLabeledImage = obj.topLeavesLabeledImage;
blobMeasurements = regionprops(labeledImage, obj.topBWForegroundImage, 'all');
obj.topNumberOfLeaves = size(blobMeasurements, 1);
obj.topLeavesDetails = {'Leaf_Number', 'Mean_Intensity', 'Area_(cm2)', 'Perimeter_(cm)', 'Centroid_X', 'Centroid_Y', 'Diameter_(cm)'};
for k = 1 : obj.topNumberOfLeaves
thisBlobsPixels = blobMeasurements(k).PixelIdxList; % Get list of pixels in current blob.
meanGL = mean(obj.topBWForegroundImage(thisBlobsPixels)); % Find mean intensity (in original image!)
blobArea = blobMeasurements(k).Area; % Get area.
blobPerimeter = blobMeasurements(k).Perimeter; % Get perimeter.
blobCentroid = blobMeasurements(k).Centroid; % Get centroid one at a time
blobECD = sqrt(4 * blobArea / pi); % Compute ECD - Equivalent Circular Diameter.
obj.topLeavesDetails = [obj.topLeavesDetails; {k, meanGL, blobArea*obj.areaPerPixel, blobPerimeter*obj.lengthPerPixelSide, blobCentroid(1), blobCentroid(2), blobECD*obj.lengthPerPixelSide}];
obj.topLeavesTextLabeledImage = insertText(obj.topLeavesTextLabeledImage,[blobCentroid(1)+obj.topLabelShiftX, blobCentroid(2)+obj.topLabelShiftY],...
num2str(k),'FontSize',obj.topTextFontSize,'BoxOpacity',0);
end
number_of_leaves = obj.topNumberOfLeaves;
top_average_color = obj.topAverageColor;
leaves_details = obj.topLeavesDetails;
top_leaves_labeled_image = uint8(obj.topLeavesLabeledImage);
top_leaves_text_labeled_image = uint8(obj.topLeavesTextLabeledImage);
end
%% Export images
% export top color corrected image
function exportTopColorCorrectedImage(obj, filePath)
img_name = obj.getImageNameFromFilePath(filePath);
if(numel(find(strcmpi(filePath(end-2:end), obj.extList)))==1)
out_path = filePath(1:end-4);
if(exist(out_path, 'dir')==0)
mkdir(out_path);
end
save_path = strcat(out_path, obj.seperator, img_name, '_Correct.png');
imwrite(uint8(obj.topColorCorrectedImage), save_path);
end
end
% export top green mask
function exportTopGreenMask(obj, filePath)
img_name = obj.getImageNameFromFilePath(filePath);
if(numel(find(strcmpi(filePath(end-2:end), obj.extList)))==1)
out_path = filePath(1:end-4);
if(exist(out_path, 'dir')==0)
mkdir(out_path);
end
save_path = strcat(out_path, obj.seperator, img_name, '_FGMask.png');
imwrite(obj.topImgMaskGreen, save_path);
end
end
% export top foreground image
function exportTopForegroundImage(obj, filePath)
img_name = obj.getImageNameFromFilePath(filePath);
if(numel(find(strcmpi(filePath(end-2:end), obj.extList)))==1)
out_path = filePath(1:end-4);
if(exist(out_path, 'dir')==0)
mkdir(out_path);
end
save_path = strcat(out_path, obj.seperator, img_name, '_ImgFG.png');
imwrite(uint8(obj.topForegroundImage), save_path);
end
end
% export top leaves cut image
function exportTopLeavesCutImage(obj, filePath)
img_name = obj.getImageNameFromFilePath(filePath);
if(numel(find(strcmpi(filePath(end-2:end), obj.extList)))==1)
out_path = filePath(1:end-4);
if(exist(out_path, 'dir')==0)
mkdir(out_path);
end
save_path = strcat(out_path, obj.seperator, img_name, '_line.png');
imwrite(obj.topLeavesCutImage, save_path);
end
end
% export top leaves text labeled image
function exportTopLeavesTextLabeledImage(obj, filePath)
img_name = obj.getImageNameFromFilePath(filePath);
if(numel(find(strcmpi(filePath(end-2:end), obj.extList)))==1)
out_path = filePath(1:end-4);
if(exist(out_path, 'dir')==0)
mkdir(out_path);
end
save_path = strcat(out_path, obj.seperator, img_name, '_Tpseudo.png');
imwrite(obj.topLeavesTextLabeledImage, save_path);
end
end
%% Export excel files
% Export leaves number
function exportLeavesData(obj, filePath, foreground_area, number_of_leaves, top_average_color, leaves_details)
img_name = obj.getImageNameFromFilePath(filePath);
if(numel(find(strcmpi(filePath(end-2:end), obj.extList)))==1)
out_path = filePath(1:end-4);
if(exist(out_path, 'dir')==0)
mkdir(out_path);
end
save_path = strcat(out_path, '_Info.xlsx');
xlswrite(save_path,cell(100, 100));
sheet = 1;
xlRange = 'A1';
xlswrite(save_path,{'Foreground_Area'},sheet,xlRange);
xlRange = 'A2';
xlswrite(save_path,foreground_area,sheet,xlRange);
xlRange = 'C1';
xlswrite(save_path,{'Number_of_Leaves'},sheet,xlRange);
xlRange = 'C2';
xlswrite(save_path,number_of_leaves,sheet,xlRange);
xlRange = 'E1';
xlswrite(save_path,{'Plant_Average_Color_(Red)', 'Plant_Average_Color_(Green)', 'Plant_Average_Color_(Blue)'},sheet,xlRange);
xlRange = 'E2';
xlswrite(save_path,top_average_color,sheet,xlRange);
xlRange = 'A5';
xlswrite(save_path,leaves_details,sheet,xlRange);
end
end
% Export Experiment Name, CS Number, Rep Number, Leaves Number and
% Foreground Area in one Excel Sheet
function exportLeavesTable(obj, filePath, rowNumber, foreground_area, number_of_leaves, top_average_color)
savePath = [];
expName = [];
roundNum = [];
rep = [];
csNum = [];
date = [];
dirComponents = strsplit(filePath, '\');
for i = 1:size(dirComponents, 2)
dirComp = dirComponents(i);
dirComp = dirComp{1};
if(isempty(rep) == 1 && length(dirComp) > 3)
if(strcmp(dirComp(1:3), "Rep")==1)
rep = dirComp;
dirCompTemp = dirComponents(i-1);
roundNum = dirCompTemp{1};
dirCompTemp = dirComponents(i-2);
expName = dirCompTemp{1};
savePath = strsplit(filePath, rep);
savePath = savePath(1);
savePath = savePath{1};
end
end
if(isempty(csNum) == 1 && length(dirComp) > 2)
if(strcmp(dirComp(1:2), "CS")==1)
csNum = dirComp;
dirCompTemp = dirComponents(i+1);
date = dirCompTemp{1};
end
end
end
save_path = strcat(savePath, 'LeavesTable_Info.xlsx');
title = {'Experiment_Name', 'Round_Number', 'Rep_Number', 'CS_Number', ...
'Date', 'Number_of_Leaves', 'Foreground_Area_(cm2)', ...
'Plant_Average_Color_(Red)', 'Plant_Average_Color_(Green)', 'Plant_Average_Color_(Blue)'};
content = {expName, roundNum, rep, csNum, date, number_of_leaves, foreground_area, top_average_color(1), top_average_color(2), top_average_color(3)};
sheet = 1;
xlswrite(save_path,title,sheet,'A1');
xlRange = strcat('A', num2str(rowNumber+1));
xlswrite(save_path,content,sheet,xlRange);
xlRange = strcat('A', num2str(rowNumber+2));
xlswrite(save_path,cell(100, 100), sheet, xlRange);
end
%% Plot graphs
% Plot area graph for each CS number
function plotAreaGraph(obj, filePath, foreground_area)
rep = [];
date = [];
csNum = [];
dirComponents = strsplit(filePath, '\');
for i = 1:size(dirComponents, 2)
dirComp = dirComponents(i);
dirComp = dirComp{1};
if(isempty(rep) == 1 && length(dirComp) > 3)
if(strcmp(dirComp(1:3), "Rep")==1)
rep = dirComp;
savePath = strsplit(filePath, rep);
savePath = savePath(1);
savePath = savePath{1};
end
end
if(isempty(csNum) == 1 && length(dirComp) > 2)
if(strcmp(dirComp(1:2), "CS")==1)
csNum = dirComp;
dirCompTemp = dirComponents(i+1);
date = dirCompTemp{1};
end
end
end
savePath = strcat(savePath, 'Area_Graphs', obj.seperator);
graphTitle = strcat('Graph of Plant Total Area Versus Time - (', csNum, ')');
if(exist(savePath, 'dir') == 0)
mkdir(savePath);
end
savePath = strcat(savePath, csNum, '.png');
if(isempty(obj.csReference_Area)==1)
obj.csReference_Area = csNum;
obj.xArray_Area = [obj.xArray_Area, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_Area = [obj.yArray_Area, foreground_area];
elseif(strcmpi(obj.csReference_Area, csNum)==0)
obj.csReference_Area = csNum;
obj.xArray_Area = [];
obj.yArray_Area = [];
obj.xCell_Area = [];
obj.yCell_Area = [];
obj.xArray_Area = [obj.xArray_Area, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_Area = [obj.yArray_Area, foreground_area];
else
if(strcmpi(rep, "Rep1") == 1)
obj.xArray_Area = [obj.xArray_Area, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_Area = [obj.yArray_Area, foreground_area];
% fig = figure('visible','off'); hold on;
% plot(obj.xArray_Area, obj.yArray_Area, '-r'); hold off;
% title(graphTitle);
% ylabel('Plant Total Area in cm2')
% xlabel('Time');
% legend('Rep 1', 'Location', 'best');
% saveas(fig, savePath);
% pause(1);
elseif(strcmpi(rep, "Rep2") == 1)
if(isempty(obj.xCell_Area)==1)
obj.xCell_Area = {obj.xArray_Area};
obj.xArray_Area = [];
end
if(isempty(obj.yCell_Area)==1)
obj.yCell_Area = {obj.yArray_Area};
obj.yArray_Area = [];
end
obj.xArray_Area = [obj.xArray_Area, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_Area = [obj.yArray_Area, foreground_area];
fig = figure('visible','off');
plot(obj.xCell_Area{1}, obj.yCell_Area{1}, '-ro'); hold on;
plot(obj.xArray_Area, obj.yArray_Area, '--b+'); hold off;
title(graphTitle);
ylabel('Plant Total Area in cm2');
xlabel('Time');
legend('Rep 1','Rep 2', 'Location', 'best');
saveas(fig, savePath);
elseif(strcmpi(rep, "Rep3") == 1)
if(size(obj.xCell_Area, 1)==1)
tempCell = {obj.xArray_Area};
obj.xCell_Area = [obj.xCell_Area; tempCell];
obj.xArray_Area = [];
end
if(size(obj.yCell_Area, 1)==1)
tempCell = {obj.yArray_Area};
obj.yCell_Area = [obj.yCell_Area; tempCell];
obj.yArray_Area = [];
end
obj.xArray_Area = [obj.xArray_Area, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_Area = [obj.yArray_Area, foreground_area];
fig = figure('visible','off');
plot(obj.xCell_Area{1}, obj.yCell_Area{1}, '-ro'); hold on;
plot(obj.xCell_Area{2}, obj.yCell_Area{2}, '--b+');
plot(obj.xArray_Area, obj.yArray_Area, ':g*'); hold off;
title(graphTitle);
ylabel('Plant Total Area in cm2');
xlabel('Time');
legend('Rep 1','Rep 2', 'Rep 3', 'Location', 'best');
saveas(fig, savePath);
elseif(strcmpi(rep, "Rep4") == 1)
if(size(obj.xCell_Area, 1)==2)
tempCell = {obj.xArray_Area};
obj.xCell_Area = [obj.xCell_Area; tempCell];
obj.xArray_Area = [];
end
if(size(obj.yCell_Area, 1)==2)
tempCell = {obj.yArray_Area};
obj.yCell_Area = [obj.yCell_Area; tempCell];
obj.yArray_Area = [];
end
obj.xArray_Area = [obj.xArray_Area, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_Area = [obj.yArray_Area, foreground_area];
fig = figure('visible','off');
plot(obj.xCell_Area{1}, obj.yCell_Area{1}, '-ro'); hold on;
plot(obj.xCell_Area{2}, obj.yCell_Area{2}, '--b+');
plot(obj.xCell_Area{3}, obj.yCell_Area{3}, ':g*');
plot(obj.xArray_Area, obj.yArray_Area, '-.m.'); hold off;
title(graphTitle);
ylabel('Plant Total Area in cm2');
xlabel('Time');
legend('Rep 1','Rep 2', 'Rep 3', 'Rep 4', 'Location', 'best');
saveas(fig, savePath);
else
if(size(obj.xCell_Area, 1)==3)
tempCell = {obj.xArray_Area};
obj.xCell_Area = [obj.xCell_Area; tempCell];
obj.xArray_Area = [];
end
if(size(obj.yCell_Area, 1)==3)
tempCell = {obj.yArray_Area};
obj.yCell_Area = [obj.yCell_Area; tempCell];
obj.yArray_Area = [];
end
obj.xArray_Area = [obj.xArray_Area, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_Area = [obj.yArray_Area, foreground_area];
fig = figure('visible','off');
plot(obj.xCell_Area{1}, obj.yCell_Area{1}, '-ro'); hold on;
plot(obj.xCell_Area{2}, obj.yCell_Area{2}, '--b+');
plot(obj.xCell_Area{3}, obj.yCell_Area{3}, ':g*');
plot(obj.xCell_Area{4}, obj.yCell_Area{4}, '-.m.');
plot(obj.xArray_Area, obj.yArray_Area, '-cx'); hold off;
title(graphTitle);
ylabel('Plant Total Area in cm2');
xlabel('Time');
legend('Rep 1','Rep 2', 'Rep 3', 'Rep 4', 'Rep5', 'Location', 'best');
saveas(fig, savePath);
end
end
end
% Plot leaf number graph for each cs number
function plotLeafCountGraph(obj, filePath, number_of_leaves)
rep = [];
date = [];
csNum = [];
dirComponents = strsplit(filePath, '\');
for i = 1:size(dirComponents, 2)
dirComp = dirComponents(i);
dirComp = dirComp{1};
if(isempty(rep) == 1 && length(dirComp) > 3)
if(strcmp(dirComp(1:3), "Rep")==1)
rep = dirComp;
savePath = strsplit(filePath, rep);
savePath = savePath(1);
savePath = savePath{1};
end
end
if(isempty(csNum) == 1 && length(dirComp) > 2)
if(strcmp(dirComp(1:2), "CS")==1)
csNum = dirComp;
dirCompTemp = dirComponents(i+1);
date = dirCompTemp{1};
end
end
end
savePath = strcat(savePath, 'Leaf_Count_Graphs', obj.seperator);
graphTitle = strcat('Graph of Leaf Count Versus Time - (', csNum, ')');
if(exist(savePath, 'dir') == 0)
mkdir(savePath);
end
savePath = strcat(savePath, csNum, '.png');
if(isempty(obj.csReference_LeafNum)==1)
obj.csReference_LeafNum = csNum;
obj.xArray_LeafNum = [obj.xArray_LeafNum, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_LeafNum = [obj.yArray_LeafNum, number_of_leaves];
elseif(strcmpi(obj.csReference_LeafNum, csNum)==0)
obj.csReference_LeafNum = csNum;
obj.xArray_LeafNum = [];
obj.yArray_LeafNum = [];
obj.xCell_LeafNum = [];
obj.yCell_LeafNum = [];
obj.xArray_LeafNum = [obj.xArray_LeafNum, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_LeafNum = [obj.yArray_LeafNum, number_of_leaves];
else
if(strcmpi(rep, "Rep1") == 1)
obj.xArray_LeafNum = [obj.xArray_LeafNum, datetime(date,'InputFormat','yyyy-MM-dd')];
obj.yArray_LeafNum = [obj.yArray_LeafNum, number_of_leaves];
% fig = figure('visible','off'); hold on;
% plot(obj.xArray_LeafNum, obj.yArray_LeafNum, '-r'); hold off;
% title(graphTitle);
% ylabel('Leaf Count');
% xlabel('Time');
% legend('Rep 1', 'Location', 'best');
% saveas(fig, savePath);