Related
I have an image and I would like to blur it in one specific direction and distance using Matlab.
I found out there is a filter called fspecial('motion',len,theta).
Here there is an example:
I = imread('cameraman.tif');
imshow(I);
H = fspecial('motion',20,45);
MotionBlur = imfilter(I,H,'replicate');
imshow(MotionBlur);
However the blurred picture is blurred in 2 directions! In this case 225 and 45 degrees.
What should it do in order to blur it just in a specific direction (e.g. 45) and not both?
I think you want what's called a "comet" kernel. I'm not sure what kernel is used for the "motion" blur, but I'd guess that it's symmetrical based on the image you provided.
Here is some code to play with that applies the comet kernel in one direction. You'll have to change things around if you want an arbitrary angle. You can see from the output that it's smearing in one direction, since there is a black band on only one side (due to the lack of pixels there).
L = 5; % kernel width
sigma=0.2; % kernel smoothness
I = imread('cameraman.tif');
x = -L:1.0:L;
[X,Y] = meshgrid(x,x);
H1 = exp((-sigma.*X.^2)+(-sigma.*Y.^2));
kernel = H1/sum((H1(:)));
Hflag = double((X>0));
comet_kernel = Hflag.*H1;
comet_kernel=comet_kernel/sum(comet_kernel(:));
smearedImage = conv2(double(I),comet_kernel,'same');
imshow(smearedImage,[]);
Updated code: This will apply an arbitrary rotation to the comet kernel. Note also the difference between sigma in the previous example and sx and sy here, which control the length and width parameters of the kernel, as suggested by Andras in the comments.
L = 5; % kernel width
sx=3;
sy=10;
theta=0;
I = imread('cameraman.tif');
x = -L:1.0:L;
[X,Y] = meshgrid(x,x);
rX = X.*cos(theta)-Y.*sin(theta);
rY = X.*sin(theta)+Y.*cos(theta);
H1 = exp(-((rX./sx).^2)-((rY./sy).^2));
Hflag = double((0.*rX+rY)>0);
H1 = H1.*Hflag;
comet_kernel = H1/sum((H1(:)))
smearedImage = conv2(double(I),comet_kernel,'same');
imshow(smearedImage,[]);
Based on Anger Density's answer I wrote this code that solves my problem completely:
L = 10; % kernel width
sx=0.1;
sy=100;
THETA = ([0,45,90,135,180,225,270,320,360])*pi/180;
for i=1:length(THETA)
theta=(THETA(i)+pi)*-1;
I = imread('cameraman.tif');
x = -L:1.0:L;
[X,Y] = meshgrid(x,x);
rX = X.*cos(theta)-Y.*sin(theta);
rY = X.*sin(theta)+Y.*cos(theta);
H1 = exp(-((rX./sx).^2)-((rY./sy).^2));
Hflag = double((0.*rX+rY)>0);
H1 = H1.*Hflag;
comet_kernel = H1/sum((H1(:)));
smearedImage = conv2(double(I),comet_kernel,'same');
% Fix edges
smearedImage(:,[1:L, end-L:end]) = I(:,[1:L, end-L:end]); % Left/Right edge
smearedImage([1:L, end-L:end], :) = I([1:L, end-L:end], :); % Top/bottom edge
% Keep only inner blur
smearedImage(L:end-L,L:end-L) = min(smearedImage(L:end-L,L:end-L),double(I(L:end-L,L:end-L)));
figure
imshow(smearedImage,[]);
title(num2str(THETA(i)*180/pi))
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
end
How can I scale the colorbar axis of a false color image?
I read this post,and copied the code but it seems not to work correctly:
MATLAB Colorbar - Same colors, scaled values
Please see the two images below. In the first (without the scaling) the coloraxis goes
[1 2 3 4 5 6]*10^4
In the second image, it goes
[0.005 0.01 0.015 0.02 0.025]
The correct scaling (with C = 100000) would be
[0.1 0.2 0.3 0.4 0.5 0.6]
Without scaling
Wrong scaling
I want that the coloraxis is scaled by 1/C and I can freely choose C, so that when the pixel value = 10^4 and C=10^6 the scale should show 10^-2.
The reason why I multiply my image first by C is to get more decimals places, because all values below 1 will be displayed as zero without the C scaling.
When I run the code I get yticks as a workspace variable with the following values:
[500 1000 1500 2000 2500]
My code:
RGB = imread('IMG_0043.tif');% Read Image
info = imfinfo('IMG_0043.CR2'); % get Metadata
C = 1000000; % Constant to adjust image
x = info.DigitalCamera; % get EXIF
t = getfield(x, 'ExposureTime');% save ExposureTime
f = getfield(x, 'FNumber'); % save FNumber
S = getfield(x, 'ISOSpeedRatings');% save ISOSpeedRatings
date = getfield(x,'DateTimeOriginal');
I = rgb2gray(RGB); % convert Image to greyscale
K = 480; % Kamerakonstante(muss experimentel eavaluiert werden)
% N_s = K*(t*S)/power(f,2))*L
L = power(f,2)/(K*t*S)*C; %
J = immultiply(I,L); % multiply each value with constant , so the Image is Calibrated to cd/m^2
hFig = figure('Name','False Color Luminance Map', 'ToolBar','none','MenuBar','none');
% Create/initialize default colormap of jet.
cmap = jet(16); % or 256, 64, 32 or whatever.
% Now make lowest values show up as black.
cmap(1,:) = 0;
% Now make highest values show up as white.
cmap(end,:) = 1;
imshow(J,'Colormap',cmap) % show Image in false color
colorbar % add colorbar
h = colorbar; % define colorbar as variable
y_Scl = (1/C);
yticks = get(gca,'YTick');
set(h,'YTickLabel',sprintfc('%g', [yticks.*y_Scl]))
ylabel(h, 'cd/m^2')% add unit label
title(date); % Show date in image
caxis auto % set axis to auto
datacursormode on % enable datacursor
img = getframe(gcf);
nowstr = datestr(now, 'yyyy-mm-dd_HH_MM_SS');
folder = 'C:\Users\Taiko\Desktop\FalseColor\';
ImageFiles = dir( fullfile(folder, '*.jpg') );
if isempty(ImageFiles)
next_idx = 1;
else
lastfile = ImageFiles(end).name;
[~, basename, ~] = fileparts(lastfile);
file_number_str = regexp('(?<=.*_)\d+$', basename, 'match' );
last_idx = str2double(file_number_str);
next_idx = last_idx + 1;
end
newfilename = fullfile( folder, sprintf('%s_%04d.jpg', nowstr, next_idx) );
imwrite(img.cdata, newfilename);
Problems:
1) You are getting YTick of the figure (gca) but not the color bar. That would give you the "pixel" coordinates of the graph, instead of the actual values. Use yticks = get(h,'YTick');.
2) caxis auto Should come before overwriting YTicks (and after enabling the color bar); otherwise the scale and ticks will mismatch.
3) Do you mean C = 100000?
Result:
I am currently doing a project on morphology of filamentous fungi during batch fermentation (Yes, I am not a software engineer.. Biotech). Where I am taken pictures of the morphology in a petri dish. I am developing a "fast" method to describe the pellets (small aggregates of fungi) that occurs during the fermentation. To do this I am writing a code in MatLab.
Depending on the color of the pellets (light or dark) the pictures are taken on differen backgrounds, black or white. I am inverting the picture if the mean gray value is below 70 to distinguish between backgrounds.
Pictures:
White background
Dark background
I have several problems:
Detecting the edge of the petri dish so it won't be regarded as an object (Currently done with the edge('log',) function). The edge is detected, but i miss some parts, think because of the lower light in top.
Proper thresholding inside the dish
Detection of pellets - right now it is done by a combination of running through each color channel, but might be done with some blob detection?
Does anybody have some inputs?
My code is as following:
close all
clear all
clc
%Empty arrays to hold data
metricD=[];
areaD=[];
perimeterD=[];
% Specify the folder where the files live.
myFolder = pwd;
% Check to make sure that folder actually exists. Warn user if it doesn't.
if ~isdir(myFolder)
errorMessage = sprintf('Error: The following folder does not exist:\n%s', myFolder);
uiwait(warndlg(errorMessage));
return;
end
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.jpg'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
% Show debugging plots
plotFig = 0;
% parameters that can be tuned
% how many colors channels we minimum want to see a spore in
% e.g. set to 1 for image "P. f Def C.tif"
labelcutOff = 1;
% remove areas larger than
removeLargerthan = 500000;
for k = 1 : length(theFiles)
baseFileName = theFiles(k).name;
fullFileName = fullfile(myFolder, baseFileName);
%% reading as an image array with im
I = imread(fullFileName);
% convert to grayscale
Ig = rgb2gray(I);
if plotFig
figure;imagesc(I)
figure;imagesc(Ig)
end
mm=mean(mean(Ig));
if mm < 70
I=imcomplement(I);
Ig = imcomplement(Ig);
end
% BLOB DETCTION
% h = fspecial('log', [15 15], 2);
% imLOG = imfilter(Ig, h);
% figure;imagesc(imLOG)
%% find petridish by edges and binary operations
% HACK - NOT HOW IT SHOULD BE DONE
Ig = wiener2(Ig,[5 5]);
imEdge = edge(Ig,'log');
circle = bwareaopen(imEdge,50);
circle = imclose(circle,strel('disk',30));
circle = bwareaopen(circle,8000);
% circle = imfill(circle,'holes');
circle = bwconvhull(circle);
circle = imerode(circle,strel('disk',150));
if plotFig
figure;imagesc(circle)
end
%% Get thresholds inside dish using otsu on each channel
imR = double(I(:,:,1)) .* circle;
imG = double(I(:,:,2)) .* circle;
imB = double(I(:,:,3)) .* circle;
thresR = graythresh(uint8(imR(circle))) *max(imR(circle));
thresG = graythresh(uint8(imG(circle))) *max(imG(circle));
thresB = graythresh(uint8(imB(circle))) *max(imB(circle));
if plotFig
figure;imagesc(imR)
figure;imagesc(imG)
figure;imagesc(imB)
end
%% classify inside dish
% check if it should be smaller or larger than
if sum(imR(circle) < thresR) > sum(imR(circle) > thresR)
labelR = imR > thresR;
else
labelR = imR < thresR;
end
if sum(imG(circle) < thresG) > sum(imG(circle) > thresG)
labelG = imG > thresG;
else
labelG = imG < thresG;
end
if sum(imB(circle) < thresB) > sum(imB(circle) > thresB)
labelB = imB > thresB;
else
labelB = imB < thresB;
end
if plotFig
figure;imagesc(labelR)
figure;imagesc(labelG)
figure;imagesc(labelB)
end
labels = (labelR + labelG + labelB) .* circle;
labels(labels < labelcutOff) = 0;
labels = imfill(labels,'holes');
labels = bwareaopen(labels,30);
if plotFig
figure;imagesc(labels)
end
%% clean up labels
labelBig = bwareaopen(labels,removeLargerthan);
labels = labels - labelBig;
if plotFig
figure;imagesc(labels)
end
BN = labels;
%% old script
stats = regionprops(BN,'Basic');
obj2 = numel(stats);
[B,L] = bwboundaries(BN,'holes');
figure
% imshow(label2rgb(L, #jet, [.5 .5 .5]))
imshow(I)
hold on
title(baseFileName)
for j = 1:length(B)
boundary = B{j};
plot(boundary(:,2), boundary(:,1),'w','LineWidth',2)
end
%region stats
stats = regionprops(L,'Area','Centroid');
%Threshold for printing in end
threshold = 0.2;
%Conversion factor pixel to cm
conversionF=9/2125;
% loop over the boundaries
for j = 1:length(B)
% obtain (X,Y) boundary coordinates corresponding to label 'j'
boundary = B{j};
% compute a simple estimate of the object's perimeter
delta_sq = diff(boundary).^2;
perimeter = sum(sqrt(sum(delta_sq,2)));
perimeterD(j,k)=perimeter*conversionF;
% obtain the area calculation corresponding to label 'k'
area = stats(j).Area;
areaD(j,k)=area*conversionF^2;
% compute the roundness metric
metric = 4*pi*area/perimeter^2;
metricD(j,k)=metric;
% display the results
metric_string = sprintf('%d. %2.2f', j,metric);
text(boundary(1,2)-50,boundary(1,1)+23,metric_string,'Color','k',...
'FontSize',14,'FontWeight','bold');
end
drawnow; % Force display to update immediately.
end
%Calculating stats
areaM=mean(areaD);
pM=mean(perimeterD);
metricD(metricD==Inf)=0;
mM=mean(metricD);
Hint:
A morphological top-hat filter fllowed by binarization (with a constant threshold ?) can be a good start. And filtering on the blob size will do a reasonable cleanup.
For the edges, try circular Hough.
I have a set of Dicom images on matlab and i would like to add a midline going through all the images
I am outputting the images via imshow3d function
thanks
Edit: here's what i have, the random points are not in the middle they just run through the image
>> clc;
>>clear;
>>%imports dicom images
>>run DicomImport.m;
>>%random points for shortest distance test
>>a = [1 10 200];
>>b = [500 512 300];
>>ab = b - a;
>>n = max(abs(ab)) + 1;
>>s = repmat(linspace(0, 1, n)', 1, 3);
>>for d = 1:3
>> s(:, d) = s(:, d) * ab(d) + a(d);
>>end
>>s = round(s);
>>Z = 593;
>>N = 512;
>>X = zeros(N, N, Z);
>>X(sub2ind(size(X), s(:, 1), s(:, 2), s(:, 3))) = 1;
>>C = find(X);
>>ans.Img(C) = 5000;
>> %shows image
>>imshow3D(ans.Img);
So it looks like ans.Img contains the 3D matrix consisting of your image stack. It looks like you've got something going, but allow me to do this a bit differently. Basically, you need to generate a set of coordinates where we can access the image stack and draw a vertical line in the middle of the each image in the image stack. Do something like this. First get the dimensions of the stack, then determine the halfway point for the columns. Next, generate a set of coordinates that will draw a line down the middle for one image. After you do this, repeat this for the rest of the slices and get the column major indices for these:
%// Get dimensions
[rows,cols,slices] = size(ans.Img);
%// Get halfway point for columns
col_half = floor(cols/2);
%// Generate coordinates for vertical line for one slice
coords_middle_row = (1:rows).';
coords_middle_col = repmat(col_half, rows, 1);
%// Generate column major indices for the rest of the slices:
ind = sub2ind(size(ans.Img), repmat(coords_middle_row, slices, 1), ...
repmat(coords_middle_col, slices, 1), ...
reshape(kron(1:slices, ones(rows, 1)), [], 1));
%// Set the pixels accordingly
ans.Img(ind) = 5000;
This code is quite similar to the answer I provided to one of your earlier question; i.e. I don't use imshow3D but the framework is similar and simpler to modify in order to suit your need. In this case, upon pressing a pushbutton a line appears at the middle of the stack and you can scroll through it with the slider. I hope this can be of help.
function LineDicom(~)
clc
clear
close all
%// Load demo data
S = load('mri');
%// Get dimensions and number of slices.
ImageHeight = S.siz(1); %// Not used here
ImageWidth = S.siz(2); %// Not used here
NumSlices = S.siz(3);
S.D = squeeze(S.D);
%// Create GUI
hFig = figure('Position',[100 100 400 400],'Units','normalized');
%// create axes with handle
handles.axes1 = axes('Position', [0.2 0.2 0.6 0.6]);
%// create y slider with handle
handles.y_slider = uicontrol('style', 'Slider', 'Min', 1, 'Max', NumSlices, 'Value',1, 'Units','normalized','position', [0.08 0.2 0.08 0.6], 'callback', #(s,e) UpdateY);
handles.SlideryListener = addlistener(handles.y_slider,'Value','PostSet',#(s,e) YListenerCallBack);
%// Create pusbutton to draw line
handles.DrawLineButton= uicontrol('style', 'push','position', [40 40 100 30],'String','Draw line', 'callback', {#DrawLine,handles});
%// Flag to know whether pushbutton has been pushed
handles.LineDrawn = false;
%// Show 1st slice
imshow(S.D(:,:,1))
guidata(hFig,handles);
%// Listeners callbacks followed by sliders callbacks. Used to display each
%// slice smoothly.
function YListenerCallBack
handles = guidata(hFig);
%// Get current slice
CurrentSlice = round(get(handles.y_slider,'value'));
hold on
imshow(S.D(:,:,CurrentSlice));
%// If button was button, draw line
if handles.LineDrawn
line([round(ImageWidth/2) round(ImageWidth/2)],[1 ImageHeight],'Color','r','LineWidth',2);
end
drawnow
guidata(hFig,handles);
end
function UpdateY(~)
handles = guidata(hFig); %// Get handles.
CurrentSlice = round(get(handles.y_slider,'value'));
hold on
imshow(S.D(:,:,CurrentSlice));
if handles.LineDrawn
line([round(ImageWidth/2) round(ImageWidth/2)],[1 ImageHeight],'Color','r','LineWidth',2);
end
drawnow
guidata(hFig,handles);
end
%// Pushbutton callback to draw line.
function DrawLine(~,~,handles)
line([round(ImageWidth/2) round(ImageWidth/2)],[1 ImageHeight],'Color','r','LineWidth',2);
handles.LineDrawn = true;
guidata(hFig,handles);
end
end
Sample output:
and after moving the slider up:
Is this what you meant? If not I'll remove that answer haha and sorry.
I have created a big heat map using matlab's imagesc command. It plots the error output for each combination of the values in x and y axes. As can be seen in the figure there are too many axes labels. This might become even denser as I plan to increase the number of points in both x and y axes - which means I will get more outputs on a finer grid.
I want to be flexible with the labels, and skip some of them. I want to do this for both X and Y. I also want to be flexible with the "ticks" and draw either all of them or maybe skip some of them. Keep in mind that both the X and Y values are not increasing in order, at first the increment is 0.01 for 9 points, then 0.1, then 1 or 3 or whatever. I will change these increments too.
I tried to show what I want the graph look like in the second image. I want roughly the labels shown in red boxes only. As I said these are not set values, and I will make the increments smaller which will lead to denser plot.
Thank you for your help.
OS: Windows 7, 8 (64 bit)
Matlab version: Matlab 2014 a
You can manipulate the ticks and labels like this:
ticksarray=[1 33 41 100 ...] % edit these to whatever you want
tickslabels={'1', '33', '41', '100'; ...} % match the size of both arrays
set(gca,'XTick',ticksarray)
set(gca,'XTickLabel',tickslabels)
The same thing applies to the y-axis.
Small working example:
x=1:100;
y=2*x.^2-3*x+2;
plot(x,y)
ticksarray=[1 33 41 100];
tickslabels={'1', '33', '41', '100'};
set(gca,'XTick',ticksarray)
set(gca,'XTickLabel',tickslabels)
Example:
figure(1)
load clown
subplot(211)
imagesc(X);
subplot(212)
imagesc(X);
h = gca;
Now you can either set a maximum number of labels per axis:
%// define maximum number of labels
maxLabel = 3;
h.XTick = linspace(h.xlim(1),h.xlim(2),maxLabel);
h.YTick = linspace(h.ylim(1),h.ylim(2),maxLabel);
or define how many labels should be skipped:
%// define number of labels to skip
skipLabel = 2;
h.XTick = h.XTick(1:skipLabel:end);
h.YTick = h.YTick(1:skipLabel:end)
You can also get a different number of ticks and labels, more complicated though:
maxLabel = 3;
maxTicks = 6;
h.XTick = linspace(h.xlim(1),h.xlim(2),maxTicks);
h.YTick = linspace(h.ylim(1),h.ylim(2),maxTicks);
h.XTickLabel( setdiff( 1:maxTicks, 1:maxTicks/maxLabel:maxTicks ) ) = repmat({''},1,maxTicks-maxLabel);
h.YTickLabel( setdiff( 1:maxTicks, 1:maxTicks/maxLabel:maxTicks ) ) = repmat({''},1,maxTicks-maxLabel);
If you use a prior version of Matlab 2014b, then you will need the set command to set all properties:
%// define maximum number of labels
maxLabel = 3;
Xlim = get(h,'Xlim');
Ylim = get(h,'Ylim');
set(h,'XTick', linspace(Xlim(1),Xlim(2),maxLabel));
set(h,'YTick', linspace(Ylim(1),Ylim(2),maxLabel));
%// or define number of labels to skip
skipLabel = 2;
XTick = get(h,'XTick');
YTick = get(h,'YTick');
set(h,'XTick', XTick(1:skipLabel:end));
set(h,'YTick', YTick(1:skipLabel:end));
%// or combined
maxLabel = 3;
maxTicks = 6;
Xlim = get(h,'Xlim');
Ylim = get(h,'Ylim');
set(h,'XTick', linspace(Xlim(1),Xlim(2),maxTicks));
set(h,'YTick', linspace(Ylim(1),Ylim(2),maxTicks));
XTickLabel = cellstr(get(h,'XTickLabel'));
YTickLabel = cellstr(get(h,'YTickLabel'));
XTickLabel( setdiff( 1:maxTicks, 1:maxTicks/maxLabel:maxTicks ),: ) = repmat({''},1,maxTicks-maxLabel);
YTickLabel( setdiff( 1:maxTicks, 1:maxTicks/maxLabel:maxTicks ),: ) = repmat({''},1,maxTicks-maxLabel);
set(h,'XTickLabel',XTickLabel);
set(h,'YTickLabel',YTickLabel);
After applying the second method proposed by #thewaywewalk I got the second figure below. Apparently the labels need to be structured as well, because they only take the first so many labels.
Then I tried to manipulate the labels as shown below, and got the third image.
skipLabel = 2;
XTick = get(h,'XTick');
YTick = get(h,'YTick');
set(h,'XTick', XTick(1:skipLabel:end));
set(h,'YTick', YTick(1:skipLabel:end));
XTickLabel = get(h,'XTickLabel');
labelsX = cell( length(1: skipLabel:length(XTick)) , 1);
j = 1;
for i = 1: skipLabel:length(XTick)
labelsX{j} = XTickLabel(i, :);
j = j + 1;
end
set(h,'XTickLabel', labelsX);
YTickLabel = get(h,'YTickLabel');
labelsY = cell( length(1: skipLabel:length(YTick)) , 1);
j = 1;
for i = 1: skipLabel:length(YTick)
labelsY{j} = YTickLabel(i, :);
j = j + 1;
end
set(h,'YTickLabel', labelsY);
The Y axis labels seem to be in place as before (right next to tick), however the X axis labels seem to be shifted to the left a little. How can I correct this?
Another note: How can I change the scientific values into normal numbers? Also, probably there is a better approach at manipulating the labels.