function varargout = magic_gui(varargin)
% Tutorial m-file to demonstrate the operation of various controls
% such as listbox, radio button, checkbox, push button, static text, and axes.
% Requires the Image Processing Toolbox.
%
% Written by Mark Hayworth, Ph.D.
% Advanced Imaging Section
% email: hayworth dot ms at pg dot com
% The Procter & Gamble Company, Cincinnati, Ohio, USA.
% December 2008 - May 2009. Updated Feb. 2013.
%
% magic_gui M-file for magic_gui.fig
% magic_gui by itself, creates a new magic_gui or raises the existing
% singleton*.
%
% H = magic_gui returns the handle to a new magic_gui or the handle to
% the existing singleton*.
%
% magic_gui('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in magic_gui.M with the given input arguments.
%
% magic_gui('Property','Value',...) creates a new magic_gui or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before magic_gui_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to magic_gui_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help magic_gui
% Last Modified by GUIDE v2.5 20-Mar-2013 15:26:39
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @magic_gui_OpeningFcn, ...
'gui_OutputFcn', @magic_gui_OutputFcn, ...
'gui_LayoutFcn', [], ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before magic_gui is made visible.
function magic_gui_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to magic_gui (see VARARGIN)
% Choose default command line output for magic_gui
handles.output = hObject;
%=====================================================================
% --- My Startup Code --------------------------------------------------
% Clear old stuff from console.
clc;
fprintf(1, 'Just entered magic_gui_OpeningFcn...\n');
% Change the current folder to the folder of this m-file.
% (The line of code below is from Brett Shoelson of The Mathworks.)
cd(fileparts(which(mfilename)));
% MATLAB QUIRK: Need to clear out any global variables you use anywhere
% otherwise it will remember their prior values from a prior running of the macro.
clear global;
handles.macroFolder = cd;
handles.maskFolder = [handles.macroFolder '/Masks'];
set(handles.figMainWindow, 'Visible', 'off');
% Load up the initial values from the mat file.
strIniFile = fullfile(handles.macroFolder, 'Magic_GUI.mat');
if exist(strIniFile, 'file')
% Pull out values and stuff them in structure initialValues.
initialValues = load(strIniFile);
% Assign the image folder from the lastUsedImageFolder field of the
% structure.
handles.ImageFolder = initialValues.lastUsedImageFolder;
end
% If the image folder does not exist, but the imdemos folder exists, then point them to that.
if exist(handles.ImageFolder, 'dir') == 0
% Folder stored in the mat file does not exist. Try the imdemos folder instead.
imdemosFolder = fullfile(matlabroot, '\toolbox\images\imdemos');
if exist(imdemosFolder, 'dir') == 0
% imdemos folder exists. Use it.
handles.ImageFolder = imdemosFolder;
else
% imdemos folder does not exist. Use current folder.
handles.ImageFolder = cd;
end
end
% handles.ImageFolder will be a valid, existing folder by the time you get here.
if exist(strIniFile, 'file')
% If the mat file is not there, save current folder out in our mat file.
% Save the image folder in our ini file.
lastUsedImageFolder = handles.ImageFolder;
save(strIniFile, 'lastUsedImageFolder');
end
set(handles.txtFolder, 'string', handles.ImageFolder);
%uiwait(msgbox(handles.ImageFolder));
% Load list of images in the image folder.
handles = LoadImageList(handles);
% Select none of the items in the listbox.
set(handles.lstImageList, 'value', []);
% Update the number of images in the Analyze button caption.
UpdateAnalyzeButtonCaption(hObject, eventdata, handles)
% Load list of mask images in the app/masks folder.
handles=LoadMaskList(handles);
% Load a splash image.
%axes(handles.axesImage);
fullSplashImageName = fullfile(handles.macroFolder, '/Splash Images/Magic Hat.png');
if exist(fullSplashImageName, 'file')
% Display splash image.
imgOriginal = imread(fullSplashImageName);
else
% Display something
imgOriginal = peaks(300);
end
% Display image array in a window on the user interface.
% Display in axes, storing handle of image for later quirk workaround.
hold off; % IMPORTANT NOTE: hold needs to be off in order for the "fit" feature to work correctly.
axesChildHandle = imshow(imgOriginal, 'InitialMagnification', 'fit', 'parent', handles.axesImage);
imageFolder = handles.ImageFolder;
h = axesChildHandle;
setappdata(h, 'imageFolder', imageFolder);
txtInfo = sprintf('MAGIC - MATLAB Analysis with Generic Imaging Code.\n\nBy Mark Hayworth, Ph.D.\nThe Procter & Gamble Company\n\nTutorial GUI to demonstrate basic functionality\nof various controls on the GUI.');
set(handles.txtInfo, 'string', txtInfo);
% !!!! QUIRK workaround.!!!!
% Make it so that if they click in the image axes, it will execute a
% button down callback called "axesImage_ButtonDownFcn".
% Now it won't -- unless you do this quirk workaround.
% Double click on the dialog box's (main figure's) background to bring up the property inspector.
% Change both the WindowButtonDownFcn and ButtonDownFcn properties so that they are blank.
% Also set the main figure's HitTest to off. Then, make sure you already have the handle to the
% image living in the axes by getting it from an imshow. Then do this:
set(axesChildHandle, 'ButtonDownFcn', @axesImage_ButtonDownFcn);
% Put everything you want to do when they click the image into the function axesImage_ButtonDownFcn()
% !!!! End QUIRK workaround.!!!!
fprintf(1, 'Done with magic_gui_OpeningFcn.\n');
% Update handles structure
guidata(hObject, handles);
% --- End of My Startup Code --------------------------------------------------
%=====================================================================
%=====================================================================
% --- Outputs from this function are returned to the command line.
function varargout = magic_gui_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
fprintf(1, 'Just entered magic_gui_OutputFcn...\n');
% Get default command line output from handles structure
varargout{1} = handles.output;
% Call special function that The Mathworks provides on their website to maximize the window and leave it in focus.
% minfig(F,1) % minimizes the figure window for the figure with handle F
% minfig(F,0) % restores figure F if F is minimized
% maxfig(F,1) % maximizes the figure window for the figure with handle F
% maxfig(F,0) % restores figure F if F is maximized s = figstate(F) % returns the state of figure { Maximized | Minimized | Normal }
% Note: This works only if the window is already displayed. If not, it will throw a java exception.
% The best place to put this is in the yourApp_OutputFcn(),
% which actually gets called as the last thing before your app is made available to the user.
checkForMaxfig = whos('maxfig');
if isempty(checkForMaxfig)
% maxfig is not installed on this computer.
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
else
maxfig(handles.figMainWindow, 1) % Maximizes the figure window for the figure with handle in the first argument.
end
fprintf(1, 'Done with magic_gui_OutputFcn.\n');
%=====================================================================
% --- Executes on clicking in lstImageList listbox.
% Display image from disk and plots histogram
function lstImageList_Callback(hObject, eventdata, handles)
% hObject handle to lstImageList (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = get(hObject,'String') returns lstImageList contents as cell array
% contents{get(hObject,'Value')} returns selected item from lstImageList
global baseImageFileName;
clear global imgOriginal;
global imgOriginal; % Declare global so that other functions can see it, if they also declare it global.
% Change mouse pointer (cursor) to an hourglass.
% QUIRK: use 'watch' and you'll actually get an hourglass not a watch.
set(gcf,'Pointer','watch');
drawnow; % Cursor won't change right away unless you do this.
% Update the number of images in the Analyze button caption.
UpdateAnalyzeButtonCaption(hObject, eventdata, handles)
% Get image name
selectedListboxItem = get(handles.lstImageList, 'value');
if isempty(selectedListboxItem)
% Bail out if nothing was selected.
% Change mouse pointer (cursor) to an arrow.
set(gcf,'Pointer','arrow');
drawnow; % Cursor won't change right away unless you do this.
return;
end
% If more than one is selected, bail out.
if length(selectedListboxItem) > 1
% Disable Draw new mask - not clear if there is an image being
% displayed.
set(handles.btnDrawNewMask, 'enable', 'off');
baseImageFileName = '';
% Change mouse pointer (cursor) to an arrow.
set(gcf,'Pointer','arrow')
drawnow; % Cursor won't change right away unless you do this.
return;
end
% If only one is selected, display it.
set(handles.axesPlot, 'visible', 'off'); % Hide plot of results since there are no results yet.
set(handles.btnDrawNewMask, 'enable', 'on'); % Enable Draw Mask Button.
ListOfImageNames = get(handles.lstImageList, 'string');
baseImageFileName = strcat(cell2mat(ListOfImageNames(selectedListboxItem)));
fullImageFileName = [handles.ImageFolder '/' baseImageFileName]; % Prepend folder.
[folder, baseFileName, extension] = fileparts(fullImageFileName);
switch lower(extension)
case {'.mov', '.wmv', '.asf'}
msgboxw('Mov and wmv format video files are not supported by MATLAB.');
% Change mouse pointer (cursor) to an arrow.
set(gcf,'Pointer','arrow');
drawnow; % Cursor won't change right away unless you do this.
return;
case '.avi'
% The only video format supported natively by MATLAB is avi.
% A more complicated video player plug in is on MATLAB File Central
% that will support more types of video. It has a bunch of DLL's and
% other files that you have to install.
% Read the file into a MATLAB movie structure.
myVideo = aviread(fullImageFileName);
myVideoParameters = aviinfo(fullImageFileName);
numberOfFrames = myVideoParameters.NumFrames;
% Extract a frame.
frameToView = uint8(floor(numberOfFrames/2)); % Take the middle frame.
imgFirstFrame = myVideo(frameToView).cdata; % The index is the frame number.
cla(handles.axesPlot, 'reset');
imshow(imgFirstFrame, 'Parent', handles.axesPlot); % Display the first frame.
% Play the movie in the axes. It doesn't stretch to fit the axes.
% The macro will wait until it finishes before continuing.
axes(handles.axesImage);
hold off;
cla(handles.axesImage, 'reset'); % Let image resize, for example demo video rhinos.avi won't fill the image buffer if we don't do this.
movie(handles.axesImage, myVideo);
cla(handles.axesPlot, 'reset'); % Clear the mini-image from the plot axes.
guidata(hObject, handles);
% Change mouse pointer (cursor) to an arrow.
set(gcf,'Pointer','arrow');
drawnow; % Cursor won't change right away unless you do this.
return;
otherwise
% Display the image.
imgOriginal = DisplayImage(handles, fullImageFileName);
end
% If imgOriginal is empty (couldn't be read), just exit.
if isempty(imgOriginal)
% Change mouse pointer (cursor) to an arrow.
set(gcf,'Pointer','arrow');
drawnow; % Cursor won't change right away unless you do this.
return;
end
% Read in mask file, or if they haven't chosen one, just have mask be
% entire shape of imgOriginal.
GetImageMask(handles);
% These declarations need to be after GetImageMask because GetImageMask clears them
% out and the association with this function is then lost.
global imgMask;
global maskVerticesXCoordinates;
global maskVerticesYCoordinates;
% Mask off the original with pre-selected mask, if they chose one.
% Then display masked image and return it in array maskedImage and
% return mask in logical array binaryMask
imageSize = size(imgOriginal);
% Convert this outline into an image.
imgMask = poly2mask(maskVerticesXCoordinates, maskVerticesYCoordinates, imageSize(1), imageSize(2));
[maskedImage logBinaryMask] = MaskAndDisplayImage(handles, imgOriginal, false);
% Analyze this image.
if get(handles.chkAutoAnalyze,'Value')
AnalyzeSingleImage(handles, maskedImage, logBinaryMask);
end
%fprintf('lstImageList_Callback.5\n');
%axes(handles.axesImage); % Switch current figure back to image box.
%fprintf('lstImageList_Callback.6\n');
% Change mouse pointer (cursor) to an arrow.
set(gcf,'Pointer','arrow');
drawnow; % Cursor won't change right away unless you do this.
guidata(hObject, handles);
return % from lstImageList_Callback()
%=====================================================================
% Reads FullImageFileName from disk into the axesImage axes.
function imageArray = DisplayImage(handles, FullImageFileName)
% Read in image.
try
[imageArray colorMap] = imread(FullImageFileName);
% colorMap will have something for an indexed image (gray scale image with a stored colormap).
% colorMap will be empty for a true color RGB image or a monochrome gray scale image.
catch ME
errorMessage = sprintf('Error opening image file with imread():\n%s', FullImageFileName);
set(handles.txtInfo, 'String', errorMessage);
msgboxw(errorMessage);
imageArray = [];
return; % Skip the rest of this function
end
try
% Display image array in a window on the user interface.
%axes(handles.axesImage);
hold off; % IMPORTANT NOTE: hold needs to be off in order for the "fit" feature to work correctly.
% Here we actually display the image in the "axesImage" axes.
axesChildHandle = imshow(imageArray, 'InitialMagnification', 'fit', 'parent', handles.axesImage);
% Display a title above the image.
[folder, basefilename, extension] = fileparts(FullImageFileName);
extension = lower(extension);
% Convert any underlines in the name into spaces because otherwise the character after the underline would be a subscript.
caption = strrep([basefilename extension], '_', ' ');
% Display the title.
title(handles.axesImage, caption, 'FontSize', 14);
% Make it so that if they click on the image, the callback function is executed.
% See note on QUIRK in startup code section.
set(axesChildHandle, 'ButtonDownFcn', @axesImage_ButtonDownFcn);
imageFolder = folder;
setappdata(axesChildHandle, 'imageFolder', imageFolder);
[rows columns numberOfColorChannels] = size(imageArray);
% Get the file date
fileInfo = dir(FullImageFileName);
txtInfo = sprintf('%s\n\n%d lines (rows) vertically\n%d columns across\n%d color channels\n', ...
[basefilename extension], rows, columns, numberOfColorChannels);
% Tell user the type of image it is.
if numberOfColorChannels == 3
colorbar 'off'; % get rid of colorbar.
txtInfo = sprintf('%s\nThis is a true color, RGB image.', txtInfo);
elseif numberOfColorChannels == 1 && isempty(colorMap)
colorbar 'off'; % get rid of colorbar.
txtInfo = sprintf('%s\nThis is a gray scale image, with no stored color map.', txtInfo);
elseif numberOfColorChannels == 1 && ~isempty(colorMap)
txtInfo = sprintf('%s\nThis is an indexed image. It has one "value" channel with a stored color map that is used to pseudocolor it.', txtInfo);
colormap(colorMap);
whos colorMap;
%fprintf('About to apply the colormap...\n');
% Thanks to Jeff Mather at the Mathworks to helping to get this working for an indexed image.
colorbar('peer', handles.axesImage);
%fprintf('Done applying the colormap.\n');
end
% Show the file time and date.
txtInfo = sprintf('%s\n\n%s', txtInfo, fileInfo.date);
set(handles.txtInfo, 'String', txtInfo);
% Plot the histogram if requested.
plotHistogram = get(handles.chkPlotHistograms, 'Value');
if plotHistogram
fprintf('About to plot histogram...\n');
PlotImageHistogram(handles, imageArray);
fprintf('Done plotting histogram.\n');
end
catch ME
errorMessage = sprintf('Error in function DisplayImage.\nError Message:\n%s', ME.message);
WarnUser(errorMessage);
end
return; % from DisplayImage
%=====================================================================
function DisplayResults(handles, resultsArray)
% Display the results
% MATLAB BUG: \t doesn't work (R2006a)
% Workaround: convert to "courier New to get fixed space font and use
% spaces or field widths to align the numbers.
global CDFPercentiles;
strHeader = sprintf('Measurement\n____________________________________________________');
strTotalArea = sprintf('Total area %7d', resultsArray(1)) ;
strMinValue = sprintf('Minimum Value %7.2f', resultsArray(2));
strMaxValue = sprintf('Minimum Value %7.2f', resultsArray(3));
strMeanValue = sprintf('Mean Value %7.2f', resultsArray(4));
strStdDev = sprintf('Std. Dev. %7.2f', resultsArray(5));
strPercentiles = sprintf('25th percentile at %5.2f\n75th percentile at %5.2f\n50th percentile (median) at %5.2f', CDFPercentiles(25), CDFPercentiles(75), CDFPercentiles(50));
strResults = sprintf('%s\n%s\n%s\n%s\n%s\n%s\n%s', strHeader, strTotalArea, strMinValue, strMaxValue, strMeanValue, strStdDev, strPercentiles);
set(handles.txtInfo, 'String', strResults);
return; % DisplayResults
%=====================================================================
% Update Analyze button and tooltip string depending on how many files in the listbox were selected.
function UpdateAnalyzeButtonCaption(hObject, eventdata, handles)
Selected = get(handles.lstImageList, 'value');
if length(Selected) > 1
buttonCaption = {'Step 6: Analyze '}; % MATLAB quirk - needs to be cell array to keep trailing spaces.
buttonCaption = strcat(buttonCaption, num2str(length(Selected)));
buttonCaption = strcat(buttonCaption, ' images');
set(handles.btnAnalyze, 'string', buttonCaption);
set(handles.btnAnalyze, 'Tooltipstring', 'Display and analyze the selected image(s)');
elseif length(Selected) == 1
set(handles.btnAnalyze, 'string', 'Step 6: Analyze 1 image');
set(handles.btnAnalyze, 'Tooltipstring', 'Display and analyze the selected image');
else
set(handles.btnAnalyze, 'string', 'Step 6: Analyze no images');
set(handles.btnAnalyze, 'Tooltipstring', 'Please select image(s) first');
end
return;
%=====================================================================
% --- Executes during object creation, after setting all properties.
function lstImageList_CreateFcn(hObject, eventdata, handles)
% hObject handle to lstImageList (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
return
%=====================================================================
% --- Executes on clicking btnSelectFolder button.
% Asks user to select a directory and then loads up the listbox (via a call
% to LoadImageList)
function btnSelectFolder_Callback(hObject, eventdata, handles)
% hObject handle to btnSelectFolder (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%msgbox(handles.ImageFolder);
returnValue = uigetdir(handles.ImageFolder,'Select folder');
% returnValue will be 0 (a double) if they click cancel.
% returnValue will be the path (a string) if they clicked OK.
if returnValue ~= 0
% Assign the value if they didn't click cancel.
handles.ImageFolder = returnValue;
handles = LoadImageList(handles);
set(handles.txtFolder, 'string' ,handles.ImageFolder);
guidata(hObject, handles);
% Save the image folder in our ini file.
lastUsedImageFolder = handles.ImageFolder;
save('Magic_GUI.mat', 'lastUsedImageFolder');
end
return
%=====================================================================
% --- Load up the listbox with tif files in folder handles.handles.ImageFolder
function handles=LoadImageList(handles)
ListOfImageNames = {};
folder = handles.ImageFolder;
if ~isempty(handles.ImageFolder)
if exist(folder,'dir') == false
warningMessage = sprintf('Note: the folder used when this program was last run:\n%s\ndoes not exist on this computer.\nPlease run Step 1 to select an image folder.', handles.ImageFolder);
msgboxw(warningMessage);
return;
end
else
msgboxw('No folder specified as input for function LoadImageList.');
return;
end
% If it gets to here, the folder is good.
ImageFiles = dir([handles.ImageFolder '/*.*']);
for Index = 1:length(ImageFiles)
baseFileName = ImageFiles(Index).name;
[folder, name, extension] = fileparts(baseFileName);
extension = upper(extension);
switch lower(extension)
case {'.png', '.bmp', '.jpg', '.tif', '.avi'}
% Allow only PNG, TIF, JPG, or BMP images
ListOfImageNames = [ListOfImageNames baseFileName];
otherwise
end
end
set(handles.lstImageList,'string',ListOfImageNames);
return
%=====================================================================
% --- Load up the listbox with tif files in folder handles.handles.ImageFolder
function handles=LoadMaskList(handles)
ListOfMaskFilenames = {'Do not use a mask'};
dirListing = dir([handles.maskFolder '/*.mat']);
for Index = 1:length(dirListing)
baseFileName = dirListing(Index).name;
ListOfMaskFilenames = [ListOfMaskFilenames baseFileName];
end
set(handles.lstMasks, 'string', ListOfMaskFilenames);
return
%=====================================================================
% --- Executes on clicking btnAnalyze button.
% Goes down through the list, displaying then analyzing each highlighted image file.
% Main processing is done by the function AnalyzeSingleImage()
function btnAnalyze_Callback(hObject, eventdata, handles)
% hObject handle to btnAnalyze (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Change mouse pointer (cursor) to an hourglass.
% QUIRK: use 'watch' and you'll actually get an hourglass not a watch.
set(gcf,'Pointer','watch');
drawnow; % Cursor won't change right away unless you do this.
% Get a list of those indexes that are selected, so we know which images to process.
Selected = get(handles.lstImageList, 'value');
numberOfSelectedFiles = length(Selected);
% Then get list of all of the filenames in the list,
% regardless of whether they are selected or not.
ListOfImageNames = get(handles.lstImageList, 'string');
% Make an array for the results.
% We will send these to Excel if requested.
% resultsArray = zeros(numberOfSelectedFiles, 6);
for j = 1 : numberOfSelectedFiles % Loop though all selected indexes.
index = Selected(j); % Get the next selected index.
% Get the filename for this selected index.
baseImageFileName = strcat(cell2mat(ListOfImageNames(index)));
imageFullFileName = fullfile(handles.ImageFolder, baseImageFileName);
% Display the image.
imgOriginal = DisplayImage(handles, imageFullFileName);
% If imgOriginal is empty (couldn't be read), skip to next file.
if isempty(imgOriginal)
continue;
end
% If you don't want to use masking, then uncomment the next two lines.
% maskedImage = imgOriginal;
% logBinaryMask = [];
% Mask off the original with pre-selected mask, if they chose one.
% Then display masked image and return it in array maskedImage and
% return mask in logical array binaryMask.
% If you don't want to use masking, then delete the next line.
[maskedImage logBinaryMask] = MaskAndDisplayImage(handles, imgOriginal, true);
% Analyze this image.
resultsArray = AnalyzeSingleImage(handles, maskedImage, logBinaryMask);
if get(handles.chkSendToExcel, 'value')
% Send the results to Excel. One workbook will be created for each image.
% Note: You could have one workbook and one worksheet for each image, (just keep the
% same excelFullFileName but change workSheetName), but Excel 2003 limits you
% to 32 worksheets or less per workbook, so be aware of that.
blankString = ' '; % Need so that both rows of columnNames cell array have the same number of elements (or else you'll get an error).
columnNames = {baseImageFileName, blankString, blankString, blankString,...
blankString, blankString, blankString; ...
'Blob #', 'Area', 'Mean Intensity', 'Perimeter', ...
'CentroidX', 'CentroidY', 'ECD'};
[folder, baseFileNameNoExtension, extension] = fileparts(baseImageFileName);
excelBaseFileName = sprintf('Results for %s.xls', baseFileNameNoExtension);
excelFullFileName = fullfile(handles.ImageFolder, excelBaseFileName);
workSheetName = 'Results';
% Write the filename into row 1, and the column headings into row 2.
xlswrite(excelFullFileName, columnNames, workSheetName, 'B1');
% Write numerical results starting on row 3.
xlswrite(excelFullFileName, resultsArray, workSheetName, 'B3');
msgboxw({'Done with analysis. Results are in Excel file:'; excelFullFileName});
end
% Prompt to allow user to inspect the image.
if j < numberOfSelectedFiles && get(handles.chkPauseAfterImage, 'value')
userPrompt = sprintf('Check out results, then\nclick Continue to process the next image.');
reply = questdlg(userPrompt, ...
'Continue?', 'Continue', 'Quit loop', 'Continue');
% reply = '' for Upper right X, otherwise it's the exact wording.
if strcmpi(reply, 'Quit loop')
set(handles.txtInfo, 'string', 'Batch processing terminated.');
break;
end
end
end
set(gcf,'Pointer','arrow');
drawnow; % Cursor won't change right away unless you do this.
guidata(hObject, handles);
return
%=====================================================================
% Mask image according to maskVerticesXCoordinates and maskVerticesYCoordinates.
% Important: imgOriginal can't be empty since MATLAB won't allow you to pass
% empty arrays as arguments.
% Inputs:
% imgOriginal is either a 2D monochrome image or a 3D color image.
% showImage = logical true if you want to display it. showImage = false to not display.
% Outputs:
% logBinaryMask is a 2D logical (binary) image of just the mask.
% maskedImage is which has been set to zero outside of the mask.
function [maskedImage logBinaryMask] = MaskAndDisplayImage(handles, imgOriginal, showImage)
% Declare our global variables so that this function can now see and access them.
global maskVerticesXCoordinates;
global maskVerticesYCoordinates;
% Mask off the original with pre-selected mask, if they chose one.
% Set up default return values.
maskedImage = [];
logBinaryMask = [];
lowValue = 0;
highValue = 255;
% Gate check for valid values.
if isempty(imgOriginal)
% No image - nothing to do!
return;
end
if isempty(maskVerticesXCoordinates) || isempty(maskVerticesYCoordinates)
% No mask coordinates - nothing to mask. Just display if requested, then exit.
if showImage
% Display masked image array in a window on the user interface.
%axes(handles.axesImage);
hold(handles.axesImage, 'off'); % Need to do this so the image will get updated and the image buffer won't be sized according to the last image that was in there.
imshow(maskedImage, [lowValue highValue], 'parent', handles.axesImage);
end
return;
end
% If we get here, we have an image array passed in, and a valid mask.
imageSize = size(imgOriginal);
% Convert this outline into a binary image.
imgMask = poly2mask(maskVerticesXCoordinates, maskVerticesYCoordinates, imageSize(1), imageSize(2));
maskSize = size(imgMask);
% Now, mask off image
% First mask sure mask is the same size as the image.
% Make sure the dimensions are the same.
% Make sure masked image is the same size as the original.
% You have to create it first with some definite size before you
% can multiply it by a mask image.
maskedImage = imgOriginal;
if maskSize(1) ~= imageSize(1) || maskSize(1) ~= imageSize(1)
% Dimensions of image and mask don't match.
% Mask is the entire image - in essence, no mask.
% errorMessage = {'Cannot show mask over the color image because', 'the mask image dimensions do not match the image dimensions.', [' Mask image dimensions: ' num2str(maskSize(1)) ' by ' num2str(maskSize(2))], [' Color image dimensions: ' num2str(imageSize(1)) ' by ' num2str(imageSize(2))]};
% msgboxw(errorMessage);
logBinaryMask = ones(size(imgOriginal)) == 1; % logical image.
else
% Image and mask image dimension match.
if length(imageSize) >= 3
numberOfColors = imageSize(3);
else
numberOfColors = 1;
end
if numberOfColors >= 2
highRValue = max(imgOriginal(:,:,1));
highGValue = max(imgOriginal(:,:,2));
highBValue = max(imgOriginal(:,:,3));
highValue = max([highRValue highGValue highBValue]); % Max over all pixels in all color bands.
for intColorBand = 1:numberOfColors
maskedImage(:,:,intColorBand) = double(imgOriginal(:,:,intColorBand)) .* double(imgMask(:,:));
end
else
% It's monochrome.
lowValue = min(imgOriginal(:));
highValue = max(imgOriginal(:));
maskedImage = double(imgOriginal) .* double(imgMask);
end
logBinaryMask = imgMask > 0; % logical image.
end
if showImage
% Display masked image array in a window on the user interface.
%axes(handles.axesImage);
hold(handles.axesImage, 'off'); % Need to do this so the image will get updated and the image buffer won't be sized according to the last image that was in there.
imshow(maskedImage, [lowValue highValue], 'parent', handles.axesImage);
end
return;
%=====================================================================
% --- Executes on button press in btnSelectAllOrNone.
function btnSelectAllOrNone_Callback(hObject, eventdata, handles)
% hObject handle to btnSelectAllOrNone (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Find out button caption and take appropriate action.
ButtonCaption = get(handles.btnSelectAllOrNone, 'string');
if strcmp(ButtonCaption, 'Step 2: Select All') == 1
% Select all items in the listbox.
% Need to find out how many items are in the listbox (both selected and
% unselected). It's quirky and inefficient but it's the only way I
% know how to do it.
% First get the whole damn listbox text into a cell array.
caListboxString = get(handles.lstImageList, 'string');
NumberOfItems = length(caListboxString); % Get length of that cell array.
AllIndices=1:NumberOfItems; % Make a vector of all indices.
% Select all indices.
set(handles.lstImageList, 'value', AllIndices);
% Finally, change caption to say "Select None"
set(handles.btnSelectAllOrNone, 'string', 'Step 2: Select None');
% It scrolls to the bottom of the list. Use the following line
% if you want the first item at the top of the list.
set(handles.lstImageList, 'ListboxTop', 1);
else
% Select none of the items in the listbox.
set(handles.lstImageList, 'value', []);
% Change caption to say Select All
set(handles.btnSelectAllOrNone, 'string', 'Step 2: Select All');
end
% Update the number of images in the Analyze button caption.
UpdateAnalyzeButtonCaption(hObject, eventdata, handles)
guidata(hObject, handles);
%=====================================================================
% --- Executes on button press in chkSendToExcel.
function chkSendToExcel_Callback(hObject, eventdata, handles)
% hObject handle to chkSendToExcel (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of chkSendToExcel
checkboxState = get(hObject,'Value');
message = sprintf('Now the results will be saved to an Excel workbook in folder\n%s', handles.ImageFolder);
if checkboxState
set(handles.txtInfo, 'string', message);
else
set(handles.txtInfo, 'string', 'Now the results will not be saved to an Excel workbook.');
end
%=====================================================================
% --- Executes on button press in chkPauseAfterImage.
function chkPauseAfterImage_Callback(hObject, eventdata, handles)
% hObject handle to chkPauseAfterImage (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of chkPauseAfterImage
checkboxState = get(hObject,'Value');
if checkboxState
set(handles.txtInfo, 'string', 'Now you will be able to inspect the results before it processes the next image.');
else
set(handles.txtInfo, 'string', 'Now the image(s) will be analyzed without pausing for you will be able to inspect the results in between images.');
end
%=====================================================================
function GetImageMask(handles)
% Make sure it's cleared out (work around of MATLAB feature).
% MATLAB QUIRK. MATLAB can remember maskVerticesXCoordinates and maskVerticesYCoordinates
% prior runs of this macro even when you haven't clicked on the mask.
% This is because if you don't erase it from the "global" workspace before you exit this m-file
% then it will remain in the global workspace.
% It will even remember it in the ImageList_Callback function even
% though imgMask has never even been mentioned prior to it getting
% there. Clearing it here seems to fix everything.
clear global maskVerticesXCoordinates;
clear global maskVerticesYCoordinates;
% Now redeclare them. They should be empty at this point.
% Declare both the logical mask image and the coordinates that created it.
global maskVerticesXCoordinates;
global maskVerticesYCoordinates;
% Declare imgOriginal. It might be filled with values here.
global imgOriginal; % Declare global so that other functions can see it, if they also declare it global.
%fprintf('GetImageMask.4\n');
% Clear any exiting polygon overlay that may be plotted on top of the image.
%axes(handles.axesImage);
%drawnow
%fprintf('GetImageMask.4a\n');
ClearLinesFromAxes(handles.axesImage);
% Get the index of the entry they've selected.
SelectedMask = get(handles.lstMasks, 'value');
if ~isempty(imgOriginal)
% An image is available.
imageSize = size(imgOriginal);
% Get mask coordinates: either derive them from the original image size,
% or read them in from a disk file.
if SelectedMask == 1
% They have selected the top entry: "Do not use a mask"
% If they've selected an image, make the mask an array of all ones
% the same size as the image.
maskVerticesXCoordinates(1) = 0;
maskVerticesXCoordinates(2) = 0;
maskVerticesXCoordinates(3) = imageSize(2);
maskVerticesXCoordinates(4) = imageSize(2);
maskVerticesYCoordinates(1) = 0;
maskVerticesYCoordinates(2) = imageSize(1);
maskVerticesYCoordinates(3) = imageSize(1);
maskVerticesYCoordinates(4) = 0;
else
% They've selected a mask file.
% Get the complete list of all mask file names listed,
% whether selected or not.
ListOfImageNames = get(handles.lstMasks, 'string');
% Get the mask file name
maskName = strcat(cell2mat(ListOfImageNames(SelectedMask)));
% Get the full name of the mask coordinates file.
[folder, baseFileName, ext] = fileparts(maskName);
coordinatesFileName = fullfile(handles.maskFolder, [baseFileName '.mat']);
load(coordinatesFileName, 'maskVerticesXCoordinates', 'maskVerticesYCoordinates');
% Clip to mask coordinates to image boundaries. Mask can't go outside the image.
maskVerticesXCoordinates(maskVerticesXCoordinates > imageSize(2)) = imageSize(2);
maskVerticesYCoordinates(maskVerticesYCoordinates > imageSize(1)) = imageSize(1);
% Plot the mask as an outline over the image.
hold on;
plot(maskVerticesXCoordinates, maskVerticesYCoordinates, 'linewidth', 2);
end
else
% They've not clicked on an image yet.
% Just read in the mask coordinates and return.
if SelectedMask == 1
% They have selected the top entry: "Do not use a mask"
% If they've selected an image, make the mask an array of all ones
% the same size as the image.
return;
else
% They've selected a mask file but no image file.
% Get the complete list of all mask file names listed,
% whether selected or not.
ListOfImageNames = get(handles.lstMasks, 'string');
% Get the mask file name
maskName = strcat(cell2mat(ListOfImageNames(SelectedMask)));
% Get the full name of the mask coordinates file.
[folder, baseFileName, ext] = fileparts(maskName);
coordinatesFileName = fullfile(handles.maskFolder, [baseFileName '.mat']);
load(coordinatesFileName, 'maskVerticesXCoordinates', 'maskVerticesYCoordinates');
% Nothing more we can do since we don't have an image,
% so just exit.
return;
end
end
return;
%=====================================================================
% Erases all lines from the image axes. The current axes should be set first using the axes()
% command before this function is called, as it works from the current axes, gca.
function ClearLinesFromAxes(h)
%fprintf('ClearLinesFromAxes.1\n');
axesHandlesToChildObjects = findobj(h, 'Type', 'line');
%fprintf('ClearLinesFromAxes.2\n');
if ~isempty(axesHandlesToChildObjects)
delete(axesHandlesToChildObjects);
end
return; % from ClearLinesFromAxes
%=====================================================================
% --- Executes on selection change in lstMasks.
% Displays mask on top of the displayed image, if imgOriginal is not empty.
% Auto-analyzes if that checkbox is checked.
function lstMasks_Callback(hObject, eventdata, handles)
% hObject handle to lstMasks (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = get(hObject,'String') returns lstMasks contents as cell array
% contents{get(hObject,'Value')} returns selected item from lstMasks
% Read the image mask file and put the result into a logical mask image called imgMask.
GetImageMask(handles);
% These declarations need to be after GetImageMask because GetImageMask clears them
% out and the association with this function is then lost.
global imgOriginal; % Every function that declares this variable global will be able to use and modity it.
if ~isempty(imgOriginal)
% Mask off the original with pre-selected mask, if they chose one.
% Then display masked image and return it in array maskedImage and
% return mask in logical array binaryMask
[maskedImage logBinaryMask] = MaskAndDisplayImage(handles, imgOriginal, false);
if get(handles.chkAutoAnalyze, 'Value')
% Analyze this image.
AnalyzeSingleImage(handles, maskedImage, logBinaryMask);
else
set(handles.txtInfo, 'String', ' ');
end
end
%axes(handles.axesImage); % Switch current figure back to image box.
guidata(hObject, handles);
return
%=====================================================================
% --- Executes during object creation, after setting all properties.
function lstMasks_CreateFcn(hObject, eventdata, handles)
% hObject handle to lstMasks (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%=====================================================================
% --- Executes on button press in btnDrawNewMask.
% Allows user to draw a polygon over image and then save the coordinates in a binary data file.
% (We could just as well use a mat format file.)
function btnDrawNewMask_Callback(hObject, eventdata, handles)
% hObject handle to btnDrawNewMask (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Declare our global variables in case they want to save them to a mat file.
global maskVerticesXCoordinates;
global maskVerticesYCoordinates;
% Prompt user to draw a region on the image.
uiwait(msgbox({'Draw a polygon over the image.' 'Right click the last vertex point to finish drawing.'}));
% Erase all previous lines.
ClearLinesFromAxes(handles.axesImage);
% Get binary image that is a mask representing the region they drew.
% binaryMask is an image of Logical data type.
[binaryMask xCoords yCoords] = roipolyold; % drop the binaryMask= and ; to see the binary image mask
% imshow(binaryMask);
% Plot the mask as an outline over the image.
hold on;
plot(xCoords, yCoords, 'linewidth', 2);
reply = questdlg({'Do you want to save the mask', 'to disk as a template?'},'Save mask?', 'Yes','No', 'Yes');
% Note: reply = '' for Upper right X, 'Yes' for Yes, 'No' for No.
if strcmp(reply, 'Yes')
defaultFileName = fullfile(handles.maskFolder, 'Polygon.mat');
[fileName, folder, FilterIndex] = uiputfile(defaultFileName, 'Save mask file name');
if FilterIndex == 0
% If the user clicks the Cancel button, closes the dialog window,
% or if the file does not exist, FilterIndex is set to 0.
% Bail out in that case.
guidata(hObject, handles);
return;
end
maskVerticesXCoordinates = xCoords;
maskVerticesYCoordinates = yCoords;
[folder, baseFileName, ext] = fileparts(fileName);
% Save the mask as a PNG-format image for later recall if desired.
% maskImageFileName = fullfile(handles.maskFolder, [baseFileName '.png']);
% imwrite(binaryMask, maskImageFileName, 'png');
% Write the coordinates out to a mat-format file.
coordinatesFileName = fullfile(handles.maskFolder, [baseFileName '.mat']);
save(coordinatesFileName, 'maskVerticesXCoordinates', 'maskVerticesYCoordinates');
% Refresh the listbox of mask filenames.
% Load list of mask images in the app/masks folder.
handles=LoadMaskList(handles);
% Now let's make sure that the one we just saved is the selected one.
% First get the complete list of all mask file names listed, whether selected or not.
ListOfImageNames = get(handles.lstMasks, 'string');
numberOfMasks = length(ListOfImageNames);
for maskNumber = 2:numberOfMasks
% Get the mask file name
maskName = strcat(cell2mat(ListOfImageNames(maskNumber)));
if strcmpi(maskName, [baseFileName '.mat'])
set(handles.lstMasks, 'value', maskNumber); % Select first entry
break; % Skip the rest of the loop since we found it.
end
end
end
guidata(hObject, handles);
return;
%=====================================================================
% --- Executes during object creation, after setting all properties.
% EVEN THOUGH THIS FUNCTION IS EMPTY, DON'T DELETE IT OR ERRORS WILL OCCUR
function axesPlot_CreateFcn(hObject, eventdata, handles)
% hObject handle to axesPlot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: place code in OpeningFcn to populate axesPlot
%=====================================================================
% --- Executes during object creation, after setting all properties.
% EVEN THOUGH THIS FUNCTION IS EMPTY, DON'T DELETE IT OR ERRORS WILL OCCUR
function axesImage_CreateFcn(hObject, eventdata, handles)
% hObject handle to axesImage (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: place code in OpeningFcn to populate axesImage
%=====================================================================
% --- Executes during object creation, after setting all properties.
% EVEN THOUGH THIS FUNCTION IS EMPTY, DON'T DELETE IT OR ERRORS WILL OCCUR
function figMainWindow_CreateFcn(hObject, eventdata, handles)
% hObject handle to figMainWindow (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
%=====================================================================
% --- Executes on mouse press over axes background.
function axesImage_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to axesImage (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% IMNPORTANT NOTE: handles is not available for some strange reason
% when we get here as a result of clicking on the image.
% That's why we use "global" and not handles or getappdata (which also requires handles).
fprintf(1, 'Just entered axesImage_ButtonDownFcn...\n');
global baseImageFileName;
if length(baseImageFileName) < 4
return;
end
% Retrieve the image folder, which was stored with the image object
% when it was displayed with DisplayImage().
imageFolder = getappdata(hObject, 'imageFolder');
fullFileName = [imageFolder '/' baseImageFileName];
if exist(fullFileName, 'file')
hEnlargedImage = figure(1); % Bring up a new window.
hImage = imshow(fullFileName);
% Make the figure fill up most of the screen.
w = 0.96;
h = 0.85;
pos = [(1-w)/2, (1-h)/2, w, h]; % [left, bottom, width, height]
% Apply to the GUI.
set(hEnlargedImage, 'Units', 'Normalized');
set(hEnlargedImage, 'Position', pos);
% disp(get(hImage,'Type'));
% disp(get(hEnlargedImage,'Type'));
% maximize(hEnlargedImage);
else
errorMessage = sprintf('The file does not exist:\n%s', fullFileName);
WarnUser(errorMessage);
end
fprintf(1, 'Leaving axesImage_ButtonDownFcn.\n');
return; % from axesImage_ButtonDownFcn
%=====================================================================
% --- Executes on button press in btnDeleteMask.
function btnDeleteMask_Callback(hObject, eventdata, handles)
% hObject handle to btnDeleteMask (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get the index of the entry they've selected.
Selected = get(handles.lstMasks, 'value');
if Selected == 1
% They have selected the top entry: "Do not use a mask"
% If so, just return.
msgboxw('You must select a mask file first.');
return;
end
% Get the complete list of all mask image names listed,
% whether selected or not.
ListOfImageNames = get(handles.lstMasks, 'string');
% Get the mask image name
baseFileName = strcat(cell2mat(ListOfImageNames(Selected)));
reply = questdlg({'Do you want to send this mask to the recycle bin?', handles.maskFolder, baseFileName},'Delete mask?', 'Yes','No', 'Yes');
% reply = '' for Upper right X, 'Yes' for Yes, 'No' for No.
if strcmp(reply, 'Yes')
% Erase any existing, displayed mask.
ClearLinesFromAxes(handles.axesImage);
maskFullFileName = fullfile(handles.maskFolder, baseFileName);
recycle('on')
delete(maskFullFileName)
% Refresh the listbox of mask filenames.
% Load list of mask images in the app/masks folder.
% QUIRK: need to set the selected index to something less than the
% index at the end of the list otherwise you get an error.
set(handles.lstMasks, 'value', 1); % Select first entry
handles=LoadMaskList(handles);
end
guidata(hObject, handles);
return;
%=====================================================================
% --- Executes on button press in btnExit.
function btnExit_Callback(hObject, eventdata, handles)
% hObject handle to btnExit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
try
fprintf(1, 'Just entered btnExit_Callback...\n');
% Get rid of variables from the global workspace so that they aren't
% hanging around the next time we try to run this m-file.
clear global;
% Cause it to shutdown.
delete(handles.figMainWindow);
fprintf(1, 'Leaving btnExit_Callback.\n');
catch ME
errorMessage = sprintf('Error in function btnExit_Callback.\nError Message:\n%s', ME.message);
WarnUser(errorMessage);
end
% --- Executes on button press in chkAutoAnalyze.
function chkAutoAnalyze_Callback(hObject, eventdata, handles)
% hObject handle to chkAutoAnalyze (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of chkAutoAnalyze
checkboxState = get(hObject,'Value');
if checkboxState
set(handles.txtInfo, 'string', 'Now the image will be analyzed as soon as it is selected.');
else
set(handles.txtInfo, 'string', 'Now the image(s) will be analyzed only when the Analyze button is clicked.');
end
% --- Executes on button press in btnMoveMask.
% Demonstrates how to call a modal dialog box and pass arguments to it and receive output variables
% back from it.
function btnMoveMask_Callback(hObject, eventdata, handles)
% hObject handle to btnMoveMask (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
Selected = get(handles.lstMasks, 'value');
if Selected == 1
% They have selected the top entry: "Do not use a mask"
% If so, just return.
msgboxw('You must select a mask file first.');
return;
end
global imgOriginal;
global maskVerticesXCoordinates;
global maskVerticesYCoordinates;
[newMaskVerticesXCoordinates newMaskVerticesYCoordinates] = MoveMask(imgOriginal, maskVerticesXCoordinates, maskVerticesYCoordinates);
maskVerticesXCoordinates = newMaskVerticesXCoordinates;
maskVerticesYCoordinates = newMaskVerticesYCoordinates;
% Delete old plot.
%axes(handles.axesImage);
h = findobj(handles.axesImage,'Type','line');
if ~isempty(h)
delete (h);
end
% Plot the new mask over the image.
plot(maskVerticesXCoordinates, maskVerticesYCoordinates, 'linewidth', 2);
return;
%=====================================================================
% Process image
% You can replace this contents of this function with whatever you want.
% Just delete it all and put your own code in here.
% For this simple tutorial, I simply thresholded the image (green band if it's a color image)
% according to MATLAB'S autothresholding method and got a distribution of blob sizes and plotted
% them.
function [resultsArray] = AnalyzeSingleImage(handles, maskedImage, binaryMask)
try
% Get the text in the edit text box. (We don't do anything with it though - it's just for demo.)
editTextContents = get(handles.edtEditText, 'String');
editTextContents = editTextContents{:}; % Convert from cell array to string.
fprintf(1, '%s\n', editTextContents);
set(handles.txtInfo, 'String', editTextContents);
resultsArray = zeros(1, 7); % Initialize to make sure that something will always be returned.
if length(size(maskedImage)) == 3
% It's a color image. Take the green band.
originalImage = maskedImage(:, :, 2);
else
% It's a monochrome image.
originalImage = maskedImage;
end
% Extract out all the pixels within the masked area so we can threshold the area within the mask.
% The result will be a column vector, but we can still use it in graythresh().
if isempty(binaryMask)
% They want to use masking.
pixelsInsideMask = uint8(maskedImage(binaryMask)); % Gives a column vector.
else
% They commented out the masking code.
pixelsInsideMask = uint8(maskedImage(:)); % Gives a column vector.
end
thresholdLevel = graythresh(pixelsInsideMask) * 255; % Find threshold according to Otsu's method.
binaryImage = (originalImage >= thresholdLevel); % Threshold to binary (a logical image)
labeledImage = bwlabel(binaryImage, 8); % Label each blob so can do calc on it
% Show colored blobs just for fun.
coloredLabels = label2rgb (labeledImage, 'hsv', 'k', 'shuffle'); % pseudo random color labels
imshow(coloredLabels);
drawnow; % Force an immediate update of the GUI.
% Make the measurements
blobMeasurements = regionprops(labeledImage, 'Area', 'Perimeter', 'PixelIdxList', 'Centroid'); % Get the blob properties of 'Area' and 'Perimeter'
numberOfBlobs = size(blobMeasurements, 1);
% bwboundaries returns a cell array, where each cell
% contains the row/column coordinates for an object in the image.
% Plot the borders of all the coins on the original
% grayscale image using the coordinates returned by bwboundaries.
hold on;
boundaries = bwboundaries(binaryImage);
for k = 1 : numberOfBlobs
thisBoundary = boundaries{k};
plot(thisBoundary(:,2), thisBoundary(:,1), 'g', 'LineWidth', 2);
end
hold off;
if numberOfBlobs > 1
resultsArray = zeros(numberOfBlobs, 7); % Pre-allocate space.
end
for blobNumber = 1 : numberOfBlobs % Loop through all blobs.
% Find the mean of each blob. (R2008a has a better way where you can pass the original image
% directly into regionprops. The way below works for all versions including earlier versions.)
thisBlobsPixels = blobMeasurements(blobNumber).PixelIdxList; % Get list of pixels in current blob.
meanGL = mean(originalImage(thisBlobsPixels)); % Find mean intensity (in original image!)
blobArea = blobMeasurements(blobNumber).Area; % Get area.
blobPerimeter = blobMeasurements(blobNumber).Perimeter; % Get perimeter.
blobCentroid = blobMeasurements(blobNumber).Centroid; % Get centroid.
% Calculate the equivalent circular diameter - the diameter the blob would have it if were perfectly circular with the same area.
blobECD = sqrt(4.0 * blobArea / pi);
resultsArray(blobNumber, 1) = blobNumber;
resultsArray(blobNumber, 2) = blobArea;
resultsArray(blobNumber, 3) = meanGL;
resultsArray(blobNumber, 4) = blobPerimeter;
resultsArray(blobNumber, 5) = blobCentroid(1); % X coordinate.
resultsArray(blobNumber, 6) = blobCentroid(2); % Y coordinate.
resultsArray(blobNumber, 7) = blobECD; % Equivalent Circular Diameter
end
% Set up the column headers.
set(handles.uitable1, 'ColumnName', {'Blob #', 'Blob Area', 'Mean GL', 'Perimeter', 'Centroid X', 'Centroid Y', 'ECD'});
% Stick the data ( a 2D numerical array) into the table.
set(handles.uitable1, 'data', resultsArray);
drawnow; % Force an immediate update of the GUI.
% Read the radio button and sort according to what's selected.
if get(handles.radOption1, 'value')
indexToSortBy = -2;
set(handles.pnlResults, 'title', 'Results sorted by area');
elseif get(handles.radOption2, 'value')
indexToSortBy = -3;
set(handles.pnlResults, 'title', 'Results sorted by intensity');
else
indexToSortBy = -7;
set(handles.pnlResults, 'title', 'Results sorted by ECD');
end
% Sort the array from largest blobArea to smallest blobArea (index #2).
sortedResults = sortrows(resultsArray, indexToSortBy);
% Put back the blob number in there (it got messed up during sorting).
sortedResults(:, 1) = 1:numberOfBlobs;
fprintf(1,'Blob #, Area, Mean GL, Perimeter, CentroidX, CentroidY, ECD\n');
txtInfo = sprintf('Blob # Area Mean GL Perimeter CentroidX CentroidY ECD\n');
for blobNumber = 1 : numberOfBlobs % Loop through all blobs.
% Print the values out to the command window.
fprintf(1,'#%d %5.1f %11.1f %8.1f %8.1f %8.1f %8.1f\n', blobNumber, sortedResults(blobNumber, 2), sortedResults(blobNumber, 3), sortedResults(blobNumber, 4), sortedResults(blobNumber, 5), sortedResults(blobNumber, 6), sortedResults(blobNumber, 7));
txtInfo = sprintf('%s#%d %5.1f %11.1f %8.1f %8.1f %8.1f %8.1f\n', txtInfo, blobNumber, sortedResults(blobNumber, 2), sortedResults(blobNumber, 3), sortedResults(blobNumber, 4), sortedResults(blobNumber, 5), sortedResults(blobNumber, 6), sortedResults(blobNumber, 7));
end
set(handles.txtInfo, 'string', txtInfo);
% Get a histogram of the blob ECD's within the masked area, and plot it.
listOfECDs = sortedResults(:, 7);
[PixelCounts, GLs] = PlotHistogram(handles, listOfECDs);
catch ME
% Some error happened if you get here.
strErrorMessage = sprintf('Error in function mnuToolsSaveScreenshot_Callback\n\nError message: %s', ME.message);
WarnUser(strErrorMessage);
end
return; % AnalyzeSingleImage
%=====================================================================
% Takes histogram of 1-D array blobSizeArray, and plots it.
function [blobCounts, areaValues] = PlotHistogram(handles, blobSizeArray)
% Get a histogram of the blobSizeArray and display it in the histogram viewport.
numberOfBins = min([100 length(blobSizeArray)]);
[blobCounts, areaValues] = hist(blobSizeArray, numberOfBins);
% Plot the number of blobs with a certain area versus that area.
axes(handles.axesPlot);
bar(areaValues, blobCounts);
title('Histogram of Blob Sizes');
return;
%=====================================================================
function CenterFigure(handles)
% The figure Position property
% does not include the window borders, so this example uses a width of 5 pixels
% on the sides and bottom and 30 pixels on the top.
borderWidth = 5;
titleBarWidth = 30;
% Ensure root units are pixels and get the size of the screen:
set(0, 'Units', 'pixels');
set(handles.figMainWindow, 'Units', 'pixels');
% Get the screen size in pixels.
screenSize = get(0,'ScreenSize');
% Get the size of the window.
initialFigurePosition = get(handles.figMainWindow, 'Position');
% Create an array that will center it.
centeredX = (screenSize(3) - initialFigurePosition(3)) / 2;
centeredY = (screenSize(4) - initialFigurePosition(4)) / 2;
centeredPosition = [centeredX,...
centeredY,...
initialFigurePosition(3),...
initialFigurePosition(4)];
set(handles.figMainWindow, 'Position', centeredPosition);
return; % from CenterFigure()
% --- Executes when selected object is changed in grpRadButtonGroup.
function grpRadButtonGroup_SelectionChangeFcn(hObject, eventdata, handles)
% hObject handle to the selected object in grpRadButtonGroup
% eventdata structure with the following fields (see UIBUTTONGROUP)
% EventName: string 'SelectionChanged' (read only)
% OldValue: handle of the previously selected object or empty if none was selected
% NewValue: handle of the currently selected object
% handles structure with handles and user data (see GUIDATA)
switch get(eventdata.NewValue,'Tag') % Get Tag of selected object.
case 'radOption1'
% Code for when radiobutton1 is selected.
txtInfo = sprintf('Option 1 is selected and the others are deselected.\n\nResults will be sorted in order of decreasing area.');
set(handles.pnlResults, 'title', 'Results sorted by area');
case 'radOption2'
% Code for when radiobutton2 is selected.
txtInfo = sprintf('Option 2 is selected and the others are deselected.\n\nResults will be sorted in order of decreasing intensity.');
set(handles.pnlResults, 'title', 'Results sorted by intensity');
case 'radOption3'
% Code for when togglebutton1 is selected.
txtInfo = sprintf('Option 3 is selected and the others are deselected.\n\nResults will be sorted in order of decreasing ECD.');
set(handles.pnlResults, 'title', 'Results sorted by ECD');
% case 'togglebutton2'
% Code for when togglebutton2 is selected.
% Continue with more cases as necessary.
otherwise
% Code for when there is no match.
end
set(handles.txtInfo, 'String', txtInfo);
return; % from grpRadButtonGroup_SelectionChangeFcn
%=============================================================================================
% --- Executes on slider movement.
function sldHorizontalScrollbar_Callback(hObject, eventdata, handles)
% hObject handle to sldHorizontalScrollbar (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
scrollbarValue = get(hObject,'Value');
caption = sprintf('H value = %.2f', scrollbarValue);
set(handles.txtHScrollbar, 'string', caption);
%=============================================================================================
% --- Executes during object creation, after setting all properties.
function sldHorizontalScrollbar_CreateFcn(hObject, eventdata, handles)
% hObject handle to sldHorizontalScrollbar (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor',[.9 .9 .9]);
end
%=============================================================================================
% --- Executes on slider movement.
function sldVerticalScrollbar_Callback(hObject, eventdata, handles)
% hObject handle to sldVerticalScrollbar (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
scrollbarValue = get(hObject,'Value');
caption = sprintf('V value = %.2f', scrollbarValue);
set(handles.txtVScrollbar, 'string', caption);
%=============================================================================================
% --- Executes during object creation, after setting all properties.
function sldVerticalScrollbar_CreateFcn(hObject, eventdata, handles)
% hObject handle to sldVerticalScrollbar (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor',[.9 .9 .9]);
end
%=============================================================================================
% --- Executes on mouse motion over figure - except title and menu.
function figMainWindow_WindowButtonMotionFcn(hObject, eventdata, handles)
% hObject handle to figMainWindow (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%=============================================================================================
function edtEditText_Callback(hObject, eventdata, handles)
% hObject handle to edtEditText (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edtEditText as text
% str2double(get(hObject,'String')) returns contents of edtEditText as a double
%=============================================================================================
% --- Executes during object creation, after setting all properties.
function edtEditText_CreateFcn(hObject, eventdata, handles)
% hObject handle to edtEditText (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%=============================================================================================
function mnuToolsSaveScreenshot_Callback(hObject, eventdata, handles)
% hObject handle to mnuToolsSaveScreenshot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% IMPORTANT NOTE: YOU MUST HAVE DOWNLOADED import_fig()
% FROM THE FILE EXCHANGE FOR THIS FUNCTION TO WORK.
try
% Save the figure
% Have user browse for a file, from a specified "starting folder."
% For convenience in browsing, set a starting folder from which to browse.
startingFolder = 'C:\Program Files\MATLAB';
if ~exist(startingFolder, 'dir')
% If that folder doesn't exist, just start in the current folder.
startingFolder = pwd;
end
% Get the name of the color image file that the user wants to save this figure into.
defaultFileName = fullfile(startingFolder, 'MAGIC_Screenshot.png');
[baseFileName, folder] = uiputfile(defaultFileName, 'Specify a file for your screenshot');
if baseFileName == 0
% User clicked the Cancel button.
return;
end
screenshotFileName = fullfile(folder, baseFileName);
% Display a message on the UI.
txtInfo = sprintf('Please wait...\nSaving screenshot as\n%s', screenshotFileName);
set(handles.txtInfo, 'String', txtInfo);
% CALL export_fig, WHICH YOU MUST HAVE DOWNLOADED.
export_fig(screenshotFileName);
message = sprintf('Screenshot saved as:\n%s', screenshotFileName);
set(handles.txtInfo, 'String', message);
msgboxw(message);
catch ME
% Some error happened if you get here.
strErrorMessage = sprintf('Error in function mnuToolsSaveScreenshot_Callback\n\nError message: %s', ME.message);
WarnUser(strErrorMessage);
WarnUser('Are you sure you downloaded export_fig, and it is on the search path?');
end
return; % from mnuToolsSaveScreenshot_Callback
%=============================================================================================
function mnuToolsMontage_Callback(hObject, eventdata, handles)
% hObject handle to mnuToolsMontage (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
try
% Change mouse pointer (cursor) to an hourglass.
% QUIRK: use 'watch' and you'll actually get an hourglass not a watch.
set(gcf,'Pointer','watch');
% Get a list of all the filenames.
ListOfImageNames = get(handles.lstImageList, 'string');
% Get a list of what files they selected.
selectedItems = get(handles.lstImageList, 'value');
% If none are selected, use them all.
numberOfSelectedImages = length(selectedItems);
if numberOfSelectedImages <= 1
numberOfSelectedImages = length(ListOfImageNames);
selectedItems = 1 : numberOfSelectedImages;
end
caption = sprintf('Please wait...Constructing montage of %d images...', numberOfSelectedImages);
title(caption, 'FontSize', 14);
set(handles.txtInfo, 'string', caption);
drawnow; % Cursor won't change right away unless you do this.
% Get a list of the selected files only.
% Warning: This will not include folders so we will have to prepend the folder.
ListOfImageNames = ListOfImageNames(selectedItems);
for k = 1 : numberOfSelectedImages % Loop though all selected indexes.
% Get the filename for this selected index.
baseImageFileName = cell2mat(ListOfImageNames(k));
imageFullFileName = fullfile(handles.ImageFolder, baseImageFileName);
ListOfImageNames{k} = imageFullFileName;
end
% Figure out how many rows and there should be.
% There is twice as much space horizontally as vertically so solve the equation 2*rows^2 = numberOfImages.
rows = ceil(sqrt(numberOfSelectedImages/2));
columns = 2 * rows;
axes(handles.axesImage);
cla(handles.axesImage, 'reset');
handleToImage = handles.axesImage;
hMontage = montage(ListOfImageNames, 'size', [rows columns]);
caption = sprintf('Displaying a montage of %d images.', numberOfSelectedImages);
title(caption, 'FontSize', 20);
set(handles.txtInfo, 'string', caption);
catch ME
errorMessage = sprintf('Error in function mnuToolsMontage_Callback.\nError Message:\n%s', ME.message);
set(handles.txtInfo, 'string', errorMessage);
LoadSplashImage(handles, handles.axesImage);
WarnUser(errorMessage);
end
% Change mouse pointer (cursor) to an arrow.
set(gcf,'Pointer','arrow');
drawnow; % Cursor won't change right away unless you do this.
return; % from mnuToolsMontage_Callback
%=====================================================================
% Plots the histogram of grayImage in axes axesImage
% If grayImage is a double, it must be normalized between 0 and 1.
function [minGL maxGL ] = PlotImageHistogram(handles, imageArray)
try
numberOfDimensions = ndims(imageArray);
if numberOfDimensions == 1 || numberOfDimensions == 2
% Grayscale 2D or 1D image.
PlotGrayscaleHistogram(handles, imageArray)
elseif numberOfDimensions == 3
% True color RGB image.
PlotRGBHistograms(handles, imageArray);
else
warningMessage = sprintf('Histograms are only supported for grayscale (2D) or color (3D) images');
WarnUser(warningMessage);
end
catch ME
errorMessage = sprintf('Error in function PlotImageHistogram.\nError Message:\n%s', ME.message);
WarnUser(errorMessage);
end
return; % PlotImageHistogram
%=====================================================================
% Plots the histogram of grayImage in axes axesImage
% If grayImage is a double, it must be normalized between 0 and 1.
function [minGL maxGL] = PlotGrayscaleHistogram(handles, grayImage)
try
% Plot the histogram in the histogram viewport.
% Make the plot visible.
SetImageVisibility(handles, handles.axesPlot, 1);
axes(handles.axesPlot); % makes existing axes handles.axesPlot the current axes.
% Get the histogram
[pixelCounts, grayLevels] = imhist(grayImage);
% Plot it.
bar(pixelCounts);
title('Histogram of Gray Image', 'FontSize', 12);
grid on;
% Get the min and max GL for fun.
minGL = min(grayImage(:));
maxGL = max(grayImage(:));
% Set up the x axis of the histogram to go from 0 to the max value allowed for this type of integer (uint8 or uint16).
theClass = class(grayImage);
% Only set xlim for integers. For example the demo image blobs.png is logical not integer even though it's grayscale.
if strfind(theClass, 'int')
xlim([0 intmax(theClass)]);
end
catch ME
errorMessage = sprintf('Error in function PlotGrayscaleHistogram.\nError Message:\n%s', ME.message);
WarnUser(errorMessage);
end
return; % PlotGrayscaleHistogram
%=====================================================================
% Plots the histogram of imgColorImageArray in axes axesImage
% If imgArray is a double, it must be normalized between 0 and 1.
function [minGL maxGL gl1Percentile gl99Percentile] = PlotRGBHistograms(handles, imgColorImageArray)
try
% Get a histogram of the entire image. But imhist only allows 2D images, not color ones.
% First get individual channels from the original image.
redBand = imgColorImageArray(:,:,1);
greenBand = imgColorImageArray(:,:,2);
blueBand = imgColorImageArray(:,:,3);
% Use 256 bins.
[redCounts, redGLs] = imhist(redBand, 256); % make sure you label the axes after imhist because imhist will destroy them.
[greenCounts, greenGLs] = imhist(greenBand, 256); % make sure you label the axes after imhist because imhist will destroy them.
[blueCounts, blueGLs] = imhist(blueBand, 256); % make sure you label the axes after imhist because imhist will destroy them.
% GLs goes from 0 (at element 1) to 255 (at element 256) but only some
% these bins have data in them. The upper ones may be 0. Find the last
% non-zero bin so we can plot just up to there to get better horizontal resolution.
maxBinUsedR = find(redCounts, 1, 'last' );
maxBinUsedG = find(greenCounts, 1, 'last' );
maxBinUsedB = find(blueCounts, 1, 'last' );
% If the entire image is zero, have the max bin be 0.
if isempty(maxBinUsedR); maxBinUsedR = 1; end;
if isempty(maxBinUsedG); maxBinUsedG = 1; end;
if isempty(maxBinUsedB); maxBinUsedB = 1; end;
% Take the largest one overall for plotting them all.
maxBinUsed = max([maxBinUsedR maxBinUsedG maxBinUsedB]);
% Get subportion of array that has non-zero data.
redCounts = redCounts(1:maxBinUsed);
greenCounts = greenCounts(1:maxBinUsed);
blueCounts = blueCounts(1:maxBinUsed);
GLs = redGLs(1:maxBinUsed);
% Because of the mask, the first bin will have a ton of zeros in it and count(1) will be sky
% high. Zero out this bin so we aren't getting the histogram of the mask.
redCounts(1) = 0;
greenCounts(1) = 0;
blueCounts(1) = 0;
% Assign the max and min for the 3 color bands.
minGL(1) = GLs(maxBinUsedR);
maxGL(2) = GLs(maxBinUsedG);
maxGL(3) = GLs(maxBinUsedB);
% Calculate the 1% and 99% value of the CDF for the 3 color bands.
gl1Percentile = ones(3, 1); % Preallocate one element for each color.
gl99Percentile = ones(3, 1); % Preallocate one element for each color.
for color = 1:3
switch color
case 1
counts = redCounts;
case 2
counts = greenCounts;
case 3
counts = blueCounts;
end
summed = sum(counts);
cdf = 0;
for bin = 1 : maxBinUsed
cdf = cdf + counts(bin);
if cdf < 0.01 * summed
gl1Percentile(color) = GLs(bin);
end
if cdf > 0.99 * summed
break;
end
end
gl99Percentile(color) = GLs(bin);
end
% Plot the histogram in the histogram viewport.
% Make the plot visible.
SetImageVisibility(handles, handles.axesPlot, 1);
axes(handles.axesPlot); % makes existing axes handles.axesPlot the current axes.
% Plot the histogram as a line curve.
plot(GLs, blueCounts, 'b', 'LineWidth', 3);
hold on;
plot(GLs, greenCounts, 'g', 'LineWidth', 3);
plot(GLs, redCounts, 'r', 'LineWidth', 3);
grid on;
title('Red, Green, and Blue Histograms');
maxCountInHistogram = max([redCounts(:); greenCounts(:); blueCounts(:)]);
set(handles.axesPlot,'YLim',[0 maxCountInHistogram]);
% Plot the sum of all of them
% sumCounts = redCounts + greenCounts + blueCounts;
% plot(GLs, sumCounts, 'k', 'LineWidth', 1); % Plot sum in black color.
% set(handles.axesPlot,'YLim',[0 max(sumCounts)]);
set(handles.axesPlot,'XTick', [0 20 40 60 80 100 120 140 160 180 200 220 240 255]);
set(handles.axesPlot,'XTickLabel', {0 20 40 60 80 100 120 140 160 180 200 220 240 255});
set(get(handles.axesPlot,'XLabel'),'string','Gray Level');
ylabel('# of Pixels');
xlim([0 255]);
hold off;
axes(handles.axesImage); % Switch current figure back to image box.
catch ME
errorMessage = sprintf('Error in function PlotRGBHistograms.\nError Message:\n%s', ME.message);
WarnUser(errorMessage);
end
return; % PlotRGBHistograms
%=============================================================================================
function mnuTools_Callback(hObject, eventdata, handles)
% hObject handle to mnuTools (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%=============================================================================================
% Pops up a message box and waits for the user to click OK.
function msgboxw(in_strMessage)
uiwait(msgbox(in_strMessage));
return;
%==========================================================================================================================
% Warn user via the command window and a popup message.
function WarnUser(warningMessage)
fprintf(1, '%s\n', warningMessage);
uiwait(warndlg(warningMessage));
return; % from WarnUser()
% --- Executes on button press in chkPlotHistograms.
function chkPlotHistograms_Callback(hObject, eventdata, handles)
% hObject handle to chkPlotHistograms (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of chkPlotHistograms
