How to make it not to go dark?

I use the below function:

function SliderDemo
clc
clear all

NumFrames = 15; %// Check below for dummy 4D matrix/image sequence
hFig = figure('Position',[100 100 500 500],'Units','normalized');

handles.axes1 = axes('Units','normalized','Position',[.2 .2 .6 .6]);

%// Create slider and listener object for smooth visualization
handles.SliderFrame = uicontrol('Style','slider','Position',[60 20 400 50],'Min',1,'Max',NumFrames,'Value',1,'SliderStep',[1/NumFrames 2/NumFrames],'Callback',@XSliderCallback);
handles.SliderxListener = addlistener(handles.SliderFrame,'Value','PostSet',@XListenerCallBack);

handles.Text1 = uicontrol('Style','Text','Position',[180 420 60 30],'String','Current frame');
handles.Edit1 = uicontrol('Style','Edit','Position',[250 420 100 30],'String','1');

%// Create dummy image sequence, here 4D sequence of grayscale images.
Img = DicomReader('S0000009.dcm')
isoImage = makeImIsoRGB(Img, [1,1,15], 1.5, 'cubic')

MyImage = isoImage;

MyMatrix = MyImage;

%// Use setappdata to store the image stack and in callbacks, use getappdata to retrieve it and use it. Check the docs for the calling syntax.

setappdata(hFig,'MyMatrix',MyMatrix); %// You could use %//setappdata(0,'MyMatrix',MyMatrix) to store in the base workspace. 

%// Display 1st frame
imshow(MyMatrix(:,:,1))

%// IMPORTANT. Update handles structure.
guidata(hFig,handles);

%// Listener callback, executed when you drag the slider.

      function XListenerCallBack

          %// Retrieve handles structure. Used to let MATLAB recognize the
          %// edit box, slider and all UI components.
          handles = guidata(gcf);

%// Here retrieve MyMatrix using getappdata.
MyMatrix = getappdata(hFig,'MyMatrix');

          %// Get current frame
          CurrentFrame = round((get(handles.SliderFrame,'Value')));
          set(handles.Edit1,'String',num2str(CurrentFrame));

          %// Display appropriate frame.
          imshow(MyMatrix(:,:,CurrentFrame),'Parent',handles.axes1);

          guidata(hFig,handles);
      end

%// Slider callback; executed when the slider is release or you press
%// the arrows.
    function XSliderCallback(~,~)

          handles = guidata(gcf);

%// Here retrieve MyMatrix using getappdata.
    MyMatrix = getappdata(hFig,'MyMatrix');

          CurrentFrame = round((get(handles.SliderFrame,'Value')));
          set(handles.Edit1,'String',num2str(CurrentFrame));

          imshow(MyMatrix(:,:,CurrentFrame),'Parent',handles.axes1);

          guidata(hFig,handles);
      end

end

Although, it perfectly operates, still from Frame 1 to 15 (which is the last frame), only the first and the last frames are visible. In among the transition of the frames (2-14) they appear black/ dark, like they fade and come back again at the final frame.

Where is the wrong part? How to make it appear normal throughout the transition of all frames?

[Rik]

Are you sure it is not the matrix itself that goes dark? I see no indication in this code why that would happen. I can't check, because makeImIsoRGB is not a function I know, so I don't know if that could contain a bug.

[Stelios Fanourakis]

No Rik, makeImIsoRGB is a made function for making the stack of images isotropic via interp3 interpolation. I have checked it. It's not the one that makes images go black.

[Stelios Fanourakis]

Now I get that error "Warning: Error executing listener callback for PostSet event on Value dynamic property in object of matlab.ui.control.UIControl class:"Error using SliderDemo/XListenerCallBack Too many input arguments. >> "

[Jan]

by the way: A clear all on top of a function is a waste of time only. Beside deleting many useful things like loaded functions and persistent variables, clear all cleans up the current workspace. But this is empty on top of a function. Therefore clear all is "cargo cult programming".

It needs a lot of time to reload the M-files from the slow hard disk after a clear all. This can costs seconds.

We cannot run your code. Therefore it is impossible for us to debug it. But it is easy for you. Simply set some breakpoints to find out, where the observed effect happens.

It is much more efficient to run imshow once only and update the cdata afterwards.

You use a nested function and share the data using guidata. This is an overkill. One of the both methods is sufficient.

But most of all consider Rik's comment: The code does not contain command, which modify a color. This means, that the source of a color change must be somewhere else in code, you did not show.

Answer 1

[Image Analyst]

Use [] in imshow:

imshow(yourImage, []);

[Stelios Fanourakis]

It's not the solution.

Answer 2

[Stelios Fanourakis]

function varargout = testImageSlider(varargin)
% TESTIMAGESLIDER MATLAB code for testImageSlider.fig
%      TESTIMAGESLIDER, by itself, creates a new TESTIMAGESLIDER or raises the existing
%      singleton*.
%
%      H = TESTIMAGESLIDER returns the handle to a new TESTIMAGESLIDER or the handle to
%      the existing singleton*.
%
%      TESTIMAGESLIDER('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in TESTIMAGESLIDER.M with the given input arguments.
%
%      TESTIMAGESLIDER('Property','Value',...) creates a new TESTIMAGESLIDER or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before testImageSlider_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to testImageSlider_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 testImageSlider

% Last Modified by GUIDE v2.5 21-Feb-2012 15:13:08

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @testImageSlider_OpeningFcn, ...
                   'gui_OutputFcn',  @testImageSlider_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 testImageSlider is made visible.
function testImageSlider_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 testImageSlider (see VARARGIN)

% Choose default command line output for testImageSlider
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes testImageSlider wait for user response (see UIRESUME)
% uiwait(handles.figure1);

% --- Outputs from this function are returned to the command line.
function varargout = testImageSlider_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)

% Get default command line output from handles structure
varargout{1} = handles.output;

function numImages_Callback(hObject, eventdata, handles)
% hObject    handle to numImages (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 numImages as text
%        str2double(get(hObject,'String')) returns contents of numImages as a double

updateSlider(handles);

function updateSlider(handles)
% This function updates the slider to have the correct min, max, value, and
%   step size

%get the current slice number which were stored in the figure axes
sliceNum = getappdata(handles.imageAxes,'sliceNum');
if(isempty(sliceNum))%may be empty if the figure has not been initialized
    sliceNum = 1;    %set it to a default
end

%get the number written in the text box which is the maximum number of
%images to be viewed
NumImageslice = str2double(get(handles.numImages,'String'));
%there are only NumImageslice - 1 images total, because we start at 1
step = 1/(NumImageslice - 1);

%set values for the slider bar
set(handles.imageSlider, 'Max',        NumImageslice);
set(handles.imageSlider, 'Min',        1);
set(handles.imageSlider, 'SliderStep', [0 1]);

%set current value to the slice we are viewing
set(handles.imageSlider, 'Value', sliceNum);

% --- Executes during object creation, after setting all properties.
function numImages_CreateFcn(hObject, eventdata, handles)
% hObject    handle to numImages (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

% --- Executes on slider movement.
function imageSlider_Callback(hObject, eventdata, handles)
% hObject    handle to imageSlider (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

%get the current value on the slider
imageSlider_value = get(hObject,'Value');

%get the current max value from the slider
numImages = get(handles.imageSlider, 'Max');

%calculate the image number to display
imageNum = floor(imageSlider_value)...
         + (sign(imageSlider_value)...
         * ( abs(imageSlider_value) - floor(imageSlider_value) )...
         * numImages);

%create a string from the number which always has 2 digits
str = sprintf('%02.0f',imageNum);

%retrieve filename data from app data
ptNum    = getappdata(handles.imageAxes, 'ptNum');
imageType = getappdata(handles.imageAxes, 'imageType');
filepath = getappdata(handles.imageAxes, 'filePath');

%create the filename as a cell string
filename = strcat(ptNum, '.', str, '.', imageType);

%create full path to the image
imageStr = (filename{1});

%read in image data
image = dicomread(imageStr);

%bring current axes in focus and show image
axes(handles.imageAxes);
imshow(image, []); %[] = [Imin Imax]

%store image data and slice number in axes
setappdata(handles.imageAxes, 'image',     image);
setappdata(handles.imageAxes, 'sliceNum',  imageSlider_value);

% --- Executes during object creation, after setting all properties.
function imageSlider_CreateFcn(hObject, eventdata, handles)
% hObject    handle to imageSlider (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 button press in loadImage.
function loadImage_Callback(hObject, eventdata, handles)
% hObject    handle to loadImage (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global image

%intercatively choose an image to display
[fileName, isCancelled] = imgetfile();
image = DicomReader(fileName)
image = makeImIsoRGB(image, [1,1,15], 2.1, 'cubic')

%scan the filename and parse the data int a cell string array, C 
C = textscan(fileName, '%s %d %s', 'delimiter', '.');

%bring axes into focus anf show image
axes(handles.imageAxes);
imshow(image(:), []); %[] = [Imin Imax]

%store relevant data in the axes
setappdata(handles.imageAxes, 'fileName',  fileName);
setappdata(handles.imageAxes, 'image',     image);
setappdata(handles.imageAxes, 'ptNum',     C{1});
setappdata(handles.imageAxes, 'sliceNum',  C{2});
setappdata(handles.imageAxes, 'imageType', C{3});

%update slider
updateSlider(handles);

This code gives me the errors "Index exceeds matrix dimensions.

Error in testImageSlider>imageSlider_Callback (line 157) imageStr = (filename{1});" and " Warning: 'slider' control cannot have a 'Value' outside of 'Min'-'Max' range Control will not be rendered until all of its parameter values are valid >> "

Any idea?

[Stelios Fanourakis]

Another code is this:

function displayIm3d(im)
sizeImg = size(im);
minSlice = 1;
maxSlice = size(im(:));
startSlice = round((maxSlice-minSlice)/2);
% Create a figure without toolbar and menubar.
hfig = figure('Toolbar','none',...
'Menubar', 'none',...
'Name','MRI Viewer',...
'NumberTitle','off',...
'IntegerHandle','off');

slider1 = uicontrol(hfig,'Style','slider','Callback',@slider1_Callback);

set(slider1,'value',startSlice); %
set(slider1,'max',maxSlice); %
set(slider1,'min',minSlice); 
slice = get(slider1,'Value'); % returns position of slider
% Display the image in a figure with imshow.
himage = imshow(im(:,:,slice),'DisplayRange',[ ]);
hpixinfo = impixelinfo(himage);
set(himage,'ButtonDownFcn',@pixelInfo)

function slider1_Callback(slider1,eventdata,handles)
% update the displayed image when the slider is adjusted
slice = round(get(slider1,'Value'));
imshow(im(:,:,slice),'DisplayRange',[]);
end

function pixelInfo(cursor,eventdata,handles)
% get coordinates of clicked pixel
[ x, y ] = ginput(1)
end
end

Where I get the error, "Error setting property 'Max' of class 'UIControl': Value must be a scalar.

Error in displayIm3d (line 16) set(slider1,'max',maxSlice); %

Warning: 'slider' control requires a scalar Value. Control will not be rendered until all of its parameter values are valid "

[Stelios Fanourakis]

Finally, I have this code

function varargout = fresh(varargin)
% FRESH MATLAB code for fresh.fig
%      FRESH, by itself, creates a new FRESH or raises the existing
%      singleton*.
%
%      H = FRESH returns the handle to a new FRESH or the handle to
%      the existing singleton*.
%
%      FRESH('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in FRESH.M with the given input arguments.
%
%      FRESH('Property','Value',...) creates a new FRESH or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before fresh_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to fresh_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 fresh

% Last Modified by GUIDE v2.5 17-May-2018 07:07:33

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @fresh_OpeningFcn, ...
                   'gui_OutputFcn',  @fresh_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 fresh is made visible.
function fresh_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 fresh (see VARARGIN)

% Choose default command line output for fresh
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes fresh wait for user response (see UIRESUME)
% uiwait(handles.figure1);

% --- Outputs from this function are returned to the command line.
function varargout = fresh_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)

% Get default command line output from handles structure
varargout{1} = handles.output;

function slider1_Callback(hObject,eventdata, handles)
% test it out - get the handles object and display the current value

global im2 S im3 im4

S = round(get(hObject,'Value'));

set(get(gca,'children'),'cdata',squeeze(im2(:,:,S,:)))
set(get(gca,'children'),'cdata',squeeze(im3(:,:,S,:)))
set(get(gca,'children'),'cdata',squeeze(im4(:,:,S,:)))

% --- Executes during object creation, after setting all properties.
function slider1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider1 (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 during object creation, after setting all properties.
function uipanel4_CreateFcn(hObject, eventdata, handles)
% hObject    handle to uipanel4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% --- Executes during object deletion, before destroying properties.
function uipanel4_DeleteFcn(hObject, eventdata, handles)
% hObject    handle to uipanel4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% --------------------------------------------------------------------
function uipanel4_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to uipanel4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% --- If Enable == 'on', executes on mouse press in 5 pixel border.
% --- Otherwise, executes on mouse press in 5 pixel border or over slider1.
function slider1_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to slider1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% --- Executes during object deletion, before destroying properties.
function slider1_DeleteFcn(hObject, eventdata, handles)
% hObject    handle to slider1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% --- Executes on button press in Load_image.
function Load_image_Callback(hObject, eventdata, handles)
% hObject    handle to Load_image (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global im im2 S sno S_Pos im3 im4

axes(handles.axes1);
[fileName, isCancelled] = imgetfile();

im = DicomReader(fileName)

im2 = makeImIsoRGB(im, [1,1,15], 2.5, 'cubic')

sno = size(im2,3); % number of slices
S = round(sno/2);
sno = size(im2); % image size
sno_a = sno(3); % number of axial slices
S_a = round(sno_a/2);
sno_s = sno(2); % number of sagittal slices
S_s = round(sno_s/2);
sno_c = sno(1); % number of coronal slices
S_c = round(sno_c/2);
S = S_a;
sno = sno_a;

imshow(squeeze(im2(:,:,S,:)))

FigPos = get(gcf,'Position');
S_Pos = [50 70 uint16(FigPos(3)-100)+1 20];

if sno>1
shand = uicontrol('Style', 'slider','Min',1,'Max',sno,'Value',S,'SliderStep',[1/(sno-1) 10/(sno-1)],'Position', S_Pos,'Callback', {@slider1_Callback, im2});

end

set(get(gca,'children'),'cdata',squeeze(im2(:,:,S,:)))
imshow(squeeze(im2(:,:,S,:)))

slice1=floor(size(im2,1)/2);
slice2=floor(size(im2,2)/2);
slice3=floor(size(im2,3)/2);

im3 = permute(im2, [3 1 2 4]);
im4 = permute(im2, [3 2 1 4]);

axes(handles.axes2);

imshow(squeeze(im3(:,:,slice2,:)),'XData',[1 592], 'YData',[1 481]);

axes(handles.axes3);

imshow(squeeze(im4(:,:,slice1,:)),'XData',[1 592], 'YData',[1 481]);

axes(handles.axes4);
vol3d('cdata', squeeze(im2), 'xdata', [0 1], 'ydata', [0 1], 'zdata', [0 0.7]);
colormap(gray);
alphamap([0 linspace(0.1, 0.8, 255)]);
axis equal off
set(gcf, 'color', 'w');
view(3);

Where the slider although created with a uicontrol at axes1. It still keeps working for axes4 where I have the volume rendering. I want to work for all the axes not just for the 4th. Where is my mistake?

[Image Analyst]

Can't really tell. Zip up the m file, fig file, and any data files we'd need to run this and we might give it a try.

[Stelios Fanourakis]

@Image Analyst. Here is the zip. Hope I included anything you need.