Matlab: How to display Matrix as Image in GUI - image

I’m working on my first GUI in Matlab. It’s gonna get kinda big but I’m starting very basic. So far all I’ve got is a button and axes.
I’m looping a matrix that is being updated every time it goes through the loop. I’d like to display this matrix in my GUI.
When I take out “axes(handles.axes1)” my GUI shuts down and a new window opens with exactly the picture I want on my GUI. When I leave it in all I get is Errors:
Reference to a cleared variable handles.
Error in RackWriter>onOff_Callback (line 141)
axes(handles.axes1)
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in RackWriter (line 42)
gui_mainfcn(gui_State, varargin{:});
Error in
#(hObject,eventdata)RackWriter('onOff_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating DestroyedObject Callback
Anyone knows what I’m doing wrong?
Thanks so much in advance
Here’s how the matrix is created and how i was planning on showing it:
% Reshape data (1D -> 2D array)
data2d = zeros(nrow, ncol);
k = 1;
for i = 1:nrow
for j = 1:ncol
data2d(row_index(i), col_index(j)) = data(k);
k = k + 1;
end
end
%resize 16x10 image to 160x100 image
data2d_resized = imresize(data2d,10);
%sensetivity
axes(handles.axes1)
imshow(data2d_resized,[0 255]);

This should do the trick:
handles.figure = imshow(data2d_resized, [0 255], 'parent', handles.axes1);
If you want to update your figure in a later stage, you can then use:
set(handles.figure, 'CData', updated_matrix);
Also, make sure to put the next line after each function in you code, it updates the handles:
guidata(hObject,handles);

function varargout = RackWriter(varargin)
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', #RackWriter_OpeningFcn, ...
'gui_OutputFcn', #RackWriter_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 RackWriter is made visible.
function RackWriter_OpeningFcn(hObject, eventdata, handles, varargin)
% Choose default command line output for RackWriter
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
axes(handles.axes2)
imshow('sensordeckelOben.jpg');
% UIWAIT makes RackWriter wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = RackWriter_OutputFcn(hObject, eventdata, handles)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in onOff.
function onOff_Callback(hObject, eventdata, handles)
% hObject handle to onOff (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%This is where my stuff begins
% Preparations
close all %close all figures
clear all %clear all workspace variables
fclose('all') %close all Files
delete(instrfindall) %Reset Com Port
delete(timerfindall) %Delete Timers
%clear handles
% setup serial
serialPort = serial('COM3');
command = 'A';
nrow = 16;
ncol = 10;
row_index = [9,10,11,12,13,14,15,16,8,7,6,5,4,3,2,1];
col_index = [1,2,3,4,5,6,7,8,9,10];
% 10x16 = 160 bytes
lendata = 160;
BaudRate = 115200;
%InputBufferSize is bein displayed (disp(serialPort.BytesAvailable))
%with only 322 Bytes. The more information it has to process, the more
%bytes that havve to be stored in the InputBufferSize. But it seams to
%not go over 400
InputBufferSize = 500;
Timeout = 1;
set(serialPort , 'BaudRate', BaudRate);
set(serialPort , 'InputBufferSize', InputBufferSize);
set(serialPort , 'Timeout', Timeout);
fopen(serialPort);
while 1
% Request data
fprintf(serialPort, command);
% Get data
%Data is read as string (CSV)
data_string = fgetl(serialPort);
data_string_array = strsplit(data_string, ',');
data = str2double(data_string_array);
% Reshape data (1D -> 2D array)
data2d = zeros(nrow, ncol);
k = 1;
for i = 1:nrow
for j = 1:ncol
data2d(row_index(i), col_index(j)) = data(k);
k = k + 1;
end
end
%resize 16x10 image to 160x100 image
data2d_resized = imresize(data2d,10);
%sensetivity [0 255]
%axes(handles.axes1)
imshow(data2d_resized,[0 50]);
%clean out the InputBufferSize
flushinput(serialPort)
end
fclose(serialPort);

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I wrote the code for this method, by don't imagine how make the animation, how I can use the set function.
In your code there are a lot of redundant and random pieces. Do not call hold on more than once, it does nothing. Also set(p) does nothing, you want to set some ps properties to something, then you use set.
Also, you are plotting the result, but not the "change". The change is a line between the previous and current, and that is the only reason you'd want to have a variable such as predx, to plot. SO USE IT!
Anyway, this following code plots your algorithm. I added a repeated line to plot in green and then delete, so you can see what the last step does. I also changed the plots in the begging to just plot in red so its more clear what is each of the things.
Change your loop for:
for i = 1:1:iteration
j = mod(i-1,m) + 1;
if (nrm(j) <= 0), continue, end;
predx = x;
x = x + ((f(j) - A(j,:)*x)*A(j,:)')/(nrm(j))^2;
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pause(0.1)
children = get(gca, 'children'); %delete the green line
delete(children(1));
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% hold on;
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This will show:

Optimizing for loop in Matlab

I'm writing a "Peak finder" in Matlab. I've never used Matlab or anything similar before this project, so I'm new to "vectorizing" my code. Essentially, the program needs to take a video of molecules and plot circles on the molecules present in each frame of the video. If a molecule is crowded then it gets a red circle, but if it is not crowded it gets a green circle.
My problem is that some of these videos have 2000 frames and my program takes up to ~25 seconds to process a single frame, which is not practical.
Using tic and toc I've found the trouble maker: A for-loop which calls a function that contains a for-loop.
function getPeaks( orgnl_img, processed_img, cut_off, radius )
% find large peaks peaks by thresholding, i.e. you accept a peak only
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color = 'g';
else
color = 'r';
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plotCircle(color, x_centroid(i), y_centroid(i), radius)
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And here is the findDistance function which contains another for-loop and determines if the circles overlap:
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I think that there must be much improvement to be done here. I would appreciate any advice.
Thanks! :)
UPDATE: Here are the profiler results. The first section of code is the "getPeaks" function
http://i.stack.imgur.com/VaLdH.png
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function plotStateVariables(uu) %
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % graph y with lable mylabel function handle = graph_y(t, y, handle, color)
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I have tried to make a Gaussian filter in Matlab without using imfilter() and fspecial().
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here's an alternative:
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