Starting R2014b Matlab has changed the way how variables are saved using save command; Matlab has also changed the way graphic handles are saved, they are saved as structures now. If you have graphic handles in workspace Matlab takes it longer to save the mat file, size of mat file is large and when you load the file all the saved figures are popped-up, which is irritating to me. It also produces a warning:
Warning: Figure is saved in Oakley_19_PDEparameterEstimation.mat. Saving graphics handle variables can cause the creation
of very large files. To save graphics figures, use savefig.
I have a simple and straightforward question:
How can I avoid saving of all graphic handles?
Please do not suggest that I can clearvars figure handles before saving them.
Thanks
You can get information about the current workspace variables using whos and save only those variables whose class is not a graphics handle object (i.e. the class name string does not include 'matlab.graphics' or 'matlab.ui'):
varData = whos;
saveIndex = cellfun(#isempty, regexp({varData.class}, 'matlab.(graphics|ui)'));
saveVars = {varData(saveIndex).name};
save('no_handles.mat', saveVars{:});
You can select which variables you save.
Example:
save('data.mat', 'var_name1', 'var_name2', 'var_name3');
where var_name1 etc... are the names of the variables you want to save.
Related
I have multiple small *.mat files, each containing 4 input images (template{1:4} and a second channel template2{1:4}) and 4 output images (region_of_interests{1:4}), a binarized ('mask') image to train a deep neural network.
I basically followed an example on Mathworks and it suggests to use a function (in this example #matreader) to read in custom file formats.
However ...
It seems impossible to load multiple images from one *.mat file using any load function as it only allows one output, and imageDatastore doen't seem to allow loading data from workspace. How could this be achieved?
Similarly, it seems impossible to load a pixelLabelDatastore from a workspace variable. As a workaround I ended up saving the contents of my *.mat file to an image (using imwrite, saving to save_dir), and re-loading it from there (in this case, the function doesn't even allow to load *.mat files.). (How) can this be achieved without re-saving the file as image?
Here my failed attempt to do so:
%main script
image_dir = pwd; %location of *.mat files
save_dir = [pwd '/a/']; %location of saved output masks
imds = imageDatastore(image_dir,'FileExtensions','.mat','ReadFcn',#matreader); %load template (input) images
pxds = pixelLabelDatastore(save_dir,{'nothing','something'},[0 255]);%load region_of_interests (output) image
%etc, etc, go on to train network
%matreader function, save as separate file
function data=matreader(filename)
in=1; %give up the 3 other images stored in template{1:4}
load(filename); %loads template and template2, containing 4x input images each
data=cat(3,template{in},template2{in}); %concatinate 2 template input images in 3rd dimension
end
%generate example data for this question, will save into a file 'example.mat' in workspace
for ind=1:4
template{ind}=rand([200,400]);
template2{ind}=rand([200,400]);
region_of_interests{ind}=rand([200,400])>.5;
end
save('example','template','template2','output')
You should be able to achieve this using the standard load and save function. Have a look at this code:
image_dir = pwd;
save_dir = pwd;
imds = imageDatastore(image_dir,'FileExtensions',{'.jpg','.tif'});
pxds = pixelLabelDatastore(save_dir,{'nothing','something'},[0 255]);
save('images.mat','imds', 'pxds')
clear
load('images.mat') % gives you the variable "imds" and "pxds" directly -> might override previous variables
tmp = load('images.mat'); % saves all variables in a struct, access it via tmp.imds and tmp.pxds
If you only want to select the variables you want to load use:
load('images.mat','imds') % loads "imds" variable
load('images.mat','pxds') % loads "pxds" variable
load('images.mat','imds','pxds') % loads both variables
EDIT
Now I get the problem, but I fear this is not how it is going to work. The Idea behind the Datastore objects is, that it is used if the data is too big to fit in memory as a whole, but every little piece is small enough to fit in memory. You can use the Datastore object than to easily process and read multiple files on a disk.
This means for you: Simply save your images not as one big *mat file but as multiple small *.mat files that only contain one image.
EDIT 2
Is it strictly necessary to use an imageDatastore for this task? If not you can use something like the following:
image_dir = pwd;
matFiles = dir([image_dir '*.mat']);
for i=1:length(matFiles)
data = load(matFiles(i).name);
img = convertMatToImage(data); % write custom function which converts the mat input to your image
% or something like this:
% for j=1:4
% img(:,:,j) = cat(3,template{j},template2{j});
% end
% process image
end
another alternative would be to create a "image" in your 'matreader' which does not only have 2 bands but to simply put all bands (all templates) on top of each other providing a "datacube" and then in an second step after iterating over all small mat files and reading them splitting the single images out of the one bigger datacube.
would look something like this:
function data=matreader(filename)
load(filename);
for in=1:4
data=cat(3,template{in},template2{in});
end
end
and in your main file, you have to simply split the data into 4 pieces.
I have never tested it but maybe it is possible to return a cell instead of a matrix?
function data=matreader(filename)
load(filename);
data = cell(1,4)
for in=1:4
data{in}=cat(3,template{in},template2{in});
end
end
Not sure if this would work.
However, the right way to go forward from here really depends on how you plan to use the images from imds and if it is really necessary to use a imageDatastore.
I would like to save the image I generate the HeatMap() function from the bioinformatics library.
I cannot figure out to have the image without manually exporting the data.
I'd prefer to use HeatMap over Imagesc because it automatically scales the data to the mean.
I do not have the Bioinformatics Library for matlab, However you should be able to get the current figure with the function gcf. It is not the most stable way, but in most cases this will work excellent. Then you can save the figure as a figure or image with saveas.
HeatMap(...);
hFig = gcf;
saveas(hFig,'myName','png'); % You can use other image types as well and also `'fig'`
There is a second way as well. The HeatMap class also contains a plot method. This method may return the figure handle to the HeatMap plot then save the image with saveas.:
hHM = HeatMap(...);
hFig = plot(hHM);
saveas(hFig,'myName','png');
I share a part of a Matlab code that I used when I analyzed some data from TCGA
#I was considering two gene expression level taken from cancer disead tissue and
# healthy tissues comparing them with this Heatmap
labela=Gene;
labelb=Gene2;
data1=[dataN(indg,:) dataC(indg,:); dataN(indg2,:) dataC(indg2,:);];
H=HeatMap(data1,'RowLabels',
{labela,labelb},'Standardize','row','Symmetric','true','DisplayRange',2);
addTitle(H,strcat('HeatMap',project));
addXLabel(H,'patients');
addYLabel(H,'geni');
#I have allocated the plot in a variable
fig=plot(H);
# Then I saved the plot
saveas(fig,strcat('D:\Bioinformatica\Tesina...
Prova2\Risultati_lihc\',dirname,'\HM.fig'));
But if you have to run one single object I advise against waisting your time in writing code (even if it is always a good thing to explore and strengthen your knowledge), I used because each time I was running a pipeline. Otherwise you can go on
1)File ----> Export Setup
2) Export
3)Save in the format you do want!
I wish to plot a simple graph of my data with sliders to change the coefficient of the y-axis data. I have created my GUI interface from quick start, with plot and sliders. I now wish to write the code (I believe in the simpleguide_OpeningFcn section) to import my data sets. My data sets are 5 different 300x1 vectors which I currently import into a a normal MATLAB file using an import function named importfile2.m.
Any help on how to get this data into the GUI for my simple plot(x,y) would be much appreciated. Cheers
An alternative would be to use setappdata and getappdata to fetch the data wherever you want from your GUI.
For example, at t he end of your importfile2.m you could use setappdata to store the data in some variable. The first argument tells MATLAB in what workspace to save it. You could, for example, use the GUI interface in itself or use the base workspace, accessible from everywhere. That's the most general way:
setappdata(0,'FancyName',YourData); %// The 0 is for the base workspace,i.e. the 'root'.
%//YourData is the actual data and 'FancyName' is whatever name you give them. It does not have to be the same name as the variable in your function. The important thing is to use the same name in getappdata as below.
If you wanted to associate the data only with the GUI figure, you would use something like this:
setappdata(handles.YourFigure_Tag,'FancyName',YourData);
To get the data in the GUI, use getappdata in its opening function (or in any callback you want) and you're good to go:
Data_inGUI = getappdata(0,'FancyName'):
A more robust way would be to store directly the data in the handles structure of the GUI, so that it's accessible from every callback:
handles.Data_inGUI = getappdata(0,'FancyName'):
guidata(hObject,handles); %// Update handles structure; important!
And that should do it. Hope that helps!
EDIT I think another solution would be to save a .mat file at the end of the import function and load it in the OpeningFcn of the GUI. Than might be simpler/faster.
EDIT 2 Following your comment below, here is what I would do:
1) In the OpeningFcn of the GUI, import the data.
[Date,OutAirTemp,SupAirtemp] = importfile3('AHU7Oct.csv')
Then you can store everything in the handles structure:
handles.Data = Date;
handles.OutAirTemp = OutAirTemp;
handles.SupAirtemp = SupAirtemp;
guidata(hObject,handles); %// Update handles structure.
Then elsewhere in the GUI (i.e. other callbacks) you can fetch the data as regular, i.e. using for example:
NewDate = handles.Date - 4 %// or whatever.
Is it a bit clearer?
I have a GUI(made using GUIDE) in which there is an axes on which I can draw. When I saved the gui, i have a .fig file and a .m file (whose names are start_gui.m and start_gui.fig). Now, I am trying to plot on these axes using an external M file, to which I have passed the GUI handles. This is as follows:
function cube_rotate(angle1,angle2,handles)
gcf=start_gui.fig; %this is the name of the gui.fig file in GUIDE
set(gcf,'CurrentAxes',handles.cube_axes)%this allows us to plot on the GUI
%plot something
end
handles.cube_axes is the name of the handle in the GUI created using guide. Inspite of passing the handles, it won't allow me to plot in the gui. It throws up an error saying:
??? Undefined variable "start_gui" or class "start_gui.fig".
start_gui.fig is the name of the GUI figure that was generated in GUIDE. How do i make it plot in the axes in start_gui.fig?
Thanks for all the help!
You've made a few errors. The first is referring to a file name without single quotes to denote a string. The second is trying to open an existing figure by assigning it as a variable named gcf. This will just give you a variable gcf which contains the string 'start_gui.fig'.
Instead, open the figure with this command:
fH = hgload('start_gui.fig');
% Then find/assign the axes handle (assuming you only have one axes in the figure):
aH = findobj(fH,'Type','axes');
% And finally plot to the axes:
plot(aH,0:.1:2*pi,sin(0:.1:2*pi));
On a secondary note, is there a reason you're not using the M-file generated by MATLAB to carry out this functionality? By using the auto-generated M-file, you'll be able to access the handles structure rather than using findobj.
The error you're getting is because of your second line: gcf=start_gui.fig;
It's looking for a variable named start_gui, which you don't have. (start_gui.fig is a filename, not a variable.)
To solve your plotting problem, take a look at this Mathworks support article.
Is it possible to store the matlab figure inside a mat file, where the variable are stored.
I got into a scenario where i generated some plot from the variable stored in the mat file. Currently im storing the figure as a separate file, this means, i have a 1 file for variables and another file for figure. But i would like to bundle them together in a single file.
How about selecting both files in the windows explorer and zip them? ;-)
Seriously, while I do not know of a way to do exactly what you want (what is it, exactly, anyway? Do you expect the figure to pop up once you've typed load variables.mat and pressed enter?) I see this way around it:
You could store the command(s) needed to generate the figure in an anonymous function or as a string and save it along with all other variables. Then, after loading the .mat file, you call that function or eval on the string and the figure will be regenerated.
x=sort(rand(1,100)); y=sort(randn(1,100)); %# sample data
makefig = #() plot(x,y,'g.'); %# anonymous figure-generating function
save myDataAndFigure
clear all
load myDataAndFigure
makefig()
...or, with a string (e.g. when including formatting and axis-labelling commands)
x=sort(rand(1,100)); y=sort(randn(1,100)); %# sample data
figcmd = 'plot(x,y,''g.''); xlabel(''sort(U(0,1)''); ylabel(''sort(N(1,0)'');'
save myDataAndFigure
clear all
load myDataAndFigure
eval(figcmd)
The latter should save memory when the involved data are large, since the anonymous function object contains all the data it needs, i.e. its own "copy" of x and y in the example.
There's an article here on fig file format and how it's actually a mat file in a disguise.
So you can take the fig and store its data in a structs and save them as a mat file, then load the mat file and make fig out of the structs you saved.
How about storing data and functions in instances of a class and unsing the functions later to plot the data?
Actually this is surprisingly easy to do.
Suppose you have just created the figure in question. Converting the figure handle into a struct yields the corresponding hierarchical elements (including the data, labels, everything) required to display the figure.
If desired, this struct may then be saved to a mat file just as though it was data. (It is, in fact.) To view the contents of the struct as a figure again simply reconvert it to a handle with struct2handle.
% The line below converts the current figure handle into a struct.
this_fig = handle2struct(gcf)
% The line below converts the struct "this_fig" back to a figure handle and displays it.
h = struct2handle(this_fig,0);