Ok, so this question is related to my ongoing task of getting text data categorized, you can refer to this question for more details on how I approached this problem.
I used the standard matlab function "nctool" (neural clustering tool) to get my inputs organized on a plane of 10x10 SOM nodes. I also got the output of this map (i.e. which of my inputs ended up on which node) saved in to the "output" variable in my workspace.
I would now like to get this data out and see if I can write another script. I'm aware of the 'save' and some of the export functions in MATLAB, however it seems that MATLAB does not support ascii export of this variable since it is a sparse matrix.
I am currently writing a script to get this thing exported out, however if someone already has a solution, please post. Otherwise I will do so after I finish testing it.
Update: I found a workaround to this fairly easily:
% convert a sparse matrix to full
output = full(output);
% output this to a file (excel)
xlswrite('test.csv',output);
Related
Unfortunately I am not too tech proficient and only have a basic MATLAB/programming background...
I have several csv data files in a folder, and would like to make a histogram plot of all of them simultaneously in order to compare them. I am not sure how to go about doing this. Some digging online gave a script:
d=dir('*.csv'); % return the list of csv files
for i=1:length(d)
m{i}=csvread(d(i).name); % put into cell array
end
The problem is I cannot now simply write histogram(m(i)) command, because m(i) is a cell type not a csv file type (I'm not sure I'm using this terminology correctly, but MATLAB definitely isn't accepting the former).
I am not quite sure how to proceed. In fact, I am not sure what exactly is the nature of the elements m(i) and what I can/cannot do with them. The histogram command wants a matrix input, so presumably I would need a 'vector of matrices' and a command which plots each of the vector elements (i.e. matrices) on a separate plot. I would have about 14 altogether, which is quite a lot and would take a long time to load, but I am not sure how to proceed more efficiently.
Generalizing the question:
I will later be writing a script to reduce the noise and smooth out the data in the csv file, and binarise it (the csv files are for noisy images with vague shapes, and I want to distinguish these shapes by setting a cut off for the pixel intensity/value in the csv matrix, such as to create a binary image showing these shapes). Ideally, I would like to apply this to all of the images in my folder at once so I can shift out which images are best for analysis. So my question is, how can I run a script with all of the csv files in my folder so that I can compare them all at once? I presume whatever technique I use for the histogram plots can apply to this too, but I am not sure.
It should probably be better to write a script which:
-makes a histogram plot and/or runs the binarising script for each csv file in the folder
-and puts all of the images into a new, designated folder, so I can sift through these.
I would greatly appreciate pointers on how to do this. As I mentioned, I am quite new to programming and am getting overwhelmed when looking at suggestions, seeing various different commands used to apparently achieve the same thing- reading several files at once.
The function csvread returns natively a matrix. I am not sure but it is possible that if some elements inside the csv file are not numbers, Matlab automatically makes a cell array out of the output. Since I don't know the structure of your csv-files I will recommend you trying out some similar functions(readtable, xlsread):
M = readtable(d(i).name) % Reads table like data, most recommended
M = xlsread(d(i).name) % Excel like structures, but works also on similar data
Try them out and let me know if it worked. If not please upload a file sample.
The function csvread(filename)
always return the matrix M that is numerical matrix and will never give the cell as return.
If you have textual data inside the .csv file, it will give you an error for not having the numerical data only. The only reason I can see for using the cell array when reading the files is if the dimensions of individual matrices read from each file are different, for example first .csv file contains data organised as 3xA, and second .csv file contains data organised as 2xB, so you can place them all into a single structure.
However, it is still possible to use histogram on cell array, by extracting the element as an array instead of extracting it as cell element.
If M is a cell matrix, there are two options for extracting the data:
M(i) and M{i}. M(i) will give you the cell element, and cannot be used for histogram, however M{i} returns element in its initial form which is numerical matrix.
TL;DR use histogram(M{i}) instead of histogram(M(i)).
For matlab: Is there a way to write the value of a vector to a file that can later be opened and read by another matlab program?
Specifically: I have a matlab program that computes a binary-valued vector $zvector$ with 10^7 entries. I want to write $zvector$ as data to an output file so that it can be emailed and easily read as input to another matlab program. Ideally, the output file would be called “Output.m” and would look like:
zvector=[
0
1
1
…
0
1
];
I like the .m format because it is easy to use for matlab input. I have experimented with matlab’s write() and fwrite() commands, with no success. I observe that these generate files that cannot be easily read as matlab-recognizable inputs (at least, I do not know how to read from them). Is there a way to accomplish my goals? Thanks.
PS: I am interested in the easiest way. If this involves a different type of file format (not a .m format) that is fine. However, in that case, can you provide both the writing and reading commands? Thanks again.
Thanks to #edwinksl for pointing me in the right direction with MAT files. I do not know the accepted practice here, but in stackexchange math it is encouraged to answer your own question if a hint from comments got you all the way there. So I will answer my own question.
The Mat format does this well. Here are example script files for reading and writing in the Mat format (see also links in above comments for more documentation):
***Script file OutputTest.m:
filename = 'TestFile.mat';
TestVector=[1 1 0 1];
save(filename, 'TestVector');
***Script file IntputTest.m
filename = 'TestFile.mat';
file=load(filename);
z =file.TestVector;
z
I'm using a lot of MATLAB for a Control class and something is really bumming me out. They want us to use a lot of Simulink even though I find the visual representation not that helpful and the interface between Simulink and MATLAB scripts hard to figure out in general.
So I have a model and I have added scopes for sinks which can save data directly to the workspace when ran from Simulink. However when I use the command sim in the script to directly use the model according to some parameters (stopTime, solving method, etc.) the results are buried in an object which is poorly documented to say the least so say I have:
simout = sim('lab','StopTime','100','Solver','ode1','FixedStep','2');
Now I have an object in my workspace but to access the data I want I need to go 3, hell 4 layers deep sometimes in the members of simout. My first question is :
Is there a way to access directly or at least know what those members are without using the tedious use of who.
I don't want to compile code to access its documentation! And help is not really helpful for those situations.
Why doesn't the Simulink model save the data when invoked like prescribed in the sink properties. I know that the line of code I mentioned overides some of the simulink block prescriptions (e.g. the solving method used).
How to know how simulink models interact with matlab scripts, granted I am a noob in coding in general, but the documentation doesn't really tell me what are the formal definitions of the model and the way it is used in matlab. I am scared at some points the default settings of 'sim' will overide some settings I set up in an earlier model which would prove to be a nasty buisiness to debug.
TL;DR Is there a quick way to access deeply buried members of an object? For example right now I have to do:
simout = sim('lab','StopTime','100','Solver','ode1','FixedStep','2');
who(simout)
ScopeData = (simout.get('ScopeData'))
signals = (ScopeData.signals)
time = (ScopeData.time)
Can I do something more C-ish of the sort of (Simout->ScopeData).signals?
And finally, why is the MATLAB suite presented like it was an app for day-traders when it is used a lot by EE people who in general need to know their coding? Why are libraries with headers and good documentation for what you are importing in your code (e.g. boost, string etc.) not used? This last option might be less pretty by hiding the mechanics, but to be able to write code properly I feel like I have to know most of the underlying mechanics of the code.
Invariably when most people start off using MATLAB or Simulink, they hate it. The main reasons I see for this is people are taught MATLAB very poorly which prevents them from understanding the power of MATLAB and when it should be used.
Before I get into describing how the MATLAB workspace, m files and Simulink are all related let's first define what each of those is separately and a few of the things you can do with them.
The MATLAB Workspace
The MATLAB workspace contains all of the variables you have created in MATLAB either explicitly via the command window or implicitly through running a .m file (don't worry I'll come back to these). The simplest method to add a variable to the MATLAB workspace is to directly type into the command window like
>> A = 1
A =
1
which adds the variable A to the workspace and assigns it a value of 1. Even simpler though is to simple type 1 like
>> 1
ans =
1
which adds the variable ans to the workspace with a value of 1. The default workspace variable for any command executed by MATLAB that is not explicitly assigned to a variable is ans.
The workspace browser in MATLAB displays information about all of the variables currently in the workspace. For instance if we were to execute, in the command window,
>> A = 5;
>> B = [6 8];
>> C = [3 6 7; 9 11 12];
>> D = eye(max(size(C)));
the workspace browser would look something like
Some Helpful Workspace Commands
The save and clear commands are helpful commands that work with the MATLAB workspace. save lets you save variables from the workspace to a file whilst clear lets you remove variables from the workspace, thus freeing up memory. clear all will clear every variable from the workspace.
m Files
An m-file (or script file) is a simple text file with a .m file extension. In it you type MATLAB commands which can be executed sequentially by executing just the m-file in the command window. For instance, lets copy our commands from above and paste them into an m-file called mfile_test.m. Now lets add the command C - A to the bottom of the m-file (note do not append a ; after the command). We can execute this m-file from the command window and see the output of all of commands within it executed sequentially
>> mfile_test.m
ans =
-2 1 2
4 6 7
m Files and Functions
m files can also contain functions. For instance we could write a function that calculates the area and circumference of a circle like
function [A, C] = circle(r)
A = pi*r*r;
C = 2*pi*r;
end
and put it in an m-file called circle.m. We could then use this like
>> circle(5)
ans =
78.5398
where ans now holds the area of a circle with a radius of 5 or
>> [A, C] = circle(5)
A =
78.5398
C =
31.4159
where A holds the area of the circle and C the circumference.
Simulink Models
Simulink is a graphical tool that can be used to model various different types of systems as well as modelling dynamic system behaviour. Simulink is closely embedded into the MATLAB ecosystem which adds additional power to it (again I'll come back to this later when describing the similarities).
Simulink models contain blocks which all exhibit different behaviour. There is also the functionality to create your own Simulink blocks should you need. Models in Simulink are made by connecting blocks of different kinds to emulate the system you want to model.
Simulink is quite extensive and I don't recommend learning it on your own. The best way to learn Simulink is invariably as part of a course, Control Systems or Systems Analysis type courses are ideal for this purpose. For that reason I'm not going to dwell on it for much longer here.
How are the MATLAB Workspace, m Files and Simulink all Related?
Well, the MATLAB workspace is available to both m files and Simulink. Variables in the MATLAB workspace can be used in both m files and Simulink.
m files that contain only scripts (and not functions) will write every variable created in them to the MATLAB workspace. m files that contain only functions won't write any of the new variables used in those functions to the MATLAB workspace. The only way a function will alter variables in the MATLAB workspace is by assigning an output value to ans or if you explicitly declare output arguments when calling the function.
Simulink and the MATLAB workspace have a very similar relationship to m files and the MATLAB workspace. Any variable in the MATLAB workspace is available for use in Simulink (in any part, including configuration). For instance in the below configuration I use the MATLAB workspace variables start_time, stop_time and step_time to set up the parameters of model. Typically I would define these in an m-file before I run my Simulink model with sim(). This is how we can relate all 3 together.
Simulink can write variables to the MATLAB workspace by adding output arguments to the sim() command. However, as you've found this can be quite nasty to navigate and extract what you really want! A better approach would be to use the Data Import/Export options in Simulink coupled with a To Workspace block to grab the outputs that you are concerned with so that you can ignore everything else.
Below I have a screenshot of the Simulink Data Import/Export pane. You can see there are options in here for us to send variables to the MATLAB workspace. Typically, the most common you would need is tout which will be a range given by start_time:step_time:stop_time from the earlier configuration pane. Other areas that would be of primary interest in this screen would be xInitial and xout which are used in Root Locus analysis.
However, all that aside one of the best blocks in Simulink is the To Workspace block. This block can be used to store variables directly in the MATLAB workspace and is one of the keys to being able to link MATLAB and Simulink. You get the power of Simulink but the computational and plotting abilities of MATLAB. I've included a screenshot of it below as well as a typical configuration I would use. The default Save Format for this block is Timeseries, however, I recommend changing this to Array as it will make your life much easier.
OK, where was I? I feel like I'm giving a lecture instead of writing an answer!
A Practical Explanation
Simulink Model
So now let's put everything we've learned into practice with a simple example. First we are going to create a simple Simulink model like this
Now we'll set up our configuration for this, as before for the Solver section
We'll also untick Limit data points to last: in the Data Import/Export section
And, that's it. Our simple Simulink model has been created and setup. For the purposes of this answer, I'm saving mine as stackoverflow_model.slx.
MATLAB Script
Now we'll create simple MATLAB script (m-file) called stackoverflow_script.m that will set up the necessary variables for our Simulink model by adding them to the MATLAB workspace. We'll then call our Simulink model and check what new variables it added to the workspace. And, finally we'll generate a simple plot to show the benefits of this approach.
So here is the MATLAB script
% Script developed to describe the relationship between the MATLAB
% workspace, m-files and Simulink
close all
clear all
% Initialise variables
start_time = 0;
stop_time = 10;
step_time = (stop_time - start_time) / 1000; % Creates 1000 + 1 points
% Choose k
k = 60;
% Execute Simulink model
sim('stackoverflow_model');
whos % To display variables returned from Simulink
% Plot results
figure;
plot(tout, yout, 'r');
title('Sample Plot');
xlabel('Time (s)');
ylabel('Output');
Putting it All Together
Now we execute this script in the command window with stackoverflow_script and sit back and marvel at the POWER of MATLAB and Simulink combined.
>> stackoverflow_script
Name Size Bytes Class Attributes
k 1x1 8 double
start_time 1x1 8 double
step_time 1x1 8 double
stop_time 1x1 8 double
tout 1001x1 8008 double
yout 1001x1 8008 double
We can see from the output above that all of the variables Simulink needs (k, start_time, step_time and stop_time) are all in the MATLAB workspace. We can also see that Simulink adds 2 new variables to the MATLAB workspace tout and yout which are simple 1001x1 vectors of doubles. No nasty structs to navigate.
And finally, this produces a nice plot
And so that concludes our whistle stop tour through MATLAB, m files and Simulink! I hope you've enjoyed it as much as I did writing it!
P.S. I haven't checked this for spelling or grammar mistakes so edits are very much welcome ;)
General
Well to put it short workspace is the variable-environement you are working in. If you run a script, your workspace is 'base', which is the same the console uses. So Matlab does have different environements, one is a kind of included environement known as path, the other one is for variables, known as workspace.
Simulink uses a different one, which prevents shadowing variable names I guess.
To check check members in the current workspace use who
To write members to another workspace use assignin
To run something in a specified workspace use evalin
Your Questions
1.
Who lists all the variables in the current workspace you don't need it for the thing you wanna do.
The whole simulink documentation isn't that good...
2.
It does...
3.
If you run a script and define variables they are defined in the base workspace. When you specify a variable in simulink by just entering its name (for example a), it does load it from the base workspace (hence this way arround no problems).
The other way arround is to either use the given export blocks, or specify export values in your own blocks by either using global or assignin.
4.
If you open the scope block and hit the options-buttion (the little gear), you can select an export option. You can aswell specify the type you wan't to use. You seem to use the struct with time option, which is the one with the most lvls, I'd suggest to use the array-type if your problem is just the fact that it is a struct.
You can also just use the Outputblock to specify the export type and name.
So I'd go with:
sim('modelname');
signals=ScopeData.signals;
time=ScopeData.time;
Or when specified as an array:
sim('modelname');
signals=ScopeData(:,2);
time=ScopeData(:,1);
In the example above I don't specify the way the model is run, however you can also specify it as you posted.
I'm just starting to learn MatLab.
This is what I'd like to convert into MatLab code:
http://postimg.org/image/jqdvcrbod/
Since a lot of my variables are functions or other variables, does that mean that when I write them as functions in MatLab I have to save each of the functions as a separate file? Is there any other way? I don't want to end up with a million separate files, but as of right now, if I write more then one function in the editor, it starts getting confused and doesn't recognize the second function.
Also, is there a way to use actual symbols (like the square root symbol instead of writing "sqrt()") like in Mathematica? I feel like long equations (like the last one) are easier on the eye that way, but that's purely aesthetics.
Is there a way to have MatLab output unassigned variables? Like in Mathematica, if I have y(x) = 2x, if i don't put anything for x, it just outputs 2x.
One quick way to do is use a package in Mathematica called ToMatlab (I attached the download link). It is able to convert Mathematica symbol syntax to Matlab .m file.
Hope this would help.
I want to know how can this function(from MATLAB) resize the columns of an input image using weights an indices previously computed.
Which equations uses to do that?
resizeColumnsCore(double(in), weights', indices');
When I looked for a function called resizeColumnsCore in MATLAB 7.11.0 (R2010b) I didn't find anything. However, I did find a MEX-file by that name in MATLAB 7.8.0 (R2009a) in this subdirectory of the Image Processing Toolbox:
C:\Program Files\MATLAB\R2009a\toolbox\images\images\private\
I guess they've phased it out or replaced it with another function in newer MATLAB versions. Now, if you want to know what the MEX-file does, you need to look at the source code it is compiled from. Luckily, it appears that this source code resizeColumnsCore.cpp can be found in the following directory:
C:\Program Files\MATLAB\R2009a\toolbox\images\images\private\src\misc\
And you can look through that code to determine the algorithms used to resize the columns of an image given a set of weights and indices.
Now, if you want to know how these input arguments to resizeColumnsCore are computed, you'll have to look at the code of a function that calls it. I know of at least one function in the IPT that calls this function: IMRESIZE. If you type edit imresize at the command prompt it will open that function in the Editor, allowing you to look through the code so you can see how the arguments to resizeColumnsCore are created.
What I can tell you for R2009a is that there is a subfunction in the file imresize.m called contributions which computes the weights and indices that are ultimately passed as arguments to resizeColumnsCore. That is where you will want to start looking to determine what algorithms are used to compute these arguments.
Looks like this isn't a proprietary MATLAB function. Could we see some code or a link to the code?