Compiling Octave 4.0 on Ubuntu 14.04

sudo apt-get install gawk gfortran gperf flex libbison-dev libqhull-dev libglpk-dev libcurl4-gnutls-dev libfltk1.3-dev librsvg2-dev libqrupdate-dev libgl2ps-dev libosmesa6-dev libarpack2-dev libqscintilla2-dev

Note, I may have missed something since I didn’t do the above from a clean install (I may have something installed that you’re missing).

Checkout the Octave 3.8 compiling page for hints about what packages you might be missing if you get errors, and leave a comment to let others know.


./configure --enable-jit --prefix=/opt/octave4.0

This resulted in:

  Build Octave GUI:                   yes
  JIT compiler for loops:             yes
  Build Java interface:               yes
  Do internal array bounds checking:  no
  Build static libraries:             no
  Build shared libraries:             yes
  Dynamic Linking:                    yes (dlopen)
  Include support for GNU readline:   yes
  64-bit array dims and indexing:     no
  OpenMP SMP multithreading:          yes
  Build cross tools:                  no

With the only Warning being about JAVA_HOME not defined.
Then I typed


OpenCV cv.CalcOpticalFlowHS Horn-Schunck smoothness lambda parameter

More details to come, but I was comparing the performance of OpenCV to Matlab Computer Vision Toolbox for the dense estimates of optical flow given by the Horn Schunck algorithm. I was getting a very different result with OpenCV vs. Matlab for the Optical Flow Estimation. It seemed that OpenCV was washing out fine details in the optical flow. After carefully comparing Matlab Computer Vision and OpenCV outputs for Horn Schunck optical flow, I found that the default lambda/smoothness parameter of 1.0 for cv.CalcOpticalFlowHS is not the same as what Matlab calls 1.0.

I need to quantify this further, but for now I found that in OpenCV cv.CalcOpticalFlowHS setting lambda=0.001 gives results that are much more like Matlab–I can see the fine details. This is just a rough guess, if I have time I’ll quantify it in my forthcoming article on segmenting terabtyes of aurora borealis video in an hour!

Speed of Matlab vs. Python Numpy Numba

Here is a comparison on my Intel i7-2600 Sandy Bridge (3 year old) desktop PC.

Python 3.4.2, Anaconda 2.1, iPython 2.2.0, Numpy 1.8.2 with Intel MKL

import numpy as np
A = np.matrix(np.random.randn(5000,5000))
B = np.matrix(np.random.randn(5000,5000))
%timeit A*B
1 loops, best of 3: 2.51 s per loop

Matlab R2014b, also with Intel MKL
A = randn(5000,5000);
B = randn(5000,5000);
f = @() A*B;
ans =

So, Numpy is about twice as fast as Matlab at this matrix multiplication.
example 2: Using Numba in iterative algorithms.

from numba import jit # inline auto compilation to C of Python code
from time import time
from numpy import diff
def f(): # declare a function
    for i in range(int(1e7)): #generator much faster than arange here!
        x = 0.5*x + i % 10
tic = time()
print('elapsed time (sec)',time()-tic)
elapsed time (sec) 0.07639932632446289

Matlab R2014b
tic, x = 0; for i = 0:1e7-1; x = 0.5*x + mod(i,10); end, toc
Elapsed time is 0.608442 seconds.

Python is 7.96 times faster than Matlab for this trivial test.
You can also find plenty of examples where Python is somewhat slower than Matlab. For me the places where Python was much faster seemed to very much outweigh the slower places.

Sparse Matrices in Python from Matlab R2014b

First of all, you can’t pass sparse matrices, so you have to have enough RAM to hold the full matrix and probably a copy or two of it. This is more just to show how it could be done, and hope that the Mathworks will improve the passing of variables in future releases of Matlab.

All commands are issued in Matlab R2014b.

a = eye(5);
A = py.numpy.reshape(a(:)',size(a));
As = py.scipy.sparse.csc_matrix(A)

As =
Python csc_matrix with properties:

dtype: [1x1 py.numpy.dtype]
has_sorted_indices: 1
nnz: 5
shape: [1x1 py.tuple]
maxprint: 50
indices: [1x1 py.numpy.ndarray]
data: [1x1 py.numpy.ndarray]
indptr: [1x1 py.numpy.ndarray]
format: [1x1 py.str]
(0, 0) 1.0
(1, 1) 1.0
(2, 2) 1.0
(3, 3) 1.0
(4, 4) 1.0

Matlab R2014b: passing matrices to/from Python

As noted in my earlier post, this is awkward because Matlab doesn’t understand Numpy arrays. Matlab understands lists, dicts, sets, scalars, and other less frequently used classes from Python. Let’s do an example with the “clown” image included with Matlab. All commands here are executed in Matlab R2014b.

First off, here are some Python packages that don’t currently work from Matlab R2014b (just hard crash Matlab)
cv2 (opencv 2.4)

NOTE: The use of the ‘F’ parameter to and from Python in the .reshape() and .ravel() methods–this is crucial or your matrix will be transposed inside Python!

load clown % 200x320 image is now in variable X
Xp = py.numpy.reshape(X(:)',size(X),'F'); % I ravel X to a row vector, and unravel with Numpy
Yp = py.scipy.ndimage.gaussian_filter(Xp,3); % SciPy works, but Scikit-image doesn't for me
% now let's come back to Matlab
Y = reshape(cell2mat(cell(Yp.ravel('F').tolist())),size(X)); % a regular Matlab 2-D matrix
imshow(Y,map) %map comes from when you load clown

% now let's do something similar in Matlab--note I didn't make the filter truncation radius the same, so the numerical results differ.
F = fspecial('gaussian',[15,15],3);
M = imfilter(X,F);

Of course normally you would be using Python for a function not readily available in Matlab, but this was a side-by-side working example.

Matlab R2014b: X11 forwarding and OpenGL

The new plotting engine in Matlab R2014b has caused some hangups and reduced quality plots for people using Matlab over X11 forwarding.

Consider starting Matlab this way:

matlab -nosoftwareopengl


If you can’t start Matlab with the -nosoftwareopengl open, omit that open and try plotting with the

set(gcf….’painters’) line as shown above for each figure.


Matlab R2014b: installing the integrated OpenCV support

Initially it appears that to use OpenCV from Matlab R2014b, you will need to write your OpenCV calls in C++, using all the usual Mex stuff. This is not very convenient to me; it would be much more convenient to use the friendly syntax of Python. However the Python support in Matlab R2014b allows passing only 1xN arrays, so there would be reshaping involved to/from Python that would slow things down.

The mexopencv package that has been available for some time (and that works with earlier versions of Matlab) seems to be more user-friendly once installed–you use it much like any other Matlab toolbox, without you needing to code in C++/Mex yourself.

Bottom line: I’ll still be using Python/OpenCV without Matlab, or even C++/OpenCV, which looks easier than using Mex with Matlab. I am glad Mathworks has taken this step; maybe the mexopencv people will make the R2014b OpenCV support easier to use by making a bunch of .cpp functions to compile once and then call.

This process gets the packages downloaded and installed:

The directory with examples is at:


Here’s how the first example, the Foreground Detector works from Matlab:

cd ~/Documents/MATLAB/SupportPackages/R2014b/opencvinterface/toolbox/vision/supportpackages/visionopencv/example/ForegroundDetector

mexOpenCV backgroundSubtractorOCV.cpp


You will see a Video Player window pop up with cars driving by, with the cars detected outlined in white rectangles.

Matlab 2014b Python: can only pass 1xN vectors!

Note that for Matlab 2014b, which is the first version of Matlab to have official support for Python, you can only to TO python a 1xN vector. You have to reshape the matrix into a 1xN vector when passing the matrix into Python, and reshape back to a matrix inside Python, but  I think Matlab will make copies at both reshapings.

Note that Numpy ndarrays are not understandable by Matlab, you will have to make your Numpy array into a 1-D list and then send it back. Yikes that’s a lot of memory copying!

I can pass



ans=[ 1.41421356  1.41421356]

but I cannot pass
Error using py.numpy.sqrt
Conversion of MATLAB 'double' to Python is only supported for 1-N vectors.

the link below seems to confirm that you cannot pass normal 2D matrices to Python from Matlab R2014b:

Cygwin64 HDF5 load() crash fix

Currently, Octave 3.8.1 in Cygwin64 was compiled with headers 1.8.12 but HDF5 library 1.8.13.

This causes Octave to seg fault Warning! ***HDF5 library version mismatched error*** and exit.

To avoid having to recompile, you can type
to startup octave
you can perhaps add to your ~/.bashrc file the line:
alias octave="HDF5_DISABLE_VERSION_CHECK=1 octave -q"