Upgrading from Matlab

Chris R. Smith

Here are some one-to-one translations for many popular functions in Matlab and python that should make it easier to switch from Matlab to Python

System functions

Matlab Function	Python Equivalent	Description
addpath	sys.path.append	Add to path

File I/O

Matlab Function	Python Equivalent	Description
dlmread	either read and parse or skimage.io.imread	Read ASCII-delimited file of numeric data into matrix
imread	pyplot.imread	read image file; N is number of files used

Data Type

Matlab Function	Python Equivalent	Description
int	numpy.int	Convert data to signed integer
double	numpy.float	Convert data to double
real	numpy.real	Return the real part of a complex number
imag	numpy.imag	Return the imaginary part of a complex number

Mathematics

Matlab Function	Python Equivalent	Description
sqrt	math.sqrt or numpy.sqrt	Square root
erf	math.erf or scipy.special.erf	Error function
atan2	math.erf or numpy.atan2	Four-quadrant inverse tangent
abs	abs or numpy.abs	Absolute value
exp	exp or numpy.exp	Exponential function
sin	sin or numpy.sin	Sine function

Array Creation

Matlab Function	Python Equivalent	Description
zeros	numpy.zeros	Create an array of zeros
meshgrid	numpy.meshgrid	Create grid of coordinates in 2 or 3 dimensions
ndgrid	numpy.mgrid or numpy.ogrid	Rectangular grid in N-D space

Advanced functions

Matlab Function	Python Equivalent	Description
permute	numpy.transpose	Rearrange dimensions of N-dimensional array
angle	numpy.angle	Phase angles for elements in complex array
max	numpy.max	Return the maximum element in an array
min	numpy.min	Return the minimum element in an array
reshape	numpy.reshape	Reshape array
mean	numpy.mean	Take mean along specified dimension
size	numpy.size	get the total number of entries in an array
cell2mat	numpy.vstack([numpy.hstack(cell) for cell in cells])	converts data structure from cell to mat; joins multiple arrays of different sizes into single array
repmat	numpy.tile	Repeat copies of an array
unwrap	np.unwrap	Shift the phase of an array so that there are no jumps of more than the desired angle (default pi)

Array Indexing

Matlab Function	Python Equivalent	Description
find	numpy.where	Find all indices of a matrix for which a logical statement is true
isnan	numpy.isnan	checks each array entry to see if it is NaN
isinf	numpy.isinf	checks each array entry to see if it is Inf
ischar	numpy.ischar	checks each array entry to see if it is a character

Advanced functions

Matlab Function	Python Equivalent	Description
fft2	numpy.fft.fft2	2D fast Fourier transform
fftshift	numpy.fft.fftshift	shift zero-frequency component to the center of the spectrum
ifftshift	numpy.fft.ifftshift	inverse fftshift
ifft2	numpy.fft.fifft2	inverse 2d fft
interp2	scipy.interpolate.RectBivariateSpline or scipy.interpolate.interp2	Interpolation for 2-D gridded data in meshgrid format
imshowpair	skimage.measure.structural_similarity	Compare differences between 2 images
imregconfig		Creates configurations to perform intensity-based image registration
imregister		Intensity-based image registration
imregtform	skimage.feature.register_translation or skimage.transform.estimate_transform	Estimate geometric transfomation to align two images
imwarp	skimage.transform.warp	Apply geometric transformation to an image
imref2d		Reference 2d image to xy-coordinates
corr2	scipy.signal.correlate2d	2d correlation coefficient
optimset		Create of edit optimizations options for passing to fminbnd, fminsearch, fzero, or lsqnonneg
lsqcurvefit	scipy.optimize.curve_fit	Solve nonlinear curve-fitting problems
fastica	sklearn.decomposition.FastICA	fast fixed-point algorithm for independent component analysis and projection pursuit
kmeans	sklearn.cluster.Kmeans	kmeans clustering
fsolve	scipy.optimize.root(func, x0, method=’anderson’)	Root finding. Scipy does not have a trust-region dogleg method that functions exactly like Matlab’s fsolve. The ‘anderson’ method reproduces the results in many cases. Other methods may need to be explored for other problems.

Basic Plotting

Matlab Function	Python Equivalent	Description
figure	matplotlib.pyplot.figure	Create a new figure object
clf	figure.clf	clear figure; shouldn’t be needed in Python since each figure will be a unique object
subplot	figure.subplots or figure.add_subplot	1st creates a set of subplots in the figure, 2nd creates one subplot and adds it to the figure
plot	figure.plot or axes.plot	Add lineplot to current figure
title	object.title	Title of plot; better to define on object creation if possible
xlabel	axes.xlabel	Label for the x-axis of plot
ylabel	axes.ylabel	Label for the y-axis of plot
imagesc	pyplot.imshow or pyplot.matshow	Scale image data to full range of colormap and display
axis	axes.axis	Axis properties
surf	axes3d.plot_surface or axes3d.plot_trisurf	Plot a 3d surface, need to uses mpl_toolkits.mplot3d and Axes3d; which you use depends on data format
shading		Set during plot creation as argument
view	axes3d.view_init	Change the viewing angle for a 3d plot
colormap	plot.colormap	Set the colormap; better to do so at plot creation if possible
colorbar	figure.add_colorbar(axes)	Add colorbar to selected axes