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|
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 |
+-----------------+--------------------------------------------+-------------------------------------------------------------------------------------------------------+
|
