Statistics using Python

Porting Code from Matlab to Python - 2017

10 October 2017 | Rajalekshmi Deepu

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 Statistics in Matlab and python
Ø Matlab:
- Proprietary software.
- Need “Statistics” toolbox. (extra cost )
Ø Python:
- Opensource
- Extended with a fantastic ecosystem of
data-centric packages like: numpy,scipy,
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matplotlib, scikit-learn,pandas, …

10. October 2017 Porting Code from Matlab to Python 3

 Numpy and Statistics(Descriptive)
Ø Contains in-built statistical functions like Mean,
Median, Standard Deviation and Variance.
Matlab Python (using Numpy)
>> load wages.dat
>>> import numpy as np
% Mean
>>> X = [16.92, 96.10, 11.82, 44.32,
>> Mean_value = mean(wages)
55.66, 10.75]
% Median
>>> mean = np.mean(X)
>> med_value = median(wages)
>>> median = np.median(X)
% Standard deviation
>>> sd = np.std(X)
>> std_value = std(wages)
>>> variance = np.var(X)
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% Variance
>> var_value = var(wages)

10. October 2017 Porting Code from Matlab to Python 4

 ScientificPython (SciPy)
Ø Scientific Computing Package for Python.
>>> help(scipy)
Ø Built on top of Numpy and uses Numpy arrays and data types.
Ø Scipy package is organized into several sub-packages.
Ø Imports all functions in the Numpy package, and several commonly
used functions from sub-packages, into the top level namespace.
e.g: scipy.var and numpy.var
both refers to function var in module numpy.core.fromnumeric
scipy.array and numpy.array
both refers to built-in function array in module numpy.core.multiarray
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10. October 2017 Porting Code from Matlab to Python 5

 SciPy and Statistics (Inferential)

Ø SciPy offers an extended collection of statistical

tools such as distributions (continuous and discrete)
and functions.
Ø Few sub packages for statistics are:
scipy.cluster --- Vector Quantization / Kmeans
scipy.stats --- Statistical Functions
scipy.stats.t --- Student’s T test

Remember: Subpackages requires an explicit import

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e.g: >>> import scipy.cluster

>>> from scipy import stats

10. October 2017 Porting Code from Matlab to Python 6

 scipy.stats
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10. October 2017 Porting Code from Matlab to Python 7

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10. October 2017 Porting Code from Matlab to Python 8

 Scipy and Matlab

Ø scipy.io.matlab - Utilities for dealing with MATLAB

files.
Ø Included functions:
• scipy.io.loadmat - Load MATLAB file. Returns dictionary
with variable names as keys, and loaded matrices as values.
• scipy.io.savemat - Save a dictionary of names and arrays
into a MATLAB-style .mat file.
• scipy.io.whosmat - List variables inside a MATLAB file.
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Jupyter Notebook: Load_List_Save_MAT_files

10. October 2017 Porting Code from Matlab to Python 9

 Matplotlib
Ø matplotlib.mlab
Numerical python functions written for compatibility
with MATLAB commands with the same names.

MATLAB compatible functions

:func:`cohere` Coherence (normalized cross spectral density)
:func:`csd` Cross spectral density using Welch's average periodogram
:func:`detrend` Remove the mean or best fit line from an array
:func:`find` Return the indices where some condition is true; numpy.nonzero is
similar but more general.
:func:`griddata` Interpolate irregularly distributed data to a regular grid.
:func:`prctile` Find the percentiles of a sequence
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:func:`prepca` Principal Component Analysis

:func:`psd` Power spectral density using Welch's average periodogram
:func:`rk4` A 4th order runge kutta integrator for 1D or ND systems
:func:`specgram` Spectrogram (spectrum over segments of time)

10. October 2017 Porting Code from Matlab to Python 10

 Principal Component Analysis (PCA)

Ø Way of identifying patterns and expressing the data

to highlight their similarities and differences.

Ø Powerful tool for analyzing high dimensional data.

Ø Enables data compression without much loss of

information by reducing the number of dimensions.
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10. October 2017 Porting Code from Matlab to Python 11

 Matlab code for PCA (An example)
rd = load_untouch_nii('edtd.nii');
rd = double(rd.img);
sz = size(rd)
nrows = sz(1)
ncols = sz(2)
nslcs = sz(4)
s = reshape(rd,nrows*ncols,nslcs);
[coeff,score] = pca(s);
s = reshape(score,nrows,ncols,nslcs);
n = make_nii(s);
save_nii(n,'results/pca.nii')
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Ref: https://de.mathworks.com/help/stats/pca.html
https://stackoverflow.com/questions/35651133/matlab-and-python-
produces-different-results-for-pca

10. October 2017 Porting Code from Matlab to Python 12

 PCA using Python (matplotlib.mlab)

Ø Hint:
- Use matplotlib.mlab.PCA
- Imported as given below:
from matplotlib.mlab import PCA
- Dataset: edtd.nii
- Ref:
http://matplotlib.org/api/mlab_api.html#matplotlib.mlab.PCA
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http://nipy.org/nibabel/nibabel_images.html
Jupyter Notebook

10. October 2017 Porting Code from Matlab to Python 13

 Scikit-learn or sklearn
Ø Meant for machine learning in Python
Ø sklearn.cluster.KMeans
Ø ‘sklearn.decomposition’ module includes matrix
decomposition algorithms, including among others
PCA, NMF or ICA.
e.g. modules:
- sklearn.decomposition.nmf - Non-negative matrix factorization
- sklearn.decomposition.pca - Principal Component Analysis

Ø Most of the algorithms of this module can be

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regarded as dimensionality reduction techniques.

10. October 2017 Porting Code from Matlab to Python 14

 PCA using Python (sklearn)

Ø Hint:
- Use sklearn.decomposition.PCA
- Imported as given below:
from sklearn.decomposition import PCA
- Dataset: edtd.nii
- Ref:
http://scikitlearn.org/stable/modules/generated/sklearn.dec
omposition.PCA.html
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http://nipy.org/nibabel/nibabel_images.html

Jupyter Notebook Optional

10. October 2017 Porting Code from Matlab to Python 15

 Other Python modules for Statistics
Ø Seaborn : Statistical data visualization
http://seaborn.pydata.org

Ø Statsmodels : Library for statistical and econometric

analysis in Python.
http://statsmodels.sourceforge.net/
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Jupyter Notebook : seaborn_savefig

10. October 2017 Porting Code from Matlab to Python 16

 References
The Python Language Reference: http://docs.python.org/2/reference/index.html
The Python Standard Library: http://docs.python.org/2/library/
https://docs.scipy.org/doc/scipy/reference/tutorial/stats.html
http://matplotlib.org/api/mlab_api.html#module-matplotlib.mlab
http://conference.scipy.org/proceedings/scipy2010/pdfs/seabold.pdf
http://seaborn.pydata.org
https://www.datacamp.com/community/data-science-cheatsheets
PEP 20 -- The Zen of Python :https://www.python.org/dev/peps/pep-0020/
https://docs.scipy.org/doc/numpy-dev/user/numpy-for-matlab-users.html
https://www.tiobe.com/tiobe-index/
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10. October 2017 Porting Code from Matlab to Python 17