NinWavelets

This is a python package for analystic wavelet transform.
Generalized Morse(GMW), Morlet and so on.
It can also perform CWT based on GMW.

This project is just my hobby, and I am not an engineer or scholar.
There may be lots of bugs. Ofcource it is free to use.
BUT you should not use this package for work! m9(^q^) PooGyaaaaa!

This is my alpha band of EEG which was processed by this package.

Why NinWavelets?

There may be some advantages.

Use wavelets which is originally Frourier transformed
- Generalized Morse
- Morlet/Gabor(Frourier transformed version)
- Shannon(It looks like Haar, when fourier transformed)
- May be more(It is scalable)
Skipping one FFT when performing CWT.
- May be better and faster if you use FFT method.
Cuda
- If you want to process long wave, it may be faster.
Compatibility
- You can use it with mne-python.(Now, sensor based only...)

There are some critical limitations, too.
See Advantages and Limitations.

Install

pip install git+https://github.com/uesseu/ninwavelets

Dependency

python 3.6.5 or newer(It involves type hint and annotation)

These are automatically installed.

Scipy
numpy
cupy

If you want to use cuda, please setup cuda.
https://developer.nvidia.com/cuda-zone
https://www.geforce.com/drivers
It is faster if you process long wave, like my EEG power example.

Optionally, if you want to process EEG/MEG, you can use this.

mne

pip install mne

At first, it was written for mne python.
but I found that, using mne function with this package is ugly way.
(Because it needs inverse Fourier transform to no purpose.)
Now it has own CWT method.

It is brand new project, and under heavily development.
Destructive changes may be made m9(^q^) PooGyaaaaa!.

Exsamples

GMW is similar to morlet wavelet, if you use default param.

You can calculate power.

from ninwavelets import Morse

morse = Morse(1000, gamma=3, beta=17.5)
freq = 60
time = np.arange(0, 0.3, 0.001)

# Now lets analyze sin wave!
sin = np.array([np.sin(time * freq * 2 * np.pi)])

result = morse.power(sin, range(1, 100))
plt.imshow(result, cmap='RdBu_r')
plt.gca().invert_yaxis()
plt.title('CWT of 60Hz sin wave')
plt.show()

You can also calculate power.

result = morse.power(sin, range(1, 100))

You can perform baseline correction.

from ninwavelets import Baseline

wave = Baseline(wave, 1000, 0, 0.2).zscore()

You can also use plot_tf(). It can plot result with colorbar.

from ninwavelets import plot_tf
plot_tf(result)

If you just want to perform cwt only, write like this.

result = morse.cwt(sin, range(1, 100))

If you are mne user, epochs can be processed. See 'NinWavelets for MNE'.

These are results from my test code.

Reference

WaveletClasses

They are classes for wavelet.
They are sub class of WaveletBase.
You can inherit 'WaveletBase' class and make your own wavelet.
I wrote some wavelets.

For example, lets see Morse class!

from ninwavelets import Morse

Morse(self, sfreq: float = 1000,
      b: float = 17.5, r: float = 3,
      length: float = 10,
      interpolate=False, cuda: bool = False) -> None:

Parameters

Param	Type	Default
sfreq	float	1000Hz	Sampling frequency.
b	float	17.5	beta value
r	float	3	gamma value. 3 may be good value.
length	float	10	Length paramater. It affects only when you plot wavelets.
interpolate	bool	False	Interpolate frequencies which is higher than nyquist freq.
cuda	bool	False	Use cuda or not. See 'Performance of wavelet transform'.

morse = Morse()

interpolate=True makes your code faster.
(Up to half time)
But, I dont know whether it is good or bad...

This is an example.
List of wavelet classes is this.
All of them are in module 'nin_wavelets.wavelets' and you can use it by this code.

from nin_wavelets import hoge

Name	Name in this package
Generalized Morse	Morse
Complex Morlet	Morlet
Complex Shannon	Shannon
Gausian(Gabor)	Morlet(gabor option is available)
MexicanHat	MexicanHat
Haar	Haar(This is not good!)

make_wavelets

Exsample.

wavelet = Morse(1000, 17.5, 3).make_wavelets([10])[0]

Make list of wavelets.

Param	Type
freq	float	List of frequencies.

Because it returnes bad wave easily,
you should use it when you plot it only.
For example, GMW with sfreq=1000, freq=3 returnes bad wave.
If you want good wave, you must set

Returns
MorseWavelet: list of np.ndarray

make_fft_waves

make_fft_waves(self, total: float, one: float,
               freqs: Iterable) -> Iterator:

Make Fourier transformed Wavelet. If the wavelet is originally Frourier transformed wavelet, it just calculate original formula. If wavelet is originally not Fourier transformed wavelet, it run FFT to make them.

cwt

CWT method.

Param	Type
wave	float	Wave drawed by numpy.
freqs	float	List of frequencies.
max_freq	float	Max freq.
reuse	bool	Reuse wavelets you made before. If true, calculation becomes faster.

def cwt(self, wave: np.ndarray,
        freqs: Union[List[float], range, np.ndarray],
        max_freq: int = 0, reuse=True) -> np.ndarray:

example

import numpy as np
freq: float = 60
length: float = 5

time: np.ndarray = np.arange(0, length, 0.001)
sin = np.array(np.sin(time * freq * 2 * np.pi))
morse = Morse()
result = morse.cwt(sin, np.arange(1, 1000, 1))
plt.imshow(np.abs(result), cmap='RdBu_r')
plt.show()

max_freq is a param to cut result.

power

power(self, wave: np.ndarray,
      freqs: Union[List[float], range, np.ndarray],
      reuse=True) -> np.ndarray:

Run cwt of mne-python, and compute power.

Param	Type
wave	float	Wave drawed by numpy.
freqs	float	List of frequencies.
max_freq	float	Max freq.
reuse	bool	Reuse wavelets you made before. If true, calculation becomes faster.

Returns
Result of cwt. np.ndarray.

MorseMNE Class(Bad way)

MorseMNE class to use function of MNE-python,
which is Great package to analyze EEG/MEG.
It is same as Morse class except cwt but
if you run cwt, it uses mne.time_frequency.tfr.cwt to run cwt.

But it is not recommended, because mne.time_frequency.tfr.cwt needs
wavelet which is 'not Fourier transformed'.
Basically, GMW is a wavelet which is originally
'Fourier transformed wavelet' and so, you need to run
InverseFourier transform before you perform CWT.
I think, this ugly class is disgusting.

By the way, there is a formula of Morlet wavelet which is Fourier transformed.
And so, I think, it may be better to use the formula
even if you use Morlet Wavelet.

Baseline Class

NinWavelets supports baseline correction.

def __init__(self, wave: Array, sfreq: float,
             start: float, stop: float) -> None:

You need to import Baseline. In this case, wave was read as 'wave'.

from ninwavelets import Baseline

baseline = Baseline(wave, 1000, 0, 0.2)
wave = baseline.zscore()

In this case, 1000 is sampling frequency. 0 ~ 0.2 second is range for baseline correction.

There are these methods.

mean: subtraction
ratio: division
percent: division after subtraction
log: log10 after division
zscore: standize after subtraction
zlog: log10 after zscore

NinWavelets for MNE

ninwavelets.EpochsWavelet is a class for Epochs class of mne.

'''python from ninwavelets import EpochsWavelet, Morse, plot_tf from mne import read_epochs

fname = 'hoge_epo.fif' epochs = read_epochs(fname) morse = Morse() result = EpochsWavelet(epochs, morse).power(range(1, 100)) plot_tf(result) '''

At first, make instance of wavelets(Morse, Morlet and so on). Then, make EpochsWavelet class. This has methods named cwt, power and itc. plot_tf is a function to plot numpy array.

WaveletBase Class

Super class of wavelets. You can inherit this class and make new wavelets.

After inherit this, you can edit these methods.

BaseWavelet.formula
BaseWavelet.trans_formula
BaseWavelet.peak_freq

At first, you need to overwrite them.
They needs to written by numpy.
These methods are used in the class,
and bothering procedures are done.

Way to inherit

This is an example. This code is sub class of BaseWavelet, and is ninwavelets.MorletWavelet.

class Morlet(WaveletBase):
    '''
    Morlet Wavelets.
    Example.
    >>> morse = Morse(1000, sigma=7.)
    >>> freq = 60
    >>> time = np.arange(0, 0.3, 0.001)
    >>> sin = np.array([np.sin(time * freq * 2 * np.pi)])
    >>> result = morse.power(sin, range(1, 100))
    >>> plt.imshow(result, cmap='RdBu_r')
    >>> plt.gca().invert_yaxis()
    >>> plt.title('CWT of 60Hz sin wave')
    >>> plt.show()

    Parameters
    ----------
    sfreq: float | Sampling frequency.
        This behaves like sfreq of mne-python.
    sigma: float | sigma value
    length: float | Length of wavelet.
        It does not make sence when you use fft only.
        Too long wavelet causes slow calculation.
        This param is cutting threshould of wavelets.
        Peak wave * length is the length of wavelet.

    Returns
    -------
    As constructor, Morse instance its self.
    '''

    def __init__(self, sfreq: float = 1000, sigma: float = 7.,
                 real_wave_length: float = 1.,
                 gabor: bool = False, interpolate: bool = False,
                 cuda: bool = False) -> None:
        super(Morlet, self).__init__(sfreq, real_wave_length,
                                     interpolate, cuda)
        self.mode = WaveletMode.Both
        self.sigma = sigma
        self.c = np.float_power(1 +
                                np.exp(-np.float_power(self.sigma, 2) / 2)
                                - 2 * np.exp(-3 / 4
                                             * np.float_power(self.sigma, 2)),
                                -1/2)
        self.k = 0 if gabor else np.exp(-np.float_power(self.sigma, 2) / 2)

    def cp_trans_formula(self, freqs: cp.ndarray,
                                 freq: float = 1.) -> cp.ndarray:
        freqs = freqs / freq * self.peak_freq(freq)
        result = (self.c * cp.pi ** (-1/4) *
                  (cp.exp(-cp.square(self.sigma-freqs) / 2) -
                   self.k * cp.exp(-cp.square(freqs) / 2)))
        return result

    def trans_formula(self, freqs: np.ndarray,
                              freq: float = 1) -> np.ndarray:
        freqs = freqs / freq * self.peak_freq(freq)
        return (self.c * np.float_power(np.pi, (-1/4)) *
                (np.exp(-np.square(self.sigma-freqs) / 2) -
                 self.k * np.exp(-np.square(freqs) / 2)))

    def formula(self, timeline: np.ndarray,
                        freq: float = 1) -> np.ndarray:
        return (self.c * np.float_power(np.pi, (-1 / 4))
                * np.exp(-np.square(timeline) / 2)
                * (np.exp(self.sigma * 1j * timeline) - self.k))

    def peak_freq(self, freq: float) -> float:
        return self.sigma / (1. - np.exp(-self.sigma * freq))

All you should do is write formula.
The formulas may be written in mathmatical papers! ;)

Perfomance of wavelet formulas

These formulas are usually complicated like this code.
And so, making wavelets takes much time.

Operator

**

is slower than 'np.float_power'.
And 'np.float_power' is slower than 'np.exp'.
These are critical for speed.

Optionally, you can write code for cupy.
cupy is faster only when data is big.
There is no method named 'cp.float_power' in cupy.
And so, I divided method for cupy.
Name is 'cp_trans_formula'.
Please write code for cupy in the method.

I performed benchmark test by my NotePC
'Dell G3 15-3579r' with Intel corei7(4.1Ghz 6core) and Geforce 1050.

Length	back ground	CWT time
1sec	cupy	1.28sec
1sec	numpy	0.872sec
50sec	cupy	7.25sec
50sec	numpy	15.9sec

Advantages and Limitations

Method

Mathmatically, DFT is not good way.
We have no good method to perform Fourier transform by digital computer.
Method of convolve is good way for Wavelet transform.
But GMW needs Frourier transform.
Further more, convolving needs long long loooong time.
It is not good for Morlet wavelet too.
There may be some methods.

1

Convolve(wave, wavelet)  # Very good, but slow!

2

iFFT(FFT(wave) * FFT(wavelet))  # Fast, and widely used. But not good.

3

iFFT(FFT(wave) * FFTed_wavelet)  # Better and faster than 2.

I adopted method 3. Not only GMW, but also Morlet wavelet will be performed by 3.

It is just my hobby

It is just my hobby. I am not professional person.
Further more, I am not an engineer or PhD or Master.
Just a man.

Licence

'This software is released under the MIT License, see LICENSE.txt.'
I wanted to write so. But, tellilng you my name thought SNS is said 'Not good!' in my country.
Mit licence requires my name... I am confused.

TODO

Other wavelets
- Morse
- Morlet
- Gabor
- Mexican hat
- Shannon
- Haar
- Scalability for unknown wavelets
More methods
- Decimation
- DWT
- 2D wavelet
Use cuda or cython and speedup!
- It was cythonized before. But it is not good for scalability.
- It may be faster with cupy if you process long wave.
Kill typos(I am a Nip and not good at English) ;(
Licence
- Whether write my name or not.
- Which licence to use.

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README.md

README.md

NinWavelets

Why NinWavelets?

Install

Dependency

Exsamples

Reference

WaveletClasses

make_wavelets

make_fft_waves

cwt

power

MorseMNE Class(Bad way)

Baseline Class

NinWavelets for MNE

WaveletBase Class

Way to inherit

Perfomance of wavelet formulas

Advantages and Limitations

Method

It is just my hobby

Licence

TODO

Files

README.md

Latest commit

History

README.md

File metadata and controls

NinWavelets

Why NinWavelets?

Install

Dependency

Exsamples

Reference

WaveletClasses

make_wavelets

make_fft_waves

cwt

power

MorseMNE Class(Bad way)

Baseline Class

NinWavelets for MNE

WaveletBase Class

Way to inherit

Perfomance of wavelet formulas

Advantages and Limitations

Method

It is just my hobby

Licence

TODO