Python Library for Signal/Image Data Analysis with Transport Methods

Last update: Dec 23, 2022

Related tags

Deep Learning PyTransKit

Overview

PyTransKit

Python Transport Based Signal Processing Toolkit

Website and documentation: https://pytranskit.readthedocs.io/

Installation

The library could be installed through pip

pip install pytranskit

Alternately, you could clone/download the repository and add the pytranskit directory to your Python path

import sys
sys.path.append('path/to/pytranskit')

from pytranskit.optrans.continuous.cdt import CDT

Low Level Functions

CDT, SCDT

Cumulative Distribution Transform (CDT) [1] tutorial [notebook] [nbviewer]
Signed Cumulative Distribution Transform (SCDT) [6] tutorial [notebook] [nbviewer]
SCDT tutorial with domain adaptation [notebook] [nbviewer]

R-CDT

Radon-CDT tutorial [notebook] [nbviewer]
3D Radon-CDT tutorial [notebook][nbviewer]

CLOT

Continuous Linear Optimal Transport Transform (CLOT) tutorial [notebook] [nbviewer]

Classification Examples

CDT Nearest Subspace (CDT-NS) classifier for 1D data [notebook] [nbviewer]
SCDT Nearest Subspace (SCDT-NS) classifier for 1D data [8] [notebook] [nbviewer]
Radon-CDT Nearest Subspace (RCDT-NS) classifier for 2D data [4] [notebook] [nbviewer]
3D Radon-CDT Nearest Subspace (3D-RCDT-NS) classifier for 3D data [notebook] [nbviewer]

Estimation Examples

Time delay estimation using CDT [5] [notebook] [nbviewer]
Time delay and linear dispersion estimation using CDT [5] [notebook] [nbviewer]

Transport-based Morphometry

Transport-based Morphometry to detect and visualize cell phenotype differences [7] [notebook] [nbviewer]

References

Resources

External website http://imagedatascience.com/transport/

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Comments

Problem installing `bluepy` from the repo.
Problem: for my machine (machine spec mentioned below), installing requirements on this repo, as given in requirements.txt throws the following error.

error: legacy-install-failure × Encountered error while trying to install package. ╰─> bluepy note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

This error is in context with mention of bluepy in requirements.txt.

Machine Specs:

miniconda venv for python 3.9.12 running on MacOS Monterey; CPU: Apple M2.

miniconda venv for python 3.10.4 running on Ubuntu Jammy Jellyfish; CPU: AMD Ryzen.

Interesting Note: I don't find bluepy being directly imported in the code on the master or the CDT-app-gui branch.

Proposed Solution:

Remove bluepy from requirements.txt

Note: This is not a problem with installing PyTranskit itself. It installs pretty gracefully through pip.
opened by Ujjawal-K-Panchal 1
Changed filter to filter_name

In the radoncdt.py file passing the option filter was not working since scikit-image expects the key filter_name.

Tutorial 2 was failing for this reason.

opened by giovastabile 0
Create a "NS" classifier

Create a "NS" classifier, as an standalone implementation of the nearest subspace classification method. The "RCDT_NS" and "CDT-NS" classifier can be a subclass of this classifier.

opened by xuwangyin 0

Issue when setting forward('rm_edge = True')

This possibly just needs an edit to reduce the size of the reference signal array alongside the reduction in size of the signal with removed edges.

File "\RCDT_Basic_Tests.py", line 115, in <module>
    Irev = rcdt.inverse(Ihat, temp, nlims)

  File "\pytranskit\optrans\continuous\radoncdt.py", line 123, in inverse
    return self.apply_inverse_map(transport_map, sig0, x1_range)

  File "\pytranskit\optrans\continuous\radoncdt.py", line 235, in apply_inverse_map
    sig1_recon = match_shape2d(sig0, sig1_recon)

  File "\pytranskit\optrans\utils\data_utils.py", line 81, in match_shape2d
    raise ValueError("A is bigger than B: "

ValueError: A is bigger than B: (250, 250) vs (248, 248)

opened by TobiasLong 0

Releases(0.1)

0.1(Oct 29, 2019)

Source code(tar.gz)
Source code(zip)

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