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ffta

Fast Free Transient Analysis of atomic force microscopy data

https://github.com/rajgiriuw/ffta

Science Score: 77.0%

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    CITATION.cff file
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    Found 12 DOI reference(s) in README
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    Links to: ieee.org
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    4 of 10 committers (40.0%) from academic institutions
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    Low similarity (9.8%) to scientific vocabulary

Keywords

frequency-analysis microscopy pycroscopy
Last synced: 6 months ago · JSON representation ·

Repository

Fast Free Transient Analysis of atomic force microscopy data

Basic Info
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 11
Topics
frequency-analysis microscopy pycroscopy
Created almost 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

PyPI version Documentation Status Coverage Status

Fast-Free Transient Analysis

A package for processing time-dependent frequency response information in atomic force microscopy data. This package is primarily geared towards electrostatic force microscopy, with the resulting output being the amplitude, phase, and instantaneous frequency as a function of time and position. This includes non-stationary Fourier mode decomposition by Daniel Shea of University of Washington.

For further information and discussion, primary point-of-contact:

Dr. Raj Giridharagopal, Ph.D. Senior Research Scientist University of Washington Department of Chemistry Seattle, Washington, USA E-mail: rgiri@uw.edu

Overview

FFTA extracts Instantaneous frequency from Time-Resolved AFM data, such as Fast Free Time-Resolved Electrostatic Force Microscopy (FF-trEFM) data[1-4]. This package also returns time-to-first frequency peak (tFP) and phase from atomic force microscopy. The use case is if your experiment records AFM deflection data and you wish to reconstruct the instantaneous frequency vs time.

This includes a few types of frequency analysis: * Hilbert Transform
* Wavelet Transform (CWT, via Morlet wavelet) * Short-time Fourier Transform (STFT) * General Mode KPFM (G-KPFM) * Nonstationary Fourier Mode Decomposition (NFMD)

References

  1. Giridharagopal R, Rayermann GE, Shao G, et al. Submicrosecond time resolution atomic force microscopy for probing nanoscale dynamics. Nano Lett. 12, 893-8 (2012). DOI: 10.1021/nl203956q
  2. Karatay DU, Harrison JA, et al. Fast time-resolved electrostatic force microscopy: Achieving sub-cycle time resolution. Rev Sci Inst. 87, 053702 (2016). DOI: 10.1063/1.4948396
  3. Giridharagopal R, Precht JA, Jariwala S, Collins L, et al. Time-Resolved Electrical Scanning Probe Microscopy of Layered Perovskites Reveals Spatial Variations in Photoinduced Ionic and Electronic Carrier Motion. ACS Nano 13, 2812-21 (2019). DOI: 10/1021/acsnano.8b08390
  4. Ginger DS, Giridharagopal R, Moore DT, Rayermann GE, Reid OG. Sub-microsecond-resolution probe microscopy. US Patent US8686358B2
  5. Shea DE, Giridharagopal R, Ginger DS, Brunton SL, Kutz JN. Extraction of instantaneous frequencies and amplitudes in nonstationary time-series data. IEEE Access. In press (as of 6/14/2021). DOI: 10.1109/ACCESS.2021.3087595

Getting started

To get started and to see some examples, check out the (very much in progress) documention.

Installation

pip install ffta

Owner

  • Name: Rajiv Giridharagopal
  • Login: rajgiriUW
  • Kind: user
  • Location: Seattle
  • Company: University of Washington

Sr. Research Scientist in UW Chemistry, contributor to pycroscopy

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: FFTA (Fast Free Transient Analysis)
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Rajiv
    family-names: Giridharagopal
license: MIT

GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 600
  • Total Committers: 10
  • Avg Commits per committer: 60.0
  • Development Distribution Score (DDS): 0.172
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Raj r****i@u****u 497
Durmus U. Karatay u****y@g****m 55
LAKESIDE\LindaT18 l****8@l****g 17
Jessica Kong j****g@g****m 9
Jeff Harrison j****n@u****u 8
lindat18 t****4@y****m 4
Durmus U. Karatay u****y@u****u 4
Ginger Lab g****b@c****u 3
= = 2
JAKE-PC\Jake j****t@g****m 1
Committer Domains (Top 20 + Academic)
uw.edu: 3 chem.washington.edu: 1 lakesideschool.org: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 1
  • Total pull requests: 14
  • Average time to close issues: 19 days
  • Average time to close pull requests: about 6 hours
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.36
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rajgiriUW (1)
Pull Request Authors
  • rajgiriUW (9)
  • kongjy (3)
  • lindat18 (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 60 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 11
  • Total maintainers: 1
pypi.org: ffta

Fast Free Transient Analysis

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 60 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 19.1%
Average: 21.4%
Dependent repos count: 21.7%
Stargazers count: 27.8%
Downloads: 28.4%
Maintainers (1)
rajgiri
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • nbsphinx *
  • sphinx >=4.5.0
  • sphinx_rtd_theme *
requirements.txt pypi
  • BGlib >=0.0.3
  • igor >=0.3
  • numexpr >=2.7.1
  • numpy >=1.18.1
  • pandas >=1.1.0
  • pyUSID >=0.0.10
  • pywavelets >=1.1.1
  • scikit-image >=0.19.2
  • scipy >=1.4.1
  • sidpy >=0.0.5
  • torch >=1.6.0
setup.py pypi
  • BGlib >=0.0.3
  • igor >=0.3
  • numexpr >=2.7.1
  • numpy >=1.18.1
  • pandas >=1.1.0
  • pyUSID >=0.0.10
  • pywavelets >=1.1.1
  • scikit-image >=0.19.2
  • scipy >=1.4.1
  • sidpy >=0.0.5
  • torch >=1.6.0
.github/workflows/actions.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite