diff --git a/.gitignore b/.gitignore
index 3c2ae5f..54233f1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
data
env
output
+trash
# Mac Stuff
*.DS_Store
diff --git a/.python-version b/.python-version
index d8a96f8..675903c 100644
--- a/.python-version
+++ b/.python-version
@@ -1 +1 @@
-chirpdet
+chirpdetection
diff --git a/Chirpdetection poster script.md b/Chirpdetection poster script.md
deleted file mode 100644
index 3868fd3..0000000
--- a/Chirpdetection poster script.md
+++ /dev/null
@@ -1,141 +0,0 @@
----
-date: 2023-01-26
-author: Patrick Weygoldt
-type: talk
-speakers:
- - name:
- affiliation:
- - name:
- affiliation:
-aliases:
-tags:
----
-# Chirp detection poster script
-
-## 10 minute presentation
-
-introduction:
-- Project goal: Develop a chirp detection algorithm
-- What are chirps?
- - short frequency excursions in ms range of EOD (electric organ discharge) of weakly el. fish.
-- Show plot:
- - spectrogram of the EODf of two fish (two lines)
- - frequency resolution 150Hz
- - nfft: number of windows/datapoints over which the Fourier transform is performed
- - frequency over time is shown
- - color indicates power
- - chirp = upper line, frequency increases shortly
- - Problem:
- - to resolve chirps on the time domain, frequency domain too coarse
- - if lower fish chirps it becomes even harder
- => time-frequency uncertainty problem (general)
-- Goal: Improve existing detection methods to detect and assign chirps for electric recordings with n fish
-
-Chirp detection algorithm
-Availabe data:
-1. Raw electrical signal (EOD of multiple fish) over n electrodes (n = 11)
-2. Tracked frequency bands on spectrogram (pre-tracked): just as in upper right plot, but with lower sampling rate (3Hz)
- - for one frequency we want the electrode on which the power of the f is the greatest
- - power of the strongest of 11 electrodes for each frequencypoint in time was used to track the frequency band
- - we cannot track freq on spectrogram's time resolution is too low for detecting chirps if you wanna distinguish between the fish
-Feature extraction (in 5s rolling window):
-1. Bandpass filter around the tracked frequency band for one individual (+-5Hz)
- - first subplot grey, red = envelope of filtered baseline
-2. Dynamic bandpass filter above baseline (+-5Hz) = 2nd subplot, gray filtered search frequency, orange = envelope
- - dynamic search window above the current fish of interest
- - Why dynamic: if another fish has a higher frequency, we need to find a window without another fish to be able to detect the chirp
- - window above fish: look if there's another fish (array stuff), True/false thing, find longest subarray
- - chirps excursions always increase the frequency and decrease the amplitude
- - to find chirp, we need to search above the fish and look for break down in amplitude
- - no peaks in filtered above = no chirp
- - amplitude break down of baseline can have multiple reasons (e.g. fish swims away, stone)
-3. Instantaneous frequency of baseline = 3rd subplot, gray filtered inst., yellow = envelope
- - calculated on filtered raw data
- - get zero crossings of each period and calculate frequency manually
- - we know that chirps are increases in frequency, here we look at the frequency feature of chirps
-Peak detection:
-1. Detect peaks on bandpass filtered and inverted baseline envelope (lower red line)
-2. Detect peaks on bandpass filtered search frequency (lower orange line)
-3. Detect peaks on absolute inst. freq (lower yellow line)
- - Peak prominence: Minimal distance from highest peak to next peak
-Peak classification:
-- all three features have to be present at once in a 20ms window (appr. chirp length) in strongest electrodes
-- mean of peak timestamps of features is saved as chirp timestamp
-
-Chirps in dyadic competitions
-1. Competition experiment by Til Raab:
- - two fish compete for one shelter
- - 6h recording, 3h light, 3h dark
- - electrical and video recordings
- - with video recordings, behavior was tracked and assigned to an antagonistic category: Chasing (on- and offset) and physical contacts
-- we did behavioral analysis with the detected chirps of our algorithm
-2. Plot: Contact an chasing event timepoints, chirps of both fish, tracked frequency bands
- - from literature: Chirps assumed as submissive signal by loser fish
-4. Winner Loser boxplot
- - chirps counts for winner and loser (n=22 recordings with winner and loser)
- - loser tends to chirp more (Wilcoxon not significant, but trend with 0.054)
- - white lines are paired fish for competition
-5. Size difference plot
- - Literature: Larger wish usually wins. (Larger resource holding potential theory, Till with rises)
- - The smaller the size difference between fish, the more chirps are emitted taken winner and loser together
- - correlation within winners and losers are not significant
- - n = 21 because one recording with equal fish size was excluded
-6. Frequency plot
- - Literature: Males are more aggressive and chirp more, males have a lower EODf
- - EODf has no effect on the competition outcome
-
-Chirps emitted by loser fish might stop chasing events
-- Chirps were centered around the timestamps of each event in a +-60s time window (for each category and each recording)
-- kernel density estimation of centered chirps (gaussian kernel with 2s width and 10ms resolution)
-- We show some example plots
-1. First plot: No correlation case for chasing offset
- - no correlation between chirping and the offset
- - this was the case for most recordings and all events
-2. Second plot: Correlation case for chirping and offset
- - For some few dyads/individuals, chirp rate increases drastically before the chasing offset
- - also slightly visible before chasing onsets
- - no correlation for physical contacts
-3. Third plot: Time of chasing events in the night VS the chirps during the chasing events and during night
- - fraction of chirps during chasings is not increased relative to the fraction of chasing events overall
- - Chirps do not seem to have an increased significance for chasing events
- - only for some few dyads the chirp rate increased during chasings
-- Gray/black areas:
- - bootstrapped data (n = 50)
- - all chirps for one recording during the night (because there more chirps)
- - all shuffled chirps again centered around event and convolved
-
-Conclusion:
-- First tests indicate that our algorithm is able to detect chirps in recordings of multiple fish
-- Algorithm results were applied on behavioral data for further analysis
-
-
-## 2 Minute presentation
-
-Introduction:
-- Project goal: Develop a chirp detection algorithm
-- What are chirps?
- - Short frequency excursions in ms range of EOD (electric organ discharge) of weakly el. fish.
- - to resolve chirps on the time domain, frequency domain too coarse, especially for multiple fish
-- Goal: Improve existing detection methods
-
-Detection algorithm
-- Improved existing detection methods by extracting 3 features that change during a chirp but are not limited by the time frequency uncertainty
- 1. Amplitude drop of EOD (show trough)
- 2. Peaks of instantaneous frequency of EOD
- 3. Peaks in the dynamically adjusted frequency band above the fish's baseline EODf (special).
-- Detected and classified peaks are chirp times
-
-Application: Chirps during competition
-- Detected over 10000 chirps in real data from a competition experiment
-- Analysis of the relationship of chirps and competition events
-- Fish competed for a shelter
-- Were able to replicate some findings from literature
- - e.g. loser fish tend to chirp more
- - Other findings are not that clear and require the consideration of more factors, e.g. sex
-- We explored how the chirp rate changes during onsets and offsets of chasing events
- - For some recordings, chirping increased strongly before the offset of a chasing, for some nothing happens
- - The number of chirps during chasings is only elevated for some dyads
-
-Conclusion
-- Algorithm can be used to detect chirps
-- We could replicate some literature findings and motivate further examination
\ No newline at end of file
diff --git a/README.md b/README.md
index 3edd598..dfdebf1 100644
--- a/README.md
+++ b/README.md
@@ -1,31 +1,5 @@
<!-- Improved compatibility of back to top link: See: https://github.com/othneildrew/Best-README-Template/pull/73 -->
<a name="readme-top"></a>
-<!--
-*** Thanks for checking out the Best-README-Template. If you have a suggestion
-*** that would make this better, please fork the repo and create a pull request
-*** or simply open an issue with the tag "enhancement".
-*** Don't forget to give the project a star!
-*** Thanks again! Now go create something AMAZING! :D
--->
-
-
-
-<!-- PROJECT SHIELDS -->
-<!--
-*** I'm using markdown "reference style" links for readability.
-*** Reference links are enclosed in brackets [ ] instead of parentheses ( ).
-*** See the bottom of this document for the declaration of the reference variables
-*** for contributors-url, forks-url, etc. This is an optional, concise syntax you may use.
-*** https://www.markdownguide.org/basic-syntax/#reference-style-links
--->
-<!-- [![Contributors][contributors-shield]][contributors-url] -->
-<!-- [![Forks][forks-shield]][forks-url] -->
-<!-- [![Stargazers][stars-shield]][stars-url] -->
-<!-- [![Issues][issues-shield]][issues-url] -->
-<!-- [![MIT License][license-shield]][license-url] -->
-<!-- [![LinkedIn][linkedin-shield]][linkedin-url] -->
-
-
<!-- PROJECT LOGO -->
<br />
@@ -37,7 +11,7 @@
<h3 align="center">chirpdetector</h3>
<p align="center">
- An algorithm to detect the chirps of weakly electric fish.
+ An algorithm to detect the chirps of weakly electric fish on multielectrode recordings.
<br />
<a href="https://github.com/github_username/repo_name"><strong>Explore the docs »</strong></a>
<br />
@@ -56,31 +30,14 @@
<details>
<summary>Table of Contents</summary>
<ol>
- <li>
- <a href="#about-the-project">About The Project</a>
- <ul>
- <li><a href="#built-with">Built With</a></li>
- </ul>
- </li>
- <li>
- <a href="#getting-started">Getting Started</a>
- <ul>
- <li><a href="#prerequisites">Prerequisites</a></li>
- <li><a href="#installation">Installation</a></li>
- </ul>
- </li>
+ <li><a href="#about-the-project">About The Project</a></li>
+ <li><a href="#getting-started">Getting Started</a></li>
<li><a href="#usage">Usage</a></li>
- <li><a href="#roadmap">Roadmap</a></li>
- <li><a href="#contributing">Contributing</a></li>
- <li><a href="#license">License</a></li>
- <li><a href="#contact">Contact</a></li>
- <li><a href="#acknowledgments">Acknowledgments</a></li>
+ <li><a href="#to-do">Roadmap</a></li>
</ol>
</details>
-
-<!-- ABOUT THE PROJECT -->
## About The Project
[![Product Name Screen Shot][product-screenshot]](https://example.com)
@@ -90,98 +47,11 @@ Here's a blank template to get started: To avoid retyping too much info. Do a se
<p align="right">(<a href="#readme-top">back to top</a>)</p>
-```sh
- .
-├── 2022-06-02-10_00
-│ ├── 2022.06.02_0.mp4
-│ ├── analysis
-│ │ ├── baseline_freq_times.npy
-│ │ ├── baseline_freqs.npy
-│ │ ├── fish_freq.npy
-│ │ ├── fish_freq_interp.npy
-│ │ ├── frame_times.npy
-│ │ ├── rise_idx.npy
-│ │ └── rise_size.npy
-│ ├── backup
-│ │ ├── fund_v.npy
-│ │ ├── ident_v.npy
-│ │ ├── idx_v.npy
-│ │ ├── meta.npy
-│ │ ├── sign_v.npy
-│ │ ├── spec.npy
-│ │ └── times.npy
-│ ├── chirp_ids.npy
-│ ├── chirps.npy
-│ ├── chirps_ids.npy
-│ ├── fill_freqs.npy
-│ ├── fill_spec.npy
-│ ├── fill_spec_shape.npy
-│ ├── fill_times.npy
-│ ├── fishgrid.cfg
-│ ├── fund_v.npy
-│ ├── ident_v.npy
-│ ├── idx_v.npy
-│ ├── LED_frames.npy
-│ ├── led_idxs.csv
-│ ├── led_times.csv
-│ ├── LED_val.npy
-│ ├── meta.npy
-│ ├── sign_v.npy
-│ ├── spec.npy
-│ ├── times.npy
-│ └── traces-grid1.raw
-└── mount_data
-```
-
-
-<!-- ### Built With -->
-
-<!-- * [![Next][Next.js]][Next-url] -->
-<!-- * [![React][React.js]][React-url] -->
-<!-- * [![Vue][Vue.js]][Vue-url] -->
-<!-- * [![Angular][Angular.io]][Angular-url] -->
-<!-- * [![Svelte][Svelte.dev]][Svelte-url] -->
-<!-- * [![Laravel][Laravel.com]][Laravel-url] -->
-<!-- * [![Bootstrap][Bootstrap.com]][Bootstrap-url] -->
-<!-- * [![JQuery][JQuery.com]][JQuery-url] -->
-
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
-
-
-<!-- GETTING STARTED -->
## Getting Started
This is an example of how you may give instructions on setting up your project locally.
To get a local copy up and running follow these simple example steps.
-<!-- ### Prerequisites -->
-
-<!-- This is an example of how to list things you need to use the software and how to install them. -->
-<!-- * npm -->
-<!-- ```sh -->
-<!-- npm install npm@latest -g -->
-<!-- ``` -->
-
-### Installation
-
-1. Get a free API Key at [https://example.com](https://example.com)
-2. Clone the repo
- ```sh
- git clone https://github.com/github_username/repo_name.git
- ```
-3. Install NPM packages
- ```sh
- npm install
- ```
-4. Enter your API in `config.js`
- ```js
- const API_KEY = 'ENTER YOUR API';
- ```
-
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
-
<!-- USAGE EXAMPLES -->
## Usage
@@ -193,68 +63,80 @@ _For more examples, please refer to the [Documentation](https://example.com)_
<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
-<!-- ROADMAP -->
-## Roadmap
+## To do
- [ ] Feature 1
- [ ] Feature 2
- [ ] Feature 3
- [ ] Nested Feature
-See the [open issues](https://github.com/github_username/repo_name/issues) for a full list of proposed features (and known issues).
-
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
-
-
-<!-- <!-1- CONTRIBUTING -1-> -->
-<!-- ## Contributing -->
-
-<!-- Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated**. -->
-
-<!-- If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". -->
-<!-- Don't forget to give the project a star! Thanks again! -->
-
-<!-- 1. Fork the Project -->
-<!-- 2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`) -->
-<!-- 3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`) -->
-<!-- 4. Push to the Branch (`git push origin feature/AmazingFeature`) -->
-<!-- 5. Open a Pull Request -->
-
-<!-- <p align="right">(<a href="#readme-top">back to top</a>)</p> -->
-
-
-
-<!-- <!-1- LICENSE -1-> -->
-<!-- ## License -->
-
-<!-- Distributed under the MIT License. See `LICENSE.txt` for more information. -->
-
-<!-- <p align="right">(<a href="#readme-top">back to top</a>)</p> -->
-
-
-
-<!-- CONTACT -->
-## Contact
-
-Your Name - [@twitter_handle](https://twitter.com/twitter_handle) - email@email_client.com
-
-Project Link: [https://github.com/github_username/repo_name](https://github.com/github_username/repo_name)
-
<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
-<!-- ACKNOWLEDGMENTS -->
-## Acknowledgments
-
-* []()
-* []()
-* []()
-
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
+<!-- # Chirp detection - GP2023 -->
+<!-- ## Git-Repository and commands -->
+
+<!-- - Go to the [Bendalab Git-Server](https://whale.am28.uni-tuebingen.de/git/) (https://whale.am28.uni-tuebingen.de/git/) -->
+<!-- - Create your own account (and tell me ;D) -->
+<!-- * I'll invite you the repository -->
+<!-- - Clone the repository -->
+<!-- - -->
+<!-- ```sh -->
+<!-- git clone https://whale.am28.uni-tuebingen.de/git/raab/GP2023_chirp_detection.git -->
+<!-- ``` -->
+
+<!-- ## Basic git commands -->
+
+<!-- - pull changes in git -->
+<!-- ```shell -->
+<!-- git pull origin <branch> -->
+<!-- ``` -->
+<!-- - commit chances -->
+<!-- ```shell -->
+<!-- git commit -m '<explaination>' file # commit one file -->
+<!-- git commit -a -m '<explaination>' # commit all files -->
+<!-- ``` -->
+<!-- - push commits -->
+<!-- ```shell -->
+<!-- git push origin <branch> -->
+<!-- ``` -->
+
+<!-- ## Branches -->
+<!-- Use branches to work on specific topics (e.g. 'algorithm', 'analysis', 'writing', ore even more specific ones) and merge -->
+<!-- them into Master-Branch when it works are up to your expectations. -->
+
+<!-- The "master" branch should always contain a working/correct version of your project. -->
+
+<!-- - Create/change into branches -->
+<!-- ```shell -->
+<!-- # list all branches (highlight active branch) -->
+<!-- git banch -a -->
+<!-- # switch into existing -->
+<!-- git checkout <existing branch> -->
+<!-- # switch into new branch -->
+<!-- git checkout master -->
+<!-- git checkout -b <new branch> -->
+<!-- ``` -->
+
+
+<!-- - Re-merging with master branch -->
+<!-- 1) get current version of master and implement it into branch -->
+<!-- ```shell -->
+<!-- git checkout master -->
+<!-- git pull origin master -->
+<!-- git checkout <branch> -->
+<!-- git rebase master -->
+<!-- ``` -->
+<!-- This resets you branch to the fork-point, executes all commits of the current master before adding the commits of you -->
+<!-- branch. You may have to resolve potential conflicts. Afterwards commit the corrected version and push it to your branch. -->
+
+<!-- 2) Update master branch master -->
+<!-- - correct way: Create -->
+<!-- ```shell -->
+<!-- git checkout master -->
+<!-- git merge <branch> -->
+<!-- git push origin master -->
+<!-- ``` -->
<!-- MARKDOWN LINKS & IMAGES -->
@@ -289,3 +171,4 @@ Project Link: [https://github.com/github_username/repo_name](https://github.com/
[JQuery.com]: https://img.shields.io/badge/jQuery-0769AD?style=for-the-badge&logo=jquery&logoColor=white
[JQuery-url]: https://jquery.com
+
diff --git a/poster_frozen/figs/algorithm.pdf b/poster_printed/figs/algorithm.pdf
similarity index 100%
rename from poster_frozen/figs/algorithm.pdf
rename to poster_printed/figs/algorithm.pdf
diff --git a/poster_frozen/figs/algorithm1.pdf b/poster_printed/figs/algorithm1.pdf
similarity index 100%
rename from poster_frozen/figs/algorithm1.pdf
rename to poster_printed/figs/algorithm1.pdf
diff --git a/poster_frozen/figs/chirps_in_chasing.pdf b/poster_printed/figs/chirps_in_chasing.pdf
similarity index 100%
rename from poster_frozen/figs/chirps_in_chasing.pdf
rename to poster_printed/figs/chirps_in_chasing.pdf
diff --git a/poster_frozen/figs/chirps_winner_loser.pdf b/poster_printed/figs/chirps_winner_loser.pdf
similarity index 100%
rename from poster_frozen/figs/chirps_winner_loser.pdf
rename to poster_printed/figs/chirps_winner_loser.pdf
diff --git a/poster_frozen/figs/efishlogo.pdf b/poster_printed/figs/efishlogo.pdf
similarity index 100%
rename from poster_frozen/figs/efishlogo.pdf
rename to poster_printed/figs/efishlogo.pdf
diff --git a/poster_frozen/figs/introplot.pdf b/poster_printed/figs/introplot.pdf
similarity index 100%
rename from poster_frozen/figs/introplot.pdf
rename to poster_printed/figs/introplot.pdf
diff --git a/poster_frozen/figs/kde.pdf b/poster_printed/figs/kde.pdf
similarity index 100%
rename from poster_frozen/figs/kde.pdf
rename to poster_printed/figs/kde.pdf
diff --git a/poster_frozen/figs/logo_all.pdf b/poster_printed/figs/logo_all.pdf
similarity index 100%
rename from poster_frozen/figs/logo_all.pdf
rename to poster_printed/figs/logo_all.pdf
diff --git a/poster_frozen/figs/timeline.pdf b/poster_printed/figs/timeline.pdf
similarity index 100%
rename from poster_frozen/figs/timeline.pdf
rename to poster_printed/figs/timeline.pdf
diff --git a/poster_frozen/main.pdf b/poster_printed/main.pdf
similarity index 100%
rename from poster_frozen/main.pdf
rename to poster_printed/main.pdf
diff --git a/poster_frozen/main.tex b/poster_printed/main.tex
similarity index 100%
rename from poster_frozen/main.tex
rename to poster_printed/main.tex
diff --git a/poster_frozen/packages.tex b/poster_printed/packages.tex
similarity index 100%
rename from poster_frozen/packages.tex
rename to poster_printed/packages.tex
diff --git a/poster_frozen/poster.pdf b/poster_printed/poster.pdf
similarity index 100%
rename from poster_frozen/poster.pdf
rename to poster_printed/poster.pdf
diff --git a/poster_frozen/style.tex b/poster_printed/style.tex
similarity index 100%
rename from poster_frozen/style.tex
rename to poster_printed/style.tex
diff --git a/requirements.txt b/requirements.txt
index ad47b80..af5d16a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,3 @@
-audioio==0.10.0
cmocean==2.0
cycler==0.11.0
ipython==8.12.0
@@ -9,5 +8,4 @@ paramiko==2.11.1
PyYAML==6.0
scipy==1.10.1
scp==0.14.5
-thunderfish==1.9.10
tqdm==4.64.1