From efd61b270c83da132e96b647fe34290a6a1c2103 Mon Sep 17 00:00:00 2001
From: Loic-Lenof <loic.lenof@gmail.com>
Date: Tue, 12 Jul 2022 16:21:57 +0200
Subject: [PATCH] Re-structuration + Update README
+ modified "audio_f" paths
+ added text to README.md
---
BBPs/1-BBP_detection.py | 6 ++--
BBPs/2-manual_verification.py | 6 ++--
Clicks/1-detection_of_clicks.py | 6 ++--
Clicks/3-projection_3features.py | 2 +-
Clicks/__pycache__/ClickUtils.cpython-39.pyc | Bin 6127 -> 0 bytes
README.md | 31 ++++++++++++++++++-
Whistles/1-Identification_of_whistles.py | 6 ++--
Whistles/2-get_stats_of_whistles.py | 6 ++--
8 files changed, 46 insertions(+), 17 deletions(-)
delete mode 100644 Clicks/__pycache__/ClickUtils.cpython-39.pyc
diff --git a/BBPs/1-BBP_detection.py b/BBPs/1-BBP_detection.py
index 5b0a901..2f7f7f5 100644
--- a/BBPs/1-BBP_detection.py
+++ b/BBPs/1-BBP_detection.py
@@ -22,9 +22,9 @@ print("Importation of packages done!")
#%% Parameters
# Paths
print("\rSetting up parameters...", end="\r")
-audio_f = "/media/loic/DOLPHINFREE/Acoustique" # Path to recordings
-csv_f = "./../CSV_data" # Path to data in csv
-save_f = "./Results" # Path to results
+audio_f = "./../Audio_data" # Path to recordings
+csv_f = "./../CSV_data" # Path to data in csv
+save_f = "./Results" # Path to results
# For functions
sr = 512000 # sample rate of the recordings
diff --git a/BBPs/2-manual_verification.py b/BBPs/2-manual_verification.py
index e540a24..5413427 100644
--- a/BBPs/2-manual_verification.py
+++ b/BBPs/2-manual_verification.py
@@ -23,9 +23,9 @@ print("Importation of packages done!")
#%% Parameters
print("\rSetting up parameters...", end="\r")
# Paths
-audio_f = "/media/loic/DOLPHINFREE/Acoustique" # Path to recordings
-csv_f = "./../CSV_data" # Path to data in csv
-save_f = "./Results" # Path to results
+audio_f = "./../Audio_data" # Path to recordings
+csv_f = "./../CSV_data" # Path to data in csv
+save_f = "./Results" # Path to results
# For functions
sr = 512000 # sample rate of the recordings
diff --git a/Clicks/1-detection_of_clicks.py b/Clicks/1-detection_of_clicks.py
index a189c6c..5739e8b 100644
--- a/Clicks/1-detection_of_clicks.py
+++ b/Clicks/1-detection_of_clicks.py
@@ -20,9 +20,9 @@ print("Importation of packages done!")
#%% Parameters
# Paths
print("\rSetting up parameters...", end="\r")
-audio_f = "/media/loic/DOLPHINFREE/Acoustique" # Path to audio data
-csv_f = "./../CSV_data" # Path to csv data
-save_f = "./Results/peaks_02052022" # Path to save results
+audio_f = "./../Audio_data" # Path to recordings
+csv_f = "./../CSV_data" # Path to csv data
+save_f = "./Results/peaks_02052022" # Path to save results
# Audio parameters
sr = 512000 # sample rate of the recordings
diff --git a/Clicks/3-projection_3features.py b/Clicks/3-projection_3features.py
index 54df7fb..ad7bd6d 100644
--- a/Clicks/3-projection_3features.py
+++ b/Clicks/3-projection_3features.py
@@ -24,7 +24,7 @@ print("Importation of packages done!")
#%% Parameters
print("\rSetting up parameters...", end="\r")
-audio_f = "/media/loic/DOLPHINFREE/Acoustique" # Path to audio data
+audio_f = "./../Audio_data" # Path to recordings
csv_f = "./../CSV_data" # Path to csv data
res_f = "./Results" # Path to save results
peaks_f = "peaks_02052022" # Path to save results
diff --git a/Clicks/__pycache__/ClickUtils.cpython-39.pyc b/Clicks/__pycache__/ClickUtils.cpython-39.pyc
deleted file mode 100644
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diff --git a/README.md b/README.md
index 5b42868..7fb42ba 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,31 @@
# Scripts-DOLPHINFREE
- Scripts used for mdpi article
+A repository containing scripts and data used in *Lehnhoff et al, 2022* (in submission process).
+
+## Description
+This repository contains the files used to analyse data obtained during the <a href="https://umr-marbec.fr/en/the-projects/dolphinfree/">DOLPHINFREE project</a>. The goal was to detect and identify clicks and whisltes in audio recordings of common dolphins.
+
+"BBPs", "Clicks" and "Whisltes" folders each treat a type of signal emitted by dolphins.
+- Each folder contains numbered scripts for step-by-step execution.
+- ___Utils.py files contain the functions necessary to the execution of the other scripts
+- "Results" and other subfolders contain... results and other outputs (surprise surprise).
+
+"Stats" folder contains the files used to carry on a statistical analysis of extracted data.
+"CSV_data" folder contains the visual observations made during experiments.
+"Audio_data" folder is empty. Files cannot be made available publicly due to the presence of copyrighted elements.
+
+## Get Started
+.py files were developped using Python 3.9.7.
+If needed, you can add missing packages to your environement using:
+```bash
+$ pip install name-package
+```
+
+.matlab files can be executed in matlab or octave.
+
+## Contact
+Feel free to contact me if you have questions, tips or anything else to say. I'd really appreciate it!
+
+Loïc Lehnhoff - <loic.lehnhoff@gmail.com>
+
+## Publication
+**IN SUBMISSION PROCESS:** Lehnhoff, L.; Glotin, H.; Bernard, S.; Dabin, W.; Le Gall, Y.; Menut, E.; Meheust, E.; Peltier, H.; Pochat, A.; Pochat, K.; Rimaud, T.; Sourget, Q.; Spitz, J.; Van Canneyt, O.; Mérigot, B. *Behavioural response of common *dolphins Delphinus* delphis to a bio-inspired acoustic device for limiting fishery by-catch.* Sustainability **2022**, 1, 0
\ No newline at end of file
diff --git a/Whistles/1-Identification_of_whistles.py b/Whistles/1-Identification_of_whistles.py
index f914876..766961b 100644
--- a/Whistles/1-Identification_of_whistles.py
+++ b/Whistles/1-Identification_of_whistles.py
@@ -22,9 +22,9 @@ print("Importation of packages complete!")
#%% Parameters
# Paths
print("\rSetting up parameters...", end="\r")
-audio_f = "/media/loic/DOLPHINFREE/Acoustique" # Path to recordings
-csv_f = "./../CSV_data" # Path to data in csv
-save_f = "./Trajectories" # Path were
+audio_f = "./../Audio_data" # Path to recordings
+csv_f = "./../CSV_data" # Path to data in csv
+save_f = "./Trajectories" # Path were
# Audio parameters
start = 0 # start time for signal (in sec)
diff --git a/Whistles/2-get_stats_of_whistles.py b/Whistles/2-get_stats_of_whistles.py
index eded8ab..af3151c 100644
--- a/Whistles/2-get_stats_of_whistles.py
+++ b/Whistles/2-get_stats_of_whistles.py
@@ -22,9 +22,9 @@ print("Importation of packages complete!")
#%% Parameters
print("\rSetting up parameters...", end="\r")
-audio_f = "/media/loic/DOLPHINFREE/Acoustique" # Path to recordings
-csv_f = "./../CSV_data" # Path to data in csv
-save_f = "./Trajectories" # Path were
+audio_f = "./../Audio_data" # Path to recordings
+csv_f = "./../CSV_data" # Path to data in csv
+save_f = "./Trajectories" # Path were
results_f = "./Evaluation"
keep_if = 1 # minimal length of a whistle to be kept
--
GitLab