Initial commit

.gitignore

+data/
+output/
+tmp/
+poetry.lock

.idea/.gitignore

+# Default ignored files
+/shelf/
+/workspace.xml

.idea/Ecoacoustics.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Poetry (Ecoacoustics)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file

.idea/inspectionProfiles/profiles_settings.xml

+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>
\ No newline at end of file

.idea/misc.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Poetry (Ecoacoustics)" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file

.idea/modules.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/Ecoacoustics.iml" filepath="$PROJECT_DIR$/.idea/Ecoacoustics.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file

.idea/vcs.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file

conf/FS1.yaml

+data:
+  path: "data/Brazil/package-1/OP1/OP1"
+
+mic:
+  sensitivity: -4   # dBV
+  gain: 18  # dB
+
+temporal_alpha_indices:
+  dB_threshold: 3 # dB
+  rejectDuration: 0.01  
+
+spectrogram:
+  window: "hann"
+  nperseg: 1024 
+  noverlap: 512
+
+spectral_alpha_indices:
+  flim_low: [0, 1500]
+  flim_mid: [1500, 8000]
+  flim_hi: [8000, 20000]
+  mask_param1: 6
+  mask_param2: 0.5

conf/INFOREST1.yaml

+data:
+  path: "data/Brazil/package-1/INFOREST1"
+
+mic:
+  sensitivity: -4   # dBV
+  gain: 18  # dB
+
+temporal_alpha_indices:
+  dB_threshold: 3 # dB
+  rejectDuration: 0.01 
+
+spectrogram:
+  window: "hann"
+  nperseg: 1024 
+  noverlap: 512
+
+spectral_alpha_indices:
+  flim_low: [0, 1500]
+  flim_mid: [1500, 8000]
+  flim_hi: [8000, 20000]
+  mask_param1: 6
+  mask_param2: 0.5

conf/INFOREST2.yaml

+data:
+  path: "data/Brazil/package-1/INFOREST2/INFOREST2"
+
+mic:
+  sensitivity: -4   # dBV
+  gain: 18  # dB
+
+temporal_alpha_indices:
+  dB_threshold: 3 # dB
+  rejectDuration: 0.01  
+
+spectrogram:
+  window: "hann"
+  nperseg: 1024 
+  noverlap: 512
+
+spectral_alpha_indices:
+  flim_low: [0, 1500]
+  flim_mid: [1500, 8000]
+  flim_hi: [8000, 20000]
+  mask_param1: 6
+  mask_param2: 0.5

conf/OP1.yaml

+data:
+  path: "data/Brazil/package-1/FS1/FS1"
+
+mic:
+  sensitivity: -4   # dBV
+  gain: 18  # dB
+
+temporal_alpha_indices:
+  dB_threshold: 3 # dB
+  rejectDuration: 0.01 
+
+spectrogram:
+  window: "hann"
+  nperseg: 1024 
+  noverlap: 512
+
+spectral_alpha_indices:
+  flim_low: [0, 1500]
+  flim_mid: [1500, 8000]
+  flim_hi: [8000, 20000]
+  mask_param1: 6
+  mask_param2: 0.5

pyproject.toml

+[tool.poetry]
+name = "ecoacoustics"
+version = "0.1.0"
+description = ""
+authors = ["Andrei Margert <andrei.margert@wur.nl>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.9"
+scikit-maad = "^1.3.12"
+jupyter = "^1.0.0"
+matplotlib = "^3.7.1"
+pandas = "<2.0.0"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

rename_files.sh

+#!/bin/bash
+
+# define the directory to work with
+dir_path=$1
+
+# iterate over the .wav files in the directory
+for old_file in "$dir_path"/*.wav
+do
+    # Extract the filename and extension
+    filename=$(basename -- "$old_file")
+    extension="${filename##*.}"
+    filename="${filename%.*}"
+
+    # Split the filename into parts using "_" as delimiter
+    IFS="_"; read -a parts <<< "$filename"; unset IFS
+
+    # Pad or truncate the XXX part to 8 characters
+    parts[0]=$(printf "%-8.8s" "${parts[0]}")
+
+    # Replace spaces with 'X'
+    parts[0]="${parts[0]// /X}"
+
+    # Construct new filename
+    new_file="${parts[0]}_${parts[1]}_${parts[2]}.$extension"
+
+    # Rename the file
+    mv -- "$old_file" "$dir_path/$new_file"
+    # Or print the new filenames without renaming
+    # echo $new_file
+done