Update A_VIRER__TEST_full_process_test.py, birdnet_test.py, and 16 mo…

…re files...
ear-team · Nov 30, 2022 · 2446574 · 2446574
1 parent c289b6e
commit 2446574
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Showing 18 changed files with 327 additions and 267 deletions.
diff --git a/article/A_VIRER__TEST_full_process_test.py b/article/A_VIRER__TEST_full_process_test.py
diff --git a/article/birdnet_test.py b/article/birdnet_test.py
@@ -12,7 +12,6 @@
 # Clear all the variables
 get_ipython().magic('reset -sf')
 
-import yaml
 from pathlib import Path
 import pandas as pd
 import matplotlib.pyplot as plt
@@ -28,15 +27,9 @@
 DIR_DATA        = Path('./data/test')               
 ANNOT_CSV_FILE  = 'manual_annotations.csv' 
 BIRDNET_CSV_FILE= "birdnet_annotations.csv" 
-CONFIG_FILE     = 'config_article.yaml' 
 
 # %%
-if __name__ == '__main__':
-
-    with open(CONFIG_FILE) as f:
-        params = yaml.load(f, Loader=bambird.get_loader())
-
-# %%         
+if __name__ == '__main__':       
 
     # BirdNET on ROIS 
     # ---------------------------------------------------------------------

diff --git a/article/birdnet_train.py b/article/birdnet_train.py
@@ -12,12 +12,12 @@
 # Clear all the variables
 get_ipython().magic('reset -sf')
 
-import yaml
 from pathlib import Path
 import pandas as pd
 import matplotlib.pyplot as plt
 plt.close("all")
 
+
 import bambird
 
 # %%
@@ -28,16 +28,10 @@
 DIR_DATA        = Path('./data/train')               
 ANNOT_CSV_FILE  = 'manual_annotations.csv' 
 BIRDNET_CSV_FILE= "birdnet_annotations.csv" 
-CONFIG_FILE     = 'config_article.yaml' 
 
 # %%
 if __name__ == '__main__':
-
-    with open(CONFIG_FILE) as f:
-        params = yaml.load(f, Loader=bambird.get_loader())
-
-# %%         
-
+
     # BirdNET on ROIS 
     # ---------------------------------------------------------------------
     # Load the dataframe with the result from BirdNET

diff --git a/article/birdnet_validation.py b/article/birdnet_validation.py
@@ -28,16 +28,10 @@
 DIR_DATA        = Path('./data/validation')               
 ANNOT_CSV_FILE  = 'manual_annotations.csv' 
 BIRDNET_CSV_FILE= "birdnet_annotations.csv" 
-CONFIG_FILE     = 'config_article.yaml' 
 
 # %%
 if __name__ == '__main__':
-
-    with open(CONFIG_FILE) as f:
-        params = yaml.load(f, Loader=bambird.get_loader())
-
-# %%         
-
+
     # BirdNET on ROIS 
     # ---------------------------------------------------------------------
     # Load the dataframe with the result from BirdNET

diff --git a/article/clustering_only_test.py b/article/clustering_only_test.py
@@ -12,13 +12,13 @@
 # Clear all the variables
 get_ipython().magic('reset -sf')
 
-import yaml
 from pathlib import Path
-import pandas as pd
 import matplotlib.pyplot as plt
 plt.close("all")
 
 import bambird
+import bambird.config as cfg
+
 # %%
 # Define constants
 # ----------------
@@ -32,8 +32,8 @@
 # %%
 if __name__ == '__main__':
 
-    with open(CONFIG_FILE) as f:
-        params = yaml.load(f, Loader=bambird.get_loader())
+    # Load the configuration file    
+    params = cfg.load_config(CONFIG_FILE)
 
     # Name of the csv file with feaetures
     FEATURES_CSV_FILE = (

diff --git a/article/clustering_only_train.py b/article/clustering_only_train.py
@@ -17,10 +17,8 @@
 import matplotlib.pyplot as plt
 plt.close("all")
 
-bambird_path = Path('/home/haupert/DATA/mes_projets/Z_THESE_FELIX_MICHAUD/CHAPITRE_1/bambird.git')
-import os
-os.sys.path.append(bambird_path.as_posix())
 import bambird
+import bambird.config as cfg
 
 # %%
 # Define constants
@@ -34,9 +32,9 @@
 
 # %%
 if __name__ == '__main__':
-
-    with open(CONFIG_FILE) as f:
-        params = yaml.load(f, Loader=bambird.get_loader())
+    
+    # Load the configuration file    
+    params = cfg.load_config(CONFIG_FILE)
 
     # Name of the csv file with feaetures
     FEATURES_CSV_FILE = (

diff --git a/article/clustering_only_validation.py b/article/clustering_only_validation.py
@@ -18,6 +18,8 @@
 plt.close("all")
 
 import bambird
+import bambird.config as cfg
+
 # %%
 # Define constants
 # ----------------
@@ -31,8 +33,8 @@
 # %%
 if __name__ == '__main__':
 
-    with open(CONFIG_FILE) as f:
-        params = yaml.load(f, Loader=bambird.get_loader())
+    # Load the configuration file    
+    params = cfg.load_config(CONFIG_FILE)
 
     # Name of the csv file with feaetures
     FEATURES_CSV_FILE = (

diff --git a/article/config_article.yaml b/article/config_article.yaml
@@ -17,14 +17,14 @@ PARAMS_XC:
   - len:30-60
   - q:">C"
   - type:song
-  #CSV_XC_FILE: 'dataset_xc_embcit.csv' # The file will contain all the metadata collected from Xeno-canto
+  CSV_XC_FILE: 'bam_dataset_xc.csv' # The file will contain all the metadata collected from Xeno-canto
 
 ################################
 # ROIS EXTRACTION PARAMETERS
 ################################
 PARAMS_EXTRACT:
   # function
-  FUNC: !fun bambird.extract_rois_core  # select the function used to extract the rois {bambird.extract_rois_core, bambird.extract_rois_full_sig}
+  FUNC: !FUNC bambird.extract_rois_core  # select the function used to extract the rois {bambird.extract_rois_core, bambird.extract_rois_full_sig}
   # Extract Audio resampling
   SAMPLE_RATE: 44100      # Sampling frequency in Hz
   # Audio preprocess

diff --git a/article/full_process_test.py b/article/full_process_test.py
@@ -12,13 +12,13 @@
 # Clear all the variables
 get_ipython().magic('reset -sf')
 
-import yaml
 from pathlib import Path
 import matplotlib.pyplot as plt
 plt.close("all")
 import pandas as pd
 
 import bambird
+import bambird.config as cfg
 
 # %%
 # Define constants
@@ -42,8 +42,8 @@
 # %%
 if __name__ == '__main__':
 
-    with open(CONFIG_FILE) as f:
-        params = yaml.load(f, Loader=bambird.get_loader())
+    # Load the configuration file    
+    params = cfg.load_config(CONFIG_FILE)
 
     # load the inital dataset with the metadata stored from XC
     df_dataset = pd.read_csv(XC_CSV_FILE, sep=';')
@@ -69,7 +69,6 @@
     # extract ROIS
     df_rois, csv_rois = bambird.multicpu_extract_rois(
                     dataset             =df_xc,
-                    fun                 =params['PARAMS_EXTRACT']['FUNC'],
                     params              =params['PARAMS_EXTRACT'],
                     save_path           =DIR_DATA / ROIS_NAME,
                     overwrite           =True,
@@ -98,7 +97,7 @@
     df_cluster, csv_cluster = bambird.find_cluster(
                     dataset     =df_features,
                     params      =params['PARAMS_CLUSTER'],
-                    save_path           =DIR_DATA / ROIS_NAME,
+                    save_path   =DIR_DATA / ROIS_NAME,
                     display     =False,
                     verbose     =True
                     )