Merge pull request #7 from Kitware/issue-4-output-folder-option

Output folder option

Author: bluemellophone

batbot/__init__.py

@@ -63,6 +63,7 @@ def pipeline(
     config=None,
     # classifier_thresh=classifier.CONFIGS[None]['thresh'],
     clean=True,
+    output_folder='.',
 ):
     """
     Run the ML pipeline on a given WAV filepath and return the classification results
@@ -93,7 +94,9 @@ def pipeline(
         tuple ( float, list ( dict ) ): classifier score, list of time windows
     """
     # Generate spectrogram
-    output_paths, metadata_path, metadata = spectrogram.compute(filepath)
+    output_paths, metadata_path, metadata = spectrogram.compute(
+        filepath, output_folder=output_folder
+    )
 
     return output_paths, metadata_path
 
@@ -161,7 +164,7 @@ def example():
         assert exists(wav_filepath)
 
     log.debug(f'Running pipeline on WAV: {wav_filepath}')
-
-    results = pipeline(wav_filepath)
+    output = './output'
+    results = pipeline(wav_filepath, output_folder=output)
 
     log.debug(results)

batbot/batbot.py

@@ -47,8 +47,9 @@ def fetch(config):
 )
 @click.option(
     '--output',
-    help='Path to output JSON (if unspecified, results are printed to screen)',
-    default=None,
+    'output_path',
+    help='Path to output folder for the results',
+    default='.',
     type=str,
 )
 # @click.option(
@@ -60,7 +61,7 @@ def fetch(config):
 def pipeline(
     filepath,
     config,
-    output,
+    output_path,
     # classifier_thresh,
 ):
     """
@@ -79,25 +80,13 @@ def pipeline(
         config = config.strip().lower()
     # classifier_thresh /= 100.0
 
-    score = batbot.pipeline(
+    batbot.pipeline(
         filepath,
         config=config,
         # classifier_thresh=classifier_thresh,
+        output_folder=output_path,
     )
 
-    data = {
-        filepath: {
-            'classifier': score,
-        }
-    }
-
-    log.debug('Outputting results...')
-    if output:
-        with open(output, 'w') as outfile:
-            json.dump(data, outfile)
-    else:
-        print(data)
-
 
 @click.command('batch')
 @click.argument(

batbot/spectrogram/__init__.py

@@ -1329,6 +1329,11 @@ def compute_wrapper(
 
     chunksize = int(50e3)
 
+    # create output folder if it doesn't exist
+    if not os.path.exists(output_folder):
+        os.makedirs(output_folder)
+        assert exists(output_folder)
+
     debug_path = get_debug_path(output_folder, wav_filepath, enabled=debug)
 
     # Load the spectrogram from a WAV file on disk

tests/test_spectrogram.py

@@ -5,4 +5,5 @@ def test_spectrogram_compute():
     from batbot.spectrogram import compute
 
     wav_filepath = abspath(join('examples', 'example2.wav'))
-    output_paths, metadata_path, metadata = compute(wav_filepath)
+    output_folder = './output'
+    output_paths, metadata_path, metadata = compute(wav_filepath, output_folder=output_folder)