some debugging changes left over from last year

NERC-CEH · Jan 14, 2025 · 112788b · 112788b
1 parent 99b9d1c
commit 112788b
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Showing 2 changed files with 27 additions and 11 deletions.
diff --git a/scripts/params.yaml b/scripts/params.yaml
@@ -1,4 +1,4 @@
 cluster:
   n_clusters: 5
 
-collection: untagged-images-lana 
+collection: untagged-images-lana
diff --git a/scripts/run_luigi_pipeline.py b/scripts/run_luigi_pipeline.py
@@ -3,31 +3,47 @@
 from cyto_ml.pipeline.pipeline_decollage import FlowCamPipeline
 from cyto_ml.data.flowcam import parse_filename
 import logging
+
 logging.basicConfig(level=logging.INFO)
 
 
 if __name__ == "__main__":
 
     parser = argparse.ArgumentParser(
-    prog='Luigi FlowCam pipeline',
-    description='Triggers the process of decollaging images, embedding spatio-temporal metadata in headers, and uploading to s3 storage',
+        prog="Luigi FlowCam pipeline",
+        description="Triggers the process of decollaging images, embedding spatio-temporal metadata in headers, and uploading to s3 storage",
     )
 
-    parser.add_argument('-o', '--output_directory', type=str, default="./data/images_decollage", help="directory for intermediate data")
-    parser.add_argument('-d', '--directory', type=str, default="./tests/fixtures/MicrobialMethane_MESO_Tank10_54.0143_-2.7770_04052023_1", help='Enable verbose mode')
-    parser.add_argument('-s', '--s3_bucket', type=str, default="untagged-images-lana")
-    parser.add_argument('-e', '--experiment_name', type=str)
+    parser.add_argument(
+        "-o",
+        "--output_directory",
+        type=str,
+        default="./data/images_decollage",
+        help="directory for intermediate data",
+    )
+    parser.add_argument(
+        "-d",
+        "--directory",
+        type=str,
+        default="./tests/fixtures/MicrobialMethane_MESO_Tank10_54.0143_-2.7770_04052023_1",
+        help="Enable verbose mode",
+    )
+    parser.add_argument("-s", "--s3_bucket", type=str, default="untagged-images-lana")
+    parser.add_argument("-e", "--experiment_name", type=str)
     args = parser.parse_args()
 
     experiment = args.experiment_name
-    if not experiment:
+    if not experiment or experiment == "":
         try:
             prefix, _, _, date, _ = parse_filename(args.directory)
-            experiment = ''.join([prefix, date])
+            experiment = "".join([prefix, date])
         except ValueError as err:
-            logging.info("Could't figure out experiment name and date from {args.directory} - please call this with --experiment_name to set this")
+            logging.info(
+                "Could't figure out experiment name and date from {args.directory} - please call this with --experiment_name to set this"
+            )
             logging.debug(err)
-            exit
+            # TODO this properly
+            experiment = str(args.directory).split("/")[-2]
 
     luigi.build(
         [