fix: correct check for parent of bound volumes and pass through args …

…to download_crop_pipeline.py

aipipeline/prediction/download_crop_pipeline.py

@@ -40,9 +40,9 @@ def run_pipeline(argv=None):
     parser = argparse.ArgumentParser(description="Download and crop unknown images.")
     parser.add_argument("--config", required=True, help="Config file path")
     parser.add_argument("--labels", required=True, help="Comma separated list of labels to download")
-    parser.add_argument("--download_args", required=False, default=[""], help="Additional arguments for download")
-    parser.add_argument("--download_dir", required=True, help="Directory to download images")
-    parser.add_argument("--skip_clean", required=False, default=False,
+    parser.add_argument("--download-args", required=False, default=[""], help="Additional arguments for download")
+    parser.add_argument("--download-dir", required=True, help="Directory to download images")
+    parser.add_argument("--skip-clean", required=False, default=False,
                                                     help="Skip cleaning of previously downloaded data")
     args, beam_args = parser.parse_known_args(argv)
     options = PipelineOptions(beam_args)
@@ -72,9 +72,16 @@ def run_pipeline(argv=None):
 
     # Make sure the download directory is not a child of the processed directory - this is a safety check
     # Otherwise, the processed data could be deleted
-    processed_dir = config_dict["data"]["processed_path"]
-    if Path(args.download_dir).is_relative_to(processed_dir):
-        raise ValueError(f"Download directory {args.download_dir} is a child of the processed directory {processed_dir}")
+    bind_volumes = config_dict["docker"]["bind_volumes"].keys()
+    # Check if the download directory is a child of any of the bind volumes in the docker config
+    found = False
+    for volume in bind_volumes:
+        if Path(args.download_dir).is_relative_to(volume):
+            found = True
+            break
+    if not found:
+        raise ValueError(
+            f"Download directory {args.download_dir} is not a child of any of the bind volumes in the docker config")
 
     if not args.skip_clean:
         clean(args.download_dir)

justfile

@@ -8,7 +8,7 @@ list:
     @just --list --unsorted
 
 # Setup the environment
-install: update
+install: update_trackers
     conda run -n aipipeline pip install https://github.com/redis/redis-py/archive/refs/tags/v5.0.9.zip
     git clone http://github.com/mbari-org/aidata.git deps/aidata
     git clone https://github.com/facebookresearch/co-tracker deps/co-tracker
@@ -17,8 +17,8 @@ install: update
     cd .. && mkdir checkpoints && cd checkpoints && wget https://huggingface.co/facebook/cotracker3/resolve/main/scaled_offline.pth
 
 # Update the environment. Run this command after checking out any code changes
-update:
-    conda env update --file environment.yml --prune
+update_trackers:
+    conda env update_trackers --file environment.yml --prune
 
 # Generate a tsne plot of the VSS database
 plot-tsne-vss project='uav':
@@ -137,7 +137,7 @@ fix-uav-metadata:
     export PYTHONPATH=.:deps/aidata
     time conda run -n aipipeline --no-capture-output python3 $PROJECT_DIR/fix_metadata.py
 
-# Compute saliency for downloaded VOC data and update the Tator database
+# Compute saliency for downloaded VOC data and update_trackers the Tator database
 compute-saliency project='uav' *more_args="":
     #!/usr/bin/env bash
     export PROJECT_DIR=./aipipeline/projects/{{project}}
@@ -155,14 +155,15 @@ crop project='uav' *more_args="":
         {{more_args}}
 
 # Download and crop Unknown detections
-download-crop-unknowns project='uav' label='Unknown' download_dir='/tmp/download':
+download-crop-unknowns project='uav' labels='Unknown' download-dir='/tmp/download' *more_args="":
     #!/usr/bin/env bash
     export PYTHONPATH=.
     time conda run -n aipipeline --no-capture-output python3 aipipeline/prediction/download_crop_pipeline.py \
-        --config ./aipipeline/projects/{{project}}/config/config_unknown.yml \
+        --config ./aipipeline/projects/{{project}}/config/config.yml \
         --skip_clean True \
-        --label {{label}} \
-        --download_dir {{download_dir}}
+        --labels {{labels}} \
+        --download-dir {{download-dir}} \
+        {{more_args}}
 
 # Download only
 download project='uav':
@@ -213,6 +214,12 @@ run-mega-inference:
     --skip-load \
     --remove-vignette \
     --min-confidence 0.2 \
-    --max-seconds 120 \
+    --max-seconds 300 \
+    --stride 1 \
     --endpoint_url http://FastAP-FastA-0RIu3xAfMhUa-337062127.us-west-2.elb.amazonaws.com/predict \
-    --video /mnt/M3/mezzanine/Ventana/2020/12/4318/V4318_20201208T203419Z_h264.mp4
+    --video /mnt/M3/mezzanine/Ventana/2020/12/4318/V4318_20201208T203419Z_h264.mp4
+
+run-mega-update_trackers:
+    #!/usr/bin/env bash
+    export PYTHONPATH=.
+    time conda run -n aipipeline --no-capture-output python3 aipipeline/projects/bio/run_strided_track.py