Add todo to issue (#5)

* start postprocess labels stage

* add todo to issue

* test todo

.github/workflows/todo.yml

@@ -0,0 +1,22 @@
+name: "Run TODO to Issue"
+on:
+  push:
+  workflow_dispatch:
+    inputs:
+      MANUAL_COMMIT_REF:
+        description: "The SHA of the commit to get the diff for"
+        required: true
+      MANUAL_BASE_REF:
+        description: "By default, the commit entered above is compared to the one directly before it; to go back further, enter an earlier SHA here"
+        required: false
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+    steps:
+      - name: "TODO to Issue"
+        uses: "alstr/todo-to-issue-action@v5"
+        env:
+          MANUAL_COMMIT_REF:
+            ${{ inputs.MANUAL_COMMIT_REF }}
+          MANUAL_BASE_REF:
+            ${{ inputs.MANUAL_BASE_REF }}

data/output.txt

@@ -0,0 +1,3 @@
+{'encounter_id': '11486', 'latitude': 36.91, 'longitude': -122.02, 'displayImgUrl': 'https://au-hw-media-m.happywhale.com/c5522187-058e-4a1a-83d7-893560ba6b2c.jpg', 'audio': array([], dtype=float32), 'start': Timestamp('2016-12-21 00:20:30'), 'end': Timestamp('2016-12-21 00:21:30'), 'classifications': []}
+{'encounter_id': '9182', 'latitude': 36.91, 'longitude': -122.02, 'displayImgUrl': 'https://au-hw-media-m.happywhale.com/d40b9e6e-07cf-4f20-8cb4-4042ba22a00b.jpg', 'audio': array([-0.00352275, -0.00346267, -0.00334585, ..., -0.00339496,
+       -0.00333035, -0.00329852], dtype=float32), 'start': Timestamp('2016-12-21 00:49:30'), 'end': Timestamp('2016-12-21 00:50:30'), 'classifications': [[0.8753612041473389], [0.746759295463562], [0.26265254616737366], [0.45787951350212097], [0.35406064987182617], [0.42348742485046387], [0.4947870969772339], [0.7287474274635315], [0.7099379897117615], [0.2122703194618225], [0.044488538056612015], [0.00849922839552164], [0.024390267208218575], [0.33750119805336], [0.6530888080596924], [0.3057247996330261], [0.1243574470281601], [0.027093390002846718], [0.011367958970367908], [0.004032353404909372], [0.026372192427515984], [0.021978065371513367], [0.006407670211046934], [0.5405446887016296], [0.34207114577293396], [0.6080849766731262], [0.5394770503044128], [0.3662146031856537], [0.16772609949111938], [0.3641503155231476], [0.060217034071683884], [0.008764371275901794], [0.012523961253464222], [0.009186000563204288], [0.022050702944397926], [0.3908870816230774], [0.15179167687892914], [0.3454047441482544], [0.4770602285861969], [0.07589100301265717], [0.5439115166664124], [0.8634722232818604], [0.985602617263794], [0.3311924636363983], [0.8832067847251892], [0.6166273951530457], [0.42301759123802185], [0.03573732450604439], [0.09752023965120316], [0.01426385436207056], [0.022987568750977516], [0.012294118292629719], [0.010207954794168472], [0.00296270614489913]]}

src/pipeline.py

@@ -5,6 +5,8 @@
 from stages.audio import RetrieveAudio, WriteAudio, WriteSiftedAudio
 from stages.sift import Butterworth
 from stages.classify import WhaleClassifier, WriteClassifications
+from stages.postprocess import PostprocessLabels
+
 
 from config import load_pipeline_config
 config = load_pipeline_config()
@@ -19,29 +21,25 @@ def run():
     }
 
     with beam.Pipeline(options=pipeline_options) as p:
-        input_data      = p             | "Create Input"        >> beam.Create([args])  
-        search_output   = input_data    | "Run Geometry Search" >> beam.ParDo(GeometrySearch())
-
-        audio_output    = search_output | "Retrieve Audio"      >> beam.ParDo(RetrieveAudio())
-        audio_output    | "Store Audio (temp)"  >> beam.ParDo(WriteAudio())
-
-        sifted_audio    = audio_output  | "Sift Audio"          >> Butterworth()
-        sifted_audio    | "Store Sifted Audio"  >> beam.ParDo(WriteSiftedAudio("butterworth"))
-
-        classifications = sifted_audio  | "Classify Audio"      >> WhaleClassifier(config)
-        classifications | "Store Classifications" >> beam.ParDo(WriteClassifications(config))
-
-
-        # # Post-process the labels
-        # postprocessed_labels = classified_audio | "Postprocess Labels" >> PostprocessLabels()
+        input_data          = p                 | "Create Input"        >> beam.Create([args])  
+        search_output       = input_data        | "Run Geometry Search" >> beam.ParDo(GeometrySearch())
+        audio_output        = search_output     | "Retrieve Audio"      >> beam.ParDo(RetrieveAudio())
+        sifted_audio        = audio_output      | "Sift Audio"          >> Butterworth()
+        classifications     = sifted_audio      | "Classify Audio"      >> WhaleClassifier(config)
+        postprocess_labels  = classifications   | "Postprocess Labels"  >> beam.ParDo(
+            PostprocessLabels(config),
+            search_output=beam.pvalue.AsSingleton(search_output),
+        )
+
+        # Store results
+        audio_output        | "Store Audio (temp)"      >> beam.ParDo(WriteAudio())
+        sifted_audio        | "Store Sifted Audio"      >> beam.ParDo(WriteSiftedAudio("butterworth"))
+        classifications     | "Store Classifications"   >> beam.ParDo(WriteClassifications(config))
+        postprocess_labels  | "Write Results"           >> beam.io.WriteToText("data/output.txt", shard_name_template="")
 
         # Output results
         # postprocessed_labels | "Write Results" >> beam.io.WriteToText("output.txt")
 
-        # For debugging, you can write the output to a text file
-        # audio_files     | "Write Audio Output"  >> beam.io.WriteToText('audio_files.txt')
-        # search_results  | "Write Search Output" >> beam.io.WriteToText('search_results.txt')
-
 
 if __name__ == "__main__":
     run()

src/stages/postprocess.py

@@ -0,0 +1,59 @@
+import apache_beam as beam
+
+from datetime import datetime
+from typing import Dict, Any, Tuple
+from types import SimpleNamespace
+from matplotlib import gridspec
+
+import librosa
+import logging
+import numpy as np
+import os 
+import time
+import pandas as pd
+
+import requests
+import math 
+import matplotlib.pyplot as plt
+import scipy.signal
+
+
+class PostprocessLabels(beam.DoFn):
+    def __init__(self, config: SimpleNamespace):
+        self.config = config
+
+        self.search_output_path_template = config.search.export_template
+        self.sifted_audio_path_template = config.sift.output_path_template
+        self.classification_path = config.classify.classification_path
+
+
+    def process(self, element: Dict[str, Any], search_output: Dict[str, Any]):
+        logging.info(f"element \n{element}")
+        logging.info(f"search_output \n{search_output}")
+        breakpoint()
+
+        classifications_df = pd.DataFrame([element], columns=["audio", "start", "end", "encounter_ids", "classifications"])
+        classifications_df = classifications_df.explode("encounter_ids").rename(columns={"encounter_ids": "encounter_id"})
+        classifications_df["encounter_id"] = classifications_df["encounter_id"].astype(str)
+
+        # TODO pool classifications in postprocessing
+
+
+        search_output = search_output.rename(columns={"id": "encounter_id"})
+        search_output["encounter_id"] = search_output["encounter_id"].astype(str)  # TODO do in one line
+        search_output = search_output[[
+            # TODO refactor to confing
+            "encounter_id",
+            "latitude",
+            "longitude",
+            "displayImgUrl",
+            # "species",  # TODO add in geo search stage (require rm local file)
+        ]]
+
+        # join dataframes
+        joined_df = pd.merge(search_output, classifications_df, how="inner", on="encounter_id")
+
+        logging.info(f"Final output: \n{joined_df.head()}")
+
+
+        return joined_df.to_dict(orient="records")