1 files changed, 178 insertions, 0 deletions
diff --git a/analysis/scripts/summarize.py b/analysis/scripts/summarize.py
new file mode 100644
index 00000000..426976c5
--- /dev/null
+++ b/analysis/scripts/summarize.py
@@ -0,0 +1,178 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+Summarize the results into a single file per dataset.
+
+For each dataset we want::
+
+    {
+        "dataset": "<name>",
+        "dataset_nobs": N,
+        "dataset_ndim": N,
+        "annotations": {
+            "<user_id>": [...],
+            "<user_id>": [...],
+            },
+        "results": {
+            "<method>": [
+                {
+                    "parameters": {
+                        "<param>": value,
+                        },
+                    "cplocations": [...],
+                    "scores": {
+                        "<score_1>": value,
+                    },
+                    "status": <status>
+                },
+                {
+                    "parameters": {
+                        "<param>": value,
+                        },
+                    "cplocations": [...],
+                    "scores": {
+                        "<score_1>": value,
+                    },
+                    "status": <status>
+                },
+                ],
+        }
+    }
+
+Basic cleanup on the change point locations will also be performed:
+
+    - deduplication
+    - removal of invalid indices. Recall that indices are 0-based. We remove 
+      any indices smaller than 1 and larger than n_obs - 2. The reason that we 
+      don't allow 0 or n_obs - 1 (both valid endpoints) is that several 
+      algorithms declare these locations as change points by default and they 
+      are meaningless.
+
+Author: Gertjan van den Burg
+Copyright (c) 2020 - The Alan Turing Institute
+License: See the LICENSE file.
+
+"""
+
+import argparse
+import json
+import os
+import sys
+
+from metrics import f_measure, covering
+
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "-a",
+        "--annotation-file",
+        help="Path to annotation file",
+        required=True,
+    )
+    parser.add_argument(
+        "-d", "--dataset-file", help="Path to dataset file", required=True
+    )
+    parser.add_argument(
+        "-r", "--result-dir", help="Directory of abed results", required=True
+    )
+    parser.add_argument("-o", "--output-file", help="File to write to")
+    return parser.parse_args()
+
+
+def load_json(filename):
+    with open(filename, "r") as fp:
+        try:
+            data = json.load(fp)
+        except json.decoder.JSONDecodeError:
+            print("Error parsing json file: %s" % filename, file=sys.stderr)
+            return {"error": "parsing error"}
+    return data
+
+
+def load_annotations(filename, dataset):
+    with open(filename, "r") as fp:
+        data = json.load(fp)
+    return data[dataset]
+
+
+def clean_cps(locations, dataset):
+    n_obs = dataset["n_obs"]
+    valid = set([x for x in locations if 1 <= x < n_obs - 1])
+    return sorted(valid)
+
+
+def main():
+    args = parse_args()
+
+    dataset = load_json(args.dataset_file)
+    annotations = load_annotations(args.annotation_file, dataset["name"])
+
+    out = {
+        "dataset": dataset["name"],
+        "dataset_nobs": dataset["n_obs"],
+        "dataset_ndim": dataset["n_dim"],
+        "annotations": annotations,
+        "results": {},
+    }
+
+    data_results = next(
+        (d for d in os.listdir(args.result_dir) if d == dataset["name"]), None
+    )
+    if data_results is None:
+        print(
+            "Couldn't find the result directory for dataset %s"
+            % dataset["name"],
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+
+    dataset_dir = os.path.join(args.result_dir, data_results)
+
+    for method in os.listdir(dataset_dir):
+        method_dir = os.path.join(dataset_dir, method)
+        for result_file in os.listdir(method_dir):
+            # print("Processing result file: %s" % result_file)
+            fname = os.path.join(method_dir, result_file)
+            result = load_json(fname)
+            if not method in out["results"]:
+                out["results"][method] = []
+
+            if result["status"].lower() == "success":
+                locations = clean_cps(result["result"]["cplocations"], dataset)
+
+                f1, precision, recall = f_measure(
+                    annotations, locations, return_PR=True
+                )
+                n_obs = dataset["n_obs"]
+                cover = covering(annotations, locations, n_obs)
+                scores = {
+                    "f1": f1,
+                    "precision": precision,
+                    "recall": recall,
+                    "cover": cover,
+                }
+            else:
+                locations = None
+                scores = None
+
+            out["results"][method].append(
+                {
+                    "parameters": result["parameters"],
+                    "task_file": result_file,
+                    "cplocations": locations,
+                    "scores": scores,
+                    "status": result['status'],
+                }
+            )
+
+    if args.output_file:
+        with open(args.output_file, "w") as fp:
+            json.dump(out, fp, indent="\t")
+    else:
+        print(json.dumps(out, indent="\t"))
+
+
+if __name__ == "__main__":
+    main()