pickle -> onnx, IsolationForest -> AADForest

.github/workflows/run_test.yml

@@ -44,6 +44,8 @@ jobs:
       run: |
         pip uninstall -y actsnfink
         pip install git+https://github.com/emilleishida/fink_sn_activelearning.git@bf8d4e263e02d42781642f872f7bc030c24792bc#egg=actsnfink
+        pip install onnx==1.12.0
+        pip install onnxruntime
 
         ./run_tests.sh
         curl -s https://codecov.io/bash | bash

fink_science/anomaly_detection/processor.py

@@ -14,13 +14,17 @@
 # limitations under the License.
 import logging
 import os
-import pickle
 import zipfile
 
 from pyspark.sql.functions import udf
 from pyspark.sql.types import DoubleType
 
 import pandas as pd
+import numpy as np
+
+from onnx import load
+import onnxruntime as rt
+
 
 from fink_science import __file__
 from fink_science.tester import spark_unit_tests
@@ -43,96 +47,133 @@ def __init__(self, forest_g, forest_r) -> None:
         self.forest_g = forest_g
 
     def anomaly_score(self, data_g, data_r):
-        scores_g = self.forest_g.score_samples(data_g)
-        scores_r = self.forest_r.score_samples(data_r)
-        return (scores_g + scores_r) / 2
+        scores_g = self.forest_g.run(None, {"X": data_g.values.astype(np.float32)})
+        scores_r = self.forest_r.run(None, {"X": data_r.values.astype(np.float32)})
+        return (scores_g[-1] + scores_r[-1]) / 2
 
 
 path = os.path.dirname(os.path.abspath(__file__))
 model_path = f"{path}/data/models/anomaly_detection"
-g_model_path = f"{model_path}/forest_g.pickle"
-r_model_path = f"{model_path}/forest_r.pickle"
+g_model_path = f"{model_path}/forest_g.onnx"
+r_model_path = f"{model_path}/forest_r.onnx"
+g_model_path_AAD = f"{model_path}/forest_g_AAD.onnx"
+r_model_path_AAD = f"{model_path}/forest_r_AAD.onnx"
 if not (os.path.exists(r_model_path) and os.path.exists(g_model_path)):
     # unzip in a tmp place
     tmp_path = '/tmp'
-    g_model_path = f"{tmp_path}/forest_g.pickle"
-    r_model_path = f"{tmp_path}/forest_r.pickle"
+    g_model_path = f"{tmp_path}/forest_g.onnx"
+    r_model_path = f"{tmp_path}/forest_r.onnx"
+    g_model_path_AAD = f"{tmp_path}/forest_g_AAD.onnx"
+    r_model_path_AAD = f"{tmp_path}/forest_r_AAD.onnx"
     # check it does not exist to avoid concurrent write
     if not (os.path.exists(r_model_path) and os.path.exists(g_model_path)):
         with zipfile.ZipFile(f"{model_path}/anomaly_detection_forest.zip", 'r') as zip_ref:
             zip_ref.extractall(tmp_path)
+    if not (os.path.exists(g_model_path_AAD) and os.path.exists(r_model_path_AAD)):
+        with zipfile.ZipFile(f"{model_path}/anomaly_detection_forest_AAD.zip", 'r') as zip_ref:
+            zip_ref.extractall(tmp_path)
 
-with open(r_model_path, 'rb') as forest_file:
-    forest_r = pickle.load(forest_file)
-with open(g_model_path, 'rb') as forest_file:
-    forest_g = pickle.load(forest_file)
-r_means = pd.read_csv(f"{model_path}/r_means.csv", header=None, index_col=0, squeeze=True)
-g_means = pd.read_csv(f"{model_path}/g_means.csv", header=None, index_col=0, squeeze=True)
-
-model = TwoBandModel(forest_g, forest_r)
-
-
-@udf(returnType=DoubleType())
-def anomaly_score(lc_features) -> float:
-    """ Returns anomaly score for an observation
 
-    Parameters
-    ----------
-    lc_features: Spark Map
-        Dict of dicts of floats. Keys of first dict - filters (fid), keys of inner dicts - names of features.
+class WrapInferenceSession:
+    """
+    The class is an additional wrapper over InferenceSession
+    to solve the pyspark serialisation problem
 
-    Returns
-    ----------
-    out: float
-        Anomaly score
+    https://github.com/microsoft/onnxruntime/pull/800#issuecomment-844326099
+    """
+    def __init__(self, onnx_bytes):
+        self.sess = rt.InferenceSession(onnx_bytes.SerializeToString())
+        self.onnx_bytes = onnx_bytes
 
-    Examples
-    ---------
-    >>> from fink_utils.spark.utils import concat_col
-    >>> from pyspark.sql import functions as F
-    >>> from fink_science.ad_features.processor import extract_features_ad
+    def run(self, *args):
+        return self.sess.run(*args)
 
-    >>> df = spark.read.load(ztf_alert_sample)
+    def __getstate__(self):
+        return {'onnx_bytes': self.onnx_bytes}
 
-    # Required alert columns, concatenated with historical data
-    >>> what = ['magpsf', 'jd', 'sigmapsf', 'fid', 'distnr', 'magnr', 'sigmagnr', 'isdiffpos']
-    >>> prefix = 'c'
-    >>> what_prefix = [prefix + i for i in what]
-    >>> for colname in what:
-    ...    df = concat_col(df, colname, prefix=prefix)
+    def __setstate__(self, values):
+        self.onnx_bytes = values['onnx_bytes']
+        self.sess = rt.InferenceSession(self.onnx_bytes.SerializeToString())
 
-    >>> cols = ['cmagpsf', 'cjd', 'csigmapsf', 'cfid', 'objectId', 'cdistnr', 'cmagnr', 'csigmagnr', 'cisdiffpos']
-    >>> df = df.withColumn('lc_features', extract_features_ad(*cols))
-    >>> df = df.withColumn("anomaly_score", anomaly_score("lc_features"))
 
-    >>> df.filter(df["anomaly_score"] < -0.5).count()
-    7
+forest_r = WrapInferenceSession(load(r_model_path))
+forest_g = WrapInferenceSession(load(g_model_path))
+forest_r_AAD = WrapInferenceSession(load(r_model_path_AAD))
+forest_g_AAD = WrapInferenceSession(load(g_model_path_AAD))
 
-    >>> df.filter(df["anomaly_score"] == 0).count()
-    84
 
-    """
+r_means = pd.read_csv(f"{model_path}/r_means.csv", header=None, index_col=0, squeeze=True)
+g_means = pd.read_csv(f"{model_path}/g_means.csv", header=None, index_col=0, squeeze=True)
 
-    if (
-        lc_features is None
-        or len(lc_features) != 2  # noqa: W503 (https://www.flake8rules.com/rules/W503.html, https://www.flake8rules.com/rules/W504.html)
-        or any(map(  # noqa: W503
-            lambda fs: (fs is None or len(fs) == 0),
-            lc_features.values()
-        ))
-    ):
-        return 0.0
-    if any(map(lambda fid: fid not in lc_features, (1, 2))):
-        logger.exception(f"Unsupported 'lc_features' format in '{__file__}/{anomaly_score.__name__}'")
-
-    data_r, data_g = (
-        pd.DataFrame.from_dict({k: [v] for k, v in lc_features[i].items()})[MODEL_COLUMNS]
-        for i in (1, 2)
-    )
-    for data, means in ((data_r, r_means), (data_g, g_means)):
-        for col in data.columns[data.isna().any()]:
-            data[col].fillna(means[col], inplace=True)
-    return model.anomaly_score(data_r, data_g)[0].item()
+model = TwoBandModel(forest_g, forest_r)
+model_AAD = TwoBandModel(forest_g_AAD, forest_r_AAD)
+
+
+def anomaly_score(lc_features, model_type='AADForest'):
+    @udf(returnType=DoubleType())
+    def anomaly_score(lc_features) -> float:
+        """ Returns anomaly score for an observation
+
+        Parameters
+        ----------
+        lc_features: Spark Map
+            Dict of dicts of floats. Keys of first dict - filters (fid), keys of inner dicts - names of features.
+
+        Returns
+        ----------
+        out: float
+            Anomaly score
+
+        Examples
+        ---------
+        >>> from fink_utils.spark.utils import concat_col
+        >>> from pyspark.sql import functions as F
+        >>> from fink_science.ad_features.processor import extract_features_ad
+
+        >>> df = spark.read.load(ztf_alert_sample)
+
+        # Required alert columns, concatenated with historical data
+        >>> what = ['magpsf', 'jd', 'sigmapsf', 'fid', 'distnr', 'magnr', 'sigmagnr', 'isdiffpos']
+        >>> prefix = 'c'
+        >>> what_prefix = [prefix + i for i in what]
+        >>> for colname in what:
+        ...    df = concat_col(df, colname, prefix=prefix)
+
+        >>> cols = ['cmagpsf', 'cjd', 'csigmapsf', 'cfid', 'objectId', 'cdistnr', 'cmagnr', 'csigmagnr', 'cisdiffpos']
+        >>> df = df.withColumn('lc_features', extract_features_ad(*cols))
+        >>> df = df.withColumn("anomaly_score", anomaly_score("lc_features"))
+
+        >>> df.filter(df["anomaly_score"] < -0.5).count()
+        7
+
+        >>> df.filter(df["anomaly_score"] == 0).count()
+        84
+
+        """
+
+        if (
+            lc_features is None
+            or len(lc_features) != 2  # noqa: W503 (https://www.flake8rules.com/rules/W503.html, https://www.flake8rules.com/rules/W504.html)
+            or any(map(  # noqa: W503
+                lambda fs: (fs is None or len(fs) == 0),
+                lc_features.values()
+            ))
+        ):
+            return 0.0
+        if any(map(lambda fid: fid not in lc_features, (1, 2))):
+            logger.exception(f"Unsupported 'lc_features' format in '{__file__}/{anomaly_score.__name__}'")
+
+        data_r, data_g = (
+            pd.DataFrame.from_dict({k: [v] for k, v in lc_features[i].items()})[MODEL_COLUMNS]
+            for i in (1, 2)
+        )
+        for data, means in ((data_r, r_means), (data_g, g_means)):
+            for col in data.columns[data.isna().any()]:
+                data[col].fillna(means[col], inplace=True)
+        if model_type == 'AADForest':
+            return model_AAD.anomaly_score(data_r, data_g)[0].item()
+        return model.anomaly_score(data_r, data_g)[0].item()
+    return anomaly_score(lc_features)
 
 
 if __name__ == "__main__":

fink_science/data/models/anomaly_detection/g_means.csv

@@ -1,18 +1,19 @@
+,0
 amplitude,0.21948567063093466
 anderson_darling_normal,0.5738338537540897
-beyond_1_std,0.2975957082645236
+beyond_1_std,0.29759570826452364
 chi2,37.704414101216535
 cusum,0.3407494402523421
-kurtosis,0.29150516293433526
-linear_fit_slope,0.0008679869820436599
-linear_fit_slope_sigma,0.002219643796867781
-linear_trend_noise,0.1395519301423175
-linear_trend_sigma,0.006530832951936918
+kurtosis,0.2915051629343353
+linear_fit_slope,0.0008679869820436663
+linear_fit_slope_sigma,0.002219643796867831
+linear_trend_noise,0.13955193014231754
+linear_trend_sigma,0.006530832951936966
 magnitude_percentage_ratio_20_10,0.7096091060287604
-magnitude_percentage_ratio_40_5,0.21345309681339728
+magnitude_percentage_ratio_40_5,0.2134530968133973
 maximum_slope,20.197335141851806
 median,16.09982754358941
-median_absolute_deviation,0.07874299095497293
+median_absolute_deviation,0.07874299095497296
 median_buffer_range_percentage_10,0.226612517162576
 skew,0.06777187504700471
 stetson_K,0.853534164617388

fink_science/data/models/anomaly_detection/r_means.csv

@@ -1,18 +1,19 @@
-amplitude,0.27761581012726816
+,0
+amplitude,0.2776158101272682
 anderson_darling_normal,0.6324932481221309
-beyond_1_std,0.2984203432923638
+beyond_1_std,0.29842034329236383
 chi2,47.98632140376363
 cusum,0.3353034770643174
 kurtosis,0.19552357158753803
-linear_fit_slope,0.0004677950689235035
-linear_fit_slope_sigma,0.004115135468353454
-linear_trend_noise,0.17699726764662013
-linear_trend_sigma,0.008118738252789526
+linear_fit_slope,0.00046779506892350695
+linear_fit_slope_sigma,0.004115135468353504
+linear_trend_noise,0.17699726764662016
+linear_trend_sigma,0.008118738252789576
 magnitude_percentage_ratio_20_10,0.7110312348018119
-magnitude_percentage_ratio_40_5,0.2119754721716743
+magnitude_percentage_ratio_40_5,0.21197547217167437
 maximum_slope,27.23340912206943
 median,17.306199665913482
-median_absolute_deviation,0.09875090359331291
-median_buffer_range_percentage_10,0.22553694294088789
+median_absolute_deviation,0.09875090359331296
+median_buffer_range_percentage_10,0.22553694294088797
 skew,0.022823198234573093
 stetson_K,0.8580286805997064