add fast topo

fedot/core/operations/evaluation/common_preprocessing.py

@@ -8,6 +8,8 @@
 from fedot.core.operations.evaluation.operation_implementations.data_operations.sklearn_transformations import \
     ImputationImplementation, KernelPCAImplementation, NormalizationImplementation, PCAImplementation, \
     PolyFeaturesImplementation, ScalingImplementation, FastICAImplementation
+from fedot.core.operations.evaluation.operation_implementations.data_operations.topological.fast_topological_extractor import \
+    FastTopologicalFeaturesImplementation
 from fedot.core.operations.evaluation.operation_implementations.data_operations.topological. \
     topological_extractor import TopologicalFeaturesImplementation
 from fedot.core.operations.operation_parameters import OperationParameters
@@ -47,7 +49,8 @@ class FedotPreprocessingStrategy(EvaluationStrategy):
         'one_hot_encoding': OneHotEncodingImplementation,
         'label_encoding': LabelEncodingImplementation,
         'fast_ica': FastICAImplementation,
-        'topological_features': TopologicalFeaturesImplementation
+        'topological_features': TopologicalFeaturesImplementation,
+        'fast_topological_features': FastTopologicalFeaturesImplementation,
     }
 
     def __init__(self, operation_type: str, params: Optional[OperationParameters] = None):

fedot/core/operations/evaluation/operation_implementations/data_operations/topological/fast_topological_extractor.py

@@ -0,0 +1,72 @@
+import math
+import sys
+from itertools import chain
+from multiprocessing import cpu_count
+from typing import Optional
+
+import numpy as np
+from gph import ripser_parallel as ripser
+
+from fedot.core.data.data import InputData, OutputData
+from fedot.core.operations.evaluation.operation_implementations.data_operations.topological.point_cloud import \
+    TopologicalTransformation
+from fedot.core.operations.evaluation.operation_implementations.data_operations.topological.topological import \
+    HolesNumberFeature, MaxHoleLifeTimeFeature, RelevantHolesNumber, AverageHoleLifetimeFeature, \
+    SumHoleLifetimeFeature, PersistenceEntropyFeature, SimultaneousAliveHolesFeature, \
+    AveragePersistenceLandscapeFeature, BettiNumbersSumFeature, RadiusAtMaxBNFeature, PersistenceDiagramsExtractor, \
+    TopologicalFeaturesExtractor
+from fedot.core.operations.evaluation.operation_implementations.implementation_interfaces import \
+    DataOperationImplementation
+from fedot.core.operations.operation_parameters import OperationParameters
+from fedot.utilities.window_size_selector import WindowSizeSelector, WindowSizeSelectorMethodsEnum
+from golem.utilities.utilities import determine_n_jobs
+
+
+class FastTopologicalFeaturesImplementation(DataOperationImplementation):
+    def __init__(self, params: Optional[OperationParameters] = None):
+        super().__init__(params)
+        self.window_size = params.get('window_size')
+        self.points_count = params.get('points_count')
+        self.max_homology_dimension = 1
+        self.shapes = None
+
+    def fit(self, input_data: InputData):
+        if self.points_count == 0:
+            self.points_count = int(input_data.features.shape[1] * 0.33)
+
+        self.shapes = None
+
+        return self
+
+    def transform(self, input_data: InputData) -> OutputData:
+        topological_features = [self._extract_features(self._slice_by_window(data, self.points_count))
+                                for data in input_data.features]
+
+        if self.shapes is None:
+            self.shapes = [max(x[dim].shape[0] for x in topological_features)
+                           for dim in range(self.max_homology_dimension + 1)]
+
+        features = list()
+        for dim in range(self.max_homology_dimension + 1):
+            _features = np.zeros((len(topological_features), self.shapes[dim]))
+            for topo_features_num, topo_features in enumerate(topological_features):
+                if len(topo_features[dim]) > 0:
+                    x = topo_features[dim][:, 1] - topo_features[dim][:, 0]
+                    _features[topo_features_num, :len(x)] = x
+            features.append(_features)
+        features = np.concatenate(features, axis=1)
+        features[np.isinf(features) | (features < 0)] = 0
+
+        return features
+
+    def _extract_features(self, x):
+        x_processed = ripser(x,
+                             maxdim=self.max_homology_dimension,
+                             coeff=2,
+                             metric='euclidean',
+                             n_threads=1,
+                             collapse_edges=False)["dgms"]
+        return x_processed
+
+    def _slice_by_window(self, data, window):
+        return [data[i:window + i] for i in range(data.shape[0] - window + 1)]

fedot/core/repository/data/data_operation_repository.json

@@ -256,6 +256,20 @@
       "presets": [
         "ts"
       ],
+      "input_type": "[DataTypesEnum.table]",
+      "output_type": "[DataTypesEnum.table]",
+      "tags": [
+        "non_applicable_for_ts",
+        "feature_space_transformation"
+      ]
+    },
+    "fast_topological_features": {
+      "meta": "custom_ts_preprocessing",
+      "presets": [
+        "ts"
+      ],
+      "input_type": "[DataTypesEnum.table]",
+      "output_type": "[DataTypesEnum.table]",
       "tags": [
         "non_applicable_for_ts",
         "feature_space_transformation"

fedot/core/repository/data/default_operation_params.json

@@ -160,5 +160,9 @@
   },
   "topological_features": {
     "n_jobs": -1
+  },
+  "fast_topological_features": {
+    "window_size": 0,
+    "points_count": 0
   }
 }