refining ClustersFactoryTest

src/SymptomsCausedByVaccines/MultiLineFitting/ClustersFactory.py

@@ -0,0 +1,55 @@
+import numpy as np
+from skspatial.objects import Line
+
+class ClustersFactory:
+
+    @staticmethod
+    def createPreferenceMatrix(points, lines, consensusThreshold):
+        preferenceMatrix = np.zeros([len(points), len(lines)], dtype = int)
+        for pointIndex, point in enumerate(points):
+            for lineIndex, line in enumerate(lines):
+                preferenceMatrix[pointIndex, lineIndex] = 1 if line.distance_point(point) <= consensusThreshold else 0
+
+        return preferenceMatrix
+    
+    @staticmethod
+    def createClusters(preferenceMatrix):
+        keep_clustering = True
+        cluster_step = 0
+
+        num_clusters = preferenceMatrix.shape[0]
+        clusters = [[i] for i in range(num_clusters)]
+
+        while keep_clustering:
+            smallest_distance = 0
+            best_combo = None
+            keep_clustering = False
+
+            num_clusters = preferenceMatrix.shape[0]
+
+            for i in range(num_clusters):
+                for j in range(i):
+                    set_a = preferenceMatrix[i]
+                    set_b = preferenceMatrix[j]
+                    intersection = np.count_nonzero(np.logical_and(set_a, set_b))
+                    union = np.count_nonzero(np.logical_or(set_a, set_b))
+                    distance = 1.*intersection/np.maximum(union, 1e-8)
+
+                    if distance > smallest_distance:
+                        keep_clustering = True
+                        smallest_distance = distance
+                        best_combo = (i,j)
+
+            if keep_clustering:
+                clusters[best_combo[0]] += clusters[best_combo[1]]
+                clusters.pop(best_combo[1])
+                set_a = preferenceMatrix[best_combo[0]]
+                set_b = preferenceMatrix[best_combo[1]]
+                merged_set = np.logical_and(set_a, set_b)
+                preferenceMatrix[best_combo[0]] = merged_set
+                preferenceMatrix = np.delete(preferenceMatrix, best_combo[1], axis=0)
+                cluster_step += 1
+
+        print("clustering finished after %d steps" % cluster_step)
+
+        return preferenceMatrix, clusters

src/SymptomsCausedByVaccines/MultiLineFitting/ClustersFactoryTest.py

@@ -0,0 +1,44 @@
+import unittest
+import numpy as np
+from skspatial.objects import Line
+from src.SymptomsCausedByVaccines.MultiLineFitting.ClustersFactory import ClustersFactory
+
+
+class ClustersFactoryTest(unittest.TestCase):
+
+    def test_createPreferenceMatrix(self):
+        # Given
+        points = [(1, 3), (10, 20)]
+        lines = [Line.from_points([0, 0], [100, 0])]
+        consensusThreshold = 4.0
+
+        # When
+        preferenceMatrix = ClustersFactory.createPreferenceMatrix(points, lines, consensusThreshold)
+
+        # Then
+        np.testing.assert_array_equal(
+            preferenceMatrix,
+            np.array(
+                [
+                    [1],
+                    [0]
+                ]))
+
+    def test_createClusters(self):
+        # Given
+        preferenceMatrix = np.array(
+                [
+                    [1],
+                    [1]
+                ])
+
+        # When
+        _, clusters = ClustersFactory.createClusters(preferenceMatrix)
+
+        # Then
+        np.testing.assert_array_equal(
+            clusters,
+            np.array(
+                [
+                    [1, 0]
+                ]))

src/SymptomsCausedByVaccines/MultiLineFitting/PreferenceMatrixFactory.py

@@ -1,14 +0,0 @@
-import numpy as np
-from skspatial.objects import Line
-
-class PreferenceMatrixFactory:
-
-    @staticmethod
-    def createPreferenceMatrix(points, lines, consensusThreshold):
-        preferenceMatrix = np.zeros([len(points), len(lines)], dtype = int)
-        for pointIndex, point in enumerate(points):
-            for lineIndex, line in enumerate(lines):
-                preferenceMatrix[pointIndex, lineIndex] = 1 if line.distance_point(point) <= consensusThreshold else 0
-
-        return preferenceMatrix
-    

src/SymptomsCausedByVaccines/MultiLineFitting/PreferenceMatrixFactoryTest.py

@@ -1,26 +0,0 @@
-import unittest
-import numpy as np
-from numpy.testing import assert_array_equal
-from skspatial.objects import Line
-from SymptomsCausedByVaccines.MultiLineFitting.PreferenceMatrixFactory import PreferenceMatrixFactory
-
-
-class PreferenceMatrixFactoryTest(unittest.TestCase):
-
-    def test_createPreferenceMatrix(self):
-        # Given
-        points = [(1, 3), (10, 20)]
-        lines = [Line.from_points([0, 0], [100, 0])]
-        consensusThreshold = 4.0
-
-        # When
-        preferenceMatrix = PreferenceMatrixFactory.createPreferenceMatrix(points, lines, consensusThreshold)
-
-        # Then
-        assert_array_equal(
-            preferenceMatrix,
-            np.array(
-                [
-                    [1],
-                    [0]
-                ]))