feat : distance method added #349 #350

pycm/pycm_distance.py

@@ -0,0 +1,129 @@
+# -*- coding: utf-8 -*-
+"""Distance/Similarity functions."""
+from __future__ import division
+from enum import Enum
+import math
+
+class DistanceType(Enum):
+    """
+    Distance metric type class.
+    >>> pycm.DistanceType.AMPLE
+    """
+
+    AMPLE = "AMPLE"
+    Anderberg = "Anderberg"
+    AndresMarzoDelta = "AndresMarzoDelta"
+    BaroniUrbaniBuserI = "BaroniUrbaniBuserI"
+    BaroniUrbaniBuserII = "BaroniUrbaniBuserII"
+
+def AMPLE_calc(TP, FP, FN, TN):
+    """
+    Calculate AMPLE.
+
+    :param TP: true positive
+    :type TP: int
+    :param TN: true negative
+    :type TN: int
+    :param FP: false positive
+    :type FP: int
+    :param FN: false negative
+    :type FN: int
+    :return: AMPLE as float
+    """
+    try:
+        part1 = TP/(TP + FP)
+        part2 = FN/(FN + TN)
+        return abs(part1 - part2)
+    except Exception:
+        return "None"
+
+def Anderberg_calc(TP, FP, FN, TN):
+    """
+    Calculate Anderberg's D.
+
+    :param TP: true positive
+    :type TP: int
+    :param TN: true negative
+    :type TN: int
+    :param FP: false positive
+    :type FP: int
+    :param FN: false negative
+    :type FN: int
+    :return: Anderberg's D as float
+    """
+    try:
+        part1 = max(TP, FP) + max(FN, TN) + max(TP, FN) + max(FP, TN)
+        part2 = max(TP + FP, FP + TN) + max(TP + FP, FN + TN)
+        n = TP + FP + FN + TN
+        return (part1 - part2) / (2 * n)
+    except Exception:
+        return "None"
+
+
+def AndresMarzoDelta_calc(TP, FP, FN, TN):
+    """
+    Calculate Andres & Marzo's Delta.
+
+    :param TP: true positive
+    :type TP: int
+    :param TN: true negative
+    :type TN: int
+    :param FP: false positive
+    :type FP: int
+    :param FN: false negative
+    :type FN: int
+    :return: Andres & Marzo's Delta as float
+    """
+    try:
+        part1 = TP + TN - 2 * math.sqrt(FP * FN)
+        n = TP + FP + FN + TN
+        return part1 / n
+    except Exception:
+        return "None"
+
+def BaroniUrbaniBuserI_calc(TP, FP, FN, TN):
+    """
+    Calculate Baroni-Urbani & Buser I.
+
+    :param TP: true positive
+    :type TP: int
+    :param TN: true negative
+    :type TN: int
+    :param FP: false positive
+    :type FP: int
+    :param FN: false negative
+    :type FN: int
+    :return: Baroni-Urbani & Buser I as float
+    """
+    try:
+        part1 = math.sqrt(TP * TN) + TP
+        part2 = part1 + FP + FN
+        return part1 / part2
+    except Exception:
+        return "None"
+
+def BaroniUrbaniBuserII_calc(TP, FP, FN, TN):
+    """
+    Calculate Baroni-Urbani & Buser II.
+
+    :param TP: true positive
+    :type TP: int
+    :param TN: true negative
+    :type TN: int
+    :param FP: false positive
+    :type FP: int
+    :param FN: false negative
+    :type FN: int
+    :return: Baroni-Urbani & Buser II as float
+    """
+    try:
+        part1 = math.sqrt(TP * TN) + TP - FP - FN
+        part2 = math.sqrt(TP * TN) + TP + FP + FN
+        return part1 / part2
+    except Exception:
+        return "None"
+
+
+
+DISTANCE_MAPPER = {DistanceType.AMPLE: AMPLE_calc, DistanceType.Anderberg: Anderberg_calc, DistanceType.AndresMarzoDelta: AndresMarzoDelta_calc, DistanceType.BaroniUrbaniBuserI:
+    BaroniUrbaniBuserI_calc, DistanceType.BaroniUrbaniBuserII: BaroniUrbaniBuserII_calc}

pycm/pycm_obj.py

@@ -6,6 +6,7 @@
 from .pycm_handler import __obj_assign_handler__, __obj_file_handler__, __obj_matrix_handler__, __obj_vector_handler__, __obj_array_handler__
 from .pycm_class_func import F_calc, IBA_calc, TI_calc, NB_calc, sensitivity_index_calc
 from .pycm_overall_func import weighted_kappa_calc, weighted_alpha_calc, alpha2_calc, brier_score_calc
+from .pycm_distance import DistanceType, DISTANCE_MAPPER
 from .pycm_output import *
 from .pycm_util import *
 from .pycm_param import *
@@ -591,6 +592,21 @@ def NB(self, w=1):
         except Exception:
             return {}
 
+    def distance(self, metric):
+        """
+        Calculate distance/similarity for all classes.
+
+        :param metric: metric
+        :type metric: DistanceType
+        :return: result as float
+        """
+        distance_dict = {}
+        if not isinstance(metric, DistanceType):
+            pycmMatrixError(DISTANCE_METRIC_TYPE_ERROR)
+        for i in self.classes:
+            distance_dict[i] = DISTANCE_MAPPER[metric](TP = self.TP[i], FP = self.FP[i], FN = self.FN[i], TN = self.TN[i])
+        return distance_dict
+
     def CI(
             self,
             param,

pycm/pycm_param.py

@@ -117,6 +117,8 @@
 
 CURVE_NONE_WARNING = "The curve axes contain non-numerical value(s)."
 
+DISTANCE_METRIC_TYPE_ERROR = "The metric type must be DistanceType"
+
 CLASS_NUMBER_THRESHOLD = 10
 
 BALANCE_RATIO_THRESHOLD = 3