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# -*- coding: utf-8 -*-
"""Class statistics functions."""
from __future__ import division
from typing import Union, Dict, List, Any
import math
from .utils import normal_quantile
from .interpret import *
from .params import CLASS_PARAMS
def sensitivity_index_calc(TPR: float, FPR: float) -> Union[float, str]:
"""
Calculate Sensitivity index (d prime).
:param TPR: sensitivity, recall, hit rate, or true positive rate
:param FPR: fall-out or false positive rate
"""
try:
return normal_quantile(TPR) - normal_quantile(FPR)
except TypeError:
return "None"
def NB_calc(TP: int, FP: int, POP: int, w: float) -> Union[float, str]:
"""
Calculate Net Benefit (NB).
:param TP: true positive
:param FP: false positive
:param POP: population or total number of samples
:param w: weight
"""
try:
NB = (TP - w * FP) / POP
return NB
except (ZeroDivisionError, TypeError):
return "None"
def TI_calc(TP: int, FP: int, FN: int, alpha: float, beta: float) -> Union[float, str]:
"""
Calculate Tversky index (TI).
:param TP: true positive
:param FP: false positive
:param FN: false negative
:param alpha: alpha coefficient
:param beta: beta coefficient
"""
try:
TI = TP / (TP + alpha * FN + beta * FP)
return TI
except (ZeroDivisionError, TypeError):
return "None"
def OOC_calc(TP: int, TOP: int, P: int) -> Union[float, str]:
"""
Calculate Otsuka-Ochiai coefficient (OOC).
:param TP: true positive
:param TOP: number of positives in predict vector
:param P: number of actual positives
"""
try:
OOC = TP / (math.sqrt(TOP * P))
return OOC
except (ZeroDivisionError, TypeError, ValueError):
return "None"
def OC_calc(TP: int, TOP: int, P: int) -> Union[float, str]:
"""
Calculate Overlap coefficient (OC).
:param TP: true positive
:param TOP: number of positives in predict vector
:param P: number of actual positives
"""
try:
overlap_coef = TP / min(TOP, P)
return overlap_coef
except (ZeroDivisionError, TypeError):
return "None"
def BB_calc(TP: int, TOP: int, P: int) -> Union[float, str]:
"""
Calculate Braun-Blanquet similarity (BB).
:param TP: true positive
:param TOP: number of positives in predict vector
:param P: number of actual positives
"""
try:
BB = TP / max(TOP, P)
return BB
except (ZeroDivisionError, TypeError):
return "None"
def AGF_calc(TP: int, FP: int, FN: int, TN: int) -> Union[float, str]:
"""
Calculate Adjusted F-score (AGF).
:param TP: true positive
:param TN: true negative
:param FP: false positive
:param FN: false negative
"""
try:
F2 = F_calc(TP=TP, FP=FP, FN=FN, beta=2)
F05_inv = F_calc(TP=TN, FP=FN, FN=FP, beta=0.5)
AGF = math.sqrt(F2 * F05_inv)
return AGF
except (TypeError, ValueError):
return "None"
def AGM_calc(TPR: float, TNR: float, GM: float, N: int, POP: int) -> Union[float, str]:
"""
Calculate Adjusted geometric mean (AGM).
:param TNR: specificity or true negative rate
:param TPR: sensitivity, recall, hit rate, or true positive rate
:param GM: geometric mean
:param N: number of actual negatives
:param POP: population or total number of samples
"""
try:
n = N / POP
if TPR == 0:
result = 0
else:
result = (GM + TNR * n) / (1 + n)
return result
except (ZeroDivisionError, TypeError):
return "None"
def Q_calc(TP: int, TN: int, FP: int, FN: int) -> Union[float, str]:
"""
Calculate Yule's Q.
:param TP: true positive
:param TN: true negative
:param FP: false positive
:param FN: false negative
"""
try:
OR = (TP * TN) / (FP * FN)
result = (OR - 1) / (OR + 1)
return result
except (ZeroDivisionError, TypeError):
return "None"
def TTPN_calc(item1: int, item2: int) -> Union[float, str]:
"""
Calculate TPR, TNR, PPV, or NPV.
:param item1: item1 in fractional expression
:param item2: item2 in fractional expression
"""
try:
result = item1 / (item1 + item2)
return result
except (ZeroDivisionError, TypeError):
return "None"
def FXR_calc(item: float) -> Union[float, str]:
"""
Calculate False negative rate, False positive rate, False discovery rate (FDR), or False omission rate (FOR).
:param item: item In expression
"""
try:
result = 1 - item
return result
except TypeError:
return "None"
def ACC_calc(TP: int, TN: int, FP: int, FN: int) -> Union[float, str]:
"""
Calculate Accuracy.
:param TP: true positive
:param TN: true negative
:param FP: false positive
:param FN: false negative
"""
try:
result = (TP + TN) / (TP + TN + FN + FP)
return result
except (ZeroDivisionError, TypeError):
return "None"
def F_calc(TP: int, FP: int, FN: int, beta: float) -> Union[float, str]:
"""
Calculate F-score.
:param TP: true positive
:param FP: false positive
:param FN: false negative
:param beta: beta coefficient
"""
try:
result = ((1 + (beta)**2) * TP) / \
((1 + (beta)**2) * TP + FP + (beta**2) * FN)
return result
except (ZeroDivisionError, TypeError):
return "None"
def MCC_calc(TP: int, TN: int, FP: int, FN: int) -> Union[float, str]:
"""
Calculate Matthews correlation coefficient (MCC).
:param TP: true positive
:param TN: true negative
:param FP: false positive
:param FN: false negative
"""
try:
result = (TP * TN - FP * FN) / \
(math.sqrt((TP + FP) * (TP + FN) * (TN + FP) * (TN + FN)))
return result
except (ZeroDivisionError, TypeError, ValueError):
return "None"
def MK_BM_calc(item1: float, item2: float) -> Union[float, str]:
"""
Calculate Informedness (BM), Markedness (MK), or Individual classification success index (ICSI).
:param item1: item1 in expression
:param item2: item2 in expression
"""
try:
result = item1 + item2 - 1
return result
except TypeError:
return "None"
def LR_calc(item1: float, item2: float) -> Union[float, str]:
"""
Calculate Likelihood ratio (LR).
:param item1: item1 in expression
:param item2: item2 in expression
"""
try:
result = item1 / item2
return result
except (ZeroDivisionError, TypeError):
return "None"
def proportion_calc(item1: int, item2: int) -> Union[float, str]:
"""
Calculate Prevalence.
:param item1: item1 in fractional expression
:param item2: item2 in fractional expression
"""
try:
result = item1 / item2
return result
except (ZeroDivisionError, TypeError):
return "None"
def G_calc(item1: float, item2: float) -> Union[float, str]:
"""
Calculate G-measure or G-mean.
:param item1: True positive rate (TPR) or True negative rate (TNR) or Positive predictive value (PPV)
:param item2: True positive rate (TPR) or True negative rate (TNR) or Positive predictive value (PPV)
"""
try:
result = math.sqrt(item1 * item2)
return result
except (TypeError, ValueError):
return "None"
def RACC_calc(TOP: int, P: int, POP: int) -> Union[float, str]:
"""
Calculate Random accuracy (RACC).
:param TOP: number of positives in predict vector
:param P: number of actual positives
:param POP: population or total number of samples
"""
try:
result = (TOP * P) / ((POP) ** 2)
return result
except (ZeroDivisionError, TypeError):
return "None"
def RACCU_calc(TOP: int, P: int, POP: int) -> Union[float, str]:
"""
Calculate Random accuracy unbiased (RACCU).
:param TOP: number of positives in predict vector
:param P: number of actual positives
:param POP: population or total number of samples
"""
try:
result = ((TOP + P) / (2 * POP))**2
return result
except (ZeroDivisionError, TypeError):
return "None"
def ERR_calc(ACC: float) -> Union[float, str]:
"""
Calculate Error rate.
:param ACC: accuracy
:type ACC: float
:return: error rate as float
"""
try:
return 1 - ACC
except TypeError:
return "None"
def jaccard_index_calc(TP: int, TOP: int, P: int) -> Union[float, str]:
"""
Calculate Jaccard index for each class.
:param TP: true positive
:param TOP: number of positives in predict vector
:param P: number of actual positives
"""
try:
return TP / (TOP + P - TP)
except (ZeroDivisionError, TypeError):
return "None"
def IS_calc(TP: int, FP: int, FN: int, POP: int) -> Union[float, str]:
"""
Calculate Information score (IS).
:param TP: true positive
:param FP: false positive
:param FN: false negative
:param POP: population or total number of samples
"""
try:
result = -math.log(((TP + FN) / POP), 2) + \
math.log((TP / (TP + FP)), 2)
return result
except (ZeroDivisionError, TypeError, ValueError):
return "None"
def CEN_misclassification_calc(
table: Dict[Any, Dict[Any, int]],
TOP: int,
P: int,
i: Any,
j: Any,
subject_class: Any,
modified: bool = False) -> Union[float, str]:
"""
Calculate Misclassification probability.
:param table: input confusion matrix
:param TOP: number of positives in predict vector
:param P: number of actual positives
:param i: table row index (class name)
:param j: table col index (class name)
:param subject_class: subject to class (class name)
:param modified: modified mode flag
"""
try:
result = TOP + P
if modified:
result -= table[subject_class][subject_class]
result = table[i][j] / result
return result
except (ZeroDivisionError, TypeError):
return "None"
def CEN_calc(
classes: List[Any],
table: Dict[Any, Dict[Any, int]],
TOP: int,
P: int,
class_name: Any,
modified: bool = False) -> Union[float, str]:
"""
Calculate Confusion Entropy (CEN) (or Modified Confusion Entropy (MCEN)).
:param classes: confusion matrix classes
:param table: input confusion matrix
:param TOP: number of positives in predict vector
:param P: number of actual positives
:param class_name: reviewed class name
:param modified: modified mode flag
"""
try:
result = 0
class_number = len(classes)
for k in classes:
if k != class_name:
P_j_k = CEN_misclassification_calc(
table, TOP, P, class_name, k, class_name, modified)
P_k_j = CEN_misclassification_calc(
table, TOP, P, k, class_name, class_name, modified)
if P_j_k != 0:
result += P_j_k * math.log(P_j_k, 2 * (class_number - 1))
if P_k_j != 0:
result += P_k_j * math.log(P_k_j, 2 * (class_number - 1))
if result != 0:
result = result * (-1)
return result
except (ZeroDivisionError, TypeError, ValueError):
return "None"
def AUC_calc(item: float, TPR: float) -> Union[float, str]:
"""
Calculate Area under the ROC/PR curve for each class (AUC/AUPR).
:param item: True negative rate (TNR) or Positive predictive value (PPV)
:param TPR: sensitivity, recall, hit rate, or true positive rate
"""
try:
return (item + TPR) / 2
except TypeError:
return "None"
def dInd_calc(TNR: float, TPR: float) -> Union[float, str]:
"""
Calculate Distance index (dInd).
:param TNR: specificity or true negative rate
:param TPR: sensitivity, recall, hit rate, or true positive rate
"""
try:
result = math.sqrt(((1 - TNR)**2) + ((1 - TPR)**2))
return result
except (TypeError, ValueError):
return "None"
def sInd_calc(dInd: float) -> Union[float, str]:
"""
Calculate Similarity index (sInd).
:param dInd: dInd
"""
try:
return 1 - (dInd / (math.sqrt(2)))
except (ZeroDivisionError, TypeError):
return "None"
def DP_calc(TPR: float, TNR: float) -> Union[float, str]:
"""
Calculate Discriminant power (DP).
:param TNR: specificity or true negative rate
:param TPR: sensitivity, recall, hit rate, or true positive rate
"""
try:
X = TPR / (1 - TPR)
Y = TNR / (1 - TNR)
return (math.sqrt(3) / math.pi) * (math.log(X, 10) + math.log(Y, 10))
except (ZeroDivisionError, TypeError, ValueError):
return "None"
def GI_calc(AUC: float) -> Union[float, str]:
"""
Calculate Gini index.
:param AUC: Area under the ROC curve
"""
try:
return 2 * AUC - 1
except TypeError:
return "None"
def lift_calc(PPV: float, PRE: float) -> Union[float, str]:
"""
Calculate Lift score.
:param PPV: Positive predictive value (PPV)
:param PRE: Prevalence
"""
try:
return PPV / PRE
except (ZeroDivisionError, TypeError):
return "None"
def AM_calc(TOP: int, P: int) -> Union[int, str]:
"""
Calculate Automatic/Manual (AM).
:param TOP: number of positives in predict vector
:param P: number of actual positives
"""
try:
return TOP - P
except TypeError:
return "None"
def OP_calc(ACC: float, TPR: float, TNR: float) -> Union[float, str]:
"""
Calculate Optimized precision (OP).
:param ACC: accuracy
:param TNR: specificity or true negative rate
:param TPR: sensitivity, recall, hit rate, or true positive rate
"""
try:
RI = abs(TNR - TPR) / (TPR + TNR)
return ACC - RI
except (ZeroDivisionError, TypeError):
return "None"
def IBA_calc(TPR: float, TNR: float, alpha: float = 1) -> Union[float, str]:
"""
Calculate Index of balanced accuracy (IBA).
:param TNR: specificity or true negative rate
:param TPR: sensitivity, recall, hit rate, or true positive rate
:param alpha: alpha coefficient
"""
try:
IBA = (1 + alpha * (TPR - TNR)) * TPR * TNR
return IBA
except TypeError:
return "None"
def BCD_calc(AM: int, POP: int) -> Union[float, str]:
"""
Calculate Bray-Curtis dissimilarity (BCD).
:param AM: Automatic/Manual
:param POP: population or total number of samples
"""
try:
return abs(AM) / (2 * POP)
except (ZeroDivisionError, TypeError, AttributeError):
return "None"
def basic_statistics(
TP: Dict[Any, int],
TN: Dict[Any, int],
FP: Dict[Any, int],
FN: Dict[Any, int]) -> Dict[str, Dict[Any, int]]:
"""
Init classes' statistics.
:param TP: true positive
:param TN: true negative
:param FP: false positive
:param FN: false negative
"""
result = {}
for i in CLASS_PARAMS:
result[i] = {}
result["TP"] = TP
result["TN"] = TN
result["FP"] = FP
result["FN"] = FN
return result
def class_statistics(
TP: Dict[Any, int],
TN: Dict[Any, int],
FP: Dict[Any, int],
FN: Dict[Any, int],
classes: List[Any],
table: Dict[Any, Dict[Any, int]]) -> Dict[str, Dict[Any, Union[float, int, str]]]:
"""
Return All statistics of classes.
:param TP: true positive
:param TN: true negative
:param FP: false positive
:param FN: false negative
:param classes: confusion matrix classes
:param table: input confusion matrix
"""
result = basic_statistics(TP, TN, FP, FN)
for i in TP:
result["POP"][i] = TP[i] + TN[i] + FP[i] + FN[i]
result["P"][i] = TP[i] + FN[i]
result["N"][i] = TN[i] + FP[i]
result["TOP"][i] = TP[i] + FP[i]
result["TON"][i] = TN[i] + FN[i]
result["HD"][i] = FP[i] + FN[i]
result["TPR"][i] = TTPN_calc(TP[i], FN[i])
result["TNR"][i] = TTPN_calc(TN[i], FP[i])
result["PPV"][i] = TTPN_calc(TP[i], FP[i])
result["NPV"][i] = TTPN_calc(TN[i], FN[i])
result["FNR"][i] = FXR_calc(result["TPR"][i])
result["FPR"][i] = FXR_calc(result["TNR"][i])
result["FDR"][i] = FXR_calc(result["PPV"][i])
result["FOR"][i] = FXR_calc(result["NPV"][i])
result["ACC"][i] = ACC_calc(TP[i], TN[i], FP[i], FN[i])
result["F1"][i] = F_calc(TP[i], FP[i], FN[i], 1)
result["F0.5"][i] = F_calc(TP[i], FP[i], FN[i], 0.5)
result["F2"][i] = F_calc(TP[i], FP[i], FN[i], 2)
result["MCC"][i] = MCC_calc(TP[i], TN[i], FP[i], FN[i])
result["BM"][i] = MK_BM_calc(result["TPR"][i], result["TNR"][i])
result["MK"][i] = MK_BM_calc(result["PPV"][i], result["NPV"][i])
result["PLR"][i] = LR_calc(result["TPR"][i], result["FPR"][i])
result["NLR"][i] = LR_calc(result["FNR"][i], result["TNR"][i])
result["DOR"][i] = LR_calc(result["PLR"][i], result["NLR"][i])
result["PRE"][i] = proportion_calc(result["P"][i], result["POP"][i])
result["PR"][i] = result["PRE"][i]
result["TOPR"][i] = proportion_calc(result["TOP"][i], result["POP"][i])
result["G"][i] = G_calc(result["PPV"][i], result["TPR"][i])
result["RACC"][i] = RACC_calc(
result["TOP"][i], result["P"][i], result["POP"][i])
result["ERR"][i] = ERR_calc(result["ACC"][i])
result["RACCU"][i] = RACCU_calc(
result["TOP"][i], result["P"][i], result["POP"][i])
result["J"][i] = jaccard_index_calc(
TP[i], result["TOP"][i], result["P"][i])
result["IS"][i] = IS_calc(TP[i], FP[i], FN[i], result["POP"][i])
result["CEN"][i] = CEN_calc(
classes, table, result["TOP"][i], result["P"][i], i)
result["MCEN"][i] = CEN_calc(
classes,
table,
result["TOP"][i],
result["P"][i],
i,
True)
result["AUC"][i] = AUC_calc(result["TNR"][i], result["TPR"][i])
result["dInd"][i] = dInd_calc(result["TNR"][i], result["TPR"][i])
result["sInd"][i] = sInd_calc(result["dInd"][i])
result["DP"][i] = DP_calc(result["TPR"][i], result["TNR"][i])
result["Y"][i] = result["BM"][i]
result["PLRI"][i] = PLR_analysis(result["PLR"][i])
result["NLRI"][i] = NLR_analysis(result["NLR"][i])
result["DPI"][i] = DP_analysis(result["DP"][i])
result["AUCI"][i] = AUC_analysis(result["AUC"][i])
result["GI"][i] = GI_calc(result["AUC"][i])
result["LS"][i] = lift_calc(result["PPV"][i], result["PRE"][i])
result["AM"][i] = AM_calc(result["TOP"][i], result["P"][i])
result["OP"][i] = OP_calc(
result["ACC"][i],
result["TPR"][i],
result["TNR"][i])
result["IBA"][i] = IBA_calc(result["TPR"][i], result["TNR"][i])
result["GM"][i] = G_calc(result["TNR"][i], result["TPR"][i])
result["Q"][i] = Q_calc(TP[i], TN[i], FP[i], FN[i])
result["QI"][i] = Q_analysis(result["Q"][i])
result["AGM"][i] = AGM_calc(
result["TPR"][i],
result["TNR"][i],
result["GM"][i],
result["N"][i],
result["POP"][i])
result["MCCI"][i] = MCC_analysis(result["MCC"][i])
result["AGF"][i] = AGF_calc(TP[i], FP[i], FN[i], TN[i])
result["OC"][i] = OC_calc(TP[i], result["TOP"][i], result["P"][i])
result["BB"][i] = BB_calc(TP[i], result["TOP"][i], result["P"][i])
result["OOC"][i] = OOC_calc(TP[i], result["TOP"][i], result["P"][i])
result["AUPR"][i] = AUC_calc(result["PPV"][i], result["TPR"][i])
result["ICSI"][i] = MK_BM_calc(result["PPV"][i], result["TPR"][i])
result["BCD"][i] = BCD_calc(result["AM"][i], result["POP"][i])
return result
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