tsadmetrics 0.1.4__py3-none-any.whl → 0.1.5__py3-none-any.whl

tsadmetrics/_tsadeval/affiliation/_integral_interval.py

@@ -0,0 +1,464 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+import math
+from .generics import _sum_wo_nan
+"""
+In order to shorten the length of the variables,
+the general convention in this file is to let:
+    - I for a predicted event (start, stop),
+    - Is for a list of predicted events,
+    - J for a ground truth event,
+    - Js for a list of ground truth events.
+"""
+
+def interval_length(J = (1,2)):
+    """
+    Length of an interval
+    
+    :param J: couple representating the start and stop of an interval, or None
+    :return: length of the interval, and 0 for a None interval
+    """
+    if J is None:
+        return(0)
+    return(J[1] - J[0])
+
+def sum_interval_lengths(Is = [(1,2),(3,4),(5,6)]):
+    """
+    Sum of length of the intervals
+    
+    :param Is: list of intervals represented by starts and stops
+    :return: sum of the interval length
+    """
+    return(sum([interval_length(I) for I in Is]))
+
+def interval_intersection(I = (1, 3), J = (2, 4)): 
+    """
+    Intersection between two intervals I and J
+    I and J should be either empty or represent a positive interval (no point)
+    
+    :param I: an interval represented by start and stop
+    :param J: a second interval of the same form
+    :return: an interval representing the start and stop of the intersection (or None if empty)
+    """
+    if I is None:
+        return(None)
+    if J is None:
+        return(None)
+        
+    I_inter_J = (max(I[0], J[0]), min(I[1], J[1]))
+    if I_inter_J[0] >= I_inter_J[1]:
+        return(None)
+    else:
+        return(I_inter_J)
+
+def interval_subset(I = (1, 3), J = (0, 6)):
+    """
+    Checks whether I is a subset of J
+    
+    :param I: an non empty interval represented by start and stop
+    :param J: a second non empty interval of the same form
+    :return: True if I is a subset of J
+    """
+    if (I[0] >= J[0]) and (I[1] <= J[1]):
+        return True
+    else:
+        return False
+
+def cut_into_three_func(I, J):
+    """
+    Cut an interval I into a partition of 3 subsets:
+        the elements before J,
+        the elements belonging to J,
+        and the elements after J
+    
+    :param I: an interval represented by start and stop, or None for an empty one
+    :param J: a non empty interval
+    :return: a triplet of three intervals, each represented by either (start, stop) or None
+    """
+    if I is None:
+        return((None, None, None))
+    
+    I_inter_J = interval_intersection(I, J)
+    if I == I_inter_J:
+        I_before = None
+        I_after = None
+    elif I[1] <= J[0]:
+        I_before = I
+        I_after = None
+    elif I[0] >= J[1]:
+        I_before = None
+        I_after = I
+    elif (I[0] <= J[0]) and (I[1] >= J[1]):
+        I_before = (I[0], I_inter_J[0])
+        I_after = (I_inter_J[1], I[1])
+    elif I[0] <= J[0]:
+        I_before = (I[0], I_inter_J[0])
+        I_after = None
+    elif I[1] >= J[1]:
+        I_before = None
+        I_after = (I_inter_J[1], I[1])
+    else:
+        raise ValueError('unexpected unconsidered case')
+    return(I_before, I_inter_J, I_after)
+  
+def get_pivot_j(I, J):
+    """
+    Get the single point of J that is the closest to I, called 'pivot' here,
+    with the requirement that I should be outside J
+    
+    :param I: a non empty interval (start, stop)
+    :param J: another non empty interval, with empty intersection with I
+    :return: the element j of J that is the closest to I
+    """
+    if interval_intersection(I, J) is not None:
+        raise ValueError('I and J should have a void intersection')
+
+    j_pivot = None # j_pivot is a border of J
+    if max(I) <= min(J):
+        j_pivot = min(J)
+    elif min(I) >= max(J):
+        j_pivot = max(J)
+    else:
+        raise ValueError('I should be outside J')
+    return(j_pivot)
+
+def integral_mini_interval(I, J):
+    """
+    In the specific case where interval I is located outside J,
+    integral of distance from x to J over the interval x \in I.
+    This is the *integral* i.e. the sum.
+    It's not the mean (not divided by the length of I yet)
+    
+    :param I: a interval (start, stop), or None
+    :param J: a non empty interval, with empty intersection with I
+    :return: the integral of distances d(x, J) over x \in I
+    """
+    if I is None:
+        return(0)
+
+    j_pivot = get_pivot_j(I, J)
+    a = min(I)
+    b = max(I)
+    return((b-a)*abs((j_pivot - (a+b)/2)))
+
+def integral_interval_distance(I, J):
+    """
+    For any non empty intervals I, J, compute the
+    integral of distance from x to J over the interval x \in I.
+    This is the *integral* i.e. the sum. 
+    It's not the mean (not divided by the length of I yet)
+    The interval I can intersect J or not
+    
+    :param I: a interval (start, stop), or None
+    :param J: a non empty interval
+    :return: the integral of distances d(x, J) over x \in I
+    """
+    # I and J are single intervals (not generic sets)
+    # I is a predicted interval in the range of affiliation of J
+    
+    def f(I_cut):
+        return(integral_mini_interval(I_cut, J))
+    # If I_middle is fully included into J, it is
+    # the distance to J is always 0
+    def f0(I_middle):
+        return(0)
+
+    cut_into_three = cut_into_three_func(I, J)
+    # Distance for now, not the mean:
+    # Distance left: Between cut_into_three[0] and the point min(J)
+    d_left = f(cut_into_three[0])
+    # Distance middle: Between cut_into_three[1] = I inter J, and J
+    d_middle = f0(cut_into_three[1])
+    # Distance right: Between cut_into_three[2] and the point max(J)
+    d_right = f(cut_into_three[2])
+    # It's an integral so summable
+    return(d_left + d_middle + d_right)
+
+def integral_mini_interval_P_CDFmethod__min_piece(I, J, E):
+    """
+    Helper of `integral_mini_interval_Pprecision_CDFmethod`
+    In the specific case where interval I is located outside J,
+    compute the integral $\int_{d_min}^{d_max} \min(m, x) dx$, with:
+    - m the smallest distance from J to E,
+    - d_min the smallest distance d(x, J) from x \in I to J
+    - d_max the largest distance d(x, J) from x \in I to J
+    
+    :param I: a single predicted interval, a non empty interval (start, stop)
+    :param J: ground truth interval, a non empty interval, with empty intersection with I
+    :param E: the affiliation/influence zone for J, represented as a couple (start, stop)
+    :return: the integral $\int_{d_min}^{d_max} \min(m, x) dx$
+    """
+    if interval_intersection(I, J) is not None:
+        raise ValueError('I and J should have a void intersection')
+    if not interval_subset(J, E):
+        raise ValueError('J should be included in E')
+    if not interval_subset(I, E):
+        raise ValueError('I should be included in E')
+
+    e_min = min(E)
+    j_min = min(J)
+    j_max = max(J)
+    e_max = max(E)
+    i_min = min(I)
+    i_max = max(I)
+  
+    d_min = max(i_min - j_max, j_min - i_max)
+    d_max = max(i_max - j_max, j_min - i_min)
+    m = min(j_min - e_min, e_max - j_max)
+    A = min(d_max, m)**2 - min(d_min, m)**2
+    B = max(d_max, m) - max(d_min, m)
+    C = (1/2)*A + m*B
+    return(C)
+
+def integral_mini_interval_Pprecision_CDFmethod(I, J, E):
+    """
+    Integral of the probability of distances over the interval I.
+    In the specific case where interval I is located outside J,
+    compute the integral $\int_{x \in I} Fbar(dist(x,J)) dx$.
+    This is the *integral* i.e. the sum (not the mean)
+    
+    :param I: a single predicted interval, a non empty interval (start, stop)
+    :param J: ground truth interval, a non empty interval, with empty intersection with I
+    :param E: the affiliation/influence zone for J, represented as a couple (start, stop)
+    :return: the integral $\int_{x \in I} Fbar(dist(x,J)) dx$
+    """
+    integral_min_piece = integral_mini_interval_P_CDFmethod__min_piece(I, J, E)
+  
+    e_min = min(E)
+    j_min = min(J)
+    j_max = max(J)
+    e_max = max(E)
+    i_min = min(I)
+    i_max = max(I)
+    d_min = max(i_min - j_max, j_min - i_max)
+    d_max = max(i_max - j_max, j_min - i_min)
+    integral_linear_piece = (1/2)*(d_max**2 - d_min**2)
+    integral_remaining_piece = (j_max - j_min)*(i_max - i_min)
+    
+    DeltaI = i_max - i_min
+    DeltaE = e_max - e_min
+    
+    output = DeltaI - (1/DeltaE)*(integral_min_piece + integral_linear_piece + integral_remaining_piece)
+    return(output)
+
+def integral_interval_probaCDF_precision(I, J, E):
+    """
+    Integral of the probability of distances over the interval I.
+    Compute the integral $\int_{x \in I} Fbar(dist(x,J)) dx$.
+    This is the *integral* i.e. the sum (not the mean)
+    
+    :param I: a single (non empty) predicted interval in the zone of affiliation of J
+    :param J: ground truth interval
+    :param E: affiliation/influence zone for J
+    :return: the integral $\int_{x \in I} Fbar(dist(x,J)) dx$
+    """
+    # I and J are single intervals (not generic sets)
+    def f(I_cut):
+        if I_cut is None:
+            return(0)
+        else:
+            return(integral_mini_interval_Pprecision_CDFmethod(I_cut, J, E))
+            
+    # If I_middle is fully included into J, it is
+    # integral of 1 on the interval I_middle, so it's |I_middle|
+    def f0(I_middle):
+        if I_middle is None:
+            return(0)
+        else:
+            return(max(I_middle) - min(I_middle))
+    
+    cut_into_three = cut_into_three_func(I, J)
+    # Distance for now, not the mean:
+    # Distance left: Between cut_into_three[0] and the point min(J)
+    d_left = f(cut_into_three[0])
+    # Distance middle: Between cut_into_three[1] = I inter J, and J
+    d_middle = f0(cut_into_three[1])
+    # Distance right: Between cut_into_three[2] and the point max(J)
+    d_right = f(cut_into_three[2])
+    # It's an integral so summable
+    return(d_left + d_middle + d_right)
+
+def cut_J_based_on_mean_func(J, e_mean):
+    """
+    Helper function for the recall.
+    Partition J into two intervals: before and after e_mean
+    (e_mean represents the center element of E the zone of affiliation)
+    
+    :param J: ground truth interval
+    :param e_mean: a float number (center value of E)
+    :return: a couple partitionning J into (J_before, J_after)
+    """
+    if J is None:
+        J_before = None
+        J_after = None
+    elif e_mean >= max(J):
+        J_before = J
+        J_after = None
+    elif e_mean <= min(J):
+        J_before = None
+        J_after = J
+    else: # e_mean is across J
+        J_before = (min(J), e_mean)
+        J_after = (e_mean, max(J))
+        
+    return((J_before, J_after))
+
+def integral_mini_interval_Precall_CDFmethod(I, J, E):
+    """
+    Integral of the probability of distances over the interval J.
+    In the specific case where interval J is located outside I,
+    compute the integral $\int_{y \in J} Fbar_y(dist(y,I)) dy$.
+    This is the *integral* i.e. the sum (not the mean)
+    
+    :param I: a single (non empty) predicted interval
+    :param J: ground truth (non empty) interval, with empty intersection with I
+    :param E: the affiliation/influence zone for J, represented as a couple (start, stop)
+    :return: the integral $\int_{y \in J} Fbar_y(dist(y,I)) dy$
+    """
+    # The interval J should be located outside I 
+    # (so it's either the left piece or the right piece w.r.t I)
+    i_pivot = get_pivot_j(J, I)
+    e_min = min(E)
+    e_max = max(E)
+    e_mean = (e_min + e_max) / 2
+    
+    # If i_pivot is outside E (it's possible), then
+    # the distance is worst that any random element within E,
+    # so we set the recall to 0
+    if i_pivot <= min(E):
+        return(0)
+    elif i_pivot >= max(E):
+        return(0)
+    # Otherwise, we have at least i_pivot in E and so d < M so min(d,M)=d
+    
+    cut_J_based_on_e_mean = cut_J_based_on_mean_func(J, e_mean)
+    J_before = cut_J_based_on_e_mean[0]
+    J_after = cut_J_based_on_e_mean[1]
+  
+    iemin_mean = (e_min + i_pivot)/2
+    cut_Jbefore_based_on_iemin_mean = cut_J_based_on_mean_func(J_before, iemin_mean)
+    J_before_closeE = cut_Jbefore_based_on_iemin_mean[0] # before e_mean and closer to e_min than i_pivot ~ J_before_before
+    J_before_closeI = cut_Jbefore_based_on_iemin_mean[1] # before e_mean and closer to i_pivot than e_min ~ J_before_after
+    
+    iemax_mean = (e_max + i_pivot)/2
+    cut_Jafter_based_on_iemax_mean = cut_J_based_on_mean_func(J_after, iemax_mean)
+    J_after_closeI = cut_Jafter_based_on_iemax_mean[0] # after e_mean and closer to i_pivot than e_max ~ J_after_before
+    J_after_closeE = cut_Jafter_based_on_iemax_mean[1] # after e_mean and closer to e_max than i_pivot ~ J_after_after
+    
+    if J_before_closeE is not None:
+        j_before_before_min = min(J_before_closeE) # == min(J)
+        j_before_before_max = max(J_before_closeE)
+    else:
+        j_before_before_min = math.nan
+        j_before_before_max = math.nan
+  
+    if J_before_closeI is not None:
+        j_before_after_min = min(J_before_closeI) # == j_before_before_max if existing
+        j_before_after_max = max(J_before_closeI) # == max(J_before)
+    else:
+        j_before_after_min = math.nan
+        j_before_after_max = math.nan
+   
+    if J_after_closeI is not None:
+        j_after_before_min = min(J_after_closeI) # == min(J_after)
+        j_after_before_max = max(J_after_closeI) 
+    else:
+        j_after_before_min = math.nan
+        j_after_before_max = math.nan
+    
+    if J_after_closeE is not None:
+        j_after_after_min = min(J_after_closeE) # == j_after_before_max if existing
+        j_after_after_max = max(J_after_closeE) # == max(J)
+    else:
+        j_after_after_min = math.nan
+        j_after_after_max = math.nan
+  
+    # <-- J_before_closeE --> <-- J_before_closeI --> <-- J_after_closeI --> <-- J_after_closeE -->
+    # j_bb_min       j_bb_max j_ba_min       j_ba_max j_ab_min      j_ab_max j_aa_min      j_aa_max
+    # (with `b` for before and `a` for after in the previous variable names)
+    
+    #                                          vs e_mean  m = min(t-e_min, e_max-t)  d=|i_pivot-t|   min(d,m)                            \int min(d,m)dt   \int d dt        \int_(min(d,m)+d)dt                                    \int_{t \in J}(min(d,m)+d)dt
+    # Case J_before_closeE & i_pivot after J   before     t-e_min                    i_pivot-t       min(i_pivot-t,t-e_min) = t-e_min    t^2/2-e_min*t     i_pivot*t-t^2/2  t^2/2-e_min*t+i_pivot*t-t^2/2 = (i_pivot-e_min)*t      (i_pivot-e_min)*tB - (i_pivot-e_min)*tA = (i_pivot-e_min)*(tB-tA)
+    # Case J_before_closeI & i_pivot after J   before     t-e_min                    i_pivot-t       min(i_pivot-t,t-e_min) = i_pivot-t  i_pivot*t-t^2/2   i_pivot*t-t^2/2  i_pivot*t-t^2/2+i_pivot*t-t^2/2 = 2*i_pivot*t-t^2      2*i_pivot*tB-tB^2 - 2*i_pivot*tA + tA^2 = 2*i_pivot*(tB-tA) - (tB^2 - tA^2)
+    # Case J_after_closeI & i_pivot after J    after      e_max-t                    i_pivot-t       min(i_pivot-t,e_max-t) = i_pivot-t  i_pivot*t-t^2/2   i_pivot*t-t^2/2  i_pivot*t-t^2/2+i_pivot*t-t^2/2 = 2*i_pivot*t-t^2      2*i_pivot*tB-tB^2 - 2*i_pivot*tA + tA^2 = 2*i_pivot*(tB-tA) - (tB^2 - tA^2)
+    # Case J_after_closeE & i_pivot after J    after      e_max-t                    i_pivot-t       min(i_pivot-t,e_max-t) = e_max-t    e_max*t-t^2/2     i_pivot*t-t^2/2  e_max*t-t^2/2+i_pivot*t-t^2/2 = (e_max+i_pivot)*t-t^2  (e_max+i_pivot)*tB-tB^2 - (e_max+i_pivot)*tA + tA^2 = (e_max+i_pivot)*(tB-tA) - (tB^2 - tA^2)
+    #
+    # Case J_before_closeE & i_pivot before J  before     t-e_min                    t-i_pivot       min(t-i_pivot,t-e_min) = t-e_min    t^2/2-e_min*t     t^2/2-i_pivot*t  t^2/2-e_min*t+t^2/2-i_pivot*t = t^2-(e_min+i_pivot)*t  tB^2-(e_min+i_pivot)*tB - tA^2 + (e_min+i_pivot)*tA = (tB^2 - tA^2) - (e_min+i_pivot)*(tB-tA)
+    # Case J_before_closeI & i_pivot before J  before     t-e_min                    t-i_pivot       min(t-i_pivot,t-e_min) = t-i_pivot  t^2/2-i_pivot*t   t^2/2-i_pivot*t  t^2/2-i_pivot*t+t^2/2-i_pivot*t = t^2-2*i_pivot*t      tB^2-2*i_pivot*tB - tA^2 + 2*i_pivot*tA = (tB^2 - tA^2) - 2*i_pivot*(tB-tA)
+    # Case J_after_closeI & i_pivot before J   after      e_max-t                    t-i_pivot       min(t-i_pivot,e_max-t) = t-i_pivot  t^2/2-i_pivot*t   t^2/2-i_pivot*t  t^2/2-i_pivot*t+t^2/2-i_pivot*t = t^2-2*i_pivot*t      tB^2-2*i_pivot*tB - tA^2 + 2*i_pivot*tA = (tB^2 - tA^2) - 2*i_pivot*(tB-tA)
+    # Case J_after_closeE & i_pivot before J   after      e_max-t                    t-i_pivot       min(t-i_pivot,e_max-t) = e_max-t    e_max*t-t^2/2     t^2/2-i_pivot*t  e_max*t-t^2/2+t^2/2-i_pivot*t = (e_max-i_pivot)*t      (e_max-i_pivot)*tB - (e_max-i_pivot)*tA = (e_max-i_pivot)*(tB-tA)
+    
+    if i_pivot >= max(J):
+        part1_before_closeE = (i_pivot-e_min)*(j_before_before_max - j_before_before_min) # (i_pivot-e_min)*(tB-tA) # j_before_before_max - j_before_before_min
+        part2_before_closeI = 2*i_pivot*(j_before_after_max-j_before_after_min) - (j_before_after_max**2 - j_before_after_min**2) # 2*i_pivot*(tB-tA) - (tB^2 - tA^2) # j_before_after_max - j_before_after_min
+        part3_after_closeI = 2*i_pivot*(j_after_before_max-j_after_before_min) - (j_after_before_max**2 - j_after_before_min**2) # 2*i_pivot*(tB-tA) - (tB^2 - tA^2) # j_after_before_max - j_after_before_min  
+        part4_after_closeE = (e_max+i_pivot)*(j_after_after_max-j_after_after_min) - (j_after_after_max**2 - j_after_after_min**2) # (e_max+i_pivot)*(tB-tA) - (tB^2 - tA^2) # j_after_after_max - j_after_after_min
+        out_parts = [part1_before_closeE, part2_before_closeI, part3_after_closeI, part4_after_closeE]
+    elif i_pivot <= min(J):
+        part1_before_closeE = (j_before_before_max**2 - j_before_before_min**2) - (e_min+i_pivot)*(j_before_before_max-j_before_before_min) # (tB^2 - tA^2) - (e_min+i_pivot)*(tB-tA) # j_before_before_max - j_before_before_min
+        part2_before_closeI = (j_before_after_max**2 - j_before_after_min**2) - 2*i_pivot*(j_before_after_max-j_before_after_min) # (tB^2 - tA^2) - 2*i_pivot*(tB-tA) # j_before_after_max - j_before_after_min
+        part3_after_closeI = (j_after_before_max**2 - j_after_before_min**2) - 2*i_pivot*(j_after_before_max - j_after_before_min) # (tB^2 - tA^2) - 2*i_pivot*(tB-tA) # j_after_before_max - j_after_before_min
+        part4_after_closeE = (e_max-i_pivot)*(j_after_after_max - j_after_after_min) # (e_max-i_pivot)*(tB-tA) # j_after_after_max - j_after_after_min
+        out_parts = [part1_before_closeE, part2_before_closeI, part3_after_closeI, part4_after_closeE]
+    else:
+        raise ValueError('The i_pivot should be outside J')
+    
+    out_integral_min_dm_plus_d = _sum_wo_nan(out_parts) # integral on all J, i.e. sum of the disjoint parts
+
+    # We have for each point t of J:
+    # \bar{F}_{t, recall}(d) = 1 - (1/|E|) * (min(d,m) + d)
+    # Since t is a single-point here, and we are in the case where i_pivot is inside E.
+    # The integral is then given by:
+    # C = \int_{t \in J} \bar{F}_{t, recall}(D(t)) dt
+    #   = \int_{t \in J} 1 - (1/|E|) * (min(d,m) + d) dt
+    #   = |J| - (1/|E|) * [\int_{t \in J} (min(d,m) + d) dt]
+    #   = |J| - (1/|E|) * out_integral_min_dm_plus_d    
+    DeltaJ = max(J) - min(J)
+    DeltaE = max(E) - min(E)
+    C = DeltaJ - (1/DeltaE) * out_integral_min_dm_plus_d
+    
+    return(C)
+
+def integral_interval_probaCDF_recall(I, J, E):
+    """
+    Integral of the probability of distances over the interval J.
+    Compute the integral $\int_{y \in J} Fbar_y(dist(y,I)) dy$.
+    This is the *integral* i.e. the sum (not the mean)
+
+    :param I: a single (non empty) predicted interval
+    :param J: ground truth (non empty) interval
+    :param E: the affiliation/influence zone for J
+    :return: the integral $\int_{y \in J} Fbar_y(dist(y,I)) dy$
+    """
+    # I and J are single intervals (not generic sets)
+    # E is the outside affiliation interval of J (even for recall!)
+    # (in particular J \subset E)
+    #
+    # J is the portion of the ground truth affiliated to I
+    # I is a predicted interval (can be outside E possibly since it's recall)
+    def f(J_cut):
+        if J_cut is None:
+            return(0)
+        else:
+            return integral_mini_interval_Precall_CDFmethod(I, J_cut, E)
+
+    # If J_middle is fully included into I, it is
+    # integral of 1 on the interval J_middle, so it's |J_middle|
+    def f0(J_middle):
+        if J_middle is None:
+            return(0)
+        else:
+            return(max(J_middle) - min(J_middle))
+    
+    cut_into_three = cut_into_three_func(J, I) # it's J that we cut into 3, depending on the position w.r.t I
+    # since we integrate over J this time.
+    #
+    # Distance for now, not the mean:
+    # Distance left: Between cut_into_three[0] and the point min(I)
+    d_left = f(cut_into_three[0])
+    # Distance middle: Between cut_into_three[1] = J inter I, and I
+    d_middle = f0(cut_into_three[1])
+    # Distance right: Between cut_into_three[2] and the point max(I)
+    d_right = f(cut_into_three[2])
+    # It's an integral so summable
+    return(d_left + d_middle + d_right)

tsadmetrics/_tsadeval/affiliation/_single_ground_truth_event.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+import math
+from ._affiliation_zone import (
+        get_all_E_gt_func, 
+        affiliation_partition)
+from ._integral_interval import (
+        integral_interval_distance,
+        integral_interval_probaCDF_precision, 
+        integral_interval_probaCDF_recall, 
+        interval_length,
+        sum_interval_lengths)
+
+def affiliation_precision_distance(Is = [(1,2),(3,4),(5,6)], J = (2,5.5)):
+    """
+    Compute the individual average distance from Is to a single ground truth J
+    
+    :param Is: list of predicted events within the affiliation zone of J
+    :param J: couple representating the start and stop of a ground truth interval
+    :return: individual average precision directed distance number
+    """
+    if all([I is None for I in Is]): # no prediction in the current area
+        return(math.nan) # undefined
+    return(sum([integral_interval_distance(I, J) for I in Is]) / sum_interval_lengths(Is))
+
+def affiliation_precision_proba(Is = [(1,2),(3,4),(5,6)], J = (2,5.5), E = (0,8)):
+    """
+    Compute the individual precision probability from Is to a single ground truth J
+    
+    :param Is: list of predicted events within the affiliation zone of J
+    :param J: couple representating the start and stop of a ground truth interval
+    :param E: couple representing the start and stop of the zone of affiliation of J
+    :return: individual precision probability in [0, 1], or math.nan if undefined
+    """
+    if all([I is None for I in Is]): # no prediction in the current area
+        return(math.nan) # undefined
+    return(sum([integral_interval_probaCDF_precision(I, J, E) for I in Is]) / sum_interval_lengths(Is))
+
+def affiliation_recall_distance(Is = [(1,2),(3,4),(5,6)], J = (2,5.5)):
+    """
+    Compute the individual average distance from a single J to the predictions Is
+    
+    :param Is: list of predicted events within the affiliation zone of J
+    :param J: couple representating the start and stop of a ground truth interval
+    :return: individual average recall directed distance number
+    """
+    Is = [I for I in Is if I is not None] # filter possible None in Is
+    if len(Is) == 0: # there is no prediction in the current area
+        return(math.inf)
+    E_gt_recall = get_all_E_gt_func(Is, (-math.inf, math.inf))  # here from the point of view of the predictions
+    Js = affiliation_partition([J], E_gt_recall) # partition of J depending of proximity with Is
+    return(sum([integral_interval_distance(J[0], I) for I, J in zip(Is, Js)]) / interval_length(J))
+
+def affiliation_recall_proba(Is = [(1,2),(3,4),(5,6)], J = (2,5.5), E = (0,8)):
+    """
+    Compute the individual recall probability from a single ground truth J to Is
+    
+    :param Is: list of predicted events within the affiliation zone of J
+    :param J: couple representating the start and stop of a ground truth interval
+    :param E: couple representing the start and stop of the zone of affiliation of J
+    :return: individual recall probability in [0, 1]
+    """
+    Is = [I for I in Is if I is not None] # filter possible None in Is
+    if len(Is) == 0: # there is no prediction in the current area
+        return(0)
+    E_gt_recall = get_all_E_gt_func(Is, E) # here from the point of view of the predictions
+    Js = affiliation_partition([J], E_gt_recall) # partition of J depending of proximity with Is
+    return(sum([integral_interval_probaCDF_recall(I, J[0], E) for I, J in zip(Is, Js)]) / interval_length(J))

tsadmetrics/_tsadeval/affiliation/generics.py

@@ -0,0 +1,135 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+from itertools import groupby
+from operator import itemgetter
+import math
+import gzip
+import glob
+import os
+
+def convert_vector_to_events(vector = [0, 1, 1, 0, 0, 1, 0]):
+    """
+    Convert a binary vector (indicating 1 for the anomalous instances)
+    to a list of events. The events are considered as durations,
+    i.e. setting 1 at index i corresponds to an anomalous interval [i, i+1).
+    
+    :param vector: a list of elements belonging to {0, 1}
+    :return: a list of couples, each couple representing the start and stop of
+    each event
+    """
+    positive_indexes = [idx for idx, val in enumerate(vector) if val > 0]
+    events = []
+    for k, g in groupby(enumerate(positive_indexes), lambda ix : ix[0] - ix[1]):
+        cur_cut = list(map(itemgetter(1), g))
+        events.append((cur_cut[0], cur_cut[-1]))
+    
+    # Consistent conversion in case of range anomalies (for indexes):
+    # A positive index i is considered as the interval [i, i+1),
+    # so the last index should be moved by 1
+    events = [(x, y+1) for (x,y) in events]
+        
+    return(events)
+
+def infer_Trange(events_pred, events_gt):
+    """
+    Given the list of events events_pred and events_gt, get the
+    smallest possible Trange corresponding to the start and stop indexes 
+    of the whole series.
+    Trange will not influence the measure of distances, but will impact the
+    measures of probabilities.
+    
+    :param events_pred: a list of couples corresponding to predicted events
+    :param events_gt: a list of couples corresponding to ground truth events
+    :return: a couple corresponding to the smallest range containing the events
+    """
+    if len(events_gt) == 0:
+        raise ValueError('The gt events should contain at least one event')
+    if len(events_pred) == 0:
+        # empty prediction, base Trange only on events_gt (which is non empty)
+        return(infer_Trange(events_gt, events_gt))
+        
+    min_pred = min([x[0] for x in events_pred])
+    min_gt = min([x[0] for x in events_gt])
+    max_pred = max([x[1] for x in events_pred])
+    max_gt = max([x[1] for x in events_gt])
+    Trange = (min(min_pred, min_gt), max(max_pred, max_gt))
+    return(Trange)
+
+def has_point_anomalies(events):
+    """
+    Checking whether events contain point anomalies, i.e.
+    events starting and stopping at the same time.
+    
+    :param events: a list of couples corresponding to predicted events
+    :return: True is the events have any point anomalies, False otherwise
+    """
+    if len(events) == 0:
+        return(False)
+    return(min([x[1] - x[0] for x in events]) == 0)
+
+def _sum_wo_nan(vec):
+    """
+    Sum of elements, ignoring math.isnan ones
+    
+    :param vec: vector of floating numbers
+    :return: sum of the elements, ignoring math.isnan ones
+    """
+    vec_wo_nan = [e for e in vec if not math.isnan(e)]
+    return(sum(vec_wo_nan))
+    
+def _len_wo_nan(vec):
+    """
+    Count of elements, ignoring math.isnan ones
+    
+    :param vec: vector of floating numbers
+    :return: count of the elements, ignoring math.isnan ones
+    """
+    vec_wo_nan = [e for e in vec if not math.isnan(e)]
+    return(len(vec_wo_nan))
+
+def read_gz_data(filename = 'data/machinetemp_groundtruth.gz'):
+    """
+    Load a file compressed with gz, such that each line of the
+    file is either 0 (representing a normal instance) or 1 (representing)
+    an anomalous instance.
+    :param filename: file path to the gz compressed file
+    :return: list of integers with either 0 or 1
+    """
+    with gzip.open(filename, 'rb') as f:
+        content = f.read().splitlines()
+    content = [int(x) for x in content]
+    return(content)
+
+def read_all_as_events():
+    """
+    Load the files contained in the folder `data/` and convert
+    to events. The length of the series is kept.
+    The convention for the file name is: `dataset_algorithm.gz`
+    :return: two dictionaries:
+        - the first containing the list of events for each dataset and algorithm,
+        - the second containing the range of the series for each dataset
+    """
+    filepaths = glob.glob('data/*.gz')
+    datasets = dict()
+    Tranges = dict()
+    for filepath in filepaths:
+        vector = read_gz_data(filepath)
+        events = convert_vector_to_events(vector)
+        # ad hoc cut for those files
+        cut_filepath = (os.path.split(filepath)[1]).split('_')
+        data_name = cut_filepath[0]
+        algo_name = (cut_filepath[1]).split('.')[0]
+        if not data_name in datasets:
+            datasets[data_name] = dict()
+            Tranges[data_name] = (0, len(vector))
+        datasets[data_name][algo_name] = events
+    return(datasets, Tranges)
+
+def f1_func(p, r):
+    """
+    Compute the f1 function
+    :param p: precision numeric value
+    :param r: recall numeric value
+    :return: f1 numeric value
+    """
+    return(2*p*r/(p+r))