tsadmetrics 0.1.3__py3-none-any.whl → 0.1.5__py3-none-any.whl

tsadmetrics/_tsadeval/affiliation/metrics.py

@@ -0,0 +1,114 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+from .generics import (
+        infer_Trange,
+        has_point_anomalies, 
+        _len_wo_nan, 
+        _sum_wo_nan,
+        read_all_as_events)
+from ._affiliation_zone import (
+        get_all_E_gt_func, 
+        affiliation_partition)
+from ._single_ground_truth_event import (
+        affiliation_precision_distance,
+        affiliation_recall_distance,
+        affiliation_precision_proba,
+        affiliation_recall_proba)
+
+def test_events(events):
+    """
+    Verify the validity of the input events
+    :param events: list of events, each represented by a couple (start, stop)
+    :return: None. Raise an error for incorrect formed or non ordered events
+    """
+    if type(events) is not list:
+        raise TypeError('Input `events` should be a list of couples')
+    if not all([type(x) is tuple for x in events]):
+        raise TypeError('Input `events` should be a list of tuples')
+    if not all([len(x) == 2 for x in events]):
+        raise ValueError('Input `events` should be a list of couples (start, stop)')
+    if not all([x[0] <= x[1] for x in events]):
+        raise ValueError('Input `events` should be a list of couples (start, stop) with start <= stop')
+    if not all([events[i][1] < events[i+1][0] for i in range(len(events) - 1)]):
+        raise ValueError('Couples of input `events` should be disjoint and ordered')
+
+def pr_from_events(events_pred, events_gt, Trange):
+    """
+    Compute the affiliation metrics including the precision/recall in [0,1],
+    along with the individual precision/recall distances and probabilities
+    
+    :param events_pred: list of predicted events, each represented by a couple
+    indicating the start and the stop of the event
+    :param events_gt: list of ground truth events, each represented by a couple
+    indicating the start and the stop of the event
+    :param Trange: range of the series where events_pred and events_gt are included,
+    represented as a couple (start, stop)
+    :return: dictionary with precision, recall, and the individual metrics
+    """
+    # testing the inputs
+    # test_events(events_pred)
+    # test_events(events_gt)
+    
+    # other tests
+    minimal_Trange = infer_Trange(events_pred, events_gt)
+    if not Trange[0] <= minimal_Trange[0]:
+        raise ValueError('`Trange` should include all the events')
+    if not minimal_Trange[1] <= Trange[1]:
+        raise ValueError('`Trange` should include all the events')
+    
+    if len(events_gt) == 0:
+        raise ValueError('Input `events_gt` should have at least one event')
+
+    if has_point_anomalies(events_pred) or has_point_anomalies(events_gt):
+        raise ValueError('Cannot manage point anomalies currently')
+
+    if Trange is None:
+        # Set as default, but Trange should be indicated if probabilities are used
+        raise ValueError('Trange should be indicated (or inferred with the `infer_Trange` function')
+
+    E_gt = get_all_E_gt_func(events_gt, Trange)
+    aff_partition = affiliation_partition(events_pred, E_gt)
+
+    # # Computing precision distance
+    # d_precision = [affiliation_precision_distance(Is, J) for Is, J in zip(aff_partition, events_gt)]
+    
+    # # Computing recall distance
+    # d_recall = [affiliation_recall_distance(Is, J) for Is, J in zip(aff_partition, events_gt)]
+
+    # Computing precision
+    p_precision = [affiliation_precision_proba(Is, J, E) for Is, J, E in zip(aff_partition, events_gt, E_gt)]
+
+    # Computing recall
+    p_recall = [affiliation_recall_proba(Is, J, E) for Is, J, E in zip(aff_partition, events_gt, E_gt)]
+
+    if _len_wo_nan(p_precision) > 0:
+        p_precision_average = _sum_wo_nan(p_precision) / _len_wo_nan(p_precision)
+    else:
+        p_precision_average = p_precision[0] # math.nan
+    p_recall_average = sum(p_recall) / len(p_recall)
+
+    dict_out = dict({'precision': p_precision_average,
+                     'recall': p_recall_average,
+                     'individual_precision_probabilities': p_precision,
+                     'individual_recall_probabilities': p_recall})
+    return(dict_out)
+
+def produce_all_results():
+    """
+    Produce the affiliation precision/recall for all files
+    contained in the `data` repository
+    :return: a dictionary indexed by data names, each containing a dictionary
+    indexed by algorithm names, each containing the results of the affiliation
+    metrics (precision, recall, individual probabilities and distances)
+    """
+    datasets, Tranges = read_all_as_events() # read all the events in folder `data`
+    results = dict()
+    for data_name in datasets.keys():
+        results_data = dict()
+        for algo_name in datasets[data_name].keys():
+            if algo_name != 'groundtruth':
+                results_data[algo_name] = pr_from_events(datasets[data_name][algo_name],
+                                                         datasets[data_name]['groundtruth'],
+                                                         Tranges[data_name])
+        results[data_name] = results_data
+    return(results)

tsadmetrics/_tsadeval/eTaPR_pkg/DataManage/File_IO.py

@@ -0,0 +1,175 @@
+from .Range import Range
+import time
+import datetime
+import pandas as pd
+
+def load_stream_2_range(stream_data: list, normal_label: int, anomaly_label: int, is_range_name: bool) -> list:
+    return_list = []
+    start_id = -1
+    end_id = -1
+    id = 0
+    range_id = 1
+
+    prev_val = -2 #Set prev_val as a value different to normal and anomalous labels
+
+    for val in stream_data:
+        if val == anomaly_label and (prev_val == normal_label or prev_val == -2): #Enter the anomaly range
+            start_id = id
+        elif val == normal_label and prev_val == anomaly_label: #Go out the anomaly range
+            name_buf = ''
+            if is_range_name:
+                name_buf = str(range_id)
+            end_id = id - 1
+            return_list.append(Range(start_id, end_id, name_buf))
+            range_id += 1
+            #start_id = 0
+
+        id += 1
+        prev_val = val
+    if start_id > end_id: #start_id != 0 and start_id != -1: #if an anomaly continues till the last point
+        return_list.append(Range.Range(start_id, id - 1, str(range_id)))
+
+    return return_list
+
+
+def load_stream_file(filename: str, normal_label: int, anomaly_label: int, is_range_name: bool) -> list:
+    return_list = []
+    start_id = -1
+    end_id = -1
+    id = 0
+    range_id = 1
+    #is_first = True
+
+    prev_val = -2 #Set prev_val as a value different to normal and anomalous labels
+
+    f = open(filename, 'r', encoding='utf-8', newline='')
+
+    for line in f.readlines():
+        val = int(line.strip().split()[0])
+
+        '''
+        #skip the first line
+        if is_first:
+            if val == anomaly_label:
+                start_id = id
+            prev_val = val
+            is_first = False
+            continue
+        '''
+
+        if val == anomaly_label and (prev_val == normal_label or prev_val == -2): #Enter the anomaly range
+            start_id = id
+        elif val == normal_label and prev_val == anomaly_label: #Go out the anomaly range
+            name_buf = ''
+            if is_range_name:
+                name_buf = str(range_id)
+            end_id = id - 1
+            return_list.append(Range.Range(start_id, end_id, name_buf))
+            range_id += 1
+            #start_id = 0
+
+        id += 1
+        prev_val = val
+    f.close()
+    if start_id > end_id: #start_id != 0 and start_id != -1: #if an anomaly continues till the last point
+        return_list.append(Range.Range(start_id, id - 1, str(range_id)))
+
+    return return_list
+
+def load_range_file(filename: str, time_format: str) -> list:
+    return_list = []
+    #is_first = True
+
+    f = open(filename, 'r', encoding='utf-8', newline='')
+    for line in f.readlines():
+        # skip the first line
+        #if is_first:
+            #is_first = False
+            #continue
+
+        items = line.strip().split(',')
+        if time_format == 'index':
+            first_idx = int(items[0])
+            last_idx = int(items[1])
+        else:
+            first_idx = string_to_unixtime(items[0], time_format)
+            last_idx = string_to_unixtime(items[1], time_format)
+
+        name_buf = ''
+        if len(items) > 2:
+            name_buf = str(items[2])
+
+        return_list.append(Range.Range(first_idx, last_idx, name_buf))
+    f.close()
+
+    for idx in range(1, len(return_list)):
+        if return_list[idx].get_time()[0] <= return_list[idx-1].get_time()[1]:
+            print("Error: ranges ({},{}) and ({},{}) are overlapped in {}".format(return_list[idx-1].get_time()[0],
+                                                                                  return_list[idx-1].get_time()[1],
+                                                                                  return_list[idx].get_time()[0],
+                                                                                  return_list[idx].get_time()[1], filename))
+            exit(0)
+
+    return return_list
+
+
+def unixtime_to_string(epoch: int, format: str) -> str:
+    return datetime.datetime.fromtimestamp(epoch).strftime(format) #'%Y-%m-%d %I:%M:%S %p'
+
+
+def string_to_unixtime(timestamp: str, format: str) -> int:
+    return int(time.mktime(datetime.datetime.strptime(timestamp, format).timetuple()))
+
+
+def save_range_list(filename: str, range_list: list) -> None:
+    f = open(filename, encoding='utf-8', mode='w')
+    for single_range in range_list:
+        first, last = single_range.get_time()
+        f.writelines(str(first)+','+str(last)+','+single_range.get_name()+'\n')
+    f.close()
+
+# Assume that the first line of input files including the information of file format and its corresponding information
+# This function handles three types of file format
+def load_file(filename: str, filetype: str) -> list:
+    assert(filetype == 'range' or filetype == 'stream')
+
+    if filetype == 'stream':
+        return load_stream_file(filename, 1, -1, True)
+    elif filetype == 'range':
+        return load_range_file(filename, 'index')
+
+
+def make_attack_file(input_files: list, sep: str, label_featname: str, input_normal_label: int, input_anomalous_label: int,
+                     output_stream_file: str, output_range_file: str, output_normal_label: int, output_anomalous_label: int) -> None:
+    label = []
+    for an_input_file in input_files:
+        temp_file = pd.read_csv(an_input_file, sep=sep)
+        label += temp_file[label_featname].values.tolist()
+
+    with open(output_stream_file, 'w') as f:
+        for a_label in label:
+            if a_label == input_normal_label:
+                f.write('{}\n'.format(output_normal_label))
+            elif a_label == input_anomalous_label:
+                f.write('{}\n'.format(output_anomalous_label))
+            else:
+                print("There is an unknown label, " + a_label, flush=True)
+                f.close()
+                return
+
+    ranges = load_stream_2_range(label, 0, 1, False)
+    save_range_list(output_range_file, ranges)
+
+def save_range_2_stream(filename: str, range_list: list, last_idx: int, normal_label: int, anomalous_label: int) -> None:
+    f = open(filename, encoding='utf-8', mode='w')
+    range_id = 0
+    for idx in range(last_idx):
+        if idx < range_list[range_id].get_time()[0]:
+            f.writelines('{}\n'.format(normal_label))
+        elif range_list[range_id].get_time()[0] <= idx <= range_list[range_id].get_time()[1]:
+            f.writelines('{}\n'.format(anomalous_label))
+        else:
+            f.writelines('{}\n'.format(normal_label))
+            if range_id < len(range_list) - 1:
+                range_id += 1
+    f.close()

tsadmetrics/_tsadeval/eTaPR_pkg/DataManage/Range.py

@@ -0,0 +1,50 @@
+# To store a single anomaly
+class Range:
+    def __init__(self, first, last, name):
+        self._first_timestamp = first
+        self._last_timestamp = last
+        self._name = name
+
+    def set_time(self, first, last):
+        self._first_timestamp = first
+        self._last_timestamp = last
+
+    def get_time(self):
+        return self._first_timestamp, self._last_timestamp
+
+    def set_name(self, str):
+        self._name = str
+
+    def get_name(self):
+        return self._name
+
+    def get_len(self):
+        return self._last_timestamp - self._first_timestamp + 1
+
+    def __eq__(self, other):
+        return self._first_timestamp == other.get_time()[0] and self._last_timestamp == other.get_time()[1]
+
+    def distance(self, other_range) -> int:
+        if min(self._last_timestamp, other_range.get_time()[1]) - max(self._first_timestamp, other_range.get_time()[0]) > 0:
+            return 0
+        else:
+            return min(abs(self._first_timestamp - other_range.get_time()[1]),
+                       abs(self._last_timestamp - other_range.get_time()[0]))
+
+    def compare(self, other_range) -> int:
+        if min(self._last_timestamp, other_range.get_time()[1]) - max(self._first_timestamp, other_range.get_time()[0]) > 0:
+            return 0
+        elif self._last_timestamp - other_range.get_time()[0] < 0:
+            return -1
+        else:
+            return 1
+
+def stream_2_ranges(self, prediction_stream: list) -> list:
+    result = []
+    for i in range(len(prediction_stream)-1):
+        start_time = 0
+        if prediction_stream[i] == 0 and prediction_stream[i+1] == 1:
+            start_time = i+1
+        elif prediction_stream[i] == 1 and prediction_stream[i+1] == 0:
+            result.append(Range(start_time, i, ''))
+    return result

tsadmetrics/_tsadeval/eTaPR_pkg/DataManage/Time_Plot.py

@@ -0,0 +1,184 @@
+import numpy as np
+import cv2 as cv
+from copy import deepcopy
+import pathlib
+
+def convert_index(org_index, max_index, graph_width, margin_left):
+    return round(float(org_index/max_index)*graph_width+margin_left)
+
+def draw_csv(ranges, img, h_floor, h_ceiling, color, max_index, graph_width, margin_left):
+    for a_range in ranges:
+        start_time = convert_index(a_range.get_time()[0], max_index, graph_width, margin_left)
+        end_time = convert_index(a_range.get_time()[1], max_index, graph_width, margin_left)
+        cv.rectangle(img, (start_time, h_floor), (end_time, h_ceiling), color, thickness=-1)
+
+def draw_csv_range(ranges, img, h_floor, h_ceiling, color, start, end):
+    for a_range in ranges:
+        if a_range.get_time()[0] <= end or a_range.get_time()[1] >= start:
+            cv.rectangle(img, (a_range.get_time()[0]-start+10, h_floor), (a_range.get_time()[1]-start+10, h_ceiling), color, thickness=-1)
+
+def shift_ranges(ranges, first_idx):
+    for a_range in ranges:
+        a_range.set_time(a_range.get_time()[0] - first_idx, a_range.get_time()[1] - first_idx)
+
+def draw_graphs(anomalies, predictions, how_show: str):
+    method_list = [ 'Anomalies', 'Predictions' ]
+    anomalies = deepcopy(anomalies)
+    predictions = deepcopy(predictions)
+    first_idx = min(anomalies[0].get_time()[0]-100, predictions[0].get_time()[0])
+    last_idx = max(anomalies[-1].get_time()[1], predictions[-1].get_time()[1])
+    marginal_idx = int(float(last_idx-first_idx)/100)
+    first_idx -= marginal_idx
+    shift_ranges(anomalies, first_idx)
+    shift_ranges(predictions, first_idx)
+    ranges_list = [ anomalies, predictions ]
+    max_index = max(anomalies[-1].get_time()[1], predictions[-1].get_time()[1]) + marginal_idx
+
+    color_list = [(70, 70, 70),  #black
+                  (60, 76, 203),  #red
+                  (193, 134, 46),  #blue
+                  (133, 160, 22),  #green
+                  (206, 143, 187),  #purple
+                  (94, 73, 52),  # darkblue
+                  (63, 208, 244)  #yellow
+                  ]
+
+    margin_left   = 10
+    margin_right  = 150
+    margin_top    = 20
+    margin_bottom = 40
+
+    graph_gap = 20
+    graph_height = 40
+    graph_width = 2000
+
+    n_results = 2
+
+    width = margin_left + graph_width + margin_right
+    height = margin_top + margin_bottom + n_results * (graph_gap + graph_height)
+    bpp = 3
+
+    img = np.ones((height, width, bpp), np.uint8)*255
+
+    img_h = img.shape[0]
+    img_w = img.shape[1]
+    img_bpp = img.shape[2]
+
+    thickness = 1
+    fontsize = 1
+    cv.line(img, (int(margin_left/2), img_h-margin_bottom), (img_w-int(margin_left/2), img_h-margin_bottom), color_list[0], thickness) #x-axis
+    pts = np.array([[img_w-int(margin_left/2), img_h-margin_bottom], [img_w-int(margin_left/2)-7, img_h-margin_bottom+5], [img_w-int(margin_left/2)-7, img_h-margin_bottom-5]], np.int32) #arrow_head
+    pts = pts.reshape((-1, 1, 2))
+    cv.fillPoly(img, [pts], color_list[0])
+    cv.putText(img, 'Relative Index', (img_w-180, img_h-15), cv.FONT_HERSHEY_COMPLEX_SMALL, fontsize, color_list[0], 1, cv.LINE_AA) #x-axis label
+
+    for i in range(margin_left, width-margin_right, int(graph_width/10)):
+        cv.line(img, (i, img_h-margin_bottom+2), (i, img_h-margin_bottom-2), color_list[0], thickness)
+        org_index = str(round((i-10) / graph_width * max_index / 1000))
+        cv.putText(img, org_index+'K', (i-len(org_index)*5, img_h-margin_bottom + 25), cv.FONT_HERSHEY_COMPLEX_SMALL, fontsize, color_list[0], 1, cv.LINE_AA)
+
+    thickness = -1
+    for idx in range(n_results):
+        cv.putText(img, method_list[idx],
+                   (width - margin_right + 2, img_h - margin_bottom - graph_gap * (idx+1) - graph_height * idx - 12),
+                   cv.FONT_HERSHEY_COMPLEX_SMALL, fontsize, color_list[0], 1, cv.LINE_AA)
+        draw_csv(ranges_list[idx], img, h_floor=img_h - margin_bottom - graph_gap * (idx+1) - graph_height * idx,
+                 h_ceiling=img_h - margin_bottom - graph_gap * (idx+1) - graph_height * (idx+1),
+                 color=color_list[(idx+1)%len(color_list)],
+                 max_index=max_index, graph_width=graph_width, margin_left=margin_left)
+
+    if how_show == 'screen' or how_show == 'all':
+        cv.imshow("drawing", img)
+    if how_show == 'file' or how_show == 'all':
+        cv.imwrite("../../brief_result.png", img)
+    if how_show != 'screen' and how_show != 'all' and how_show != 'file':
+        print('Parameter Error')
+    cv.waitKey(0);
+
+
+def draw_multi_graphs(anomalies, predictions_list, predictions_name_list, how_show: str):
+    method_list = [ 'Anomalies' ] + predictions_name_list
+
+    anomalies = deepcopy(anomalies)
+    predictions_list = deepcopy(predictions_list)
+
+    first_idx = anomalies[0].get_time()[0]-100
+    last_idx = anomalies[-1].get_time()[1]
+    for single_prediction in predictions_list:
+        first_idx = min(first_idx, single_prediction[0].get_time()[0])
+        last_idx = max(last_idx, single_prediction[-1].get_time()[1])
+
+    marginal_idx = int(float(last_idx-first_idx)/100)
+    first_idx -= marginal_idx
+    shift_ranges(anomalies, first_idx)
+    for single_prediction in predictions_list:
+        shift_ranges(single_prediction, first_idx)
+
+    ranges_list = [ anomalies ] + predictions_list
+
+    max_index = anomalies[-1].get_time()[1]
+    for single_prediction in predictions_list:
+        max_index = max(max_index, single_prediction[-1].get_time()[1])
+    max_index = max_index + marginal_idx
+
+    color_list = [(0, 0, 0),  #black
+                  (60, 76, 203),  #red
+                  (193, 134, 46),  #blue
+                  (133, 160, 22),  #green
+                  (206, 143, 187),  #purple
+                  (94, 73, 52),  # darkblue
+                  (63, 208, 244)  #yellow
+                  ]
+
+    margin_left   = 10
+    margin_right  = 180
+    margin_top    = 20
+    margin_bottom = 40
+
+    graph_gap = 20
+    graph_height = 40
+    graph_width = 2000
+
+    n_results = len(ranges_list)
+
+    width = margin_left + graph_width + margin_right
+    height = margin_top + margin_bottom + n_results * (graph_gap + graph_height)
+    bpp = 3
+
+    img = np.ones((height, width, bpp), np.uint8)*255
+
+    img_h = img.shape[0]
+    img_w = img.shape[1]
+    img_bpp = img.shape[2]
+
+    thickness = 1
+    fontsize = 1.4
+    cv.line(img, (int(margin_left/2), img_h-margin_bottom), (img_w-int(margin_left/2), img_h-margin_bottom), color_list[0], thickness) #x-axis
+    pts = np.array([[img_w-int(margin_left/2), img_h-margin_bottom], [img_w-int(margin_left/2)-7, img_h-margin_bottom+5], [img_w-int(margin_left/2)-7, img_h-margin_bottom-5]], np.int32) #arrow_head
+    pts = pts.reshape((-1, 1, 2))
+    cv.fillPoly(img, [pts], color_list[0])
+    cv.putText(img, 'Relative Index', (img_w-180, img_h-15), cv.FONT_HERSHEY_COMPLEX_SMALL, 1, color_list[0], 1, cv.LINE_AA) #x-axis label
+
+    for i in range(margin_left, width-margin_right, int(graph_width/10)):
+        cv.line(img, (i, img_h-margin_bottom+2), (i, img_h-margin_bottom-2), color_list[0], thickness)
+        org_index = str(round((i-10) / graph_width * max_index / 1000))
+        cv.putText(img, org_index+'K', (i-len(org_index)*5, img_h-margin_bottom + 25), cv.FONT_HERSHEY_COMPLEX_SMALL, 1, color_list[0], 1, cv.LINE_AA)
+
+    thickness = -1
+    for idx in range(n_results):
+        cv.putText(img, method_list[idx],
+                   (width - margin_right + 2, img_h - margin_bottom - graph_gap * (idx+1) - graph_height * idx - 12),
+                   cv.FONT_HERSHEY_COMPLEX_SMALL, fontsize, color_list[0], 1, cv.LINE_AA)
+        draw_csv(ranges_list[idx], img, h_floor=img_h - margin_bottom - graph_gap * (idx+1) - graph_height * idx,
+                 h_ceiling=img_h - margin_bottom - graph_gap * (idx+1) - graph_height * (idx+1),
+                 color=color_list[(idx+1)%len(color_list)],
+                 max_index=max_index, graph_width=graph_width, margin_left=margin_left)
+
+    if how_show == 'screen' or how_show == 'all':
+        cv.imshow("drawing", img)
+    if how_show == 'file' or how_show == 'all':
+        print("The file is saved at " + str(pathlib.Path(__file__).parent.absolute()))
+        cv.imwrite("./brief_result.png", img)
+    if how_show != 'screen' and how_show != 'all' and how_show != 'file':
+        print('Parameter Error')
+    cv.waitKey(0);