tsadmetrics 0.1.1__tar.gz → 0.1.3__tar.gz

tsadmetrics-0.1.3/PKG-INFO

@@ -0,0 +1,22 @@
+Metadata-Version: 2.1
+Name: tsadmetrics
+Version: 0.1.3
+Summary: Librería para evaluación de detección de anomalías en series temporales
+Home-page: https://github.com/pathsko/TSADmetrics
+Author: Pedro Rafael Velasco Priego
+Author-email: Pedro Rafael Velasco Priego <i12veprp@uco.es>
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: joblib==1.4.2
+Requires-Dist: numpy==1.24.4
+Requires-Dist: pandas==2.0.3
+Requires-Dist: PATE==0.1.1
+Requires-Dist: patsy==0.5.6
+Requires-Dist: python-dateutil==2.9.0.post0
+Requires-Dist: pytz==2024.1
+Requires-Dist: scikit-learn==1.3.2
+Requires-Dist: scipy==1.10.1
+Requires-Dist: six==1.16.0
+Requires-Dist: statsmodels==0.14.1
+Requires-Dist: threadpoolctl==3.5.0
+Requires-Dist: tzdata==2024.1

tsadmetrics-0.1.3/pyproject.toml

@@ -0,0 +1,30 @@
+[project]
+name = "tsadmetrics"
+version = "0.1.3"
+description = "Librería para evaluación de detección de anomalías en series temporales"
+authors = [
+  { name = "Pedro Rafael Velasco Priego", email = "i12veprp@uco.es" }
+]
+dependencies = [
+    "joblib==1.4.2",
+    "numpy==1.24.4",
+    "pandas==2.0.3",
+    "PATE==0.1.1",
+    "patsy==0.5.6",
+    "python-dateutil==2.9.0.post0",
+    "pytz==2024.1",
+    "scikit-learn==1.3.2",
+    "scipy==1.10.1",
+    "six==1.16.0",
+    "statsmodels==0.14.1",
+    "threadpoolctl==3.5.0",
+    "tzdata==2024.1"
+]
+requires-python = '>=3.8'
+
+[tool.setuptools]
+packages = ["tsadmetrics","tsadmetrics._tsadeval"]  
+
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"

{tsadmetrics-0.1.1 → tsadmetrics-0.1.3}/setup.py

@@ -5,14 +5,14 @@ with open("README.md", "r", encoding="utf-8") as fh:
 
 setup(
     name="tsadmetrics",
-    version="0.1.1",
+    version="0.1.3",
     author="Pedro Rafael Velasco Priego",
     author_email="i12veprp@uco.es",
     description="A library for time series anomaly detection metrics and evaluation.",
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/pathsko/TSADmetrics",
-    packages=find_packages(where="src"),
+    packages=find_packages(where='./'),
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
@@ -20,7 +20,7 @@ setup(
         "Intended Audience :: Science/Research",
         "Topic :: Scientific/Engineering :: Artificial Intelligence",
     ],
-    python_requires=">=3.6",
+    python_requires=">=3.8",
     install_requires=[
         "joblib==1.4.2",
         "numpy==1.24.4",
@@ -46,5 +46,4 @@ setup(
             "myst-parser",
         ],
     },
-    package_dir={"": "src"},
 )

{tsadmetrics-0.1.1/src → tsadmetrics-0.1.3}/tsadmetrics/__init__.py

@@ -2,13 +2,11 @@ from .binary_metrics import *
 from .non_binary_metrics import *
 from .utils import *
 
-import sys
-import os
-sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "_tsadeval")))
+
 
 
 __author__ = 'Pedro Rafael Velasco Priego i12veprp@uco.es'
-__version__ = "0.0.1"
+__version__ = "0.1.3"
 __all__ = ['point_wise_recall', 'point_wise_precision', 'point_wise_f_score','point_adjusted_recall',
             'point_adjusted_precision', 'point_adjusted_f_score', 'segment_wise_recall', 'segment_wise_precision',
             'segment_wise_f_score','delay_th_point_adjusted_recall', 'delay_th_point_adjusted_precision',

tsadmetrics-0.1.3/tsadmetrics/_tsadeval/auc_roc_pr_plot.py

@@ -0,0 +1,295 @@
+# import numpy as np
+# from scipy.stats import norm
+# from matplotlib import pyplot as plt
+
+# from metrics import f1_from_pr
+
+
+# class Two_1d_normal_distributions:
+#     def __init__(self, P_ampl, N_ampl, P_mu, N_mu, P_std, N_std, color="b", betas=None):
+#         self.P_ampl = P_ampl
+#         self.N_ampl = N_ampl
+#         self.P_mu = P_mu
+#         self.N_mu = N_mu
+#         self.P_std = P_std
+#         self.N_std = N_std
+#         self.betas = (1 / 8, 1 / 4, 1 / 2, 1, 2, 4, 8, 16, 32) if betas == None else betas
+
+#         self.color = color
+#         self.N_color = "k"
+#         self.P_color = "r"
+
+#     def make(self, delta=0.05, steps=10001, start=-8, stop=8):
+#         index = 0
+
+#         # For plotting grahps
+#         self.fpr = []
+#         self.precision = []
+#         self.recall = []
+
+#         # For plotting x´s and o´s on the graphs
+#         self.x_fpr = []
+#         self.x_precision = []
+#         self.x_recall = []
+#         self.xs = 0
+#         self.x_threshold = []
+#         self.o_fpr = []
+#         self.o_precision = []
+#         self.o_recall = []
+#         self.os = 0
+#         self.o_threshold = []
+
+#         # Track maximum f scores for various beta values
+#         self.max_f = {i: 0 for i in self.betas}
+#         self.max_f_fpr = {i: 0 for i in self.betas}
+#         self.max_f_precision = {i: 0 for i in self.betas}
+#         self.max_f_recall = {i: 0 for i in self.betas}
+#         self.max_f_thresholds = {i: 0 for i in self.betas}
+
+#         for threshold in np.linspace(start, stop, steps):
+#             TN = self.N_ampl * norm.cdf(threshold, loc=self.N_mu, scale=self.N_std)
+#             FP = self.N_ampl - TN
+#             FN = self.P_ampl * norm.cdf(threshold, loc=self.P_mu, scale=self.P_std)
+#             TP = self.P_ampl - FN
+#             self.fpr.append(FP / (FP + TN))
+#             self.precision.append(TP / (TP + FP))
+#             self.recall.append(TP / (TP + FN))
+
+#             for beta in self.betas:
+#                 if f1_from_pr(p=self.precision[-1], r=self.recall[-1], beta=beta) > self.max_f[beta]:
+#                     self.max_f[beta] = f1_from_pr(p=self.precision[-1], r=self.recall[-1], beta=beta)
+#                     self.max_f_fpr[beta] = self.fpr[-1]
+#                     self.max_f_precision[beta] = self.precision[-1]
+#                     self.max_f_recall[beta] = self.recall[-1]
+#                     self.max_f_thresholds[beta] = threshold
+
+#             if (FN) / (self.P_ampl) >= self.xs * delta + delta * 0.5:
+#                 self.x_fpr.append(FP / (FP + TN))
+#                 self.x_precision.append(TP / (TP + FP))
+#                 self.x_recall.append(TP / (TP + FN))
+#                 self.xs += 1
+#                 # print(xs, TN+FN)
+#                 self.x_threshold.append(threshold)
+#             if (TN / self.N_ampl) >= self.os * delta + delta * 0.5:
+#                 self.o_fpr.append(FP / (FP + TN))
+#                 self.o_precision.append(TP / (TP + FP))
+#                 self.o_recall.append(TP / (TP + FN))
+#                 self.os += 1
+#                 self.o_threshold.append(threshold)
+#                 # print(os, TN+FN)
+
+#     def plot_roc_pr(self, roc_ax, pr_ax, plot_xs=True, plot_os=True, plot_fs=False):
+#         roc_ax.plot(self.fpr, self.recall, self.color, zorder=1)
+#         pr_ax.plot(self.precision, self.recall, self.color, zorder=1)
+#         if plot_xs:
+#             roc_ax.plot(self.x_fpr, self.x_recall, "x", color=self.color, zorder=1)
+#             pr_ax.plot(self.x_precision, self.x_recall, "x", color=self.color, zorder=1)
+#         if plot_os:
+#             roc_ax.plot(self.o_fpr, self.o_recall, "o", color=self.color, fillstyle="none", zorder=1)
+#             pr_ax.plot(self.o_precision, self.o_recall, "o", color=self.color, fillstyle="none", zorder=1)
+#         if plot_fs:
+#             roc_ax.plot(
+#                 list(self.max_f_fpr.values()),
+#                 list(self.max_f_recall.values()),
+#                 ".",
+#                 linestyle="None",
+#                 zorder=2,
+#                 color="k",
+#             )  # self.color)
+#             pr_ax.plot(
+#                 list(self.max_f_precision.values()), list(self.max_f_recall.values()), ".", zorder=2, color="k"
+#             )  # self.color)
+#             for beta in self.betas:
+#                 # roc_ax.plot([self.max_f_fpr[beta]],[self.max_f_recall[beta]], marker=f"$1/{int(1/beta)}$" if beta<1 else f"${beta}$", linestyle= "None", zorder=2, color="k")
+#                 # pr_ax.plot([self.max_f_precision[beta]], [self.max_f_recall[beta]], marker=f"$1/{int(1/beta)}$" if beta<1 else f"${beta}$", zorder=2, color="k")
+#                 if self.color == "forestgreen":  # need to place the numbers differently
+#                     roc_ax.text(
+#                         self.max_f_fpr[beta],
+#                         self.max_f_recall[beta],
+#                         f" $1/{int(1/beta)}$" if beta < 1 else f" ${beta}$",
+#                         horizontalalignment="left",
+#                         verticalalignment="top",
+#                         color=self.color,
+#                     )
+#                     pr_ax.text(
+#                         self.max_f_precision[beta],
+#                         self.max_f_recall[beta],
+#                         f"$1/{int(1/beta)}$" if beta < 1 else f"${beta}$",
+#                         horizontalalignment="left",
+#                         verticalalignment="bottom",
+#                         color=self.color,
+#                     )
+#                 else:
+#                     roc_ax.text(
+#                         self.max_f_fpr[beta],
+#                         self.max_f_recall[beta],
+#                         f"$1/{int(1/beta)}$" if beta < 1 else f"${beta}$",
+#                         horizontalalignment="right",
+#                         verticalalignment="bottom",
+#                         color=self.color,
+#                     )
+#                     pr_ax.text(
+#                         self.max_f_precision[beta],
+#                         self.max_f_recall[beta],
+#                         f"$1/{int(1/beta)}$ " if beta < 1 else f"${beta}$ ",
+#                         horizontalalignment="right",
+#                         verticalalignment="top",
+#                         color=self.color,
+#                     )
+
+#             # adjust axes to get the numbers within the figure
+#             xmin, xmax = roc_ax.get_xlim()
+#             xmin, xmax = pr_ax.get_xlim()
+#             roc_ax.set_xlim([xmin - 0.04, xmax])
+#             pr_ax.set_xlim([xmin - 0.01, xmax])
+#         pr_ax.set_xlabel("Precision")
+#         pr_ax.set_ylabel("Recall")
+#         roc_ax.set_xlabel("False positive rate")
+#         roc_ax.set_ylabel("Recall")
+
+#     def plot_roc_prec(self):
+#         plt.plot(self.fpr, self.recall, self.color, zorder=1)
+#         plt.plot(self.fpr, self.precision, self.color, zorder=1)
+#         plt.show()
+
+#     def plot_roc_pr_lines(self, ax):
+#         ax.plot(self.fpr, np.array(self.recall) + 1, self.color, zorder=1)
+#         ax.plot(np.array(self.precision) * (-1) + 1, self.recall, self.color, zorder=1)
+#         for i in range(0, len(self.recall), 5):
+#             ax.plot(
+#                 [self.fpr[i], 1 - self.precision[i]],
+#                 [self.recall[i] + 1, self.recall[i]],
+#                 marker="o",
+#                 color=self.N_color,
+#                 zorder=1,
+#                 alpha=0.3,
+#             )
+
+#     def plot_distributions(
+#         self, axes, start=-5, stop=7, steps=1001, normalize=True, plot_xs=True, plot_os=True, plot_fs=False, threshold=0
+#     ):
+#         grid = np.linspace(start, stop, steps)
+#         fill_alpha = 0.2
+
+#         y = lambda x: norm.pdf(x, loc=self.N_mu, scale=self.N_std) * (1 if normalize else self.N_ampl)
+#         axes[0].plot(
+#             grid,
+#             y(grid),
+#             color=self.N_color,
+#             label=f"pdf_N/{self.N_ampl}",
+#         )
+
+#         axes[0].fill_between(
+#             grid[grid <= threshold], 0, y(grid[grid <= threshold]), alpha=fill_alpha, lw=0, color="darkgreen"
+#         )
+#         axes[0].fill_between(
+#             grid[grid >= threshold], 0, y(grid[grid >= threshold]), alpha=fill_alpha, lw=0, color="orchid"
+#         )
+#         tn_x = min(self.N_mu, threshold - 0.75)
+#         fp_x = max(self.N_mu, threshold + 0.75)
+#         axes[0].text(tn_x, y(tn_x) / 2 - 0.005, "TN", horizontalalignment="center", verticalalignment="top")
+#         axes[0].text(fp_x, y(fp_x) / 2 - 0.005, "FP", horizontalalignment="center", verticalalignment="top")
+#         # add thresholdline, on the whole y-range
+#         ymin, ymax = axes[0].get_ylim()
+#         axes[0].plot([threshold, threshold], [ymin - 1, ymax + 1], "--", color="gray", lw=1)
+#         axes[0].set_ylim([ymin - 0.02, ymax])
+
+#         # same for anomal distributions
+#         y = lambda x: norm.pdf(x, loc=self.P_mu, scale=self.P_std) * (1 if normalize else self.P_ampl)
+#         axes[1].plot(
+#             grid,
+#             y(grid),
+#             color=self.P_color,
+#             label=f"pdf_P/{self.P_ampl}",
+#         )
+#         axes[1].fill_between(
+#             grid[grid <= threshold], 0, y(grid[grid <= threshold]), alpha=fill_alpha, lw=0, color="chocolate"
+#         )
+#         axes[1].fill_between(
+#             grid[grid >= threshold], 0, y(grid[grid >= threshold]), alpha=fill_alpha, lw=0, color="darkcyan"
+#         )
+#         fn_x = min(self.P_mu, threshold - 0.75)
+#         tp_x = max(self.P_mu, threshold + 0.75)
+#         axes[1].text(fn_x, y(fn_x) / 2, "FN", horizontalalignment="center", verticalalignment="top")
+#         axes[1].text(tp_x, y(tp_x) / 2, "TP", horizontalalignment="center", verticalalignment="top")
+
+#         # add thresholdline, on the whole y-range
+#         ymin, ymax = axes[1].get_ylim()
+#         axes[1].plot([threshold, threshold], [ymin - 1, ymax + 1], "--", color="gray", lw=1)
+#         axes[1].set_ylim([ymin, ymax])
+
+
+#     def plot_cdf(self, ax, start=-6, stop=8, steps=1001, normalize=True):
+#         grid = np.linspace(start, stop, steps)
+
+#         ax.plot(
+#             grid,
+#             norm.cdf(grid, loc=self.N_mu, scale=self.N_std) * (1 if normalize else self.N_ampl),
+#             color=self.N_color,
+#             label=f"pdf_N/{self.N_ampl}",
+#         )
+#         ax.plot(
+#             grid,
+#             norm.cdf(grid, loc=self.P_mu, scale=self.P_std) * (1 if normalize else self.P_ampl),
+#             color=self.P_color,
+#             label=f"pdf_P/{self.P_ampl}",
+#         )
+
+
+# if __name__ == "__main__":
+
+#     # Make detector distributions
+
+#     t1 = Two_1d_normal_distributions(
+#         1, 49, 1.8, -1, 2, 1, color="mediumblue", betas=(1 / 8, 1 / 4, 1 / 2, 1, 2, 4, 8, 16)
+#     )
+#     t2 = Two_1d_normal_distributions(
+#         1, 49, 1, -1, 1, 1, color="forestgreen", betas=(1 / 8, 1 / 4, 1 / 2, 1, 2, 4, 8, 16)
+#     )
+
+#     t1.make(steps=1001, delta=0.1)
+#     t2.make(steps=1001, delta=0.1)
+
+    
+#     #  Make roc and pr plots
+
+#     figsize = (4, 4)
+
+#     roc_fig, roc_ax = plt.subplots(figsize=figsize)
+#     pr_fig, pr_ax = plt.subplots(figsize=figsize)
+#     t1.plot_roc_pr(roc_ax, pr_ax, False, False, True)
+#     t2.plot_roc_pr(roc_ax, pr_ax, False, False, True)
+#     roc_fig.tight_layout()
+#     pr_fig.tight_layout()
+#     roc_fig.savefig("auc_roc_f.pdf")
+#     pr_fig.savefig("auc_pr_f.pdf")
+#     plt.show()
+#     plt.close("all")
+
+
+#     # Make distribution plots
+
+#     figsize = (5, 3)
+
+#     for beta in t1.betas:  # [16,4,1,1/4,1/8]:
+#         fig, axes = plt.subplots(2, 2, figsize=figsize, sharex=True, sharey=True)
+#         t1.plot_distributions(
+#             [axes[0][0], axes[1][0]], plot_xs=False, plot_os=False, plot_fs=True, threshold=t1.max_f_thresholds[beta]
+#         )
+#         t2.plot_distributions(
+#             [axes[0][1], axes[1][1]], plot_xs=False, plot_os=False, plot_fs=True, threshold=t2.max_f_thresholds[beta]
+#         )
+
+#         axes[0][0].set_title(f"Blue detector", color=t1.color)
+#         axes[0][1].set_title("Green detector", color=t2.color)
+#         axes[1][0].set_xlabel("Anomaly \n score", color=t1.color)
+#         axes[1][1].set_xlabel("Anomaly \n score", color=t2.color)
+#         shadowaxes = fig.add_subplot(111, xticks=[], yticks=[], frame_on=False)
+#         shadowaxes.set_ylabel("Probability density", labelpad=25)
+#         fig.tight_layout()
+#         axes[0][0].set_ylabel("Normal\nsamples", labelpad=25)
+#         axes[1][0].set_ylabel("Anomalous\nsamples", labelpad=25)
+
+#         plt.subplots_adjust(hspace=0.0)
+#         plt.savefig(f"auc_distributions_b{beta}.pdf")
+#         plt.show()

tsadmetrics-0.1.3/tsadmetrics/_tsadeval/discontinuity_graph.py

@@ -0,0 +1,109 @@
+# from maketable import *
+
+
+# class Score_graphs_table(Table):
+#     def __init__(self, metric_names, results, marks=[]):
+#         self.metric_names = metric_names
+#         self.results = results
+#         self.marks = marks
+#         super().__init__(Table_content([], [], []), scale=2)
+#         self.x_factor = 1 / 20 * self.scale
+#         self.y_factor = 1 / 2
+#         self.y_shift = -0.2
+
+#         self.row_length = 2
+#         self.n_rows = len(metric_names)
+
+#     def add_top_row(self):
+#         self.string += "Metric"
+#         self.string += "&"
+#         self.string += "Score"
+#         self.end_row()
+
+#     def add_next_row(self):
+#         self.string += self.metric_names[self.rows_added]
+#         self.string += "&"
+#         self.add_graph(self.rows_added + 1)
+#         self.end_row()
+#         self.rows_added += 1
+
+#     def add_graph(self, number):
+#         self.add_line(f"\\begin{{tikzpicture}}[baseline=-\\the\\dimexpr\\fontdimen22\\textfont2\\relax]")
+#         for x in self.marks:
+#             self.add_line(
+#                 f"\draw[-, gray] ({x*self.x_factor},{self.y_shift}) -- ({x*self.x_factor},{0.2*self.y_factor + self.y_shift});"
+#             )
+#         self.add_line(
+#             f"\draw[-, gray] (0,{self.y_shift}) -- ({self.x_factor*(len(self.results[self.metric_names[number-1]])-1)},{self.y_shift});"
+#         )
+#         self.add_line("\\foreach \\i/\\a in")
+#         self.add_line(
+#             str(
+#                 [
+#                     (round(i * self.x_factor, 3), round(a * self.y_factor + self.y_shift, 3))
+#                     for i, a in enumerate(self.results[self.metric_names[number - 1]])
+#                 ]
+#             )
+#             .replace(",", "/")
+#             .replace(")/", ",")
+#             .replace("(", "")
+#             .replace("[", "{")
+#             .replace("]", "}")
+#             .replace(")}", "}{")
+#         )
+#         self.add_line("\\coordinate (now) at (\\i,\\a) {};")
+#         self.add_line("  \\ifthenelse{\\equal{\\i}{0.0}}{}{")
+#         self.add_line("  \\draw[-, teal, thick] (prev) -- (now);")
+#         self.add_line("  }")
+#         self.add_line("  \\coordinate (prev) at (\\i,\\a) {};")
+#         self.add_line("}")
+#         self.add_line("\\end{tikzpicture}")
+
+
+# def score_graphs():
+#     # define scenario
+#     ts_length = 100
+#     pred_length = 5
+#     gt_length = 20
+#     gt_start = 40
+#     marks = [35, 40, 55, 60]
+#     assert pred_length % 2 == 1
+
+#     # prepare metrics list
+#     All_metrics.remove(metrics.Range_PR)
+#     all_metrics_and_rffront = [*All_metrics, metrics.Range_PR, Range_PR_front]
+
+#     # make results and names
+#     metric_names = []
+#     result = {}
+#     for metric in all_metrics_and_rffront:
+#         # set names
+#         if metric == metrics.TaF:
+#             metric_names.append(metric(5, [3, 4], [3], delta=10).name)
+#         elif metric == metrics.Time_Tolerant:
+#             metric_names.append(metric(5, [3, 4], [3], d=10).name)
+#         else:
+#             metric_names.append(metric(5, [3, 4], [3]).name)
+
+#         # get results
+#         current_result = []
+#         for pred_mid in range(pred_length // 2, ts_length - pred_length // 2):
+#             gt = [[gt_start, gt_start + gt_length - 1]]
+#             pred = [[pred_mid - pred_length // 2, pred_mid + pred_length // 2]]
+#             if metric == metrics.TaF:
+#                 current_result.append(metric(ts_length, gt, pred, delta=10).get_score())
+#             elif metric == metrics.Time_Tolerant:
+#                 current_result.append(metric(ts_length, gt, pred, d=10).get_score())
+#             else:
+#                 current_result.append(metric(ts_length, gt, pred).get_score())
+#         current_result = np.array(current_result)
+#         current_result = (current_result - min(current_result)) / (max(current_result) - min(current_result))
+#         result[metric_names[-1]] = current_result
+
+#     # make the table
+#     table = Score_graphs_table(metric_names, result, marks)
+#     table.write()
+#     print(table)
+
+
+# score_graphs()