sierra-research 1.3.6__py3-none-any.whl → 1.5.0__py3-none-any.whl

sierra/core/pipeline/stage3/run_collator.py

@@ -1,317 +0,0 @@
-# Copyright 2019 John Harwell, All rights reserved.
-#
-#  SPDX-License-Identifier: MIT
-
-"""Classes for collating data within a :term:`Batch Experiment`.
-
-Collation is the process of "lifting" data from :term:`Experimental Runs
-<Experimental Run>` across all :term:`Experiment` for all experiments in a
-:term:`Batch Experiment` into a single CSV (a reduce operation).  This is needed
-to correctly calculate summary statistics for performance measures in stage 4:
-you can't just run the calculated stddev through the calculations for
-flexibility (for example) because comparing curves of stddev is not
-meaningful. Stage 4 needs access to raw-(er) run data to construct a
-`distribution` of performance measure values to then calculate the summary
-statistics (such as stddev) over.
-
-"""
-
-# Core packages
-import multiprocessing as mp
-import typing as tp
-import queue
-import logging
-import pathlib
-
-# 3rd party packages
-import pandas as pd
-import numpy as np
-import psutil
-
-# Project packages
-import sierra.core.variables.batch_criteria as bc
-import sierra.core.plugin_manager as pm
-from sierra.core import types, storage, utils, config
-
-
-class ExperimentalRunParallelCollator:
-    """Generates :term:`Collated .csv` files for each :term:`Experiment`.
-
-    :term:`Collated .csv` files generated from :term:`Output .csv` files across
-     :term:`Experimental Runs <Experimental Run>`.  Gathered in parallel for
-     each experiment for speed, unless disabled with ``--processing-serial``.
-
-    """
-
-    def __init__(self, main_config: dict, cmdopts: types.Cmdopts):
-        self.main_config = main_config
-        self.cmdopts = cmdopts
-        self.logger = logging.getLogger(__name__)
-
-    def __call__(self, criteria: bc.IConcreteBatchCriteria) -> None:
-        if self.cmdopts['processing_serial']:
-            n_gatherers = 1
-            n_processors = 1
-        else:
-            # Aways need to have at least one of each! If SIERRA is invoked on a
-            # machine with 2 or less logical cores, the calculation with
-            # psutil.cpu_count() will return 0 for # gatherers.
-            n_gatherers = max(1, int(psutil.cpu_count() * 0.25))
-            n_processors = max(1, int(psutil.cpu_count() * 0.75))
-
-        pool = mp.Pool(processes=n_gatherers + n_processors)
-
-        m = mp.Manager()
-        gatherq = m.Queue()
-        processq = m.Queue()
-
-        exp_to_proc = utils.exp_range_calc(self.cmdopts,
-                                           self.cmdopts['batch_output_root'],
-                                           criteria)
-
-        for exp in exp_to_proc:
-            gatherq.put((self.cmdopts['batch_output_root'], exp.name))
-
-        self.logger.debug("Starting %d gatherers, method=%s",
-                          n_gatherers,
-                          mp.get_start_method())
-
-        gathered = [pool.apply_async(ExperimentalRunParallelCollator._gather_worker,
-                                     (gatherq,
-                                      processq,
-                                      self.main_config,
-                                      self.cmdopts['project'],
-                                      self.cmdopts['storage_medium'])) for _ in range(0, n_gatherers)]
-
-        self.logger.debug("Starting %d processors, method=%s",
-                          n_processors,
-                          mp.get_start_method())
-        processed = [pool.apply_async(ExperimentalRunParallelCollator._process_worker,
-                                      (processq,
-                                       self.main_config,
-                                       self.cmdopts['batch_stat_collate_root'],
-                                       self.cmdopts['storage_medium'],
-                                       self.cmdopts['df_homogenize'])) for _ in range(0, n_processors)]
-
-        # To capture the otherwise silent crashes when something goes wrong in
-        # worker threads. Any assertions will show and any exceptions will be
-        # re-raised.
-        self.logger.debug("Waiting for workers to finish")
-        for g in gathered:
-            g.get()
-
-        for p in processed:
-            p.get()
-
-        pool.close()
-        pool.join()
-        self.logger.debug("All threads finished")
-
-    @staticmethod
-    def _gather_worker(gatherq: mp.Queue,
-                       processq: mp.Queue,
-                       main_config: types.YAMLDict,
-                       project: str,
-                       storage_medium: str) -> None:
-        module = pm.module_load_tiered(project=project,
-                                       path='pipeline.stage3.run_collator')
-        gatherer = module.ExperimentalRunCSVGatherer(main_config,
-                                                     storage_medium,
-                                                     processq)
-        while True:
-            # Wait for 3 seconds after the queue is empty before bailing
-            try:
-                batch_output_root, exp = gatherq.get(True, 3)
-                gatherer(batch_output_root, exp)
-                gatherq.task_done()
-
-            except queue.Empty:
-                break
-
-    @staticmethod
-    def _process_worker(processq: mp.Queue,
-                        main_config: types.YAMLDict,
-                        batch_stat_collate_root: pathlib.Path,
-                        storage_medium: str,
-                        df_homogenize: str) -> None:
-        collator = ExperimentalRunCollator(main_config,
-                                           batch_stat_collate_root,
-                                           storage_medium,
-                                           df_homogenize)
-        while True:
-            # Wait for 3 seconds after the queue is empty before bailing
-            try:
-                item = processq.get(True, 3)
-
-                exp_leaf = list(item.keys())[0]
-                gathered_runs, gathered_dfs = item[exp_leaf]
-                collator(gathered_runs, gathered_dfs, exp_leaf)
-                processq.task_done()
-            except queue.Empty:
-                break
-
-
-class ExperimentalRunCSVGatherer:
-    """Gather :term:`Output .csv` files across all runs within an experiment.
-
-    This class can be extended/overriden using a :term:`Project` hook. See
-    :ref:`ln-sierra-tutorials-project-hooks` for details.
-
-    Attributes:
-
-        processq: The multiprocessing-safe producer-consumer queue that the data
-                  gathered from experimental runs will be placed in for
-                  processing.
-
-        storage_medium: The name of the storage medium plugin to use to extract
-                        dataframes from when reading run data.
-
-        main_config: Parsed dictionary of main YAML configuration.
-
-        logger: The handle to the logger for this class. If you extend this
-                class, you should save/restore this variable in tandem with
-                overriding it in order to get logging messages have unique
-                logger names between this class and your derived class, in order
-                to reduce confusion.
-
-    """
-
-    def __init__(self,
-                 main_config: types.YAMLDict,
-                 storage_medium: str,
-                 processq: mp.Queue) -> None:
-        self.processq = processq
-
-        self.storage_medium = storage_medium
-        self.main_config = main_config
-
-        self.run_metrics_leaf = main_config['sierra']['run']['run_metrics_leaf']
-
-        self.logger = logging.getLogger(__name__)
-
-    def __call__(self,
-                 batch_output_root: pathlib.Path,
-                 exp_leaf: str):
-        """
-        Gather CSV data from all experimental runs in an experiment.
-
-        Gathered data is put in a queue for processing.
-
-        Arguments:
-
-            exp_leaf: The name of the experiment directory within the
-                      ``batch_output_root``.
-
-        """
-        self.logger.info('Gathering .csvs: %s...', exp_leaf)
-
-        exp_output_root = batch_output_root / exp_leaf
-
-        runs = sorted(exp_output_root.iterdir())
-
-        gathered = []
-        for run in runs:
-            run_output_root = run / self.run_metrics_leaf
-            gathered.append(self.gather_csvs_from_run(run_output_root))
-
-        names = [run.name for run in runs]
-        self.processq.put({exp_leaf: (names, gathered)})
-
-    def gather_csvs_from_run(self,
-                             run_output_root: pathlib.Path) -> tp.Dict[tp.Tuple[str, str],
-                                                                       pd.DataFrame]:
-        """Gather all data from a single run within an experiment.
-
-        Returns:
-
-           dict: A dictionary of <(CSV file name, CSV performance column),
-                 dataframe> key-value pairs. The CSV file name is the leaf part
-                 of the path with the extension included.
-
-        """
-
-        intra_perf_csv = self.main_config['sierra']['perf']['intra_perf_csv']
-        intra_perf_leaf = intra_perf_csv.split('.')[0]
-        intra_perf_col = self.main_config['sierra']['perf']['intra_perf_col']
-
-        reader = storage.DataFrameReader(self.storage_medium)
-        perf_path = run_output_root / (intra_perf_leaf +
-                                       config.kStorageExt['csv'])
-        perf_df = reader(perf_path, index_col=False)
-
-        return {
-            (intra_perf_leaf, intra_perf_col): perf_df[intra_perf_col],
-        }
-
-
-class ExperimentalRunCollator:
-    """Collate gathered :term:`Output .csv` files together (reduce operation).
-
-    :term:`Output .csv`s gathered from N :term:`Experimental Runs <Experimental
-    Run>` are combined together into a single :term:`Summary .csv` per
-    :term:`Experiment` with 1 column per run.
-
-    """
-
-    def __init__(self,
-                 main_config: types.YAMLDict,
-                 batch_stat_collate_root: pathlib.Path,
-                 storage_medium: str,
-                 df_homogenize: str) -> None:
-        self.main_config = main_config
-        self.batch_stat_collate_root = batch_stat_collate_root
-        self.df_homogenize = df_homogenize
-
-        self.storage_medium = storage_medium
-
-        # To support inverted performance measures where smaller is better
-        self.invert_perf = main_config['sierra']['perf'].get('inverted', False)
-        self.intra_perf_csv = main_config['sierra']['perf']['intra_perf_csv']
-
-        utils.dir_create_checked(self.batch_stat_collate_root, exist_ok=True)
-
-    def __call__(self,
-                 gathered_runs: tp.List[str],
-                 gathered_dfs: tp.List[tp.Dict[tp.Tuple[str, str], pd.DataFrame]],
-                 exp_leaf: str) -> None:
-        collated = {}
-
-        for run in gathered_runs:
-            run_dfs = gathered_dfs[gathered_runs.index(run)]
-
-            for csv_leaf, col in run_dfs.keys():
-                csv_df = run_dfs[(csv_leaf, col)]
-
-                # Invert performance if configured.
-                if self.invert_perf and csv_leaf in self.intra_perf_csv:
-                    csv_df = 1.0 / csv_df
-
-                    # Because of the requirement that P(N) >= 0 for flexibility
-                    # (1/0 = inf gives a crash with DTW), if the current level
-                    # of performance is 0, it stays 0.
-                    #
-                    # This is a bit of a hack. But also not a hack at all,
-                    # because infinite performance is not possible. This
-                    # is... Schrodinger's Hack.
-                    csv_df = csv_df.replace([-np.inf, np.inf], 0)
-
-                if (csv_leaf, col) not in collated:
-                    collated[(csv_leaf, col)] = pd.DataFrame(index=csv_df.index,
-                                                             columns=gathered_runs)
-                collated[(csv_leaf, col)][run] = csv_df
-
-        for (csv_leaf, col) in collated:
-            writer = storage.DataFrameWriter(self.storage_medium)
-            df = utils.df_fill(collated[(csv_leaf, col)], self.df_homogenize)
-            fname = f'{exp_leaf}-{csv_leaf}-{col}' + config.kStorageExt['csv']
-            opath = self.batch_stat_collate_root / fname
-            writer(df, opath, index=False)
-
-
-__api__ = [
-    'ExperimentalRunParallelCollator',
-    'ExperimentalRunCSVGatherer',
-    'ExperimentalRunCollator'
-
-
-]