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

sierra/core/pipeline/stage3/statistics_calculator.py

@@ -1,478 +0,0 @@
-# Copyright 2019 John Harwell, All rights reserved.
-#
-#  SPDX-License-Identifier: MIT
-
-"""
-Classes for generating statistics within and across experiments in a batch.
-"""
-
-# Core packages
-import re
-import multiprocessing as mp
-import typing as tp
-import queue
-import time
-import datetime
-import logging
-import pathlib
-
-# 3rd party packages
-import pandas as pd
-import psutil
-
-# Project packages
-import sierra.core.variables.batch_criteria as bc
-from sierra.core import types, utils, stat_kernels, storage, config
-
-
-class GatherSpec:
-    """
-    Data class for specifying .csv files to gather from an :term:`Experiment`.
-    """
-
-    def __init__(self,
-                 exp_name: str,
-                 item_stem: str,
-                 imagize_csv_stem: tp.Optional[str]):
-        self.exp_name = exp_name
-        self.item_stem = item_stem
-        self.imagize_csv_stem = imagize_csv_stem
-
-    def for_imagizing(self):
-        return self.imagize_csv_stem is not None
-
-
-class BatchExpParallelCalculator:
-    """Process :term:`Output .csv` files for each experiment in the batch.
-
-    In parallel for speed.
-    """
-
-    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:
-
-        exp_to_avg = utils.exp_range_calc(self.cmdopts,
-                                          self.cmdopts['batch_output_root'],
-                                          criteria)
-
-        template_input_leaf = pathlib.Path(self.cmdopts['template_input_file']).stem
-
-        avg_opts = {
-            'template_input_leaf': template_input_leaf,
-            'df_skip_verify': self.cmdopts['df_skip_verify'],
-            'dist_stats': self.cmdopts['dist_stats'],
-            'project_imagizing': self.cmdopts['project_imagizing'],
-            'processing_mem_limit': self.cmdopts['processing_mem_limit'],
-            'storage_medium': self.cmdopts['storage_medium'],
-            'df_homogenize': self.cmdopts['df_homogenize']
-        }
-
-        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))
-
-        with mp.Pool(processes=n_gatherers + n_processors) as pool:
-            self._execute(exp_to_avg, avg_opts, n_gatherers, n_processors, pool)
-
-    def _execute(self,
-                 exp_to_avg: tp.List[pathlib.Path],
-                 avg_opts: types.SimpleDict,
-                 n_gatherers: int,
-                 n_processors: int,
-                 pool) -> None:
-        m = mp.Manager()
-        gatherq = m.Queue()
-        processq = m.Queue()
-
-        for exp in exp_to_avg:
-            gatherq.put(exp)
-
-        # Start some threads gathering .csvs first to get things rolling.
-        self.logger.debug("Starting %d gatherers, method=%s",
-                          n_gatherers,
-                          mp.get_start_method())
-        gathered = [pool.apply_async(BatchExpParallelCalculator._gather_worker,
-                                     (gatherq,
-                                      processq,
-                                      self.main_config,
-                                      avg_opts)) for i in range(0, n_gatherers)]
-
-        self.logger.debug("Starting %d processors, method=%s",
-                          n_processors,
-                          mp.get_start_method())
-        processed = [pool.apply_async(BatchExpParallelCalculator._process_worker,
-                                      (processq,
-                                       self.main_config,
-                                       self.cmdopts['batch_stat_root'],
-                                       avg_opts)) for i 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,
-                       avg_opts: tp.Dict[str, str]) -> None:
-        gatherer = ExpCSVGatherer(main_config, avg_opts, processq)
-
-        # Wait for 3 seconds after the queue is empty before bailing, at the
-        # start. If that is not long enough then exponentially increase from
-        # there until you find how long it takes to get the first item in the
-        # queue, and use that as the appropriate timeout (plus a little
-        # margin).
-        timeout = 3
-        got_item = False
-        n_tries = 0
-        while n_tries < 2:
-            try:
-                exp_output_root = gatherq.get(True, timeout)
-
-                gatherer(exp_output_root)
-                gatherq.task_done()
-                got_item = True
-
-            except queue.Empty:
-                if got_item:
-                    break
-
-                timeout *= 2
-                n_tries += 1
-
-    @staticmethod
-    def _process_worker(processq: mp.Queue,
-                        main_config: types.YAMLDict,
-                        batch_stat_root: pathlib.Path,
-                        avg_opts: tp.Dict[str, str]) -> None:
-        calculator = ExpStatisticsCalculator(main_config,
-                                             avg_opts,
-                                             batch_stat_root)
-
-        # Wait for 3 seconds after the queue is empty before bailing, at the
-        # start. If that is not long enough then exponentially increase from
-        # there until you find how long it takes to get the first item in the
-        # queue, and use that as the appropriate timeout (plus a little
-        # margin).
-        timeout = 3
-        got_item = False
-        n_tries = 0
-        while n_tries < 2:
-            try:
-                item = processq.get(True, timeout)
-                key = list(item.keys())[0]
-
-                calculator(key, item[key])
-                processq.task_done()
-                got_item = True
-
-            except queue.Empty:
-                if got_item:
-                    break
-
-                timeout *= 2
-                n_tries += 1
-
-
-class ExpCSVGatherer:
-    """Gather all :term:`Output .csv` files from all runs within an experiment.
-
-    "Gathering" in this context means creating a dictionary mapping which .csv
-    came from where, so that statistics can be generated both across and with
-    experiments in the batch.
-    """
-
-    def __init__(self,
-                 main_config: types.YAMLDict,
-                 gather_opts: dict,
-                 processq: mp.Queue) -> None:
-        self.processq = processq
-        self.gather_opts = gather_opts
-
-        # Will get the main name and extension of the config file (without the
-        # full absolute path).
-        self.template_input_fname = self.gather_opts['template_input_leaf']
-
-        self.main_config = main_config
-
-        self.run_metrics_leaf = main_config['sierra']['run']['run_metrics_leaf']
-        self.videos_leaf = 'videos'
-        self.project_imagize = gather_opts['project_imagizing']
-
-        self.logger = logging.getLogger(__name__)
-
-    def __call__(self, exp_output_root: pathlib.Path) -> None:
-        """Process the CSV files found in the output save path."""
-        if not self.gather_opts['df_skip_verify']:
-            self._verify_exp_outputs(exp_output_root)
-
-        self.logger.info('Processing .csvs: %s...', exp_output_root.name)
-
-        pattern = "{}_{}_output".format(re.escape(self.gather_opts['template_input_leaf']),
-                                        r'\d+')
-
-        runs = list(exp_output_root.iterdir())
-        assert(all(re.match(pattern, r.name) for r in runs)),\
-            f"Extra files/not all dirs in '{exp_output_root}' are exp runs"
-
-        # Maps (unique .csv stem, optional parent dir) to the averaged dataframe
-        to_gather = self._calc_gather_items(runs[0], exp_output_root.name)
-
-        for item in to_gather:
-            self._wait_for_memory()
-            gathered = self._gather_item_from_sims(exp_output_root, item, runs)
-
-            # Put gathered .csv list  in the process queue
-            self.processq.put(gathered)
-
-        self.logger.debug("Enqueued %s items from %s for processing",
-                          len(to_gather),
-                          exp_output_root.name)
-
-    def _calc_gather_items(self,
-                           run_output_root: pathlib.Path,
-                           exp_name: str) -> tp.List[GatherSpec]:
-        to_gather = []
-
-        sim_output_root = run_output_root / self.run_metrics_leaf
-
-        # The metrics folder should contain nothing but .csv files and
-        # directories. For all directories it contains, they each should contain
-        # nothing but .csv files (these are for video rendering later).
-        for item in sim_output_root.iterdir():
-            csv_stem = item.stem
-
-            if item.is_file():
-                to_gather.append(GatherSpec(exp_name=exp_name,
-                                            item_stem=csv_stem,
-                                            imagize_csv_stem=None))
-            else:
-                # This takes FOREVER, so only do it if we absolutely need to
-                if not self.project_imagize:
-                    continue
-
-                for csv_fname in item.iterdir():
-                    to_gather.append(GatherSpec(exp_name=exp_name,
-                                                item_stem=csv_stem,
-                                                imagize_csv_stem=csv_fname.stem))
-
-        return to_gather
-
-    def _gather_item_from_sims(self,
-                               exp_output_root: pathlib.Path,
-                               item: GatherSpec,
-                               runs: tp.List[pathlib.Path]) -> tp.Dict[GatherSpec,
-                                                                       tp.List[pd.DataFrame]]:
-        gathered = {}  # type: tp.Dict[GatherSpec, pd.DataFrame]
-
-        for run in runs:
-            sim_output_root = run / self.run_metrics_leaf
-
-            if item.for_imagizing():
-                item_path = sim_output_root / item.item_stem / \
-                    (item.imagize_csv_stem + config.kStorageExt['csv'])
-            else:
-                item_path = sim_output_root / \
-                    (item.item_stem + config.kStorageExt['csv'])
-
-            reader = storage.DataFrameReader(self.gather_opts['storage_medium'])
-            df = reader(item_path, index_col=False)
-
-            if df.dtypes[0] == 'object':
-                df[df.columns[0]] = df[df.columns[0]].apply(lambda x: float(x))
-
-            if item not in gathered:
-                gathered[item] = []
-
-            gathered[item].append(df)
-
-        return gathered
-
-    def _wait_for_memory(self) -> None:
-        while True:
-            mem = psutil.virtual_memory()
-            avail = mem.available / mem.total
-            free_percent = avail * 100
-            free_limit = 100 - self.gather_opts['processing_mem_limit']
-
-            if free_percent >= free_limit:
-                return
-
-            self.logger.info("Waiting for memory: avail=%s,min=%s",
-                             free_percent,
-                             free_limit)
-            time.sleep(1)
-
-    def _verify_exp_outputs(self, exp_output_root: pathlib.Path) -> None:
-        """
-        Verify the integrity of all runs in an experiment.
-
-        Specifically:
-
-        - All runs produced all CSV files.
-
-        - All runs CSV files with the same name have the same # rows and
-          columns.
-
-        - No CSV files contain NaNs.
-        """
-        experiments = exp_output_root.iterdir()
-
-        self.logger.info('Verifying results in %s...', str(exp_output_root))
-
-        start = time.time()
-
-        for exp1 in experiments:
-            csv_root1 = exp1 / self.run_metrics_leaf
-
-            for exp2 in experiments:
-                csv_root2 = exp2 / self.run_metrics_leaf
-
-                if not csv_root2.is_dir():
-                    continue
-
-                self._verify_exp_outputs_pairwise(csv_root1, csv_root2)
-
-        elapsed = int(time.time() - start)
-        sec = datetime.timedelta(seconds=elapsed)
-        self.logger.info("Done verifying results in %s: %s",
-                         exp_output_root,
-                         sec)
-
-    def _verify_exp_outputs_pairwise(self,
-                                     csv_root1: pathlib.Path,
-                                     csv_root2: pathlib.Path) -> None:
-        for csv in csv_root2.iterdir():
-            path1 = csv
-            path2 = csv_root2 / csv.name
-
-            # .csvs for rendering that we don't verify (for now...)
-            if path1.is_dir() or path2.is_dir():
-                self.logger.debug("Not verifying '%s': contains rendering data",
-                                  str(path1))
-                continue
-
-            assert (utils.path_exists(path1) and utils.path_exists(path2)),\
-                f"Either {path1} or {path2} does not exist"
-
-            # Verify both dataframes have same # columns, and that
-            # column sets are identical
-            reader = storage.DataFrameReader(self.gather_opts['storage_medium'])
-            df1 = reader(path1)
-            df2 = reader(path2)
-
-            assert (len(df1.columns) == len(df2.columns)), \
-                (f"Dataframes from {path1} and {path2} do not have "
-                 "the same # columns")
-            assert(sorted(df1.columns) == sorted(df2.columns)),\
-                f"Columns from {path1} and {path2} not identical"
-
-            # Verify the length of all columns in both dataframes is the same
-            for c1 in df1.columns:
-                assert(all(len(df1[c1]) == len(df1[c2]) for c2 in df1.columns)),\
-                    f"Not all columns from {path1} have same length"
-
-                assert(all(len(df1[c1]) == len(df2[c2]) for c2 in df1.columns)),\
-                    (f"Not all columns from {path1} and {path2} have "
-                     "the same length")
-
-
-class ExpStatisticsCalculator:
-    """Generate statistics from output files for all runs within an experiment.
-
-    .. IMPORTANT:: You *CANNOT* use logging ANYWHERE during processing .csv
-       files. Why ? I *think* because of a bug in the logging module itself. If
-       you get unlucky enough to spawn the process which enters the __call__()
-       method in this class while another logging statement is in progress (and
-       is therefore holding an internal logging module lock), then the
-       underlying fork() call will copy the lock in the acquired state. Then,
-       when this class goes to try to log something, it deadlocks with itself.
-
-       You also can't just create loggers with unique names, as this seems to be
-       something like the GIL, but for the logging module. Sometimes python
-       sucks.
-    """
-
-    def __init__(self,
-                 main_config: types.YAMLDict,
-                 avg_opts: dict,
-                 batch_stat_root: pathlib.Path) -> None:
-        self.avg_opts = avg_opts
-
-        # will get the main name and extension of the config file (without the
-        # full absolute path)
-        self.template_input_fname = self.avg_opts['template_input_leaf']
-
-        self.main_config = main_config
-        self.batch_stat_root = batch_stat_root
-
-        self.intra_perf_csv = main_config['sierra']['perf']['intra_perf_csv']
-        self.intra_perf_col = main_config['sierra']['perf']['intra_perf_col']
-
-    def __call__(self,
-                 gather_spec: GatherSpec,
-                 gathered_dfs: tp.List[pd.DataFrame]) -> None:
-
-        csv_concat = pd.concat(gathered_dfs)
-
-        exp_stat_root = self.batch_stat_root / gather_spec.exp_name
-        utils.dir_create_checked(exp_stat_root, exist_ok=True)
-
-        # Create directory for averaged .csv files for imagizing later.
-        if gather_spec.for_imagizing():
-            utils.dir_create_checked(exp_stat_root / gather_spec.item_stem,
-                                     exist_ok=True)
-
-        by_row_index = csv_concat.groupby(csv_concat.index)
-
-        dfs = {}
-        if self.avg_opts['dist_stats'] in ['none', 'all']:
-            dfs.update(stat_kernels.mean.from_groupby(by_row_index))
-
-        if self.avg_opts['dist_stats'] in ['conf95', 'all']:
-            dfs.update(stat_kernels.conf95.from_groupby(by_row_index))
-
-        if self.avg_opts['dist_stats'] in ['bw', 'all']:
-            dfs.update(stat_kernels.bw.from_groupby(by_row_index))
-
-        for ext in dfs:
-            opath = exp_stat_root / gather_spec.item_stem
-
-            if gather_spec.for_imagizing():
-                opath /= (gather_spec.imagize_csv_stem + ext)
-
-            else:
-                opath = opath.with_suffix(ext)
-
-            df = utils.df_fill(dfs[ext], self.avg_opts['df_homogenize'])
-            writer = storage.DataFrameWriter(self.avg_opts['storage_medium'])
-            writer(df, opath, index=False)
-
-
-__api__ = [
-    'GatherSpec',
-    'BatchExpParallelCalculator',
-    'ExpCSVGatherer',
-    'ExpStatisticsCalculator'
-]