How to use _track_progress method in lisa

Best Python code snippet using lisa_python

parser.py

Source:parser.py

...29        self.progress = 030        self.network = []31        self.process_pool = Pool(processes=4)32        self._count_atoms()33        self._track_progress()34    def _count_atoms(self):35        with open(self.filename,'r') as infile:36            try:37                self._atoms_number = int(infile.readline())38            except:39                print("Could not read the number of atoms,please make sure the .xyz file has the correct format.")40                exit()41    def _make_last_movie_frame(self):42        os.system("rm last_frame.xyz")43        os.system("rm last.xyz")44        cmd = "tail -"+str(self._atoms_number)+" fibro.xyz >> last_frame.xyz "45        with open("last_frame.xyz",'w') as outfile:46            outfile.write("{}\nAtoms. Timestep: 0\n".format(self._atoms_number))47        os.system(cmd)48        cmd = "cat last_frame.xyz last_frame.xyz >> last.xyz"49        os.system(cmd)50    def _track_progress(self):51        if os.path.exists("log.lammps"):52            os.system("tail -1 log.lammps >> progress.txt")53            with open("progress.txt") as infile:54                try:55                    self.progress = int(re.findall(r'\d+', infile.readline())[0])56                except:57                    print("Could not find the last frame, run the simulation for longer!")58            os.system("rm progress.txt")59        else:60            print("Warning: Could not find the LAMMPS log file.")61    def go_through_frames(self,filename):62        frame_index = 063        types = []64        xs = []; ys = []; zs = []65        jobs = []66        fibril_analyser = FibrilAnalyser()67        with open(filename, 'r') as infile:68            for item in infile:69                if len(item.split()) == 1 and types:70                    frame_index += 171                    types = np.asarray(types);xs=np.asarray(xs);ys=np.asarray(ys);zs=np.asarray(zs)72                    if args.verbose and not args.last_frame:73                        print("Processing frame......{}".format(frame_index))74                    self.process_pool.apply_async(fibril_analyser.analyse_fibril_distribution,75                    args=(args.nematic_cutoff,args.radial_cutoff,types,xs,ys,zs))76                    types=[];xs=[];ys=[];zs=[]77                if len(item.split()) > 3:78                    atom_type,x,y,z=item.split()79                    atom_type = str(atom_type)80                    x, y, z = float(x), float(y), float(z)81                    types.append(int(atom_type))82                    xs.append(x);ys.append(y);zs.append(z)83        self.process_pool.close()84        self.process_pool.join()85if __name__ == "__main__":86    parser = Parser(args.movie_name)87    parser._count_atoms()88    parser._track_progress()89    if args.last_frame:90        print("analysing last frame")91        parser._make_last_movie_frame()92        parser.go_through_frames("last.xyz")93    else:94        parser.go_through_frames(args.movie_name)95    print("Successfully analysed all frames!")...

rollout_saver.py

Source:rollout_saver.py

1import shelve2import argparse3import json4import numpy as np5import os6import os.path as osp7import torch8from pathlib import Path9from typing import List, Optional, Tuple, Union, Dict10from collections import defaultdict11from grf_imitation.infrastructure.datas import Batch, convert_batch_to_dict12from grf_imitation.infrastructure.utils import utils13class RolloutSaver:14    """15    Utility class for storing rollouts.16    Each rollout is stored with a key based on the episode number (0-indexed),17    and the number of episodes is stored with the key "num_episodes",18    so to load the shelf file, use something like:19    with shelve.open('rollouts.pkl') as rollouts:20       for episode_id in range(rollouts["episodes"]):21          rollout = rollouts[str(episode_id)]22    If outfile is None, this class does nothing.23    """24    def __init__(25        self,26        exp_dir=None,27        num_steps=None,28        num_episodes=None,29        track_progress=False,30        save_info=False,31    ):32        self._exp_dir = exp_dir33        self._track_progress = track_progress34        self._outfile = None # exp_dir/rollouts/rollouts35        self._progressfile = None # exp_dir/rollouts/__progress_rollouts36        self._shelf = None37        self._episodes = 038        self._steps = 039        self._num_episodes = num_episodes40        self._num_steps = num_steps41        self._save_info = save_info42        if self._exp_dir:43            self._rollout_dir = osp.join(self._exp_dir, 'evaluation')44            os.makedirs(self._rollout_dir, exist_ok=True)45            self._outfile = osp.join(self._rollout_dir, 'rollouts') 46    def _get_tmp_progress_filename(self):47        outpath = Path(self._outfile)48        return outpath.parent / ("progress_" + outpath.name)49    @property50    def outfile(self):51        return self._outfile52    @property53    def is_invalid(self):54        return self._exp_dir is None55    def __enter__(self):56        if self._outfile:57            self._shelf = shelve.open(self._outfile)58        if self._track_progress:59            self._progressfile = self._get_tmp_progress_filename().open(mode='w')60        return self61    62    def __exit__(self, type, value, traceback):63        if self._shelf:64            # Close the shelf file, and store the number of episodes for ease65            self._shelf['episodes'] = self._episodes66            self._shelf.close()67        if self._track_progress:68            # Remove the temp progress file:69            # self._get_tmp_progress_filename().unlink()70            self._progressfile.close()71    def _get_progress(self):72        if self._num_episodes:73            return f"{self._episodes} / {self._num_episodes} episodes completed"74        elif self._num_steps:75            return f"{self._steps} / {self._num_steps} steps completed"76        else:77            return f"{self._episodes} episodes completed"78    def store(self, batch: Batch):79        if self._outfile:80            # don't save img_obs to save space81            self._shelf[str(self._episodes)] = convert_batch_to_dict(batch, ignore_keys=['img_obs'])82        self._episodes += 183        if self._progressfile:84            log_str = f"episode reward: {batch.rew[:, :4].sum() // 4}\t" + self._get_progress() + "\n"85            print(log_str)86            self._progressfile.write(log_str)87            self._progressfile.flush()88    @property89    def rollout_dir(self):...

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