def _write_aspect_lex(parsed_data: Union[str, PathLike],
generated_aspect_lex: dict, out_dir: PathLike):
parsed_docs = _load_parsed_docs_from_dir(parsed_data)
aspect_dict = {}
max_examples = 20
label = 'AS'
for doc in parsed_docs.values():
for sent_text, _ in doc.sent_iter():
for term, lemma in generated_aspect_lex.items():
if term in sent_text.lower():
_find_aspect_in_sentence(term, lemma, sent_text,
aspect_dict, label, max_examples,
False)
if lemma != '' and lemma in sent_text.lower():
_find_aspect_in_sentence(term, lemma, sent_text,
aspect_dict, label, max_examples,
True)
# write aspect lex to file
header_row = ["Term", "Alias1", "Alias2", "Alias3"]
for k in range(1, max_examples + 1):
header_row.append("Example" + str(k))
aspect_table = [header_row]
for [term, lemma], sentences in aspect_dict.items():
term_row = [term, lemma, '', '']
for sent in sentences:
term_row.append(sent)
aspect_table.append(term_row)
out_dir.mkdir(parents=True, exist_ok=True)
out_file_path = out_dir / 'generated_aspect_lex.csv'
_write_table(aspect_table, out_file_path)
print('Aspect lexicon written to {}'.format(out_file_path))
def extract_download(
url: str,
directory: PathLike,
filenames: [str] = None,
known_hash: str = None,
overwrite: bool = False,
):
if not isinstance(directory, Path):
directory = Path(directory)
if filenames is None:
filenames = []
if not directory.exists():
directory.mkdir(parents=True, exist_ok=True)
temporary_filename = directory / 'temp.tar.gz'
logging.debug(f'downloading {url} -> {temporary_filename}')
temporary_filename = pooch.retrieve(url,
known_hash=known_hash,
fname=temporary_filename)
logging.debug(f'extracting {temporary_filename} -> {directory}')
with tarfile.open(temporary_filename) as local_file:
if len(filenames) > 0:
for filename in filenames:
if filename in local_file.getnames():
path = directory / filename
if not path.exists() or overwrite:
if path.exists():
os.remove(path)
local_file.extract(filename, directory)
else:
local_file.extractall(directory)
def init_dir(adir: PathLike, exist_ok=False, parents=False, rmtree=False):
adir = Path(adir)
if adir.is_dir():
if rmtree:
shutil.rmtree(adir)
adir.mkdir(exist_ok=exist_ok, parents=parents)
return adir
def plot_dataset(
dataset: xr.Dataset,
num_chains: int = 8,
therm_frac: float = 0.,
title: str = None,
outdir: os.PathLike = None,
subplots_kwargs: dict[str, Any] = None,
plot_kwargs: dict[str, Any] = None,
ext: str = 'png',
):
plot_kwargs = {} if plot_kwargs is None else plot_kwargs
subplots_kwargs = {} if subplots_kwargs is None else subplots_kwargs
if outdir is None:
import os
tstamp = get_timestamp('%Y-%m-%d-%H%M%S')
outdir = Path(os.getcwd()).joinpath('plots', f'plots-{tstamp}')
outdir.mkdir(exist_ok=True, parents=True)
for idx, (key, val) in enumerate(dataset.data_vars.items()):
color = f'C{idx%9}'
plot_kwargs['color'] = color
fig, subfigs, ax = plot_metric(
val=val.values,
key=str(key),
title=title,
outdir=None,
therm_frac=therm_frac,
num_chains=num_chains,
plot_kwargs=plot_kwargs,
subplots_kwargs=subplots_kwargs,
)
if outdir is not None:
outfile = Path(outdir).joinpath(f'{key}.{ext}')
Path(outfile.parent).mkdir(exist_ok=True, parents=True)
outfile = outfile.as_posix()
if subfigs is not None:
# edgecolor = plt.rcParams['axes.edgecolor']
plt.rcParams['axes.edgecolor'] = plt.rcParams['axes.facecolor']
ax = subfigs[0].subplots(1, 1)
# ax = fig[1].subplots(constrained_layout=True)
cbar_kwargs = {
# 'location': 'top',
# 'orientation': 'horizontal',
}
im = val.plot(ax=ax, cbar_kwargs=cbar_kwargs)
# ax.set_ylim(0, )
im.colorbar.set_label(f'{key}') # , labelpad=1.25)
sns.despine(subfigs[0], top=True, right=True,
left=True, bottom=True)
if outdir is not None:
print(f'Saving figure to: {outfile}')
plt.savefig(outfile, dpi=400, bbox_inches='tight')
else:
fig.savefig(outfile, dpi=400, bbox_inches='tight')
return dataset
def write_csvs(
dirname: PathLike, adata: AnnData, skip_data: bool = True, sep: str = ','
):
"""See :meth:`~anndata.AnnData.write_csvs`.
"""
dirname = Path(dirname)
if dirname.suffix == '.csv':
dirname = dirname.with_suffix('')
logger.info("writing '.csv' files to %s", dirname)
if not dirname.is_dir():
dirname.mkdir(parents=True, exist_ok=True)
dir_uns = dirname / 'uns'
if not dir_uns.is_dir():
dir_uns.mkdir(parents=True, exist_ok=True)
d = dict(
obs=adata._obs,
var=adata._var,
obsm=adata._obsm.to_df(),
varm=adata._varm.to_df(),
)
if not skip_data:
d['X'] = pd.DataFrame(
adata._X.toarray() if issparse(adata._X) else adata._X
)
d_write = {**d, **adata._uns}
not_yet_raised_sparse_warning = True
for key, value in d_write.items():
if issparse(value):
if not_yet_raised_sparse_warning:
warnings.warn(
'Omitting to write sparse annotation.', WriteWarning
)
not_yet_raised_sparse_warning = False
continue
filename = dirname
if key not in {'X', 'var', 'obs', 'obsm', 'varm'}:
filename = dir_uns
filename /= f'{key}.csv'
df = value
if not isinstance(value, pd.DataFrame):
value = np.array(value)
if np.ndim(value) == 0:
value = value[None]
try:
df = pd.DataFrame(value)
except Exception as e:
warnings.warn(
f'Omitting to write {key!r} of type {type(e)}.',
WriteWarning,
)
continue
df.to_csv(
filename,
sep=sep,
header=key in {'obs', 'var', 'obsm', 'varm'},
index=key in {'obs', 'var'},
)
def write_csvs(dirname: PathLike,
adata: AnnData,
skip_data: bool = True,
sep: str = ","):
"""See :meth:`~anndata.AnnData.write_csvs`."""
dirname = Path(dirname)
if dirname.suffix == ".csv":
dirname = dirname.with_suffix("")
logger.info(f"writing .csv files to {dirname}")
if not dirname.is_dir():
dirname.mkdir(parents=True, exist_ok=True)
dir_uns = dirname / "uns"
if not dir_uns.is_dir():
dir_uns.mkdir(parents=True, exist_ok=True)
d = dict(
obs=adata._obs,
var=adata._var,
obsm=adata._obsm.to_df(),
varm=adata._varm.to_df(),
)
if not skip_data:
d["X"] = pd.DataFrame(
adata._X.toarray() if issparse(adata._X) else adata._X)
d_write = {**d, **adata._uns}
not_yet_raised_sparse_warning = True
for key, value in d_write.items():
if issparse(value):
if not_yet_raised_sparse_warning:
warnings.warn("Omitting to write sparse annotation.",
WriteWarning)
not_yet_raised_sparse_warning = False
continue
filename = dirname
if key not in {"X", "var", "obs", "obsm", "varm"}:
filename = dir_uns
filename /= f"{key}.csv"
df = value
if not isinstance(value, pd.DataFrame):
value = np.array(value)
if np.ndim(value) == 0:
value = value[None]
try:
df = pd.DataFrame(value)
except Exception as e:
warnings.warn(
f"Omitting to write {key!r} of type {type(e)}.",
WriteWarning,
)
continue
df.to_csv(
filename,
sep=sep,
header=key in {"obs", "var", "obsm", "varm"},
index=key in {"obs", "var"},
)
def download_mesh(url: str, directory: PathLike, overwrite: bool = False):
if not isinstance(directory, Path):
directory = Path(directory)
if not directory.exists():
directory.mkdir(parents=True, exist_ok=True)
if not (directory / 'fort.14').exists() or overwrite:
logging.info(f'downloading mesh files to {directory}')
extract_download(url, directory, ['fort.13', 'fort.14'])
return directory
def train(
self, episodes: int,
validation: int = None,
save_path: PathLike = None,
gamma: float = 1.0, epsilon: float = 0.2,
) -> None:
"""
:param episodes:
:param validation:
:param save_path: path to save models and logs.
:param gamma: γ - discount factor. Is used to balance immediate and future reward.
:param epsilon: ε - chance to get random move in ε-greedy policy
"""
if save_path:
save_path = pathlib.Path(save_path) / f'SIGMOID_24_negative_reward_gamma_{gamma}_epsilon_{epsilon}_q_learning'
save_path.mkdir(exist_ok=False, parents=False)
for episode in tqdm(range(episodes)):
if validation is not None and not (episode + 1) % validation:
self.validate(path=save_path)
if save_path:
self.save(save_path, episode + 1)
self.model.train()
players = (self.agent_cls(self.model), self.agent_cls(self.model))
game = bg.Game(players=players)
with self.e_greedy_get_action(episode, epsilon=epsilon):
for agent, new_board, prev_board, move, available_moves in game.play_step_by_step():
agent: agents.NNAgent
pred_q = agent.estimate(board=prev_board)
if new_board.status:
reward = new_board.status
self.update(pred_q, torch.Tensor([reward]))
with prev_board.reverse() as reversed_board:
self.update(agent.estimate(board=reversed_board), torch.Tensor([-reward]))
break
else:
estimated_moves = list(agent.estimate_moves(available_moves=available_moves, board=prev_board))
agent_checkers, opp_checkers = prev_board.to_schema()
if estimated_moves:
max_q = np.max(estimated_moves)
new_q = gamma * max_q
else:
# it is too bad, if we could not make any step.
new_q = torch.Tensor([-1])
self.update(pred_q, new_q)
def ensure_directory(directory: PathLike) -> Path:
"""
ensure that a directory exists
:param directory: directory path to ensure
:returns: path to ensured directory
"""
if not isinstance(directory, Path):
directory = Path(directory)
directory = directory.expanduser()
if directory.is_file():
directory = directory.parent
if not directory.exists():
directory.mkdir(parents=True, exist_ok=True)
return directory
def _download_file(
fname: Union[AVAILABLE_MODELS, AVAILABLE_DATA],
branch: str,
save_dir: PathLike,
type: Literal["model", "data"],
) -> Path:
"""Download a file to disk if it does not already exist.
Args:
fname: The file name.
branch: Which branch of the unlockNN repository to download from.
save_dir: The directory to check for already-downloaded models and
in which to save newly downloaded models.
type: The type of file.
Returns:
The path to the downloaded file/folder.
"""
save_dir = Path(save_dir)
if not save_dir.exists():
save_dir.mkdir()
specific_dir = save_dir / (
f"{fname}-{branch}" + (".parquet" if type == "data" else "")
)
# Add .pkl extension only if we're downloading data
url = MODELS_URL if type == "model" else DATA_URL
download_url = url.format(branch=branch, fname=fname)
if not specific_dir.exists():
r = requests.get(download_url)
if type == "model":
tar_f = tarfile.open(fileobj=BytesIO(r.content))
tar_f.extractall(specific_dir)
tar_f.close()
else:
specific_dir.write_bytes(r.content)
return specific_dir
def download_file(
url: PathLike,
filename: PathLike = None,
directory: PathLike = None,
show_progress: bool = True,
silent: bool = False,
timeout: int = 5,
) -> str:
"""
Download a file from a url and save it to the local filesystem. The file is saved to the
current directory by default, or to `directory` if specified. If a filename is not given,
the filename of the URL will be used.
:param url: URL that points to the file to download
:param filename: Name of the local file to save. Should point to the name of the file only,
not the full path. If None the filename from the url will be used
:param directory: Directory to save the file to. Will be created if it doesn't exist
If None the file will be saved to the current working directory
:param show_progress: If True, show an TQDM ProgressBar
:param silent: If True, do not print a message if the file already exists
:return: path to downloaded file
"""
try:
opener = urllib.request.build_opener()
opener.addheaders = [("User-agent", "Mozilla/5.0")]
urllib.request.install_opener(opener)
urlobject = urllib.request.urlopen(url, timeout=timeout)
if filename is None:
filename = urlobject.info().get_filename() or Path(urllib.parse.urlparse(url).path).name
except urllib.error.URLError as error:
if isinstance(error.reason, socket.timeout):
raise Exception(
"Connection timed out. If you access the internet through a proxy server, please "
"make sure the proxy is set in the shell from where you launched Jupyter. If your "
"internet connection is slow, you can call `download_file(url, timeout=30)` to "
"wait for 30 seconds before raising this error."
) from None
except urllib.error.HTTPError as e:
raise Exception(f"File downloading failed with error: {e.code} {e.msg}") from None
filename = Path(filename)
if len(filename.parts) > 1:
raise ValueError(
"`filename` should refer to the name of the file, excluding the directory. "
"Use the `directory` parameter to specify a target directory for the downloaded file."
)
# create the directory if it does not exist, and add the directory to the filename
if directory is not None:
directory = Path(directory)
directory.mkdir(parents=True, exist_ok=True)
filename = directory / Path(filename)
# download the file if it does not exist, or if it exists with an incorrect file size
urlobject_size = int(urlobject.info().get("Content-Length", 0))
if not filename.exists() or (os.stat(filename).st_size != urlobject_size):
progress_callback = DownloadProgressBar(
total=urlobject_size,
unit="B",
unit_scale=True,
unit_divisor=1024,
desc=str(filename),
disable=not show_progress,
)
urllib.request.urlretrieve(url, filename, reporthook=progress_callback.update_to)
if os.stat(filename).st_size >= urlobject_size:
progress_callback.update(urlobject_size - progress_callback.n)
progress_callback.refresh()
else:
if not silent:
print(f"'{filename}' already exists.")
return filename.resolve()
def make_path(p: PathLike) -> Path:
p = Path(p)
p.mkdir(exist_ok=True, parents=True)
return p