def scrape(input_path,
output_path="~/Downloads",
max_workers=20,
sample_size=None,
silly=None):
# Read products from input csv
prod_dicts = read_product_link_csv(input_path)
products = list(map(Product.from_dict, prod_dicts))
# Trim list of products if sample_size was provided
if sample_size is not None and sample_size < len(products):
products = products[:sample_size]
# Uses concurrent.futures.TheadPoolExecutor.map() to fetch results
print(f"Scraping metadata for {len(products)} products.")
thread_map(lambda p: p.update_metadata(),
products,
max_workers=max_workers)
if silly:
products = sillify(products)
# Write to file
write_product_link_csv(output_path, [p.to_dict() for p in products],
listing_type="scrape")
def process_downloads(self, sites, collection):
"""
Method to download and process files
:param sites: List of file to download and process
:type sites: list
:param collection: Mongodb Collection name
:type collection: str
:return:
:rtype:
"""
worker_size = min(32, os.cpu_count() + 4)
start_time = time.time()
thread_map(self.download_site, sites, desc="Downloading files")
if self.do_process:
thread_map(
self.file_to_queue,
self.file_queue.get_full_list(),
desc="Processing downloaded files",
)
self._process_queue_to_db(worker_size, collection=collection)
# checking if last-modified was in the response headers and not set to default
if "01-01-1970" != self.last_modified.strftime("%d-%m-%Y"):
setColUpdate(self.feed_type.lower(), self.last_modified)
self.logger.info("Duration: {}".format(
timedelta(seconds=time.time() - start_time)))
def preprocess_idrid_grade(root_dir: str, output_dir: str, n_workers: int, train: bool):
root_path = Path(root_dir)
output_path = Path(output_dir) / "idrid_grade"
img_output_path = output_path / "img"
img_output_path.mkdir(parents=True, exist_ok=True)
img_transformed_output_path = output_path / "transformed"
img_transformed_output_path.mkdir(parents=True, exist_ok=True)
train_test_path = "a. Training Set" if train else "b. Testing Set"
retina_path = root_path / "1. Original Images" / train_test_path
print(retina_path)
image_names = [f.name for f in retina_path.glob("**/*")]
# Worker function that wraps the image processing function.
def worker(image_name: str):
process_image(
image_name=image_name,
retina_path=retina_path,
img_output_path=img_output_path,
img_transformed_output_path=img_transformed_output_path,
)
print(f"Preprocessing IDRiD Grade ({train_test_path}) with {n_workers} workers...")
thread_map(worker, image_names, max_workers=n_workers)
def test_thread_map():
"""Test contrib.concurrent.thread_map"""
with closing(StringIO()) as our_file:
a = range(9)
b = [i + 1 for i in a]
try:
assert thread_map(lambda x: x + 1, a, file=our_file) == b
except ImportError:
raise SkipTest
assert thread_map(incr, a, file=our_file) == b
def _search_columns(col, *filters):
outputs = synth_db.query(NHMOutput).filter(
NHMOutput.Output_ID.notin_(self._added), *filters)
thread_workers = context.config.resource_opt(
'dois.threads', 20)
with self, ThreadPoolExecutor(
thread_workers) as thread_executor:
thread_map(lambda x: _extract_doi(self, x, col),
outputs.all(),
desc=col,
unit=' records',
leave=False,
position=1)
def process_df(df, f, group_name):
# We save as [C, H, W]
train_shape = (len(df), 3, 512, 512)
train_labels = df["level"].to_numpy()
grp = f.create_group(group_name)
grp.create_dataset(
"images",
shape=train_shape,
dtype=np.uint8,
# compression="lzf",
)
grp.create_dataset("labels", shape=train_labels.shape, dtype=np.uint8)
grp["labels"][...] = train_labels
grp_images = grp["images"]
def process_image(i):
path = df["path"].iloc[i]
img = open_colour_image(path)
img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
contour = find_eye(img)
x, y, w, h = cv2.boundingRect(contour)
img = img[y : y + h, x : x + w]
img = pad_to_square(img, w, h, [BLACK, BLACK, BLACK])
img = cv2.resize(img, (512, 512))
scale = 512
img = cv2.addWeighted(
img, 4, cv2.GaussianBlur(img, (0, 0), scale / 30), -4, 128
)
# Remove outer 10% boundary effects
b = np.zeros(img.shape)
b = cv2.circle(
b,
(img.shape[1] // 2, img.shape[0] // 2),
int(scale * 0.9) // 2,
(1, 1, 1),
-1,
8,
0,
)
img = img * b + 128 * (1 - b)
img = np.transpose(img, (2, 0, 1))
grp_images[i, ...] = img[None]
thread_map(process_image, range(len(df)), max_workers=8)
def run_multithread(self,
max_workers: int | None = None,
quiet: bool = False) -> None:
"""
Run the process for all genes in the Population.
Parameters
----------
:max_workers: Number of concurrent workers. If `None`, the algorithm will get the
maximum possible (default: `None`).
:quiet: If `False`, a bar will show the simulation progress (default: `False`).
Updates
-------
self.datasets.results DataFrame
"""
def sim(x):
index, row = x
return pd.DataFrame(self.process(**row),
index=pd.Series([index], name='id'))
iterable = self.datasets.population.iterrows()
if quiet:
with ThreadPoolExecutor(max_workers=max_workers) as executor:
creature_result_list = executor.map(sim, iterable)
else:
population_size = self.population.size
creature_result_list = thread_map(sim,
iterable,
total=population_size,
position=1,
desc='Simulating Population',
max_workers=max_workers)
self.datasets.results = pd.concat(creature_result_list)
def process(files, output):
print('Total files: {}'.format(len(files)))
links = []
print('Extracting links from files...')
for filename in files:
name_file = path.basename(filename)
realname = name_file.replace('.txt', '').replace('_', ' ')
alias = make_alias(realname)
ifile = open(filename, 'r')
reader = csv.reader(ifile, delimiter=' ')
for row in reader:
entry = Link(
row[0],
row[1],
row[2],
row[3],
row[4],
row[5],
row[6],
row[7],
row[8],
realname,
alias,
)
links.append(entry)
shuffle(links)
return thread_map(retrieve, links, [output] * len(links), max_workers=128)
def num_exposures_needed(runs, metrics=default_metrics):
"""
Generate the approximate number of exposures needed for a low-enough
reconstruction error when choosing with a given strategy.
"""
data_gen = DataGenerator(
raw_path=DATA_DIR / "dngs",
out_path=DATA_DIR / "correct_exposures",
compute_scores=False,
)
exp = data_gen.exposures
exposures = list(flatten((exp[exp < 0], exp[exp > 0])))
all_image_names = data_gen.image_names
stats_fun = partial(compute_stats,
data_gen=data_gen,
exposures=exposures,
metrics=metrics)
err_list = flatten(thread_map(
stats_fun,
sample(all_image_names, k=runs),
))
df = pd.DataFrame.from_records(err_list, index="image_name")
return df
def check_images(data_dir: str) -> Tuple[List[str], List[str]]:
'''Iterate through a directory of images and find corrupt images
Args:
data_dir: Path to the directory containing the images
Returns:
(healthy_images, corrupt_images)
'''
dataset = LightlyDataset(input_dir=data_dir)
filenames = dataset.get_filenames()
def _is_corrupt(filename):
try:
image = Image.open(os.path.join(data_dir, filename))
image.load()
except (IOError, UnidentifiedImageError):
return True
else:
return False
mapped = concurrent.thread_map(_is_corrupt,
filenames,
chunksize=min(32, len(filenames)))
healthy_images = [
f for f, is_corrupt in zip(filenames, mapped) if not is_corrupt
]
corrupt_images = [
f for f, is_corrupt in zip(filenames, mapped) if is_corrupt
]
return healthy_images, corrupt_images
def enhance_recipe_1m_data():
output_file = Path('comment_scraping/data/recipe1m_with_reviews.json')
if output_file.exists():
with output_file.open('r') as f:
data_with_reviews = json.load(f)
else:
data_with_reviews = []
with open('../data/recipe1m.json') as file:
data = json.load(file)
data = filter_recipe1m_data_after_url(data)
processed_ids = {elem['id'] for elem in data_with_reviews}
data = [elem for elem in data if elem['id'] not in processed_ids]
print(len(data))
print("loaded recipe1m data")
chunksize = 2000
chunked_data = [data[x:x + chunksize] for x in range(0, len(data), chunksize)]
for chunk in tqdm(chunked_data, desc='Chunks'):
chunk_reviews = thread_map(enhance_recipe, chunk, max_workers=1000, total=len(chunk), desc='Processing Chunk')
chunk_reviews = [review for review in chunk_reviews if review]
data_with_reviews.extend(chunk_reviews)
with output_file.open('w') as f:
json.dump(data_with_reviews, f)
print("Finished scraping comments.")
def fetch(self):
submodules_paths = self.repo.listall_submodules()
diff_to_tree = self.revision_commit.tree.diff_to_tree()
files_to_blame = [p.delta.new_file.path for p in diff_to_tree
if not p.delta.is_binary and p.delta.new_file.path not in submodules_paths]
results = thread_map(self.blame_file, files_to_blame)
return [rec for val in results for rec in val]
def search_aio(keywords, keywords_file, api_key, max_workers=3, ret=0, keep_cache=False, case_sensitive=False):
# new entrance and save memory
# fetch paper details
logging.info("searching from NCBI PMC.......")
key_encoded = quote(keywords)
paper_links = search_links(key_encoded, ret)
try:
if ret == 0:
result = thread_map(search_aio_sub, [(x, keywords_file, api_key, keep_cache, case_sensitive)
for x in paper_links], max_workers=max_workers)
else:
result = thread_map(search_aio_sub, [(x, keywords_file, api_key, keep_cache, case_sensitive)
for x in paper_links[:ret]], max_workers=max_workers)
return list(filter(lambda x: x is not None, result))
except Exception as e:
logging.exception("search exception (big one)")
def fetch_products_threaded(category, page_size, max_workers=20, dry_run=False):
n_prods = get_number_of_products(category)
n_pages = get_number_of_pages(n_prods, page_size)
fetch_func = fetch_func_factory(category, page_size)
page_range = [1] if dry_run else range(1, n_pages + 1)
res = thread_map(fetch_func, page_range, max_workers=max_workers)
return [p for r in res for p in r]
def get_daily_prices(
api_key: str,
base_url: str,
historical: Optional[pd.DataFrame] = None) -> pd.DataFrame:
if historical is not None:
price_func = partial(_get_raw_prices, api_key=api_key)
df = pd.concat(
thread_map(price_func,
historical.symbol.unique(),
desc="get symbol prices."))
return df
def parse(self, sources: List[str], aux: Dict[str, DataFrame], **parse_opts):
props: Dict[str, str] = parse_opts["properties"]
data = aux["knowledge_graph"].merge(aux["metadata"])[["key", "wikidata"]].set_index("key")
# Load wikidata using parallel processing
map_iter = data.wikidata.iteritems()
map_func = partial(WikidataPipeline._process_item, props)
records = concurrent.thread_map(map_func, map_iter, total=len(data))
# Return all records in DataFrame form
return DataFrame.from_records(records)
def get_images(self):
with self.session as s:
print("Scraping Image Urls...")
self.get_image_urls(s, self.url, page_count=True, page_title=True)
print(f"Found Total {self.total_pages} Pages")
print("Scraping On Page: ", 1)
if self.total_pages > 1:
for i in range(2, self.total_pages + 1):
print("Scraping On Page: ", i)
self.get_image_urls(s, f"{self.url}&page={i}")
time.sleep(1.5)
print(f"Found {len(self.image_urls)} Images")
if not Path.exists(self.file_path):
Path.mkdir(self.file_path)
thread_map(self._download_images, range(0, len(self.image_urls)), max_workers=2)
def update(self, context, target, *synth_sources):
"""
Retrieve and store metadata for each the DOIs stored in the OutputDOIs resource.
"""
with self:
super(DOIMetadata, self).update(context, target, *synth_sources)
self._handled = set()
self._added = set()
self._errors = {}
doi_cache = OutputDOIs(context)
with doi_cache:
found_dois = list(set(doi_cache.data.values()))
workers = context.config.resource_opt('doimetadata.threads', 20)
with self, ThreadPoolExecutor(workers) as executor:
thread_map(lambda x: self._get_metadata(self, x),
found_dois,
desc='Crossref',
unit=' dois',
leave=False,
position=1)
def _get_origin_metadata_locally_or_by_urls(
data_files: List[Union[Path, Url]],
max_workers=64,
use_auth_token: Optional[Union[bool, str]] = None) -> Tuple[str]:
return thread_map(
partial(_get_single_origin_metadata_locally_or_by_urls,
use_auth_token=use_auth_token),
data_files,
max_workers=max_workers,
tqdm_class=logging.tqdm,
desc="Resolving data files",
disable=len(data_files) <= 16 or not logging.is_progress_bar_enabled(),
)
def __init__(self, data_path: str, shuffle=False, train=True, max_len=500):
super().__init__()
logger.info("Loading data from {}".format(data_path))
gc.disable()
files = glob.glob(f"{data_path}*")
logger.info("File list {}".format(", ".join(files)))
dfs = thread_map(feather.read_feather, files, max_workers=16)
self.data_df = pd.concat(dfs)
gc.enable()
logger.info(
f"Loaded dataset from {data_path} with {len(self.data_df)} samples"
)
self.max_len = max_len
def parse_dataframes(self, dataframes: List[DataFrame],
aux: Dict[str, DataFrame], **parse_opts):
# Get all the weather stations with data up until 2020
stations_url = "https://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-inventory.txt"
stations = read_csv(
stations_url,
sep=r"\s+",
names=("id", "lat", "lon", "measurement", "year_start",
"year_end"),
)
stations = stations[stations.year_end == 2020][[
"id", "lat", "lon", "measurement"
]]
# Filter stations that at least provide max and min temps
measurements = ["TMIN", "TMAX"]
stations = stations.groupby(["id", "lat",
"lon"]).agg(lambda x: "|".join(x))
stations = stations[stations.measurement.apply(
lambda x: all(m in x for m in measurements))]
stations = stations.reset_index()
# Get all the POI from metadata and go through each key
metadata = dataframes[0][["key", "latitude", "longitude"]].dropna()
# Convert all coordinates to radians
stations["lat"] = stations.lat.apply(math.radians)
stations["lon"] = stations.lon.apply(math.radians)
metadata["lat"] = metadata.latitude.apply(math.radians)
metadata["lon"] = metadata.longitude.apply(math.radians)
# Use a cache to avoid having to query the same station multiple times
station_cache: Dict[str, DataFrame] = {}
# Make sure the stations and the cache are sent to each function call
map_func = partial(WeatherPipeline.station_records, station_cache,
stations)
# We don't care about the index while iterating over each metadata item
map_iter = [record for _, record in metadata.iterrows()]
# Shuffle the iterables to try to make better use of the caching
shuffle(map_iter)
# Bottleneck is network so we can use lots of threads in parallel
records = concurrent.thread_map(map_func,
map_iter,
total=len(metadata))
return concat(records)
def _get_origin_metadata_locally_or_by_urls(
data_files: List[Union[Path, Url]],
max_workers=64,
use_auth_token: Optional[Union[bool, str]] = None) -> Tuple[str]:
return thread_map(
partial(_get_single_origin_metadata_locally_or_by_urls,
use_auth_token=use_auth_token),
data_files,
max_workers=max_workers,
tqdm_class=tqdm,
desc="Resolving data files",
disable=len(data_files) <= 16
or logging.get_verbosity() == logging.NOTSET,
)
def main(args):
# Phase 0 - copy all urmp wavs to corresponding folders
CWD = Path(hydra.utils.get_original_cwd())
os.chdir(CWD)
if args.urmp is not None:
urmp_path = CWD / args.urmp.source_folder
urmp_audio_files = list(
urmp_path.glob(f'./*/{args.urmp.mono_regex}*.wav'))
target_dir = CWD / 'data_tmp'
target_dir.mkdir(exist_ok=True)
create_mono_urmp_partial = partial(
create_mono_urmp,
audio_files=urmp_audio_files,
target_dir=target_dir,
instruments_dict=args.urmp.instruments)
thread_map(create_mono_urmp_partial,
list(args.urmp.instruments.keys()))
# create hd5 datasets for each sample rate to be used later during training
data_processor = hydra.utils.instantiate(args.data_processor)
loudness_metrics = LoudnessMetrics(args.srs)
data_processor.run_on_dirs(CWD / args.input_dir, CWD / args.output_dir,
loudness_metrics)
def execute_in_threads(func: Callable, sequence: Generator,
max_sequence_length: int, **kwargs) -> List:
"""Executing 'func' in ThreadPoolExecutor for each
set of arguments received from 'sequence' generator
:param func: Callable to be executed in ThreadPoolExecutor.
:param sequence: A generator yielding sets of arguments
that are passed to 'func' on each call.
:param max_sequence_length: Limits maximum number of 'func' calls in
order to avoid possible infinite generator to block script execution.
It is also passed as 'total' parameter to 'tqdm' progress bar.
"""
results = thread_map(func,
islice(sequence, max_sequence_length),
total=max_sequence_length,
**kwargs)
return list(results)
def main():
wiki = MediaWiki(url=URL)
gen_entry_lam = lambda x: gen_entry(wiki, x)
print("Retriving all titles")
titles = getAllTitles(wiki)
titles.sort()
print("Retriving summaries for titles")
entries = thread_map(gen_entry_lam, titles, max_workers=MAX_THREADS)
entries = list(filter(None, entries))
print("Creating file lines")
file_lines = dic_creator.create_file_text_lines(entries)
print("Writing to file")
with open("content.html", "w") as file:
file.writelines(file_lines)
def request_etags(
urls: List[str],
use_auth_token: Optional[Union[str, bool]] = None,
max_workers=64,
tqdm_kwargs: Optional[dict] = None,
) -> List[Optional[str]]:
tqdm_kwargs = tqdm_kwargs if tqdm_kwargs is not None else {}
tqdm_kwargs["desc"] = tqdm_kwargs.get("desc", "Get ETags")
tqdm_kwargs["disable"] = tqdm_kwargs.get(
"disable",
len(urls) <= 16 or logging.get_verbosity() == logging.NOTSET)
return thread_map(
partial(request_etag, use_auth_token=use_auth_token),
urls,
max_workers=max_workers,
tqdm_class=tqdm,
**tqdm_kwargs,
)
def download(
base_url: str = hdrplus_bucket_base,
out: Union[str, Path] = default_download_dir,
image_names: Optional[List[str]] = None,
max_threads=10,
) -> List[Optional[Path]]:
if image_names is None:
image_names = list(get_image_names(base_url))
out = coerce_path(out)
if not out.exists():
out.mkdir(parents=True)
downloaded_files = thread_map(
partial(download_file, out_path=out),
image_names,
max_workers=max_threads,
chunksize=min(50, len(image_names)),
)
return downloaded_files
def convert(args):
def ffmpeg_convert(fname):
outfile = fname.replace('.m4a',
'.wav').replace('voxceleb2', 'voxceleb2_wav')
if outfile in out_files:
return 0
outdir = os.path.dirname(outfile)
os.makedirs(outdir, exist_ok=True)
out = subprocess.call(
'ffmpeg -v quiet -y -i %s -ac 1 -vn -acodec pcm_s16le -ar 16000 %s'
% (fname, outfile))
# if out != 0:
# raise ValueError('Conversion failed %s'%fname)
return out
files = glob.glob('%s/voxceleb2/*/*/*.m4a' % args.save_path)
files.sort()
os.makedirs(os.path.join(args.save_path, 'voxceleb2_wav'), exist_ok=True)
out_files = glob.glob('%s/voxceleb2_wav/*/*/*.wav' % args.save_path)
print('Converting files from AAC to WAV')
out = thread_map(ffmpeg_convert, files)
def process_downloads(self, sites):
"""
Method to download and process files
:param sites: List of file to download and process
:type sites: list
:return:
:rtype:
"""
start_time = time.time()
thread_map(self.download_site, sites, desc="Downloading files")
if self.do_process:
thread_map(
self.file_to_queue,
self.file_queue.getall(),
desc="Processing downloaded files",
)
chunks = []
for batch in iter(lambda: list(islice(self.queue, 10000)), []):
chunks.append(batch)
thread_map(self._db_bulk_writer,
chunks,
desc="Transferring queue to database")
# checking if last-modified was in the response headers and not set to default
if "01-01-1970" != self.last_modified.strftime("%d-%m-%Y"):
self.setColUpdate(self.feed_type.lower(), self.last_modified)
self.logger.info("Duration: {}".format(
timedelta(seconds=time.time() - start_time)))
sleep(interval)
# NB: may not clear instances with higher `position` upon completion
# since this worker may not know about other bars #796
if write_safe:
# we think we know about other bars (currently only py3 threading)
if n == 6:
tqdm.write("n == 6 completed")
return n + 1
if __name__ == '__main__':
freeze_support() # for Windows support
L = list(range(NUM_SUBITERS))[::-1]
print("Simple thread mapping")
thread_map(partial(progresser, write_safe=not PY2), L, max_workers=4)
print("Simple process mapping")
process_map(partial(progresser), L, max_workers=4)
print("Manual nesting")
for i in trange(16, desc="1"):
for _ in trange(16, desc="2 @ %d" % i, leave=i % 2):
sleep(0.01)
print("Multi-processing")
tqdm.set_lock(RLock())
p = Pool(initializer=tqdm.set_lock, initargs=(tqdm.get_lock(), ))
p.map(partial(progresser, progress=True), L)
print("Multi-threading")
