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Checking for missing files in parallel #224

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merged 2 commits into from
Sep 7, 2022
Merged

Checking for missing files in parallel #224

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9c7e4b6
Checking for missing miles in parallel
AllenDowney Sep 7, 2022
b5fd541
Adding pqdm to setup.cfg
AllenDowney Sep 7, 2022
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1 change: 1 addition & 0 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ install_requires =
openpyxl
pandas>1.2.0
pandas_path
pqdm
pydantic
python-dotenv
pytorch-lightning>=1.6.0
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24 changes: 19 additions & 5 deletions zamba/models/config.py
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Expand Up @@ -7,9 +7,11 @@
import appdirs
import ffmpeg
from loguru import logger
import numpy as np
import pandas as pd
from pydantic import BaseModel
from pydantic import DirectoryPath, FilePath, validator, root_validator
from pqdm.threads import pqdm
import torch
from tqdm import tqdm
import yaml
Expand Down Expand Up @@ -100,11 +102,23 @@ def check_files_exist_and_load(
# we can have multiple rows per file with labels so limit just to one row per file for these checks
files_df = df[["filepath"]].drop_duplicates()

# check data exists
logger.info(
f"Checking all {len(files_df):,} filepaths exist. Can take up to a minute for every couple thousand files."
)
exists = files_df["filepath"].path.exists()
# check for missing files
logger.info(f"Checking all {len(files_df):,} filepaths exist. Trying fast file checking...")

# try to check files in parallel
paths = files_df["filepath"].apply(Path)
exists = pqdm(paths, Path.exists, n_jobs=16)
exists = np.array(exists)

# if fast checking fails, fall back to slow checking
# if an I/O error is in `exists`, the array has dtype `object`
if exists.dtype != bool:
logger.info(
"Fast file checking failed. Running slower check, which can take 30 seconds per thousand files."
)
exists = files_df["filepath"].path.exists()

# select the missing files
invalid_files = files_df[~exists]

# if no files exist
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