From cd17f4117c3b16668d66532d72e86351a4ebb6ce Mon Sep 17 00:00:00 2001
From: Fabian Schindler <fabian.schindler.strauss@gmail.com>
Date: Tue, 25 Aug 2020 11:00:06 +0200
Subject: [PATCH] Adding timer class, cleanup
---
preprocessor/preprocessor/preprocess.py | 126 +++++++++++++++++-------
1 file changed, 89 insertions(+), 37 deletions(-)
diff --git a/preprocessor/preprocessor/preprocess.py b/preprocessor/preprocessor/preprocess.py
index 29ecdb56..2c167570 100644
--- a/preprocessor/preprocessor/preprocess.py
+++ b/preprocessor/preprocessor/preprocess.py
@@ -8,6 +8,7 @@ import shutil
from typing import List
from contextlib import contextmanager
from pprint import pformat
+from time import time
from .transfer import get_downloader, get_uploader
from .archive import unpack_files
@@ -45,15 +46,6 @@ def custom_preprocessor(source_dir, target_dir, path, args=None, kwargs=None):
func(source_dir, target_dir, *(args or []), **(kwargs or {}))
-def georeference(source_dir: os.PathLike, target_dir: os.PathLike, type: str, **options: dict):
- """ Apply georeferencing to the files in source_dir to create georeferenced
- image files in target_dir.
- Georeferencing type specifies what geoereferencing shall be applied. Options
- are 'GCP', 'RPC', 'world', ...
- """
- # TODO: implement
- pass
-
def custom_postprocessor(source_dir, target_dir, path, args=None, kwargs=None):
""" Preprocessing step for a custom preprocessing.
"""
@@ -77,6 +69,25 @@ def flatten(l):
return [item for sublist in l for item in sublist]
+class Timer:
+ """ Helper timer class to allow logging of timing values
+ """
+ def __init__(self):
+ self.start = None
+ self.end = None
+
+ def __enter__(self):
+ self.start = time()
+ return self
+
+ def __exit__(self, *args, **kwargs):
+ self.end = time()
+
+ @property
+ def elapsed(self):
+ return (self.end if self.end is not None else time()) - self.start
+
+
# -----------------------------------------------------------------------------
@contextmanager
@@ -86,8 +97,7 @@ def workdir(config, use_dir: os.PathLike=None):
if use_dir:
os.chdir(use_dir)
yield use_dir
-
- if config.get('keep_temp'):
+ elif config.get('keep_temp'):
dirname = mkdtemp(prefix=prefix, dir=workdir)
os.chdir(dirname)
yield dirname
@@ -100,7 +110,7 @@ def workdir(config, use_dir: os.PathLike=None):
def preprocess_file(config: dict, file_path: os.PathLike, use_dir: os.PathLike=None):
""" Runs the preprocessing of a single file.
"""
- with workdir(config, use_dir) as dirname:
+ with workdir(config, use_dir) as dirname, Timer() as preprocess_timer:
logger.info('Preprocessing %s in %s' % (file_path, dirname))
# check if we can reuse a previous download
@@ -112,13 +122,21 @@ def preprocess_file(config: dict, file_path: os.PathLike, use_dir: os.PathLike=N
downloader = get_downloader(
source_config['type'], source_config.get('args'), source_config.get('kwargs')
)
- source_archive_path = downloader.download(file_path, 'download')
+
+ with Timer() as download_timer:
+ source_archive_path = downloader.download(file_path, 'download')
+
+ logger.info(
+ 'Downloaded file %s in %f seconds'
+ % (file_path, download_timer.elapsed)
+ )
+
else:
source_archive_path = os.path.join('download', os.path.basename(file_path))
logger.info('Download dir already exists, skipping...')
# fetch the metadata XML file from the downloaded archive
- metadata_files = unpack_files(source_archive_path, 'unpack', glob=config['metadata_glob'])
+ metadata_files = unpack_files(source_archive_path, 'extra', glob=config['metadata_glob'])
# open the XML to retrieve the product type and level
product_type, product_level = extract_product_type_and_level(metadata_files, config)
@@ -135,30 +153,37 @@ def preprocess_file(config: dict, file_path: os.PathLike, use_dir: os.PathLike=N
os.mkdir('unpack')
logger.info('Unpacking original files...')
# select and unpack files according to configuration
- data_files = flatten([
- unpack_files(
- source_archive_path,
- 'unpack',
- glob=glob,
- recursive=preprocess_config.get('nested', False),
- )
- for glob in preprocess_config['data_file_globs']
- ])
- metadata_files = flatten([
- unpack_files(
- source_archive_path,
- 'unpack',
- glob=glob,
- recursive=preprocess_config.get('nested', False),
- )
- for glob in preprocess_config['additional_file_globs']
- ])
- logger.info('Unpacked files: %s' % ', '.join(metadata_files, data_files))
+ with Timer() as unpack_timer:
+ data_files = flatten([
+ unpack_files(
+ source_archive_path,
+ 'unpack',
+ glob=glob,
+ recursive=preprocess_config.get('nested', False),
+ )
+ for glob in preprocess_config['data_file_globs']
+ ])
+ metadata_files = flatten([
+ unpack_files(
+ source_archive_path,
+ 'unpack',
+ glob=glob,
+ recursive=preprocess_config.get('nested', False),
+ )
+ for glob in preprocess_config.get('additional_file_globs', [])
+ ])
+
+ logger.info(
+ 'Unpacked files: %s in %f seconds'
+ % (', '.join(metadata_files + data_files), unpack_timer.elapsed)
+ )
else:
logger.info('Unpack dir already exists, skipping...')
previous_step = 'unpack'
+
+ force_refresh = False
# make processing steps
for step in ['custom_preprocessor', 'subdatasets', 'georeference', 'calc', 'stack_bands', 'output', 'custom_postprocessor']:
step_config = preprocess_config.get(step)
@@ -167,14 +192,26 @@ def preprocess_file(config: dict, file_path: os.PathLike, use_dir: os.PathLike=N
continue
# run the step if it was not already run
- if not os.path.isdir(step):
+ if not os.path.isdir(step) or force_refresh:
+ if os.path.isdir(step):
+ logger.info('Forcing refresh of existing directory %s' % step)
+ shutil.rmtree(step)
+
logger.info('Running preprocessing step %s' % step)
os.mkdir(step)
preprpocessor = STEP_FUNCTIONS[step]
- preprpocessor(previous_step, step, **step_config)
+
+ with Timer() as step_timer:
+ preprpocessor(previous_step, step, **step_config)
+
+ logger.info(
+ 'Finished preprocessing step %s after %f seconds.'
+ % (step, step_timer.elapsed)
+ )
else:
- logger.info('%s dir already exists, skipping...' % step)
+ logger.info('%s dir already exists, skipping step...' % step)
+ force_refresh = True
previous_step = step
@@ -197,4 +234,19 @@ def preprocess_file(config: dict, file_path: os.PathLike, use_dir: os.PathLike=N
]
# send all files in the upload directory to the target storage
- uploader.upload(upload_filenames, file_path)
+ logger.info(
+ 'Starting uploading of %d files to %s'
+ % (len(upload_filenames), file_path)
+ )
+ with Timer() as upload_timer:
+ uploader.upload(upload_filenames, file_path)
+
+ logger.info(
+ 'Finished uploading after %f seconds.'
+ % (upload_timer.elapsed)
+ )
+
+ logger.info(
+ 'Finished preprocessing of %s after %f seconds.'
+ % (file_path, preprocess_timer.elapsed)
+ )
--
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