initial commit
miili
3 years ago
commit
e984aa721d
@ -0,0 +1,138 @@
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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||||
# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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||||
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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||||
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||||
# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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||||
# SageMath parsed files
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*.sage.py
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|
||||
# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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||||
# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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@ -0,0 +1 @@
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pyrocko
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@ -0,0 +1,26 @@
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import setuptools
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setuptools.setup(
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name="idas-convert",
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version="0.0.1",
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author="Marius Paul Isken",
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author_email="isken@example.com",
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description="Convert iDAS TDMS data to anything",
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url="https://git.pyrocko.org/pyrocko/idas-tdms-converter",
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package_dir={
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'idas_convert': 'src'
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},
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packages=[
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'idas_convert',
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],
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entry_points={
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'console_scripts': [
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'idas_convert = idas_convert:main',
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]},
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classifiers=[
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"Programming Language :: Python :: 3",
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"Operating System :: OS Independent",
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],
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python_requires='>=3.6',
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)
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@ -0,0 +1,289 @@
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import time
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import logging
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import numpy as num
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import os
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import subprocess
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from pyrocko import io, trace
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from pyrocko.io.tdms_idas import detect as detect_tdms
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from pyrocko.util import tts
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from itertools import repeat
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from concurrent.futures import ThreadPoolExecutor
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger('idas_convert')
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op = os.path
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PADDING = .5
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NTHREADS = 8
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BATCH_SIZE = 1
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def detect_files(path):
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if op.isfile(path):
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return [path]
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return [op.join(root, f)
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for root, dirs, files in os.walk(path)
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for f in files]
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def ensure_staged_files(files, stage_bytes, waterlevel=None):
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nbytes = 0
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nbytes_unstaged = 0
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if waterlevel is None:
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waterlevel = stage_bytes / 2
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unstaged_files = []
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for fn in files:
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stats = os.stat(fn)
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size = stats.st_size
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nbytes += size
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if stats.st_blocks == 0:
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nbytes_unstaged += size
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unstaged_files.append(fn)
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if nbytes >= stage_bytes:
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break
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if nbytes_unstaged > waterlevel:
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logger.info('staging additional %d bytes', nbytes)
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for fn in unstaged_files:
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fn_tapes = fn.strip('/projects/ether/')
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logger.debug('staging file %s', fn_tapes)
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subprocess.call(
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args=['stage', '-D', '/archive_FO1/RAW', fn_tapes],
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check=True)
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logger.info('staginged %d bytes', nbytes)
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else:
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logger.info('staging waterlevel ok')
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def downsample_data(args):
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trace, deltat, tmin_limit = args
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trace.downsample_to(deltat)
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if tmin_limit \
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and tmin_limit > trace.tmin \
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and tmin_limit < trace.tmax:
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trace.chop(
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tmin=tmin_limit,
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tmax=trace.tmax,
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inplace=True)
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trace.ydata = trace.ydata.astype(num.int32)
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# tmean = (trace.tmax - trace.tmin) / 2
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# mean = num.mean(trace.ydata)
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# max = num.max(trace.ydata)
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# std = num.std(trace.ydata)
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return trace
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# return trace, tmean, mean, max, std
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def load_idas(fn):
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logger.info('loading %s', op.basename(fn))
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return io.load(fn, format='tdms_idas')
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def convert_tdsm(
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files, outpath,
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downsample_to=1./200, network='ID', record_length=4096,
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stage_ahead=None,
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nthreads=NTHREADS, batch_size=BATCH_SIZE):
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nfiles = len(files)
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tmin_limit = None
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trs_prev = []
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ifn = 0
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while files:
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t0 = time.time()
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trs_new = []
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this_files = []
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while files and len(this_files) < batch_size:
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fn = files.pop(0)
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ifn += 1
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stat = os.stat(fn)
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fn_wait = False
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if stat.st_blocks == 0:
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logger.warning('waiting for file %s', fn)
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fn_wait = time.time()
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while stat.st_blocks == 0:
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stat = os.stat(fn)
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time.sleep(1.)
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logger.warning('file %s available. Waited %.2f s',
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time.time() - fn_wait)
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with open(fn, 'rb') as f:
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if not detect_tdms(f.read(512)):
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logger.warning('not a tdms file %s', fn)
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continue
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this_files.append(fn)
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if stage_ahead:
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ensure_staged_files(files, stage_ahead, waterlevel=stage_ahead/2)
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with ThreadPoolExecutor(max_workers=len(this_files)) as executor:
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trs_loaded = list(executor.map(load_idas, this_files))
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tmins = []
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for trs in trs_loaded:
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if not trs:
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logger.warning('loaded empty traces')
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continue
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tmins.append(trs[0].tmin)
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trs_new.extend(trs)
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trs_latest = trs_loaded[num.argmax(tmins)]
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t_load = time.time() - t0
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if not trs_new:
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logger.error('empty input data')
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continue
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if trs_prev:
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deltat = trs_new[0].deltat
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prev_tmax = [tr.tmax for tr in trs_prev]
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if max(tmins) - min(prev_tmax) > 2*deltat:
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logger.warning('gap detected at %s', tts(min(prev_tmax)))
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trs_prev = []
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trs = sorted(trs_prev + trs_new, key=lambda tr: tr.full_id)
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trs_prev = []
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for tr in trs_latest:
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try:
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trs_prev.append(tr.chop(
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tmin=tr.tmax - PADDING,
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tmax=tr.tmax,
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inplace=False))
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except trace.NoData:
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pass
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t = time.time()
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trs = trace.degapper(trs)
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with ThreadPoolExecutor(max_workers=nthreads) as executor:
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trs_ds = list(executor.map(
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downsample_data,
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zip(trs,
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repeat(downsample_to),
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repeat(tmin_limit))))
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tmin_limit = max([tr.tmax + tr.deltat for tr in trs_ds])
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t_ds = time.time() - t
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for tr in trs_ds:
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tr.set_network(network)
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t = time.time()
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io.save(
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trs_ds, outpath,
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format='mseed',
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record_length=record_length,
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append=True)
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t_save = time.time() - t
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elapsed = time.time() - t0
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files_left = len(files)
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logger.info(
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'processed %d/%d files: in %.2f s '
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'(FIR: %.2f, IO: %.2f/%.2f, remaining %.2f s)',
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ifn, nfiles, elapsed, t_ds, t_load, t_save,
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elapsed * (files_left / batch_size))
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def main():
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import argparse
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def data_size(size):
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mag = dict(k=3, M=6, G=9, T=12, P=15)
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if size is None:
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return None
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size = size.strip()
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v = int(size.strip(''.join(mag.keys())))
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if not v:
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return None
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for suffix, m in mag.items():
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if size.endswith(suffix):
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return v*10**m
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raise ValueError('cannot interpret size %s' % size)
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parser = argparse.ArgumentParser(
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'Convert and downsample iDAS TDMS to MiniSeed for archiving')
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parser.add_argument(
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'paths', type=str, nargs='+',
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help='TDMS paths to convert.')
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parser.add_argument(
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'--downsample', type=int,
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default=200,
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help='Target sample rate for mseed. Default: %(default)s')
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parser.add_argument(
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'--network',
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default='ID', type=lambda s: str(s)[:2],
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help='Network code for MiniSeeds. Default: %(default)s')
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parser.add_argument(
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'--record_length', type=int,
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default=4096,
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help='MiniSeeds record length. Default: %(default)s')
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parser.add_argument(
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'--threads', type=int,
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default=NTHREADS,
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help='Number of threads for processing data. Default: %(default)s')
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parser.add_argument(
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'--batchsize', type=int,
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default=BATCH_SIZE,
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help='Number of parallel loaded TDMS files and processed at once.'
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' Default: %(default)s')
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parser.add_argument(
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'--outpath', type=str,
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default='%(tmin_year)s%(tmin_month)s%(tmin_day)s/%(network)s.%(station)s_%(tmin_year)s%(tmin_month)s%(tmin_day)s.mseed', # noqa
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help='Outfile in pyrocko.io.save format. Default: %(default)s')
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parser.add_argument(
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'--stage-ahead', type=data_size, default=None,
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help='Amount of data to stage before conversion in bytes. Suffix with'
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' M, G, T, P. e.g. 4T.')
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parser.add_argument(
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'--verbose', '-v', action='count',
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default=0,
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help='Verbosity, add mutliple to increase verbosity.')
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args = parser.parse_args()
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log_level = logging.INFO - args.verbose * 10
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log_level = log_level if log_level > logging.DEBUG else logging.DEBUG
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logging.basicConfig(level=log_level)
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paths = args.paths
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||||
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||||
if isinstance(paths, str):
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||||
paths = [paths]
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logger.info('detecting files...')
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||||
files = []
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||||
for path in paths:
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files.extend(detect_files(path))
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||||
logger.info('sorting %d files', len(files))
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files = sorted(files, key=lambda f: op.basename(f))
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convert_tdsm(
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files, outpath=args.outpath, downsample_to=1./args.downsample,
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||||
network=args.network, record_length=args.record_length,
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nthreads=args.threads, batch_size=args.batchsize)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
Loading…
Reference in New Issue