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initial commit

This commit is contained in:
Michael Buehlmann 2024-04-14 17:22:33 -04:00
commit 3de616f198
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__pycache__
.venv

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cosmicweb_music/cosmICweb.py Executable file
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import os
import sys
import tempfile
import subprocess
import click
import requests
from collections import namedtuple
from datetime import datetime
import logging
# Logger
logger = logging.getLogger()
handler = logging.StreamHandler()
formatter = logging.Formatter(
"%(asctime)s %(levelname)-8s %(message)s", "%Y-%m-%d %H:%M:%S"
)
handler.setFormatter(formatter)
logger.addHandler(handler)
logger.setLevel("INFO")
# Some constants
DEFAULT_URL = "https://cosmicweb.astro.univie.ac.at"
EDITOR = os.environ.get("EDITOR", "vim")
# Types
Ellipsoid = namedtuple(
"Ellipsoid", ["center", "shape", "traceback_radius", "radius_definition"]
)
DownloadConfig = namedtuple(
"DownloadConfig",
[
"simulation_name",
"halo_names",
"halo_urls",
"traceback_radius",
"api_token",
"MUSIC",
"settings",
"accessed_at",
],
)
def query_yes_no(question, default="yes"):
"""Ask a yes/no question via raw_input() and return their answer.
"question" is a string that is presented to the user.
"default" is the presumed answer if the user just hits <Enter>.
It must be "yes" (the default), "no" or None (meaning
an answer is required of the user).
The "answer" return value is True for "yes" or False for "no".
"""
valid = {"yes": True, "y": True, "ye": True, "no": False, "n": False}
if default is None:
prompt = " [y/n] "
elif default == "yes":
prompt = " [Y/n] "
elif default == "no":
prompt = " [y/N] "
else:
raise ValueError("invalid default answer: '%s'" % default)
while True:
sys.stdout.write(question + prompt)
choice = input().lower()
if default is not None and choice == "":
return valid[default]
elif choice in valid:
return valid[choice]
else:
sys.stdout.write("Please respond with 'yes' or 'no' " "(or 'y' or 'n').\n")
# Routines
def fetch_ellipsoids(url, api_token, attempts):
for i in range(attempts):
try:
r = requests.get(url, headers={"Authorization": "Token " + api_token})
# This will raise an error if not successful
r.raise_for_status()
except requests.exceptions.HTTPError as e:
logging.warning("Failed fetching (attempt {}/{}) ...".format(i, attempts))
else:
content = r.json()
return [
Ellipsoid(
center=e["ellips_center"],
shape=e["ellips_matrix"],
radius_definition=e["radius_definition"],
traceback_radius=e["traceback_radius"],
)
for e in content
]
logging.error("Unable to download ellipsoids from {}".format(url))
return None
def fetch_ellipsoid(url, api_token, traceback_radius, attempts=3):
ellipsoids = fetch_ellipsoids(url, api_token, attempts)
if ellipsoids is not None:
return next(
(e for e in ellipsoids if e.traceback_radius == traceback_radius), None
)
return None
def fetch_downloadstore(cosmicweb_url, target):
try:
r = requests.get(cosmicweb_url + "/api/music/store/" + target)
# This will raise an error if not successful
r.raise_for_status()
except requests.exceptions.HTTPError as e:
logging.critical("Failed downloading from cosmICweb.")
sys.exit("Error")
content = r.json()
sim = content["simulation"]
halo_urls = [
"{url}/simulation/{sid}/halo/{hid}".format(
url=sim["api_url"], sid=sim["api_id"], hid=h
)
for h in content["halos"]
]
return DownloadConfig(
simulation_name=sim["name"],
halo_names=["halo_{}".format(h) for h in content["halos"]],
halo_urls=halo_urls,
traceback_radius=content["traceback_radius"],
api_token=sim["api_token"],
MUSIC=sim["ics"],
settings=content["configuration"],
accessed_at=datetime.now(),
)
def fetch_publication(cosmicweb_url, publication_name, traceback_radius):
try:
r = requests.get(cosmicweb_url + "/api/publications/" + publication_name)
# This will raise an error if not successful
r.raise_for_status()
except requests.exceptions.HTTPError as e:
logging.critical("Failed downloading from cosmICweb.")
sys.exit("Error")
content = r.json()
sim = content["simulation"]
halo_names = [h["name"] for h in content["halos"]]
halo_urls = [
"{url}/simulation/{sid}/halo/{hid}".format(
url=sim["api_url"], sid=sim["api_id"], hid=h["id"]
)
for h in content["halos"]
]
return DownloadConfig(
simulation_name=sim["name"],
halo_names=halo_names,
halo_urls=halo_urls,
traceback_radius=traceback_radius,
api_token=sim["api_token"],
MUSIC=sim["ics"],
settings={},
accessed_at=datetime.now(),
)
def edit_template(template):
with tempfile.NamedTemporaryFile(suffix=".tmp", mode="r+") as tf:
tf.write(template)
tf.flush()
# Call the editor. backupcopy=yes prevents vim from creating copy and rename
subprocess.call([EDITOR, "+set backupcopy=yes", tf.name])
tf.seek(0)
template = tf.read()
return template
def music_config_to_template(music_config, configuration):
# TODO: apply configuraton, add header
return (
"[SETUP]\n" + music_config["setup"] + "\n\n<ELLIPSOID_TEMPLATE>\n\n"
"[COSMOLOGY]\n" + music_config["cosmology"] + "\n\n"
"[RANDOM]\n" + music_config["random"] + "\n\n"
"[POISSON]\n" + music_config["poisson"]
)
def compose_template(template, ellipsoid):
# TODO: add ellipsoid header (rtb, halo_name, etc)
shape_0 = ", ".join("{:13.6e}".format(e) for e in ellipsoid.shape[0])
shape_1 = ", ".join("{:13.6e}".format(e) for e in ellipsoid.shape[1])
shape_2 = ", ".join("{:13.6e}".format(e) for e in ellipsoid.shape[2])
center = ", ".join("{:13.6e}".format(x) for x in ellipsoid.center)
ellipsoid_lines = (
"region = ellipsoid\n"
"region_ellipsoid_matrix[0] = {s0}\n"
"region_ellipsoid_matrix[1] = {s1}\n"
"region_ellipsoid_matrix[2] = {s2}\n"
"region_ellipsoid_center = {c}\n".format(
s0=shape_0, s1=shape_1, s2=shape_2, c=center
)
)
return template.replace("<ELLIPSOID_TEMPLATE>", ellipsoid_lines)
def write_music_file(output_file, music_config):
dirname = os.path.dirname(output_file)
if not os.path.exists(dirname):
logging.debug("Creating directory {}".format(dirname))
os.makedirs(dirname)
with open(output_file, "w") as f:
f.write(music_config)
def call_music():
pass
def process_config(config, args):
ellipsoids = []
for halo_name, url in zip(config.halo_names, config.halo_urls):
logging.info("Fetching ellipsoids from halo " + halo_name)
ellipsoids.append(
fetch_ellipsoid(
url + "/ellipsoids",
config.api_token,
config.traceback_radius,
args.attempts,
)
)
# Edit template
logging.info("Creating MUSIC template")
music_template = music_config_to_template(config.MUSIC, config.settings)
if query_yes_no(
"Do you want to edit the MUSIC template before creating the IC files?\n"
"(changing zstart, levelmin, levelmax, etc.)",
default="no",
):
logging.debug("Editing MUSIC template")
music_template = edit_template(music_template)
logging.debug("Finished editing MUSIC template")
# Store template to file
for halo_name, ellipsoid in zip(config.halo_names, ellipsoids):
if ellipsoid is None:
logging.warning(
"Ellipsoid for halo {} not available, skipping".format(halo_name)
)
continue
logging.info("Composing MUSIC configuration file for halo {}".format(halo_name))
music_config = compose_template(music_template, ellipsoid)
if args.create_subdirs and len(ellipsoids) > 1:
output_file = os.path.join(args.output_path, str(halo_name), "ics.cfg")
else:
output_file = os.path.join(
args.output_path, "/ics_{}.cfg".format(halo_name)
)
logging.info(
"Storing MUSIC configuration file for halo {} in {}".format(
halo_name, output_file
)
)
write_music_file(output_file, music_config)
# TODO: Execute MUSIC?
def downloadstore_mode(args, target: str):
logging.info("Fetching download configuration from the cosmICweb server")
config = fetch_downloadstore(args.cosmicweb_url, target)
if args.output_path == "./":
args.output_path = "./cosmICweb-zooms-{}".format(config.simulation_name)
logging.debug("Output directory set to " + args.output_path)
logging.info("Download configuration successfully fetched")
process_config(config, args)
def publication_mode(args, publication_name: str, traceback_radius: int):
logging.info(
"Fetching publication " + args.publication_name + " from the cosmICweb server"
)
config = fetch_publication(args.cosmicweb_url, publication_name, traceback_radius)
args.output_path = os.path.join(args.output_path, publication_name)
logging.debug("Output directory set to " + args.output_path)
logging.info("Publication successfully fetched")
process_config(config, args)
def dir_path(p):
if os.path.isdir(p):
return p
else:
raise NotADirectoryError(p)
@click.group()
@click.option(
"--url", default=DEFAULT_URL, help="overwrite URL of the cosmICweb server"
)
@click.option(
"--output-path",
type=dir_path,
default="./",
help="Download target for IC files. If downloading publication, will create a subfolder with the name of the publication",
)
@click.option("--common-directory", is_flag=True)
@click.option(
"--attempts", type=int, default=3, help="number of attempts to download ellipsoids"
)
@click.option("--verbose", is_flag=True)
@click.pass_context
def cli(ctx, url, output_path, common_directory, attempts, verbose):
if verbose:
logger.setLevel("DEBUG")
ctx.obj = {
"url": url,
"output_path": output_path,
"common_directory": common_directory,
"attempts": attempts,
}
@cli.command(help="Download ICs using a target UUID generated on cosmICweb")
@click.argument("target")
@click.pass_context
def get(ctx, target):
args = ctx.obj
downloadstore_mode(args, target)
@cli.command(help="Download published ICs using the publication name")
@click.argument("publication_name")
@click.option("--traceback_radius", type=click.Choice([1, 2, 4, 10]), default=2)
@click.pass_context
def publication(ctx, publication_name, traceback_radius):
args = ctx.obj
publication_mode(args, publication_name, traceback_radius)
if __name__ == "__main__":
cli()
# if __name__ == "__main__":
# parser = argparse.ArgumentParser()
# parser.add_argument(
# "--url",
# dest="cosmicweb_url",
# default=DEFAULT_URL,
# help="overwrite URL of the cosmicweb server",
# )
# parser.add_argument(
# "--output-path",
# type=dir_path,
# default="./",
# help="Download target for IC files. If downloading publication, will create a subfolder with the "
# "name of the publication",
# )
# parser.add_argument(
# "--common-directory", dest="create_subdirs", action="store_false"
# )
# parser.add_argument(
# "--attempts",
# type=int,
# default=3,
# help="number of attempts to download ellipsoids",
# )
# parser.add_argument("--verbose", action="store_true")
# subparsers = parser.add_subparsers(dest="mode")
# # Downloading from publications
# publication_parser = subparsers.add_parser(
# "publication", help="download publications"
# )
# publication_parser.add_argument("publication_name", help="name of the publication")
# publication_parser.add_argument(
# "--traceback_radius", type=int, choices=[1, 2, 4, 10], default=2, help=""
# )
# # Downloading from download object
# download_parser = subparsers.add_parser("get")
# download_parser.add_argument("target")
# args = parser.parse_args()
# if args.verbose:
# logger.setLevel("DEBUG")
# if args.mode == "get":
# downloadstore_mode(args)
# elif args.mode == "publication":
# publication_mode(args)
# else:
# raise NotImplementedError("unknown subparser")

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19
pyproject.toml Normal file
View file

@ -0,0 +1,19 @@
[tool.poetry]
name = "cosmicweb-music"
version = "0.1.0"
description = ""
authors = ["Michael Buehlmann <buehlmann.michi@gmail.com>"]
readme = "README.md"
[tool.poetry.scripts]
cosmicweb-music = "cosmicweb_music.cosmICweb:cli"
[tool.poetry.dependencies]
python = "^3.9"
click = "^8.1.7"
requests = "^2.31.0"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"