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#!/usr/bin/env python
# Copyright (c) 2019, Anthony Latorre <tlatorre at uchicago>
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
# any later version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
# more details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <https://www.gnu.org/licenses/>.
"""
Script to combine the fit results from jobs submitted to the grid.
This script first runs zdab-cat on the zdab file to get the data cleaning words
and SNOMAN fitter results for every event in the file. It then adds any fit
results from the other files listed on the command line and prints the results
as YAML to stdout.
Example:
$ cat-grid-jobs ~/mc_atm_nu_no_osc_genie_010000_0.mcds ~/grid_job_results/*.txt > output.txt
"""
from __future__ import print_function, division
import yaml
try:
from yaml import CLoader as Loader, CDumper as Dumper
except ImportError:
from yaml import Loader, Dumper
import os
import sys
# Check that a given file can be accessed with the correct mode.
# Additionally check that `file` is not a directory, as on Windows
# directories pass the os.access check.
def _access_check(fn, mode):
return (os.path.exists(fn) and os.access(fn, mode) and not os.path.isdir(fn))
def which(cmd, mode=os.F_OK | os.X_OK, path=None):
"""Given a command, mode, and a PATH string, return the path which
conforms to the given mode on the PATH, or None if there is no such
file.
`mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result
of os.environ.get("PATH"), or can be overridden with a custom search
path.
"""
# If we're given a path with a directory part, look it up directly rather
# than referring to PATH directories. This includes checking relative to the
# current directory, e.g. ./script
if os.path.dirname(cmd):
if _access_check(cmd, mode):
return cmd
return None
if path is None:
path = os.environ.get("PATH", None)
if path is None:
try:
path = os.confstr("CS_PATH")
except (AttributeError, ValueError):
# os.confstr() or CS_PATH is not available
path = os.defpath
# bpo-35755: Don't use os.defpath if the PATH environment variable is
# set to an empty string
# PATH='' doesn't match, whereas PATH=':' looks in the current directory
if not path:
return None
path = path.split(os.pathsep)
if sys.platform == "win32":
# The current directory takes precedence on Windows.
curdir = os.curdir
if curdir not in path:
path.insert(0, curdir)
# PATHEXT is necessary to check on Windows.
pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
# See if the given file matches any of the expected path extensions.
# This will allow us to short circuit when given "python.exe".
# If it does match, only test that one, otherwise we have to try
# others.
if any(cmd.lower().endswith(ext.lower()) for ext in pathext):
files = [cmd]
else:
files = [cmd + ext for ext in pathext]
else:
# On other platforms you don't have things like PATHEXT to tell you
# what file suffixes are executable, so just pass on cmd as-is.
files = [cmd]
seen = set()
for dir in path:
normdir = os.path.normcase(dir)
if not normdir in seen:
seen.add(normdir)
for thefile in files:
name = os.path.join(dir, thefile)
if _access_check(name, mode):
return name
return None
# from https://stackoverflow.com/questions/287871/how-to-print-colored-text-in-terminal-in-python
class bcolors:
HEADER = '\033[95m'
OKBLUE = '\033[94m'
OKGREEN = '\033[92m'
WARNING = '\033[93m'
FAIL = '\033[91m'
ENDC = '\033[0m'
BOLD = '\033[1m'
UNDERLINE = '\033[4m'
def print_warning(msg):
print(bcolors.WARNING + msg + bcolors.ENDC,file=sys.stderr)
warned = False
def print_warning_once(msg):
global warned
if not warned:
print_warning(msg)
print("skipping further warnings")
warned = True
def print_fail(msg):
print(bcolors.FAIL + msg + bcolors.ENDC,file=sys.stderr)
if __name__ == '__main__':
import argparse
import matplotlib.pyplot as plt
import numpy as np
from subprocess import check_call
from os.path import join, split
import os
import sys
import h5py
import glob
parser = argparse.ArgumentParser("concatenate fit results from grid jobs into a single file")
parser.add_argument("zdab", help="zdab input file")
parser.add_argument("directory", help="directory with grid results")
parser.add_argument("-o", "--output", type=str, help="output filename", required=True)
args = parser.parse_args()
zdab_cat = which("zdab-cat")
if zdab_cat is None:
print("couldn't find zdab-cat in path!",file=sys.stderr)
sys.exit(1)
# First we get the full event list along with the data cleaning word, FTP
# position, FTK, and RSP energy from the original zdab and then add the fit
# results.
#
# Note: We send stderr to /dev/null since there can be a lot of warnings
# about PMT types and fit results
with open(os.devnull, 'w') as f:
check_call([zdab_cat,args.zdab,"-o",args.output],stderr=f)
total_events = 0
events_with_fit = 0
total_fits = 0
with h5py.File(args.output,"a") as fout:
total_events = fout['ev'].shape[0]
for filename in glob.glob(join(args.directory,'*.hdf5')):
head, tail = split(filename)
with h5py.File(filename) as f:
if 'git_sha1' not in f.attrs:
print_fail("No git sha1 found for %s. Skipping..." % tail)
continue
# Check to see if the git sha1 match
if fout.attrs['git_sha1'] != f.attrs['git_sha1']:
print_warning_once("git_sha1 is %s for current version but %s for %s" % (fout.attrs['git_sha1'],f.attrs['git_sha1'],tail))
# get fits which match up with the events
valid_fits = f['fits'][np.isin(f['fits'][:][['run','gtid']],fout['ev'][:][['run','gtid']])]
# Add the fit results
fout['fits'].resize((fout['fits'].shape[0]+valid_fits.shape[0],))
fout['fits'][-valid_fits.shape[0]:] = valid_fits
events_with_fit += len(np.unique(valid_fits[['run','gtid']]))
total_fits += len(np.unique(f['fits']['run','gtid']))
# Print out number of fit results that were added. Hopefully, this will
# make it easy to catch an error if, for example, this gets run with a
# mismatching zdab and fit results
print("added %i/%i fit results to a total of %i events" % (events_with_fit, total_fits, total_events),file=sys.stderr)
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