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import argparse
import logging
import os
import os.path as osp
import re
import sys
from textwrap import dedent
from extra_data import RunDirectory
from extra_data.components import identify_multimod_detectors
log = logging.getLogger(__name__)
def parse_number(number:str):
try:
return float(number)
except ValueError:
return int(number, 0)
def main(argv=None):
example = dedent("""
Example:
extra-data-make-virtual-cxi -o ./out_file.h5 --min-modules 15 \\
--fill-value data 0 --fill-value gain 1 /path/to/source/run
""")
ap = argparse.ArgumentParser(
'extra-data-make-virtual-cxi', epilog=example,
formatter_class=argparse.RawDescriptionHelpFormatter,
description='Write a virtual CXI file to access the detector data.'
)
ap.add_argument('run_dir', help="Path to an EuXFEL run directory")
# Specifying a proposal directory & a run number is the older interface.
# If the run_number argument is passed, run_dir is used as proposal.
ap.add_argument('run_number', nargs="?", help=argparse.SUPPRESS)
ap.add_argument(
'-o', '--output',
help="Filename or path for the CXI output file. "
"By default, it is written in the proposal's scratch directory."
)
ap.add_argument(
'--min-modules', type=int, default=None, metavar='N',
help='Include trains where at least N modules have data (default:'
' half+1 of all detector modules).'
)
ap.add_argument(
'--n-modules', type=int, default=None, metavar='N',
help='Number of detector modules in the experiment setup.'
' Should be used only for JUNGFRAU data.'
)
ap.add_argument(
'--fill-value', action='append', nargs=2, metavar=('DS', 'V'),
help='define fill value (V) for individual dataset (DS). Datasets are'
' "data", "gain" and "mask". (defaults: data: nan (proc, float32)'
' or 0 (raw, uint16); gain: 0; mask: 0xffffffff)'
)
ap.add_argument(
'--exc-suspect-trains', action='store_true',
help='Exclude suspect trains. This tries to avoid some issues with'
' incorrect train IDs in the data, but may mean less data is'
' available.'
)
args = ap.parse_args(argv)
out_file = args.output
fill_values = None
if args.fill_value:
fill_values = {ds: parse_number(value) for ds, value in args.fill_value}
logging.basicConfig(level=logging.INFO)
if args.run_number:
# proposal directory, run number
run = 'r%04d' % int(args.run_number)
proposal = args.run_dir
run_dir = osp.join(args.run_dir, 'proc', run)
if out_file is None:
out_file = osp.join(proposal, 'scratch', '{}_detectors_virt.cxi'.format(run))
else:
# run directory
run_dir = os.path.abspath(args.run_dir)
if out_file is None:
m = re.search(r'/(raw|proc)/(r\d{4})/?$', run_dir)
if not m:
sys.exit("ERROR: '-o outfile' option needed when "
"input directory doesn't look like .../proc/r0123")
proposal = run_dir[:m.start()]
fname = '{}_{}_detectors_virt.cxi'.format(*m.group(2, 1))
out_file = osp.join(proposal, 'scratch', fname)
out_dir = osp.dirname(osp.abspath(out_file))
if not os.access(run_dir, os.R_OK):
sys.exit("ERROR: Don't have read access to {}".format(run_dir))
if not os.access(out_dir, os.W_OK):
sys.exit("ERROR: Don't have write access to {}".format(out_dir))
log.info("Reading run directory %s", run_dir)
inc_suspect = not args.exc_suspect_trains
run = RunDirectory(run_dir, inc_suspect_trains=inc_suspect)
_, det_class = identify_multimod_detectors(run, single=True)
n_modules = det_class.n_modules
kwargs = {}
if n_modules == 0:
n_modules = args.n_modules
kwargs['n_modules'] = n_modules
min_modules = args.min_modules
if min_modules is None:
min_modules = 1 if (n_modules is None) else (n_modules // 2) + 1
det = det_class(run, min_modules=min_modules, **kwargs)
det.write_virtual_cxi(out_file, fill_values)
if __name__ == '__main__':
main()
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