def r2d(dg, overwrite=False, nwfs=None, vrb=False):
"""
"""
# print(dg.file_keys)
# print(dg.file_keys.columns)
with open(f'config_dsp.json') as f:
dsp_config = json.load(f, object_pairs_hook=OrderedDict)
for i, row in dg.file_keys.iterrows():
f_raw = f"{dg.lh5_dir}/{row['raw_path']}/{row['raw_file']}"
f_dsp = f"{dg.lh5_dir}/{row['dsp_path']}/{row['dsp_file']}"
if "sysn" in f_raw:
tmp = {'sysn': 'geds'} # hack for lpgta
f_raw = f_raw.format_map(tmp)
f_dsp = f_dsp.format_map(tmp)
if not overwrite and os.path.exists(f_dsp):
print('file exists, overwrite not set, skipping f_dsp:\n ',
f_dsp)
continue
raw_to_dsp(f_raw,
f_dsp,
dsp_config,
n_max=nwfs,
verbose=vrb,
overwrite=overwrite)
def r2d(dg, overwrite=False, nwfs=None, vrb=False):
"""
"""
# print(dg.fileDB)
# print(dg.fileDB.columns)
with open(f'{dg.experiment}_dsp.json') as f:
dsp_config = json.load(f, object_pairs_hook=OrderedDict)
for i, row in dg.fileDB.iterrows():
f_raw = f"{dg.lh5_dir}/{row['raw_path']}/{row['raw_file']}"
f_dsp = f"{dg.lh5_dir}/{row['dsp_path']}/{row['dsp_file']}"
if "sysn" in f_raw:
tmp = {'sysn': 'geds'} # hack for lpgta
f_raw = f_raw.format_map(tmp)
f_dsp = f_dsp.format_map(tmp)
raw_to_dsp(f_raw,
f_dsp,
dsp_config,
n_max=nwfs,
verbose=vrb,
overwrite=overwrite)
def r2d(dg, overwrite=False, nwfs=None, verbose=False, user=False):
"""
$ ./processing.py -q 'run==[something]' --r2d
"""
# load default DSP config file
dsp_dir = os.path.expandvars('$CAGE_SW/processing/metadata')
with open(dsp_dir + '/config_dsp.json') as f:
dsp_config = json.load(f, object_pairs_hook=OrderedDict)
for i, row in dg.fileDB.iterrows():
lh5_dir = dg.lh5_user_dir if user else dg.lh5_dir
f_raw = f"{dg.lh5_dir}/{row['raw_path']}/{row['raw_file']}"
f_dsp = f"{lh5_dir}/{row['dsp_path']}/{row['dsp_file']}"
if "sysn" in f_raw:
tmp = {'sysn': 'geds'} # hack for lpgta
f_raw = f_raw.format_map(tmp)
f_dsp = f_dsp.format_map(tmp)
if not overwrite and os.path.exists(f_dsp):
print('file exists, overwrite not set, skipping f_dsp:\n ',
f_dsp)
continue
cyc = row['cycle']
if row.skip:
print(f'Cycle {cyc} has been marked junk, will not process.')
continue
# load updated dsp config file (optional)
if row.dsp_id > 0:
with open(dsp_dir + f'/dsp/dsp_{row.dsp_id:02d}.json') as f:
dsp_config = json.load(f, object_pairs_hook=OrderedDict)
print(f'Using DSP config: {dsp_dir}' +
f'/dsp/dsp_{row.dsp_id:02d}.json')
# NOTE: there is currently no smart DSP DB lookup here,
# so the "db defaults" values in each of the JSON files will be used.
print(f'Processing cycle {cyc}')
raw_to_dsp(f_raw,
f_dsp,
dsp_config,
n_max=nwfs,
verbose=verbose,
overwrite=overwrite)
def r2d_file(f_raw, f_dsp, overwrite=True, nwfs=None, vrb=False):
"""
single-file mode, for testing
"""
print('raw_to_dsp, single-file mode.')
print(' input:', f_raw)
print(' output:', f_dsp)
# always overwrite
if os.path.exists(f_dsp):
os.remove(f_dsp)
with open('oppi_dsp.json') as f:
dsp_config = json.load(f, object_pairs_hook=OrderedDict)
raw_to_dsp(f_raw, f_dsp, dsp_config, n_max=nwfs, verbose=vrb,
overwrite=overwrite)
def r2d(dg, overwrite=False, nwfs=None, verbose=False, user=False):
"""
$ ./processing.py -q 'run==[something]' --r2d
"""
# print(dg.fileDB)
# print(dg.fileDB.columns)
with open(
os.path.expandvars(
'$CAGE_SW/processing/metadata/config_dsp.json')) as f:
dsp_config = json.load(f, object_pairs_hook=OrderedDict)
for i, row in dg.fileDB.iterrows():
lh5_dir = dg.lh5_user_dir if user else dg.lh5_dir
f_raw = f"{dg.lh5_dir}/{row['raw_path']}/{row['raw_file']}"
f_dsp = f"{lh5_dir}/{row['dsp_path']}/{row['dsp_file']}"
if "sysn" in f_raw:
tmp = {'sysn': 'geds'} # hack for lpgta
f_raw = f_raw.format_map(tmp)
f_dsp = f_dsp.format_map(tmp)
if not overwrite and os.path.exists(f_dsp):
print('file exists, overwrite not set, skipping f_dsp:\n ',
f_dsp)
continue
cyc = row['cycle']
if row.skip:
print(f'Cycle {cyc} has been marked junk, will not process.')
continue
print(f'Processing cycle {cyc}')
raw_to_dsp(f_raw,
f_dsp,
dsp_config,
n_max=nwfs,
verbose=verbose,
overwrite=overwrite)
import argparse, os, pathlib
import pygama
from pygama.io.raw_to_dsp import raw_to_dsp
import json
from collections import OrderedDict
argparser = argparse.ArgumentParser()
argparser.add_argument("--metadata",
help="metadata path",
type=str,
required=True)
argparser.add_argument("input", help="input file", type=str)
argparser.add_argument("output", help="output file", type=str)
args = argparser.parse_args()
f_config = os.path.join(f"{args.metadata}", "config_dsp.json")
with open(f_config) as f:
config_dic = json.load(f, object_pairs_hook=OrderedDict)
pathlib.Path(os.path.dirname(args.output)).mkdir(parents=True, exist_ok=True)
# ToDo: Atomic file creation
raw_to_dsp(args.input, args.output, config_dic, verbose=True, overwrite=False)