def main():
parser = argparse.ArgumentParser(
description="Find peaks within the NeXus data")
parser.add_argument('-d', '--directory', required=True,
help='scan directory')
parser.add_argument('-e', '--entries', default=['f1', 'f2', 'f3'],
nargs='+', help='names of entries to be searched')
parser.add_argument('-t', '--threshold', type=float,
help='peak threshold - defaults to maximum counts/10')
parser.add_argument('-f', '--first', type=int, help='first frame')
parser.add_argument('-l', '--last', type=int, help='last frame')
parser.add_argument('-o', '--overwrite', action='store_true',
help='overwrite existing peaks')
parser.add_argument('-p', '--parent', default=None,
help='The parent .nxs file to use')
parser.add_argument('-q', '--queue', action='store_true',
help='add to server task queue')
args = parser.parse_args()
for entry in args.entries:
reduce = NXReduce(entry, args.directory, find=True,
threshold=args.threshold,
first=args.first, last=args.last,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxfind()
def main():
parser = argparse.ArgumentParser(
description="Find peaks within the NeXus data")
parser.add_argument('-d',
'--directory',
required=True,
help='scan directory')
parser.add_argument('-e',
'--entries',
nargs='+',
help='names of entries to be searched')
parser.add_argument('-t', '--threshold', type=float, help='peak threshold')
parser.add_argument('-f', '--first', type=int, help='first frame')
parser.add_argument('-l', '--last', type=int, help='last frame')
parser.add_argument('-P',
'--pixels',
type=int,
help='minimum pixels in a peak')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing peaks')
parser.add_argument('-p',
'--parent',
default=None,
help='The parent .nxs file to use')
parser.add_argument('-m',
'--monitor',
action='store_true',
help='monitor progress in the command line')
parser.add_argument('-q',
'--queue',
action='store_true',
help='add to server task queue')
args = parser.parse_args()
if args.entries:
entries = args.entries
else:
entries = NXMultiReduce(args.directory).entries
for entry in entries:
reduce = NXReduce(entry,
args.directory,
find=True,
threshold=args.threshold,
first=args.first,
last=args.last,
min_pixels=args.pixels,
overwrite=args.overwrite,
monitor_progress=args.monitor)
if args.queue:
reduce.queue('nxfind', args)
else:
reduce.nxfind()
def main():
parser = argparse.ArgumentParser(
description="Find peaks within the NeXus data")
parser.add_argument('-d',
'--directory',
required=True,
help='scan directory')
parser.add_argument('-e',
'--entries',
default=['f1', 'f2', 'f3'],
nargs='+',
help='names of entries to be searched')
parser.add_argument('-t',
'--threshold',
type=float,
help='peak threshold - defaults to maximum counts/10')
parser.add_argument('-f', '--first', type=int, help='first frame')
parser.add_argument('-l', '--last', type=int, help='last frame')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing peaks')
parser.add_argument('-p',
'--parent',
default=None,
help='The parent .nxs file to use')
parser.add_argument('-q',
'--queue',
action='store_true',
help='add to server task queue')
args = parser.parse_args()
for entry in args.entries:
reduce = NXReduce(entry,
args.directory,
find=True,
threshold=args.threshold,
first=args.first,
last=args.last,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxfind()
def main():
parser = argparse.ArgumentParser(
description="Set scan file as parent by creating a symbolic link")
parser.add_argument('-d', '--directory', required=True,
help='scan directory')
parser.add_argument('-e', '--entries', default=['f1', 'f2', 'f3'],
nargs='+', help='names of entries to be searched')
parser.add_argument('-t', '--threshold', type=float,
help='peak threshold - defaults to maximum counts/10')
parser.add_argument('-f', '--first', type=int, help='first frame')
parser.add_argument('-l', '--last', type=int, help='last frame')
parser.add_argument('-r', '--radius', type=int, default=200,
help='radius of mask around each peak (in pixels)')
parser.add_argument('-w', '--width', type=int, default=3,
help='width of masked region (in frames)')
parser.add_argument('-n', '--norm', default=50000,
help='normalization to monitor1')
parser.add_argument('-s', '--start', action='store_true',
help='start data reduction')
parser.add_argument('-o', '--overwrite', action='store_true',
help='overwrite existing parent')
args = parser.parse_args()
reduce = NXReduce(directory=args.directory, overwrite=args.overwrite)
reduce.make_parent()
if args.start:
for entry in args.entries:
reduce = NXReduce(entry, args.directory,
link=True, maxcount=True, find=True, mask=True,
threshold=args.threshold,
first=args.first, last=args.last,
radius=args.radius, width=args.width, norm=args.norm,
overwrite=args.overwrite)
reduce.nxlink()
reduce.nxmax()
reduce.nxfind()
reduce.nxmask()
def main():
parser = argparse.ArgumentParser(
description="Set scan file as parent by creating a symbolic link")
parser.add_argument('-d',
'--directory',
required=True,
help='scan directory')
parser.add_argument('-e',
'--entries',
default=['f1', 'f2', 'f3'],
nargs='+',
help='names of entries to be searched')
parser.add_argument('-t',
'--threshold',
type=float,
help='peak threshold - defaults to maximum counts/10')
parser.add_argument('-f', '--first', type=int, help='first frame')
parser.add_argument('-l', '--last', type=int, help='last frame')
parser.add_argument('-r',
'--radius',
type=int,
default=200,
help='radius of mask around each peak (in pixels)')
parser.add_argument('-w',
'--width',
type=int,
default=3,
help='width of masked region (in frames)')
parser.add_argument('-n',
'--norm',
default=50000,
help='normalization to monitor1')
parser.add_argument('-s',
'--start',
action='store_true',
help='start data reduction')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing parent')
args = parser.parse_args()
reduce = NXReduce(directory=args.directory, overwrite=args.overwrite)
reduce.make_parent()
if args.start:
for entry in args.entries:
reduce = NXReduce(entry,
args.directory,
link=True,
maxcount=True,
find=True,
mask=True,
threshold=args.threshold,
first=args.first,
last=args.last,
radius=args.radius,
width=args.width,
norm=args.norm,
overwrite=args.overwrite)
reduce.nxlink()
reduce.nxmax()
reduce.nxfind()
reduce.nxmask()