def main():
parser = argparse.ArgumentParser(
description="Find maximum counts of the signal in the specified path")
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 processed')
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 maximum')
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, maxcount=True,
first=args.first, last=args.last,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxmax()
def main():
parser = argparse.ArgumentParser(
description="Link data and metadata to NeXus file")
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('-o', '--overwrite', action='store_true',
help='overwrite existing peaks')
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, link=True,
overwrite=args.overwrite)
if args.queue:
reduce.queue('nxlink', args)
else:
reduce.nxlink()
def main():
parser = argparse.ArgumentParser(
description="Refine lattice parameters and goniometer angles")
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 processed')
parser.add_argument('-l', '--lattice', action='store_true',
help='refine lattice parameters')
parser.add_argument('-o', '--overwrite', action='store_true',
help='overwrite existing maximum')
parser.add_argument('-q', '--queue', action='store_true',
help='add to server task queue')
args = parser.parse_args()
for i, entry in enumerate(args.entries):
if i == 0:
lattice = args.lattice
else:
lattice = False
reduce = NXReduce(entry, args.directory, refine=True,
lattice=lattice, overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxrefine()
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="Perform CCTW transform")
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 processed')
parser.add_argument('-m',
'--mask',
action='store_true',
help='use 3D mask')
parser.add_argument('-qh', nargs=3, help='Qh - min, step, max')
parser.add_argument('-qk', nargs=3, help='Qk - min, step, max')
parser.add_argument('-ql', nargs=3, help='Ql - min, step, max')
parser.add_argument('-r',
'--radius',
default=200,
help='radius of mask around each peak (in pixels)')
parser.add_argument('-w',
'--width',
default=3,
help='width of masked region (in frames)')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing transforms')
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,
transform=True,
mask=args.mask,
Qh=args.qh,
Qk=args.qk,
Ql=args.ql,
radius=args.radius,
width=args.width,
overwrite=args.overwrite)
if args.mask:
if args.queue:
reduce.queue()
else:
reduce.nxmasked_transform()
else:
if args.queue:
reduce.queue()
else:
reduce.nxtransform()
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="Perform CCTW transform")
parser.add_argument('-d',
'--directory',
required=True,
help='scan directory')
parser.add_argument('-e',
'--entries',
nargs='+',
help='names of entries to be processed')
parser.add_argument('-qh', nargs=3, help='Qh - min, step, max')
parser.add_argument('-qk', nargs=3, help='Qk - min, step, max')
parser.add_argument('-ql', nargs=3, help='Ql - min, step, max')
parser.add_argument('-R',
'--regular',
action='store_true',
help='perform regular transform')
parser.add_argument('-M',
'--mask',
action='store_true',
help='perform transform with 3D mask')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing transforms')
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,
transform=True,
Qh=args.qh,
Qk=args.qk,
Ql=args.ql,
regular=args.regular,
mask=args.mask,
overwrite=args.overwrite)
if args.queue:
reduce.queue('nxtransform', args)
else:
if reduce.regular:
reduce.nxtransform()
if reduce.mask:
reduce.nxtransform(mask=True)
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="Refine lattice parameters and goniometer angles")
parser.add_argument('-d',
'--directory',
required=True,
help='scan directory')
parser.add_argument('-e',
'--entries',
nargs='+',
help='names of entries to be processed')
parser.add_argument('-l',
'--lattice',
action='store_true',
help='refine lattice parameters')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing maximum')
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 i, entry in enumerate(entries):
if i == 0:
lattice = args.lattice
else:
lattice = False
reduce = NXReduce(entry,
args.directory,
refine=True,
lattice=lattice,
overwrite=args.overwrite)
if args.queue:
reduce.queue('nxrefine', args)
else:
reduce.nxrefine()
def main():
parser = argparse.ArgumentParser(
description="Find maximum counts of the signal in the specified path")
parser.add_argument('-d',
'--directory',
required=True,
help='scan directory')
parser.add_argument('-e',
'--entries',
nargs='+',
help='names of entries to be processed')
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 maximum')
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,
maxcount=True,
first=args.first,
last=args.last,
overwrite=args.overwrite,
monitor_progress=args.monitor)
if args.queue:
reduce.queue('nxmax', args)
else:
reduce.nxmax()
def main():
parser = argparse.ArgumentParser(
description="Prepare 3D mask around Bragg peaks")
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 processed')
parser.add_argument('-o', '--overwrite', action='store_true',
help='overwrite existing mask')
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, prepare=True,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxprepare()
def main():
parser = argparse.ArgumentParser(
description="Perform CCTW transform")
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 processed')
parser.add_argument('-m', '--mask', action='store_true', help='use 3D mask')
parser.add_argument('-qh', nargs=3, help='Qh - min, step, max')
parser.add_argument('-qk', nargs=3, help='Qk - min, step, max')
parser.add_argument('-ql', nargs=3, help='Ql - min, step, max')
parser.add_argument('-r', '--radius', default=200,
help='radius of mask around each peak (in pixels)')
parser.add_argument('-w', '--width', default=3,
help='width of masked region (in frames)')
parser.add_argument('-o', '--overwrite', action='store_true',
help='overwrite existing transforms')
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, transform=True, mask=args.mask,
Qh=args.qh, Qk=args.qk, Ql=args.ql,
radius=args.radius, width=args.width,
overwrite=args.overwrite)
if args.mask:
if args.queue:
reduce.queue()
else:
reduce.nxmasked_transform()
else:
if args.queue:
reduce.queue()
else:
reduce.nxtransform()
def main():
parser = argparse.ArgumentParser(
description="Copy instrument parameters from a parent file")
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('-p', '--parent', help='file name of file to copy from')
parser.add_argument('-o', '--overwrite', action='store_true',
help='overwrite existing peaks')
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, parent=args.parent, copy=True,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxcopy()
def main():
parser = argparse.ArgumentParser(
description="Copy instrument parameters from a parent file")
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('-p',
'--parent',
help='file name of file to copy from')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing peaks')
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,
parent=args.parent,
copy=True,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxcopy()
def main():
parser = argparse.ArgumentParser(
description="Find maximum counts of the signal in the specified path")
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 processed')
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 maximum')
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,
maxcount=True,
first=args.first,
last=args.last,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxmax()
def add_tasks(self):
if self.grid is None:
raise NeXusError('Need to update status')
for scan in self.enabled_scans:
for entry in self.entries:
reduce = NXReduce(entry, scan)
if self.selected(scan, 'link'):
reduce.link = True
if self.selected(scan, 'max'):
reduce.maxcount = True
if self.selected(scan, 'find'):
reduce.find = True
if self.selected(scan, 'copy'):
reduce.copy = True
if self.selected(scan, 'refine'):
reduce.refine = True
if self.selected(scan, 'prepare'):
reduce.prepare = True
if self.selected(scan, 'transform'):
reduce.transform = True
if self.selected(scan, 'masked_transform'):
reduce.mask = True
if self.selected(scan, 'overwrite'):
reduce.overwrite = True
reduce.queue()
if self.selected(scan, 'link'):
self.queued(scan, 'link')
if self.selected(scan, 'max'):
self.queued(scan, 'max')
if self.selected(scan, 'find'):
self.queued(scan, 'find')
if self.selected(scan, 'copy'):
self.queued(scan, 'copy')
if self.selected(scan, 'refine'):
self.queued(scan, 'refine')
if self.selected(scan, 'prepare'):
self.queued(scan, 'prepare')
if self.selected(scan, 'transform'):
self.queued(scan, 'transform')
if self.selected(scan, 'masked_transform'):
self.queued(scan, 'masked_transform')
if self.selected(scan, 'combine'):
reduce = NXMultiReduce(scan, self.entries)
if self.selected(scan, 'overwrite'):
reduce.overwrite = True
reduce.queue()
self.queued(scan, 'combine')
if self.selected(scan, 'masked_combine'):
reduce = NXMultiReduce(scan, self.entries, mask=True)
if self.selected(scan, 'overwrite'):
reduce.overwrite = True
reduce.queue()
self.queued(scan, 'masked_combine')
self.scans[scan]
self.deselect_all()
def add_tasks(self):
if self.grid is None:
raise NeXusError('Need to update status')
for scan in self.enabled_scans:
for entry in self.entries:
reduce = NXReduce(entry, scan)
if self.selected(scan, 'link'):
reduce.link = True
if self.selected(scan, 'max'):
reduce.maxcount = True
if self.selected(scan, 'find'):
reduce.find = True
if self.selected(scan, 'copy'):
reduce.copy = True
if self.selected(scan, 'refine'):
reduce.refine = True
if self.selected(scan, 'transform'):
reduce.transform = True
if self.selected(scan, 'masked_transform'):
reduce.mask = True
if self.selected(scan, 'overwrite'):
reduce.overwrite = True
reduce.queue()
if self.selected(scan, 'link'):
self.queued(scan, 'link')
if self.selected(scan, 'max'):
self.queued(scan, 'max')
if self.selected(scan, 'find'):
self.queued(scan, 'find')
if self.selected(scan, 'copy'):
self.queued(scan, 'copy')
if self.selected(scan, 'refine'):
self.queued(scan, 'refine')
if self.selected(scan, 'transform'):
self.queued(scan, 'transform')
if self.selected(scan, 'masked_transform'):
self.queued(scan, 'masked_transform')
if self.selected(scan, 'combine'):
reduce = NXMultiReduce(scan, self.entries)
if self.selected(scan, 'overwrite'):
reduce.overwrite = True
reduce.queue()
self.queued(scan, 'combine')
if self.selected(scan, 'masked_combine'):
reduce = NXMultiReduce(scan, self.entries, mask=True)
if self.selected(scan, 'overwrite'):
reduce.overwrite = True
reduce.queue()
self.queued(scan, 'masked_combine')
self.scans[scan]
self.deselect_all()
def main():
parser = argparse.ArgumentParser(
description="Perform data reduction on entries")
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 processed')
parser.add_argument('-l',
'--link',
action='store_true',
help='link wrapper file to raw data')
parser.add_argument('-m',
'--max',
action='store_true',
help='find maximum counts')
parser.add_argument('-f', '--find', action='store_true', help='find peaks')
parser.add_argument('-c',
'--copy',
action='store_true',
help='copy parameters')
parser.add_argument('-r',
'--refine',
action='store_true',
help='refine lattice parameters')
parser.add_argument('-t',
'--transform',
action='store_true',
help='perform CCTW transforms')
parser.add_argument('-M',
'--mask',
action='store_true',
help='perform CCTW transforms with 3D mask')
parser.add_argument('-b',
'--combine',
action='store_true',
help='combine CCTW transforms')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing maximum')
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,
link=args.link,
maxcount=args.max,
find=args.find,
copy=args.copy,
refine=args.refine,
transform=args.transform,
mask=args.mask,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxreduce()
if args.combine:
reduce = NXMultiReduce(args.directory,
entries=args.entries,
mask=args.mask,
overwrite=args.overwrite)
if args.queue:
reduce.queue()
else:
reduce.nxcombine()
def main():
parser = argparse.ArgumentParser(
description="Prepare 3D mask around Bragg peaks")
parser.add_argument('-d',
'--directory',
required=True,
help='scan directory')
parser.add_argument('-e',
'--entries',
nargs='+',
help='names of entries to be processed')
parser.add_argument('--t1',
type=float,
default=2,
help='threshold for smaller convolution')
parser.add_argument('--h1',
type=int,
default=11,
help='size of smaller convolution')
parser.add_argument('--t2',
type=float,
default=0.8,
help='threshold for larger convolution')
parser.add_argument('--h2',
type=int,
default=51,
help='size of larger convolution')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing mask')
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,
prepare=True,
overwrite=args.overwrite,
monitor_progress=args.monitor)
reduce.mask_parameters['threshold_1'] = args.t1
reduce.mask_parameters['horizontal_size_1'] = args.h1
reduce.mask_parameters['threshold_2'] = args.t2
reduce.mask_parameters['horizontal_size_2'] = args.h2
if args.queue:
reduce.queue('nxprepare', args)
else:
reduce.nxprepare()
def main():
parser = argparse.ArgumentParser(
description="Perform data reduction on entries")
parser.add_argument('-d',
'--directory',
required=True,
help='scan directory')
parser.add_argument('-e',
'--entries',
nargs='+',
help='names of entries to be processed')
parser.add_argument('-l',
'--link',
action='store_true',
help='link wrapper file to raw data')
parser.add_argument('-m',
'--max',
action='store_true',
help='find maximum counts')
parser.add_argument('-f', '--find', action='store_true', help='find peaks')
parser.add_argument('-c',
'--copy',
action='store_true',
help='copy parameters')
parser.add_argument('-r',
'--refine',
action='store_true',
help='refine lattice parameters')
parser.add_argument('-p',
'--prepare',
action='store_true',
help='prepare 3D masks')
parser.add_argument('-t',
'--transform',
action='store_true',
help='perform CCTW transforms')
parser.add_argument('-C',
'--combine',
action='store_true',
help='combine CCTW transforms')
parser.add_argument('-P',
'--pdf',
action='store_true',
help='perform PDF transforms')
parser.add_argument('-R',
'--regular',
action='store_true',
help='perform regular CCTW transforms')
parser.add_argument('-M',
'--mask',
action='store_true',
help='perform CCTW transforms with 3D mask')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='overwrite existing maximum')
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=entry,
directory=args.directory,
link=args.link,
maxcount=args.max,
find=args.find,
copy=args.copy,
refine=args.refine,
prepare=args.prepare,
transform=args.transform,
combine=args.combine,
pdf=args.pdf,
regular=args.regular,
mask=args.mask,
overwrite=args.overwrite)
if args.queue:
reduce.queue('nxreduce', args)
else:
reduce.combine = reduce.pdf = False
reduce.nxreduce()
if (args.combine or args.pdf) and not args.queue:
reduce = NXMultiReduce(args.directory,
combine=args.combine,
pdf=args.pdf,
regular=args.regular,
mask=args.mask,
overwrite=args.overwrite)
reduce.nxreduce()