merged nxs2echo and convert2hdf (5af40a98) · Commits · Zolnierczuk, Piotr / pysen

pysen/inout/convert2hdf.py→pysen/inout/converters.py

+49 −0

Original line number	Diff line number	Diff line
		#!/usr/bin/env python
		""" a script to convert .echo files to .hfd5 format
		""" scripts to convert .echo files to/from .hfd5 format
		"""
		import argparse

		@@ -7,27 +7,43 @@ from pysen import version, setup_logger
		from pysen.inout import convert_files

		def main():
		"the main"
		parser = argparse.ArgumentParser(description='convert echo file into HDF5')
		parser.set_defaults(loglevel=1, compression='gzip', out='.', convert='echo', overwrite=False)
		"run function for the connverters"
		description="<unknown>"
		#
		description='convert NeXus file to old TACO format (or old .echo file to .h5)'
		parser = argparse.ArgumentParser(description=description)
		parser.set_defaults(loglevel=1, out='.', converter='to_taco')
		parser.add_argument('filename', metavar='file', nargs='+', help='filenames to process')
		parser.add_argument('--outdir', '-o', dest='out',
		help='set output directory (default %(default)s)')
		parser.add_argument('--force','-f', dest='overwrite', action='store_true',
		help='force conversion, i.e. overwrite existing HDF files')
		parser.add_argument('--no-compression', '-C', dest='compression', action='store_const',
		const=None, help='turn off gzip compression')
		parser.add_argument('--from-taco', '-e', dest='converter', action='store_const',
		const='from_taco', help='convert from TACO .echo to .h5')
		parser.add_argument('--verbose', '-v', dest='loglevel', action='count',
		help='verbose output')
		parser.add_argument('--quiet', '-q', dest='loglevel', action='store_const',
		const=0, help='verbose output')
		parser.add_argument('--version', action='version',
		version='%(prog)s pysen={version}'.format(version=version(full=True)))
		# nexus to TACO
		parser.add_argument('--npix', '-P', type=int, dest='npix', default=32,
		help='set number of detector pixels (default %(default)s)')
		parser.add_argument('--ntof', '-T', type=int, dest='ntof', default=42,
		help='set number of tof channels (default %(default)s)')
		parser.add_argument('--step', '-S', type=float, dest='step', default=None,
		help='set precession phase step (default: find it from the NeXus file)')
		# .echo to .h5 options
		parser.add_argument('--force','-f', dest='overwrite', action='store_true', default=False,
		help='force conversion, i.e. overwrite existing HDF files')
		parser.add_argument('--no-compression', '-C', dest='compression', action='store_const', default='gzip',
		const=None, help='turn off gzip compression')

		kwargs = vars(parser.parse_args())
		loglevel = kwargs.pop('loglevel')
		filenames = kwargs.pop('filename')
		outdir = kwargs.pop('out')
		setup_logger(loglevel)
		convert_files(filenames, outdir, **kwargs)

		args = parser.parse_args()
		setup_logger(args.loglevel)
		convert_files(args.filename, args.out, compression=args.compression,
		overwrite=args.overwrite, converter='from_taco')

		if __name__ == "__main__":
		main()

pysen/inout/hdf.py

+7 −6

Original line number	Diff line number	Diff line
		@@ -247,7 +247,6 @@ def convert_to_hdf(filename, outdir, **kwargs):
		WriterClassType = { 'application/nexus-nse-echo' : EchoWriter,
		'application/nexus-nse-diffraction' : DiffractionWriter,
		'application/nexus-nse-transmission' : TransmissionWriter }

		def convert_to_taco(filename, outdir, **kwargs):
		"""convert *.nxs.h5 file into old TACO style
		echo, translation,diffrun dat file
		@@ -255,24 +254,26 @@ def convert_to_taco(filename, outdir, **kwargs):
		file_type = get_nsefiletype(filename)
		writer_class = WriterClassType.get(file_type, None)
		if not isinstance(writer_class, type):
		raise RuntimeError("file {filename} unknown file type {file_type}")
		raise RuntimeError(f"Unknown file type {file_type}")
		writer = writer_class()
		if not writer.read_nexus(filename, **kwargs):
		return None
		res = writer.save(outdir=outdir)
		return res

		ConverterType = { 'to_taco' : convert_to_taco,
		'from_taco' : convert_to_hdf}

		def convert_files(filenames, outdir, **kwargs):
		"""convert *.nxs.h5 file to/from old TACO style files"""
		log = logging.getLogger()
		converter = { 'to_taco' : convert_to_taco,
		'from_taco' : convert_to_hdf}.get(kwargs.pop('converter', 'from_taco'))
		converter = ConverterType.get(kwargs.pop('converter', 'from_taco'))
		for filename in filenames:
		try:
		basename = os.path.basename(filename)
		outfile = converter(filename, outdir, **kwargs)
		log.info('converted %s to %s', basename, outfile)
		except RuntimeError as exc:
		log.warning("error converting %s: %s", basename, exc)
		log.warning("error converting %s: (%s)", basename, exc)
		except OSError as exc:
		log.warning("error converting %s: %s", basename, exc.strerror)
		log.warning("error converting %s: (%s)", basename, exc.strerror)

pysen/inout/nxs2echo.py

deleted100755 → 0

+0 −38

Original line number	Diff line number	Diff line
		#!/usr/bin/env python
		"""Simple nexus to echo converter
		Piotr Zolnierczuk, zolnierczukp AT ornl.gov
		Oak Ridge National Lab, 2024
		"""
		import argparse

		from pysen import version, setup_logger
		from pysen.inout import convert_files

		def main():
		"the main"
		parser = argparse.ArgumentParser(description='convert nxs.h5 files to old TACO format')
		parser.set_defaults(ntof=42, npix=32, step=None, outdir='.', loglevel=1)
		parser.add_argument('filename', metavar='file', nargs='+', help='filenames to process')
		parser.add_argument('--outdir', '-o', dest='out',
		help='set output directory (default %(default)s)')
		parser.add_argument('--npix', '-P', type=int, dest='npix',
		help='set number of detector pixels (default %(default)s)')
		parser.add_argument('--ntof', '-T', type=int, dest='ntof',
		help='set number of tof channels (default %(default)s)')
		parser.add_argument('--step', '-S', type=float, dest='step',
		help='set precession phase step (default: find it from the NeXus file)')
		parser.add_argument('--verbose', '-v', dest='loglevel', action='count',
		help='verbose output')
		parser.add_argument('--quiet', '-q', dest='loglevel', action='store_const',
		const=0, help='verbose output')
		parser.add_argument('--version', action='version',
		version='%(prog)s pysen={version}'.format(version=version(full=True)))

		args = parser.parse_args()
		setup_logger(args.loglevel)
		convert_files(args.filename, args.out, npix=args.npix, ntof=args.ntof, step=args.step,
		converter='to_taco')

		if __name__ == "__main__":
		main()
		#EOF

pysen/revision.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -3,8 +3,8 @@ PySEN revision module
		"""
		import sys
		__version__ = "2.1"
		__release__ = "a1"
		__date__ = "Feb 27, 2025"
		__release__ = "a2"
		__date__ = "Mar 24, 2025"

		def version(full=False):
		"get pysen version number"

setup.py

+5 −3

Original line number	Diff line number	Diff line
		@@ -41,12 +41,14 @@ setup(
		package_dir = { 'pysen': 'pysen' } ,
		entry_points={
		'console_scripts': [
		'convert2hdf = pysen.inout.convert2hdf:main',
		'nxs2echo = pysen.inout.nxs2echo:main',
		'nseplot = pysen.plot.nseplot:main',
		'nxs2echo = pysen.inout.converters:main',
		#
		'nsefilemon = pysen.ui.filemon:main',
		'nsesimecho = pysen.ui.pysimecho:main',
		]
		],
		#'gui_scripts': [
		#]
		},
		scripts = [
		'scripts/pysen_completion',