savepoint (a8fac9db) · Commits · Zolnierczuk, Piotr / pysen

pysen/inout/init.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -7,5 +7,6 @@ from .reader import ( read_echo, read_magnetic, read_xyz, # NOQA
		read_datreat , read_transmission ) # NOQA
		from .writer import EchoWriter, DiffractionWriter # NOQA
		from .scans import EchoScan, DiffractionScan, XYZScan # NOQA
		from .utils import get_nsefiletype
		# from .legacy_writer import write_csv, generate_echo # NOQA
		# from .legacy_history import extract_data, list_variables, parse_date # NOQA

pysen/inout/convert2hdf.py

+20 −14

Original line number	Diff line number	Diff line
		@@ -7,23 +7,29 @@ import argparse
		import logging

		from pysen import version, setup_logger
		from pysen.inout import convert_to_hdf
		from pysen.inout import convert_to_hdf, get_nsefiletype

		def convert_file(filenames, outdir, **kwargs):
		"""convert magnetic up/down .dat file into an HDF file """
		log = logging.getLogger()
		for filename in filenames:
		# get the file extension and the header
		filetype = get_nsefiletype(filename)
		basename = os.path.basename(filename)
		_, file_ext = os.path.splitext(filename)
		try:
		if file_ext=='.echo':
		#if file_ext=='.echo':
		if filetype=='application/nse-echo':
		log.debug('reading echo data %s', filename)
		outfile = convert_to_hdf(filename, outdir, data_type='echo', **kwargs)
		elif file_ext=='.xyz':
		elif filetype=='application/nse-xyz':
		log.debug('reading xyz data %s', filename)
		outfile = convert_to_hdf(filename, outdir, data_type='xyz', **kwargs)
		elif file_ext=='.dat':
		elif filetype=='application/nexus-nse-echo':
		log.debug('reading NeXus echo data %s', filename)
		outfile = convert_to_hdf(filename, outdir, data_type='nexus_echo', **kwargs)
		else:
		_, file_ext = os.path.splitext(basename)
		if file_ext=='.dat':
		header=''
		with open(filename, 'r', encoding='ascii') as _fd:
		header = _fd.readline()
		@@ -31,9 +37,9 @@ def convert_file(filenames, outdir, **kwargs):
		log.debug('reading magnetic data %s', filename)
		outfile = convert_to_hdf(filename, outdir, data_type='magnetic', **kwargs)
		else:
		raise RuntimeError("Unknown file type")
		raise RuntimeError("Unknown file type (.dat)")
		else:
		raise RuntimeError("Unknown file type")
		raise RuntimeError("Unknown file type %s" % filetype)
		log.info('written HDF5 file %s', outfile)
		except RuntimeError as exc:
		log.warning("error converting %s: %s", basename, exc)

pysen/inout/hdf.py

+13 −14

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@ import numpy as np
		from ..revision import version as version_info
		from ..iostrings import encode
		from .reader import read_echo, read_magnetic, read_xyz
		from .writer import EchoWriter, make_echofilename
		from .writer import EchoWriter
		from .utils import get_nsefiletype

		#FIXME: we need to work on the idea of a schema (or not???)
		@@ -178,11 +178,11 @@ class HdfConverter:

		def read_nexus_echo(filename, outdir='.'):
		"read nexus echo file"
		echo = EchoWriter(make_echofilename(filename))
		echo = EchoWriter()
		if not echo.read_nexus(filename):
		raise RuntimeError("Error reading NeXus file {filename}")
		echo.to_echo(outdir)
		return read_echo(echo.echofile)
		echofile = echo.save(outdir)
		return read_echo(echofile)


		def _make_outfilename(filename, filetype=None, outdir='.'):
		@@ -222,13 +222,6 @@ def convert_to_hdf(filename, outdir, **kwargs):
		# outfile
		filetype = get_nsefiletype(filename)
		basename = os.path.basename(filename)

		if data_type is None: # guess data type based on file
		reader = data_reader.get(filetype)
		else: # data type given
		reader = data_reader.get(data_type)
		data = reader(filename)

		outfile = _make_outfilename(basename, outdir=outdir, filetype=filetype)

		_log.info('converting %s to HDF5', basename)
		@@ -238,6 +231,12 @@ def convert_to_hdf(filename, outdir, **kwargs):
		if t_out > t_src:
		_log.info('file %s is newer than %s', outfile, filename)
		return outfile

		if data_type is None: # guess data type based on file
		reader = data_reader.get(filetype)
		else: # data type given
		reader = data_reader.get(data_type)
		data = reader(filename)
		converter = HdfConverter(outfile, mode=mode, version=version_info())
		converter.write(data, compression=compression, schema=schema)
		return outfile

pysen/inout/writer.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -119,6 +119,7 @@ class DiffractionWriter(DiffractionScan):
		fd.write(f"\"flip ratio\" {fr:g}\n")

		self.log.info("%s: done", diffrun)
		return diffrun


		class EchoWriter(EchoScan):
		@@ -318,5 +319,6 @@ class EchoWriter(EchoScan):
		for phase in self.data[tau]:
		fd.write(self.phase_point(phase))
		self.log.info("%s: done", echofile)
		return echofile

		# EOF

pysen/plot/nseplot.py

+9 −3

Original line number	Diff line number	Diff line
		@@ -16,7 +16,7 @@ import matplotlib.pyplot as plt

		from pysen import version, setup_logger, DEFAULT_LOG_LEVEL
		from pysen.config import INST_POSITIONS, INST_MODES, DEFAULT_ACCELERATOR_POWER, coverage
		from pysen.inout import convert_to_hdf
		from pysen.inout import convert_to_hdf, get_nsefiletype
		from pysen.echo import get_symmetry_phase, make_phase_table
		from pysen.plot import ( plot_echo, plot_atari, plot_map,
		plot_xyz, plot_xyz_nexus, plot_magnetic_fields,
		@@ -33,9 +33,15 @@ def action_default(filenames, **kwargs):
		log = logging.getLogger()
		for filename in filenames:
		try:
		basename , ext = os.path.splitext(os.path.basename(filename))
		if ext != ".h5":
		filetype = get_nsefiletype(filename)
		#basename , ext = os.path.splitext(os.path.basename(filename))
		print(filetype, filename)
		if filetype=='application/nse-echo':
		filename = convert_to_hdf(filename, outdir, data_type='echo')
		elif filetype=='application/nexus-nse-echo':
		filename = convert_to_hdf(filename, outdir, data_type='nexus_echo')


		with h5py.File(filename, 'r') as hdf5file:
		action(hdf5file, taus, **kwargs)
		if savefig: