rethinkig ui (a78c4393) · Commits · Zolnierczuk, Piotr / pysen

README.rst

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		The pysen package is a collection of Python modules and scripts
		for the SNS-NSE instrument (BL-15)
		but may be also useful for any neutron spin echo experimenter.
		pysen
		------

		The pysen package is a collection of Python modules and scripts that aid experiment planning, data collection, reduction, and analysis
		at the Neutron Spin Echo instrument (SNS-NSE) located at Beam Line 15 of the First Target Station at the Spallation Neutron Source.
		It may be also useful for any other neutron spin echo experimenter.

doc/source/_static/atari_example.png

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doc/source/intro.rst

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		@@ -2,20 +2,77 @@
		Introduction
		============================

		The pysen package is a collection of Python modules and scripts that aid experiment planning, data collection, reduction, and analysis
		at the Neutron Spin Echo instrument (SNS-NSE) located at Beam Line 15 of the First Target Station at the Spallation Neutron Source.
		It may be also useful for any other neutron spin echo experimenter.



		.. toctree::


		The Quick Start Guide
		=========================================

		The PySEN GUI
		-----------------------------------------

		Generic Usage
		--------------

		The most common usage pattern involves the ``nseplot`` command, followed by a subcommand what to plot.

		``nseplot <subcommand> [subcomand-options] [filename(s)]``

		For example,

		``nseplot atari -t1 /SNS/NSE/IPTS-4531/s10922.echo``

		which produces the following result:

		.. figure:: _static/atari_example.png

		Plot created by the above ``nseplot atari`` command.


		Each command provides a short help via ``--help`` option:

		``nseplot atari --help``


		or::


		usage: nseplot atari [-h] [--version] [--save-figure file] [--save-file file] [--verbose \| --quiet] [--tau TAU] [--t1 TBIN1]
		[--t2 TBIN2] [--x1 XPIX1] [--x2 XPIX2] [--y1 YPIX1] [--y2 YPIX2] [--whole-detector] [--vmin VMIN]
		[--vmax VMAX] [--logz] [--normalize] [--only-echo] [--incoherent] [--phase0 PHASE0]
		filename [filename ...]

		positional arguments:
		filename file to process

		optional arguments:
		-h, --help show this help message and exit
		--version, -V show program's version number and exit
		--save-figure file, -S file
		save figure to a file (do not show)
		--save-file file, -s file
		save data to a csv file

		--verbose, -v verbose output
		--quiet, -q suppres output
		--tau TAU, -t TAU set tau to display (default=0)
		--t1 TBIN1, -b TBIN1 set min TOF bin (default=0)
		--t2 TBIN2, -B TBIN2 set max TOF bin (default=None)
		--x1 XPIX1 set min X pix (default=10)
		--x2 XPIX2 set max X pix (default=22)
		--y1 YPIX1 set min Y pix (default=10)
		--y2 YPIX2 set max Y pix (default=22)
		--whole-detector, -W show sum over entire detector area
		--vmin VMIN set min vertical scale (default=0)
		--vmax VMAX set max vertical scale (default=None)
		--logz detector image log vertical scale
		--normalize, -n normalize results
		--only-echo show only echo (no up/down)
		--incoherent, -I treat data as from incoherent scatterer
		--phase0 PHASE0 set inital phase for echo fitting (default=None)

pysen/plot/cmdline.py

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		@@ -13,11 +13,12 @@ from pysen.plot import plot_echo, plot_atari

		class NsePlotApp(cmd.Cmd):
		"""Simple NSE plotting utility"""
		prompt = 'nsepy> '
		prompt = 'nseplot> '
		intro = """
		Welcome to NSEpy !!!
		Welcome to NSE Plot!!!

		"""
		filenames = []

		def preloop(self):
		self.cmdqueue.append(" ".join(sys.argv[1:]))
		@@ -51,7 +52,7 @@ class NsePlotApp(cmd.Cmd):
		center_only=False, whole_detector=False,
		map_type='all', phase0=None,
		incoherent=False, max_chi2=1e3)
		parser.add_argument('file', metavar='filename', help='file to process', nargs='+')
		#parser.add_argument('file', metavar='filename', help='file to process', nargs='+')
		parser.add_argument('--tau', '-t', dest='tau', type=int,
		help='set tau to display (default=%(default)s)')
		parser.add_argument('--t1' , '-b', dest='tbin1', type=int,
		@@ -73,18 +74,28 @@ class NsePlotApp(cmd.Cmd):
		try:
		args = parser.parse_args(line.split())
		except argparse.ArgumentError as exc:
		print('Catching an argumentError', exc)
		return

		kwargs = vars(args)
		try:
		for filename in args.file:
		with h5py.File(filename, 'r') as hdf5file:
		func(hdf5file, iecho=args.tau, **kwargs)
		for f in self.filenames:
		func(f, iecho=args.tau, **kwargs)
		plt.show()
		except OSError as exc:
		print(exc)

		def do_ls(self, _line):
		for f in self.filenames:
		print(f.filename)

		def do_load(self, line):
		self.filenames.append(h5py.File(line, 'r'))

		def do_clear(self, _line):
		for f in self.filenames:
		f.close()
		self.filenames = []

		def do_echo(self, line):
		"plot echo"
		self.plot_command("echo", line)

pysen/plot/nseplot.py

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		@@ -3,6 +3,7 @@

		import os.path
		import argparse
		import cmd

		import numpy as np
		import h5py
		@@ -14,7 +15,7 @@ from pysen.inout import convert_to_hdf
		from pysen.plot import ( plot_echo, plot_atari, plot_map,
		plot_xyz, plot_magnetic_fields,
		plot_diffrun, plot_transmission, plot_datreat)
		#from pysen.plot.cmdline import NsePlotApp


		def action_default(filenames, **kwargs):
		"default action for echo, atari, etc"
		@@ -145,6 +146,15 @@ def add_subparser(name, parent, sub, helpmsg=None, filearg=None):
		parser_name.add_argument('file', metavar='filename', help='file to process', nargs=filearg)
		return parser_name.add_argument_group()

		class NsePlotApp(cmd.Cmd):
		"""Simple NSE plotting utility"""
		prompt = 'nseplot> '
		intro = """
		Welcome to NSE Plot!!!
		"""



		def main():
		"the main"

		@@ -154,7 +164,7 @@ def main():
		parser_top.set_defaults(loglevel=1, outdir='.')
		parser_top.add_argument('--version', '-V', action='version',
		version='%(prog)s pysen={version}'.format(version=version(full=True)))
		subparsers = parser_top.add_subparsers(dest='plot', required=True, help='what to plot')
		subparsers = parser_top.add_subparsers(dest='plot', required=False, help='what to plot')

		# common arguments
		parser = argparse.ArgumentParser(add_help=False)
		@@ -169,11 +179,11 @@ def main():
		# version option
		parser.add_argument('--version', '-V', action='version',
		version='%(prog)s pysen={version}'.format(version=version(full=True)))
		#
		# save figure/data options
		parser.add_argument('--save-figure', '-S', dest='savefig', metavar='file',
		help='save figure to a file (do not show)')
		parser.add_argument('--save-file', '-s', dest='savefile', metavar='file',
		help='save data to a csv file')
		help='save data to a .csv file')
		# mutually exclusive [ -v \| -q ]
		group_vrb = parser.add_mutually_exclusive_group()
		group_vrb.add_argument('--verbose', '-v', dest='loglevel', action='count',
		@@ -189,7 +199,7 @@ def main():
		help='show only echo (no up/down)')
		grp_echo.add_argument('--incoherent', '-I', dest='incoherent', action='store_true',
		help='treat data as from incoherent scatterer')
		grp_echo.add_argument('--absolute-y', '-Y', dest='absy', metavar='YMAX', type=float,
		grp_echo.add_argument('--absolute-y', '-Y', dest='absy', metavar='V', type=float,
		help='use the same vertical scale for all pixels')
		grp_echo.add_argument('--num-pix', '-N', dest='npix', metavar='N', type=int,
		help='set pixel binning (default=%(default)s)')
		@@ -295,9 +305,9 @@ def main():
		log = setup_logger(args.loglevel)
		log.debug('program arguments %s', args)

		#if not args.plot
		# NsePlotApp().cmdloop()
		# return
		if not args.plot:
		NsePlotApp().cmdloop()
		return

		plt.rcParams.update({'figure.max_open_warning': 0})
		if args.savefig: