nseplot almost done (e4dc1fd5) · Commits · Zolnierczuk, Piotr / pysen

misc/show-all-help.sh

0 → 100755

+15 −0

Original line number	Diff line number	Diff line
		#!/bin/bash

		nseplotcmd=./pysen/plot/nseplot.py
		commands=$($nseplotcmd -h \| grep '^\s*{' \| head -1 \| tr '{},' ' ')
		echo $commands
		echo
		#
		for c in $commands; do
		echo "====> command: $c"
		$nseplotcmd $c --help
		echo
		done


		# vim: filetype=bash

pysen/echo/init.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -4,3 +4,4 @@ echo fit/plot module

		from .fit import fit_echo_current, Spectrum # NOQA
		from .reduce import get_symmetry_phase, reduce_echo # NOQA
		from .make_phase_table import make_phase_table # NOQA

pysen/echo/make_phase_table.py

+8 −92

Original line number	Diff line number	Diff line
		#!/usr/bin/env python
		"PHASE TABLE"
		import time
		import sys
		import os.path

		import logging
		import argparse

		import numpy as np
		import h5py
		import matplotlib.pyplot as plt

		from scipy.interpolate import interp2d

		from pysen import config, setup_logger
		from pysen.echo import get_symmetry_phase
		from pysen.inout import convert_to_hdf
		from pysen import config
		from pysen.mathutil import simple_cluster

		def brute_force_interpolation(vals, xvals, yvals, x, y):
		@@ -33,7 +27,7 @@ def brute_force_interpolation(vals, xvals, yvals, x, y):
		return res


		def make_phase_table(phtab, polyfit=0, ncur=9, nphi=11, pos=2, threshold=0.2):
		def make_phase_table(phtab, polyfit=0, ncur=10, nphi=11, pos='p2', threshold=0.2):
		"make phase table"
		#
		log = logging.getLogger()
		@@ -50,8 +44,8 @@ def make_phase_table(phtab, polyfit=0, ncur=9, nphi=11, pos=2, threshold=0.2):
		phase = phtab[:,:,2]

		if polyfit>0:
		mini00, maxi00 = 0.0, 80.0 # FIXME: hard coded
		minphi, maxphi = -2.0, config.phi_limits('p%d' % pos)[1]
		mini00, maxi00 = 0.0, 90.0 # FIXME: hard coded
		minphi, maxphi = -2.0, config.phi_limits(pos)[1]
		else:
		mini00, maxi00 = np.amin(i00), np.amax(i00)
		minphi, maxphi = np.amin(phi), np.amax(phi)
		@@ -83,11 +77,10 @@ def make_phase_table(phtab, polyfit=0, ncur=9, nphi=11, pos=2, threshold=0.2):
		# fill in data
		z[:,i] = np.polyval(a,yphi)
		plt.plot(yphi, np.polyval(a,yphi), '--', lw=1, label=r'i$_{00}$=%.1f' % c)
		f = interp2d(x,y,z, kind='linear', fill_value=None, bounds_error=False) #, fill_value=0)
		f = interp2d( x, y, z, kind='linear', fill_value=None, bounds_error=False)
		else:
		# interpolate using measured data
		f = interp2d(i00, phi, phase, kind='linear',
		fill_value=None, bounds_error=False) #, fill_value=0)
		f = interp2d(i00, phi, phase, kind='linear', fill_value=None, bounds_error=False)
		x, y = np.meshgrid(i00_set, phi_set)
		z = f(i00_set, phi_set)

		@@ -112,7 +105,6 @@ def make_phase_table(phtab, polyfit=0, ncur=9, nphi=11, pos=2, threshold=0.2):
		max_abs = abs(ph_dif)
		if abs(ph_rel) > max_rel:
		max_rel = abs(ph_rel)

		log.info("i00=%9.5f phi=%9.5f, i5_fit=%8.5f i5_tab=%8.5f i5_int=%8.5f diff=(%+.4fA, %+.3f%%)",
		maincur, theta0, ph_fit, ph_tab, ph_int, ph_dif, ph_rel)
		log.info("max(diff)=(%.4fA,%.3f%%)", max_abs, max_rel)
		@@ -128,81 +120,5 @@ def make_phase_table(phtab, polyfit=0, ncur=9, nphi=11, pos=2, threshold=0.2):
		plt.xlabel(r'$\phi$ [deg]')
		plt.ylabel(r'i$_{00}$ [A]')
		#
		plt.suptitle('Phase Table')

		plt.suptitle('Phase Table Plot')
		return xi00, yphi, phase_table, (max_abs, max_rel)



		def main():
		"the main"
		# default bin selection
		selection = dict(tbin1=4, tbin2=38, xpix1=5, xpix2=27, ypix1=5, ypix2=27)
		#
		parser = argparse.ArgumentParser(description='phase table plot')
		parser.set_defaults(loglevel=1, pos=2, polyfit=2, figfile=None, threshold=0.2)
		parser.add_argument('file', metavar='filename', help='file to process', nargs='+')
		parser.add_argument('--pos', '-p', dest='pos', type=int,
		help='set instrument position (default=%(default)s)')
		parser.add_argument('--polyfit', '-f', dest='polyfit', type=int,
		help='use polyfit')
		parser.add_argument('--savefig', '-S', dest='figfile', metavar='filename',
		help='save plot to a file')
		parser.add_argument('--threshold', dest='threshold', metavar='thr', type=float,
		help='clustering threshold (advanced option)')
		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')
		args = parser.parse_args()

		log = setup_logger(args.loglevel)
		log.debug('program arguments %s', args)

		phtab = None
		for filename in args.file:
		_ , ext = os.path.splitext(os.path.basename(filename))
		if ext==".echo":
		hfile = convert_to_hdf(filename, '.', data_type='echo')
		else:
		hfile = filename
		log.info('======> input data %s', filename)
		with h5py.File(hfile, 'r') as hdf5file:
		res = get_symmetry_phase(hdf5file, **selection)
		#res = get_symmetry_phase(hdf5file)
		if phtab is None:
		phtab = res
		else:
		phtab = np.vstack((phtab,res))

		plt.figure(figsize=(12,5))


		i00, phi, phase, max_diff = make_phase_table(phtab, args.polyfit, pos=args.pos, threshold=args.threshold)


		if args.pos:
		print("input phasetable")
		print("phasetable pos%s rebuild" % args.pos)
		print("c time: ", time.asctime())
		print("c max interpolation error [%.3gA, %.3f%%]" % (max_diff[0],max_diff[1]))
		print("c command used:")
		print("c ", " ".join(sys.argv))
		print("*\t angles ", end='')
		for p in phi:
		print("%7.4f " % p, end='')
		print("\nc amperes(main) --- phase current(i5)")
		for i,c in enumerate(i00):
		print("*\t%7.3f " % c,end='')
		for j,_ in enumerate(phi):
		print("%7.4f " % phase[j,i], end='')
		print()
		print("eof")

		if args.figfile:
		plt.savefig(args.figfile)
		else:
		plt.show()

		if __name__ == "__main__":
		main()

pysen/plot/nseplot.py

+75 −8

Original line number	Diff line number	Diff line
		@@ -3,11 +3,13 @@
		nseplot: command line interface to pysen modules

		"""
		import sys
		import os.path
		import argparse
		import functools
		import logging
		import h5py
		import time

		import numpy as np
		import matplotlib as mpl
		@@ -16,6 +18,7 @@ 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.echo import get_symmetry_phase, make_phase_table
		from pysen.plot import ( plot_echo, plot_atari, plot_map,
		plot_xyz, plot_magnetic_fields,
		plot_coverage,
		@@ -142,6 +145,64 @@ def action_qtau(filenames, **kwargs):
		if savefig:
		plt.savefig(savefig)

		def action_phase_table(filenames, **kwargs):
		""""""
		phtab = None
		log = logging.getLogger()
		savefig = kwargs.pop('savefig')
		savefile = kwargs.pop('savefile')
		polyfit = kwargs.pop('polyfit')
		pos = kwargs.pop('pos')
		threshold = kwargs.pop('threshold')
		for filename in filenames:
		_ , ext = os.path.splitext(os.path.basename(filename))
		if ext==".echo":
		hfile = convert_to_hdf(filename, '.', data_type='echo')
		else:
		hfile = filename
		log.info('======> input data %s', filename)
		with h5py.File(hfile, 'r') as hdf5file:
		res = get_symmetry_phase(hdf5file, **kwargs)
		if phtab is None:
		phtab = res
		else:
		phtab = np.vstack((phtab,res))

		plt.figure(figsize=(12,5))
		i00, phi, phase, max_diff = make_phase_table(phtab, polyfit, pos=pos, threshold=threshold)
		if savefig:
		plt.savefig(savefig)

		def print_phase_table(stream=None):
		if stream:
		orig_stdout = sys.stdout
		sys.stdout = stream
		print("input phasetable")
		print("phasetable pos%s rebuild" % pos[-1])
		print("c time: ", time.asctime())
		print("c max interpolation error [%.3gA, %.3f%%]" % (max_diff[0],max_diff[1]))
		print("c command used:")
		print("c %s" % " ".join(sys.argv))
		print("*\t angles ", end='')
		for p in phi:
		print("%7.4f " % p, end='')
		print("\nc amperes(main) --- phase current(i5)")
		for i,c in enumerate(i00):
		print("*\t%7.3f " % c,end='')
		for j,_ in enumerate(phi):
		print("%7.4f " % phase[j,i], end='')
		print()
		print("eof")
		if stream:
		sys.stdout = orig_stdout

		if savefile:
		with open(savefile, 'w+') as fd:
		print_phase_table(fd)
		else:
		print_phase_table()



		# ============================================================================================
		# arguments
		@@ -158,7 +219,7 @@ def arguments_common():
		pars.add_argument('--save-figure', '-S', dest='savefig', metavar='file',
		help='save figure to a file (do not show)')
		pars.add_argument('--save-file', '-s', dest='savefile', metavar='file',
		help='save data to a .csv file')
		help='save data to a file')
		# mutually exclusive [ -v \| -q ]
		verbose = pars.add_mutually_exclusive_group()
		verbose.add_argument('--verbose', '-v', dest='loglevel', action='count',
		@@ -389,9 +450,16 @@ def add_ptab_options(subparser, parents=None):
		pars = subparser.add_parser('phase_table', parents=parents,
		help='phase table',
		description='phase table')
		pars.set_defaults(axis=-1)
		pars.add_argument('--axis', dest='axis', type=int,
		help='set axis to plot (default=%(default)s)')
		pars.set_defaults(pos='p2', polyfit=2, threshold=0.2)
		# defaults
		pars.set_defaults(tbin1=4, tbin2=38, xpix1=5, xpix2=27, ypix1=5, ypix2=27)
		pars.add_argument('file', metavar='filename', help='file to process', nargs='+')
		pars.add_argument('--pos' , '-p', dest='pos', choices=INST_POSITIONS,
		help='set instrument position: (default %(default)s)')
		pars.add_argument('--polyfit', '-f', dest='polyfit', type=int,
		help='use polyfit')
		pars.add_argument('--threshold', dest='threshold', metavar='thr', type=float,
		help='clustering threshold (advanced option)')

		# ============================================================================================
		# the main command line interface
		@@ -407,10 +475,9 @@ def main():

		parser = argparse.ArgumentParser(description=description)
		parser.set_defaults(loglevel=DEFAULT_LOG_LEVEL)
		subparsers = parser.add_subparsers(dest='plot', required=True,
		subparsers = parser.add_subparsers(dest='plot', required=False,
		help='plot command',
		description=None)
		parser.add_argument('--commands', action='version', version='waka')
		parser.add_argument('--version', '-V', action='version',
		version='%(prog)s pysen={version}'.format(version=version(full=True)))
		# echo plot
		@@ -432,7 +499,7 @@ def main():
		# qtau plot
		add_qtau_options(subparsers, parents=[pars_com,])
		# phase table
		add_ptab_options(subparsers, parents=[pars_com,])
		add_ptab_options(subparsers, parents=[pars_com,pars_tof, pars_pix])

		# ===================================
		args = parser.parse_args()
		@@ -447,7 +514,7 @@ def main():

		action = dict( echo=action_echo, atari=action_atari, maps=action_maps, bfield=action_bfield,
		xyz=action_xyz, diffrun=action_diffrun, transmission=action_transmission,
		datreat=action_datreat, qtau=action_qtau).get(args.plot, None)
		datreat=action_datreat, qtau=action_qtau, phase_table=action_phase_table).get(args.plot, None)
		if action is None:
		raise RuntimeError('missing in action')

pysen/plot/nseplotlib.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -449,9 +449,11 @@ def plot_echo(hdfile, iecho=0, **kwargs):
		n_idx = { 'dn': hdfile['/'].attrs['point_to_down'],
		'up': hdfile['/'].attrs['point_to_up'] ,
		'nphases': hdfile['/'].attrs['no_of_phases'] }
		#TODO: this does not work for J-NSE data
		nt = hdfile['/detector'].attrs['no_t_channels']
		ny = hdfile['/detector'].attrs['no_y_channels']
		nx = hdfile['/detector'].attrs['no_x_channels']

		nph = n_idx['dn']
		miny, maxy = np.inf, 0