mag field reading (cc5343e2) · Commits · Zolnierczuk, Piotr / pysen

pysen/io/hdf.py

+46 −13

Original line number	Diff line number	Diff line
		@@ -17,16 +17,19 @@ SCHEMA_DEFAULT = {
		'sns-nse': {
		'array.plain' : ('phase', 'phase_current', 'proton_charge',),
		'array.compressible' : ('counter', 'counter_ccard', 'detector'),
		'array.phase' : ('Bfield','Temperature',), # 'Pressure'),
		'attribute.drop' : ('start', 'end', ),
		},
		'sns-nse-detimage': {
		'array.plain' : (),
		'array.compressible' : (),
		'attribute.drop' : (),
		'array.phase' : (),
		},
		'j-nse' : {
		'array.plain' : ('phase', ),
		'array.compressible' : ('counters', 'detector'),
		'array.phase' : (),
		'attribute.drop' : (),
		},
		}
		@@ -93,43 +96,73 @@ class HdfConverter:

		arrays_plain = self._schema.get('array.plain', [])
		arrays_compressible = self._schema.get('array.compressible', [])
		arrays_phase = self._schema.get('array.phase',[])

		for name, data in echo.items():
		subgroup = grpecho.create_group(name)
		self._log.debug('writing HDF5 echo point %s %s', grpecho.name, name)
		if name == 'phase': # list
		#
		for vname in arrays_plain:
		value = np.asarray([phasept[vname] for phasept in data])
		subgroup.create_dataset(vname, data=value)

		#
		for vname in arrays_compressible:
		value = np.asarray([phasept[vname] for phasept in data])
		subgroup.create_dataset(vname, data=value,
		compression=self.compression, shuffle=shuffle)
		#
		self.write_phaseinfo(data, subgroup, arrays_phase)

		else:
		self.write_pars(subgroup, data)


		def write_pars(self, group, data):
		def write_pars(self, group, data, **kwargs):
		"""write "regular" group"""
		attribute_drop = self._schema.get('attribute.drop', [])
		drop_key = kwargs.get('drop', self._schema.get('attribute.drop', []))
		for key, value in data.items():
		if key in attribute_drop:
		if key in drop_key:
		continue
		keys = key.split(".")
		subgroup, subkey = self.make_subgroup(key, group)
		if isinstance(value, np.ndarray):
		subgroup.create_dataset(subkey, data=value)
		elif key:
		value = encode(value)
		subgroup.attrs[subkey] = value

		def write_phaseinfo(self, data, group, names):
		"write phase info for names"
		phasedict = dict()
		for phasept in data:
		for key in phasept:
		if key.startswith(names):
		phasedict.setdefault(key,[])
		phasedict[key].append(phasept[key])

		for vname in phasedict:
		phasegrp, phasekey = self.make_subgroup(vname, group)
		varray = np.asarray(phasedict[vname])
		nph,_ = varray.shape
		varray = varray.reshape(nph,-1,2)
		varrd = np.asarray(varray[:,:,0], dtype=float)
		varru = np.asarray(varray[:,:,1])
		dset = phasegrp.create_dataset(phasekey, data=varrd)
		dset.attrs['unit'] = "%s" % varru[0,0]

		@staticmethod
		def make_subgroup(key, group):
		"create subgroup if necessary"
		key = key.lower()
		keys = key.split(".")
		if len(keys)>1:
		subgroup = group.require_group(keys[0])
		subkey = ".".join(keys[1:])
		else:
		subgroup = group
		subkey = key
		return subgroup, subkey

		if isinstance(value, np.ndarray):
		subgroup.create_dataset(subkey, data=value)
		elif key:
		value = encode(value)
		subgroup.attrs[subkey] = value


		def echo_to_hdf(filename, outdir, **kwargs):

pysen/revision.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -2,9 +2,9 @@
		PySEN revision module
		"""
		import sys
		__version__ = "0.6.1"
		__version__ = "0.7.0"
		__release__ = "dev1"
		__date__ = "Feb 11, 2019"
		__date__ = "Feb 13, 2019"
		#
		VERSION = __version__
		RELEASE = __release__

scripts/atariplot.py

+6 −1

Original line number	Diff line number	Diff line
		@@ -52,7 +52,12 @@ def atari_plot(hdfile, iecho=0, **kwargs):
		lam0 = physics.attrs['lambda']
		phase0 = float(tech.attrs['i5'][0])

		lmax = np.array(params['lambdaTable']).flatten()
		try:
		lmax = params['lambdatable']
		except:
		lmax = params['lambdaTable']
		lmax = np.array(lmax).flatten()

		dlam = np.ones_like(lmax)*(lmax[1]-lmax[0])

		phasesens = float(params['phaseangle'].attrs['sensitivities'][0])

scripts/echoplot.py

+6 −1

Original line number	Diff line number	Diff line
		@@ -76,7 +76,12 @@ def echo_plot(hdfile, iecho=0, **kwargs):
		lam0 = physics.attrs['lambda']
		phase0 = float(tech.attrs['i5'][0])

		lmax = np.array(params['lambdaTable']).flatten()
		try:
		lmax = params['lambdatable']
		except:
		lmax = params['lambdaTable']
		lmax = np.array(lmax).flatten()

		dlam = np.ones_like(lmax)*(lmax[1]-lmax[0])

		phasesens = float(params['phaseangle'].attrs['sensitivities'][0])

scripts/mag_field.py

0 → 100755

+147 −0

Original line number	Diff line number	Diff line
		#!/usr/bin/env python
		"ATARI Plot"

		import os.path
		import logging

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

		from pysen import ANGSTROM, NANOSECOND, OMEGA_N, MICROTM, version
		from pysen.io import echo_to_hdf
		from pysen.atarilib import fit_echo_current, Spectrum

		GAUSS2UT = 1e2 # Gauss -> micro-Tesla

		def bfield_plot(hdfile, iecho=0, **kwargs):
		"echo plot"
		#
		npix = kwargs.pop('npix', 2) # pix
		#
		tbin1 = kwargs.pop('tbin1',0) # TOF bins
		tbin2 = kwargs.pop('tbin2',None)
		#
		min_counts = kwargs.pop('min_counts', 10.0)
		max_chi2 = kwargs.pop('max_chi2' ,500.0)
		min_amp = kwargs.pop('min_amp' , 0.0)
		# FIXME: HARDCODED
		xpix1 = kwargs.pop('xpix1', 10)
		xpix2 = kwargs.pop('xpix2', 22)
		ypix1 = kwargs.pop('ypix1', 10)
		ypix2 = kwargs.pop('ypix2', 22)

		base = os.path.splitext(os.path.basename(hdfile.filename))[0]

		comment = hdfile.attrs['master_comment']
		comment = comment.decode("utf-8")
		sample = comment.split()[0]

		ntaus = hdfile.attrs['scan_length']
		nph = hdfile['/'].attrs['point_to_down']

		results = {}

		for echo in list(hdfile['/data'].values()):
		if iecho is not None and echo.attrs['id'] != iecho:
		print("skipping ", echo.name)
		continue
		else:
		print("processing", echo.name)
		pass

		phase = echo['phase']
		physics = echo['phys']
		params = echo['params']
		tech = echo['tech']

		tau0 = physics.attrs['fouriertime']/NANOSECOND
		q0 = physics.attrs['hkl'][0]
		lam0 = physics.attrs['lambda']
		cur0 = float(tech.attrs['i5'][0])
		phasesens = float(params['phaseangle'].attrs['sensitivities'][0])


		bfield = phase['bfield']
		cur = phase['phase_current'][:, 0] # actual value
		dj = np.radians(phasesens*(cur-cur0))/OMEGA_N/lam0

		nplots = int(np.ceil(np.sqrt(len(bfield))))

		fig, axes = plt.subplots(nplots,nplots, figsize=(9,6))
		fig.subplots_adjust(hspace=0.3, wspace=0.3)
		fig.suptitle(r'%s \| %s \| $\lambda$=%.2g$\AA$ $Q$=%.3f$\AA^{-1}$ $\tau$=%.3fns' % (sample, base, lam0/ANGSTROM, q0, tau0))

		for iplt, bsensor in enumerate(bfield):
		bmag = bfield[bsensor]
		ax = axes[iplt//nplots,iplt%nplots]
		t = dj[:nph]/MICROTM
		label = bsensor.split('.')[-1]
		v0 = np.sqrt(np.sum(bmag[:nph,:]*2,axis=-1))GAUSS2UT
		#
		a,b = np.polyfit(t,v0,deg=1)
		v1 = np.polyval([a,b],t)
		r = np.corrcoef(t,v0)
		r = r[1,0]
		chi2 = np.sum((v0-v1)**2)
		maxd = max(abs(v0-v1))
		#
		va = np.average(v0)
		vd = max(abs(v0-va))
		vmin = va-max(vd,0.5)
		vmax = va+max(vd,0.5)
		ax.plot(t,v0, '.', label=label)
		ax.plot(t,v1, '-')
		ax.set_ylim(bottom=vmin, top=vmax)
		ax.legend(loc='best')
		if chi2>1e-2:
		ax.set_facecolor('yellow')
		for iplt in range(iplt+1, nplots*nplots):
		ax = axes[iplt//nplots,iplt%nplots]
		ax.axis('off')


		def main():
		"the main"
		import argparse

		parser = argparse.ArgumentParser(description='echo plot')
		parser.set_defaults(loglevel=logging.INFO, outdir='.')
		parser.add_argument('file', metavar='filename', help='file to process', nargs='+')
		parser.add_argument('--echo', '-e', dest='echo', type=int, default=None,
		help='set echo to display (default=%(default)s)')
		parser.add_argument('--t1', '-t', dest='tbin1', type=int, default=0,
		help='set min TOF bin (default=%(default)s)')
		parser.add_argument('--t2', '-T', dest='tbin2', type=int, default=None,
		help='set max TOF bin (default=%(default)s)')
		parser.add_argument('--verbose', '-v', dest='loglevel', action='store_const',
		const=logging.DEBUG, help='verbose output')
		parser.add_argument('--quiet', '-q', dest='loglevel', action='store_const',
		const=logging.WARNING, help='verbose output')
		parser.add_argument('--version', action='version',
		version='%(prog)s pysen={version}'.format(version=version(full=True)))
		args = parser.parse_args()

		if args.loglevel>=logging.INFO:
		log_format=r'%(message)s'
		else:
		log_format=r'%(levelname)s: %(funcName)s: %(message)s'

		logging.basicConfig(level=args.loglevel, format=log_format)
		log = logging.getLogger()

		kwargs = vars(args)
		for filename in args.file:
		basename , ext = os.path.splitext(os.path.basename(filename))
		if ext==".echo":
		log.info('converting %s to HDF', basename)
		hfile = echo_to_hdf(filename, args.outdir)
		else:
		hfile = filename
		with h5py.File(hfile, 'r') as hdf5file:
		bfield_plot(hdf5file, iecho=args.echo, **kwargs)
		plt.show()

		if __name__ == "__main__":
		main()