getting ready for "direct nexus access" (65fb972c) · Commits · Zolnierczuk, Piotr / pysen

misc/nxs_xyz.py

0 → 100755

+87 −0

Original line number	Diff line number	Diff line
		#!/usr/bin/env python
		"Simple Atari Plot for NeXus SNS-NSE Files"
		import logging
		import argparse

		import matplotlib.pyplot as plt

		from pysen.inout.scans import XYZScan
		from pysen.plot.xyzplotlib import xyz_decomposition, plot_xyz_nexus

		class XYZ_Plot(XYZScan):
		"XYZ PLOT"
		def xyz_analysis(self):
		""" xyz analysis"""
		rates = {}

		for key, data in self.xyz.items():
		rates[key]=0.0
		if data['pcharge']>0:
		rates[key] = data['selection_counts']/data['pcharge']*1e12
		self.log.info("%s: %-6.6s = %10.2f counts/C", self.info['base'], key.upper(), rates[key])
		#
		res = xyz_decomposition(rates)
		#
		stot = res['sum_ave']
		self.log.info("%s:", self.info['base'])
		for key in ('n_coh', 'i_inc', 'm_mag'):
		self.log.info("%s: %-6.6s = %10.2f counts/C (%.2f%%)",
		self.info['base'], key.upper(), res[key], res[key]/stot*100)
		for key in ('m_up/2', 'm_dn/2',):
		self.log.info("%s: %-6.6s = %10.2f counts/C",
		self.info['base'], key.upper(), res[key])
		self.log.info("%s: TOT = %10.2f counts/C", self.info['base'], stot)
		#

		def plot(self, **kwargs):
		"plot xyz"
		plot_xyz_nexus(self.xyz, self.info, **kwargs)
		self.xyz_analysis()


		def main():
		"the main"
		parser = argparse.ArgumentParser()
		parser.set_defaults(ntof=42, npix=32,
		xpix1=10,xpix2=-10,ypix1=10,ypix2=-10, whole_detector=False,
		show=True, save=False)
		parser.add_argument('filename', metavar='file', nargs='+', help='filename to plot')

		parser.add_argument('--x1' , dest='xpix1', type=int,
		help='set min. X pix (default=%(default)s)')
		parser.add_argument('--x2' , dest='xpix2', type=int,
		help='set max. X pix (default=%(default)s)')
		parser.add_argument('--y1' , dest='ypix1', type=int,
		help='set min. Y pix (default=%(default)s)')
		parser.add_argument('--y2' , dest='ypix2', type=int,
		help='set max. Y pix (default=%(default)s)')
		parser.add_argument('--whole-detector', '-W', dest='whole_detector', action='store_true',
		help='use the whole detector')
		#
		parser.add_argument('--npix' , dest='npix', type=int,
		help='set number of pixels (default=%(default)s)')
		parser.add_argument('--ntof' , dest='ntof', type=int,
		help='set number of pixels (default=%(default)s)')
		#
		parser.add_argument('--no-show', '-N', dest='show', action='store_false',
		help='do not show plots')
		parser.add_argument('--save', '-S', dest='save', action='store_true',
		help='save figure to a file')
		args = parser.parse_args()


		logging.basicConfig(format='%(levelname)s %(message)s', level=logging.INFO)

		kwargs = vars(args)
		filenames = kwargs.pop('filename')
		for file_name in filenames:
		scan = XYZ_Plot()
		scan.read_nexus(file_name, **kwargs)
		scan.plot(**kwargs) #vmax=100)

		if args.show:
		plt.show()


		if __name__ == "__main__":
		main()

pysen/inout/init.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -5,6 +5,6 @@ from .hdf import HdfConverter, convert_to_hdf # NOQA
		from .reader import ( read_echo, read_magnetic, read_xyz, # NOQA
		read_detimage, read_datfile, read_diffrun, # NOQA
		read_datreat , read_transmission ) # NOQA
		from .writer import EchoScan, make_echofilename
		from .writer import EchoWriter, make_echofilename
		# from .legacy_writer import write_csv, generate_echo # NOQA
		# from .legacy_history import extract_data, list_variables, parse_date # NOQA

pysen/inout/nexus.py

+9 −5

Original line number	Diff line number	Diff line
		@@ -158,25 +158,29 @@ def process_scan_point(events, pcharge, ltot, begin=None, end=None, values=None)
		res['neutron'] = np.vstack((lam,pix))
		return res

		def dummy_scanpoint_callback(_args, *_kwargs):
		def _dummy_callback(_args, *_kwargs):
		"""dummy process scan point (for testing)
		a caller to process scan should override it"""
		return True

		# process scan
		def process_nexus(filename, scan_point_callback=dummy_scanpoint_callback, **kwargs):
		def process_nexus(filename, **kwargs):
		"process nexus file (scan indices)"
		scan_type = kwargs.pop('scan_type', None)
		scanpoint_cb = kwargs.pop('scanpoint_cb', _dummy_callback)
		#
		log = logging.getLogger('nexus')
		base = os.path.basename(filename)
		nxsfile = h5py.File(filename, 'r')

		# get file info
		info = get_run_info(nxsfile)
		if scan_type and scan_type not in info.get('notes','').lower():
		log.warning('not an %s scan (%s)', scan_type, info['notes'])
		return None
		if info['proton_charge']<=0.0:
		log.warning("%s: empty run (pcharge=%g)", base, info['proton_charge'])
		return None


		# get the scan indices
		scan_index = timevalue_array(nxsfile, 'scan_index', dtype=TimeIntValueDType)
		scan_index_len = len(scan_index)
		@@ -214,7 +218,7 @@ def process_nexus(filename, scan_point_callback=dummy_scanpoint_callback, **kwar
		it = info[key]['time']<=scan_index[i]['time'] # tau set before scan
		res[key] = info[key][it]['value'][-1]

		if not scan_point_callback(res, filename=base,
		if not scanpoint_cb(res, filename=base,
		begin=scan_index[i], end=scan_index[k], **kwargs):
		break
		else:

pysen/inout/nxs2echo.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -7,7 +7,7 @@ import os.path
		import logging
		import argparse

		from pysen.inout import EchoScan, make_echofilename
		from pysen.inout import EchoWriter, make_echofilename

		def main():
		"the main"
		@@ -38,7 +38,7 @@ def main():
		if not os.path.exists(file_name):
		log.warning("file '%s' does not exist", file_name)
		continue
		echo = EchoScan(make_echofilename(file_name))
		echo = EchoWriter(make_echofilename(file_name))
		if not echo.read_nexus(file_name,
		npix=args.npix, ntof=args.ntof, phase_step=args.step):
		continue

pysen/inout/scans.py

0 → 100644

+163 −0

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

		import numpy as np

		from ..config import NXCHAN as NPIX, NTCHAN as NTOF
		from .nexus import process_nexus, print_nexus_info, X0_PIX, Y0_PIX, XWID2, YWID2

		# BUNCH OF HARD CODED CONSTANTS
		# TO DO: some of this is repeated in nexus.py file (merge!)
		DEFAULT_PHASE_STEP = 45.0 # degrees

		TAU_IDX = 1000
		DN_IDX = 100
		UP_IDX = 200


		def get_tau_index(scan_idx):
		"return tau, phase index"
		idx = scan_idx['value']
		return (idx // TAU_IDX, idx % TAU_IDX)


		class EchoScan:
		"""Read SNS-NSE EPICS/NeXus echo scan file"""
		def __init__(self):
		"the constructor"
		self.log = logging.getLogger()
		self.data = {}
		self.info = None

		def phasepoint_callback(self, data, **kwargs):
		"phase point callback"
		filename = kwargs.get('filename', '<unset>')
		begin = kwargs.get('begin')
		end = kwargs.get('end')
		itau, iphase = get_tau_index(begin)
		self.data.setdefault(itau, [])
		if not self.data[itau]:
		self.log.info("%s: processing tau=%2d", filename, itau)
		self.log.debug("tau:phase=%2d:%3d index=%4d (%10.3f - %10.3f) %10.3eC %10d",
		itau, iphase, begin['value'], begin['time'], end['time'],
		data['pcharge'], data['phase'])
		data['iphase'] = iphase
		self.data[itau].append(data)
		return True

		def get_taus_and_phases(self):
		"""Get number of taus and phases"""
		indices = self.info['scan_indices']
		ctau = 0
		taus = []
		res = []
		for idx in sorted(set(indices[indices['value']>0]['value'])):
		itau = idx // TAU_IDX
		ipha = idx % TAU_IDX
		if itau != ctau:
		if res:
		taus.append((ctau, res))
		ctau = itau
		res = []
		res.append(ipha)

		if res:
		taus.append((ctau, res))

		nphases = 0
		ntaus = len(taus)
		for t,p in taus:
		has_dn, has_up = False, False
		if DN_IDX in p:
		has_dn = True
		p.remove(DN_IDX)
		if UP_IDX in p:
		has_up = True
		p.remove(UP_IDX)
		if not (has_dn and has_up):
		self.log.warning('%s: up and/or down phase missing for tau=%d', self.info['base'], t)
		if not nphases:
		nphases=len(p)
		if nphases!=len(p):
		self.log.warning('%s: tau %s has different number of phases %d (previously %d)',
		self.info['base'], t, len(p), nphases)
		return ntaus, nphases


		def read_nexus(self, nxsfile, **kwargs):
		"""read nexus file"""
		self.log.info("reading nexus file %s", nxsfile)
		#
		kwargs.setdefault('npix', NPIX)
		kwargs.setdefault('ntof', NTOF)
		kwargs.setdefault('phase_step', DEFAULT_PHASE_STEP)
		#
		self.info = process_nexus(nxsfile, scanpoint_cb=self.phasepoint_callback, scan_type='echo')
		if self.info is None:
		return False
		self.info.update(**kwargs)

		ntaus, nphases = self.get_taus_and_phases()
		self.log.info('%s: found %s taus, with %d phases in each tau', self.info['base'], ntaus, nphases)

		lmin = self.info.get('lmin', 5.0)
		lmax = self.info.get('lmax', 8.0)
		self.info['xbin'] = np.linspace(X0_PIX-XWID2, X0_PIX+XWID2, self.info['npix']+1)
		self.info['ybin'] = np.linspace(Y0_PIX-YWID2, Y0_PIX+YWID2, self.info['npix']+1)
		self.info['tbin'] = np.linspace(lmin, lmax, self.info['ntof']+1)
		self.info['nphases'] = nphases
		# debug
		self.log.debug("nexus info: %s", print_nexus_info(self.info))
		return True

		class XYZScan:
		"""Read SNS-NSE EPICS/NeXus xyz scan file"""
		def __init__(self):
		"the constructor"
		self.log = logging.getLogger()
		self.xyz = {}
		self.info = None

		def phasepoint_callback(self, data, **kwargs):
		"phase point callback"
		filename = kwargs.get('filename', '<unset>')
		begin = kwargs.get('begin')
		xyz = { 10: 'z_up',
		11: 'z_dn',
		20: 'y_up',
		21: 'y_dn',
		30: 'x_up',
		31: 'x_dn',}.get(begin['value'])

		rate=0.0
		if data['pcharge']>0:
		rate = data['neutron'].shape[1]/data['pcharge']*1e12
		self.xyz.setdefault(xyz, data)
		self.log.debug("%s: processing xyz=%s, pc=%.5f, rate=%10.1f", filename, xyz, data['pcharge']*1e-12, rate)
		return True

		def read_nexus(self, nxsfile, **kwargs):
		"""read nexus file"""
		self.log.info("reading nexus file %s", nxsfile)
		#
		kwargs.setdefault('npix', NPIX)
		kwargs.setdefault('ntof', NTOF)
		#
		self.info = process_nexus(nxsfile, scanpoint_cb=self.phasepoint_callback, scan_type='xyz')
		if self.info is None:
		return False
		self.info.update(**kwargs)
		#

		lmin = self.info.get('lmin', 5.0)
		lmax = self.info.get('lmax', 8.0)
		self.info['xbin'] = np.linspace(X0_PIX-XWID2, X0_PIX+XWID2, self.info['npix']+1)
		self.info['ybin'] = np.linspace(Y0_PIX-YWID2, Y0_PIX+YWID2, self.info['npix']+1)
		self.info['tbin'] = np.linspace(lmin, lmax, self.info['ntof']+1)
		self.log.debug("nexus info: %s", print_nexus_info(self.info))
		return True
		# EOF