added diffraction conversion to nxs2echo (ba2bf344) · Commits · Zolnierczuk, Piotr / pysen

pysen/inout/nexus.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -186,7 +186,7 @@ def _dummy_callback(_args, *_kwargs):
		return True

		# process scan
		def process_nexus(filename, **kwargs):
		def process_nexus_scan(filename, **kwargs):
		"process nexus file (scan indices)"
		scan_type = kwargs.pop('scan_type', None)
		scanpoint_cb = kwargs.pop('scanpoint_cb', _dummy_callback)

pysen/inout/nxs2echo.py

+10 −6

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

		from pysen.inout import EchoWriter
		from pysen.inout import EchoWriter, DiffractionWriter, get_nsefiletype

		def main():
		"the main"
		@@ -37,11 +37,15 @@ def main():
		if not os.path.exists(file_name):
		log.warning("file '%s' does not exist", file_name)
		continue

		writer = EchoWriter()
		#writer = DiffractionWriter()
		if not writer.read_nexus(file_name, npix=args.npix, ntof=args.ntof,
		phase_step=args.step):
		file_type = get_nsefiletype(file_name)
		writer_class = { 'application/nexus-nse-echo' : EchoWriter,
		'application/nexus-diffraction' : DiffractionWriter,
		}.get(file_type, None)
		if not isinstance(writer_class, type):
		log.warning("file '%s' unknown file type %s", file_name, file_type)
		continue
		writer = writer_class()
		if not writer.read_nexus(file_name, npix=args.npix, ntof=args.ntof, phase_step=args.step):
		continue
		writer.save(outdir=args.outdir)

pysen/inout/scans.py

+34 −2

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ 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
		from .nexus import process_nexus_scan, print_nexus_info, X0_PIX, Y0_PIX, XWID2, YWID2

		# BUNCH OF HARD CODED CONSTANTS

		@@ -45,7 +45,7 @@ class BaseScan:
		kwargs.setdefault('ntof', NTOF)
		scan_type = kwargs.setdefault('scan_type', None)
		#
		self.info = process_nexus(nxsfile, scanpoint_cb=self.phasepoint_callback,
		self.info = process_nexus_scan(nxsfile, scanpoint_cb=self.phasepoint_callback,
		scan_type=scan_type)
		if self.info is None:
		return False
		@@ -61,6 +61,38 @@ class BaseScan:
		self.log.debug("nexus info: %s", print_nexus_info(self.info))
		return True

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

		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)
		scan_type = kwargs.setdefault('scan_type', None)
		#
		self.info = process_nexus_scan(nxsfile, scanpoint_cb=self.phasepoint_callback,
		scan_type=scan_type)
		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)
		#
		# debug
		self.log.debug("nexus info: %s", print_nexus_info(self.info))
		return True

		class DiffractionScan(BaseScan):
		"""Read SNS-NSE EPICS/NeXus diffraction scan file

test/test_fit.py

+9 −1

Original line number	Diff line number	Diff line
		@@ -22,10 +22,12 @@ class FitModelTestCase(unittest.TestCase):
		err = 0.01

		def setUp(self):
		# initalize random number generator for unit testing
		rng = np.random.default_rng(1966)
		t = np.logspace(np.log10(self.tmin), np.log10(self.tmax), 101)
		sqt = kww( t,self.t0, self.beta)*self.norm
		sqt_err = self.err*sqt
		sqt = sqt+np.random.normal(0,sqt_err)
		sqt = sqt+rng.normal(0,sqt_err)
		self.t = t
		self.sqt = (sqt, sqt_err)

		@@ -36,6 +38,12 @@ class FitModelTestCase(unittest.TestCase):
		"basic fitting test"
		model = FitModel(FitFunction('kww', norm=True))
		model.fit(tau=self.t, sqt=self.sqt[0], sqt_err=self.sqt[1])

		#print("Normalized KWW function", model.__doc__.split('\n')[0])
		#print((model.results['pars'][0]-self.t0 )/self.t0 < self.err)
		#print((model.results['pars'][1]-self.beta)/self.beta, self.err)
		#print((model.results['pars'][2]-self.norm)/self.norm, self.err)

		self.assertEqual("Normalized KWW function", model.__doc__.split('\n')[0])
		self.assertTrue(abs(model.results['pars'][0]-self.t0 )/self.t0 < self.err)
		self.assertTrue(abs(model.results['pars'][1]-self.beta)/self.beta < self.err)

test/test_inout_nexus.py

+8 −3

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ import h5py
		import numpy as np

		from pysen.inout.nexus import (pixel_decompose, timevalue_array, get_slice_average,
		process_nexus, get_run_info, time_format)
		process_nexus_scan, get_run_info, time_format)

		TestDataDir = os.path.join(os.path.dirname(__file__), 'data')

		@@ -93,9 +93,14 @@ class InOut_Nexus_TestCase(unittest.TestCase):
		self.assertAlmostEqual(t, times[i] , places=1, msg=f"time {key}[{i}]: {t:.2f}!={times[i]:.2f}")
		self.assertAlmostEqual(v, vals[key][i], places=2, msg=f"value {key}[{i}]: {v:.2f}!={vals[key][i]:.2f}")

		def z_test_z_process_nexus(self):
		def z_test_z_process_nexus_plain(self):
		"test nexus processing"
		res = process_nexus(self.filename)
		res = process_nexus_scan(self.filename)
		print(res)

		def z_test_z_process_nexus_scan(self):
		"test nexus processing"
		res = process_nexus_scan(self.filename)
		print(res)

		if __name__ == "__main__":