handle missing up/down phases (6392579c) · Commits · Zolnierczuk, Piotr / pysen

pysen/inout/reader.py

+5 −5

Original line number	Diff line number	Diff line
		@@ -488,7 +488,7 @@ def read_echo(filename):
		slength = result.scan.pop('scan0_length' , -1)
		nphase = result.scan.get('no_of_phases')

		_log.debug('read preamble')
		_log.debug('read preamble: sparam=%s, slength=%s, nphase=%s', sparam, slength, nphase)
		data = []
		act_slength = 0
		while True:
		@@ -507,10 +507,10 @@ def read_echo(filename):
		for _ip in range(nphase) ]
		data.append(AttrDict(zip(('tech', 'phys', 'params', 'phase'),
		( tech, physics , params, phasept))))
		_log.info(r'read %s=%d/%d', sparam, act_slength, slength)
		_log.info(r'read_echo %s=%d/%d', sparam, act_slength, slength)
		#print('.',end='', flush=True)
		except RuntimeError as exc:
		_log.warning('read %s=%d/%d failed (%s), skipping it...', sparam, act_slength, slength, str(exc))
		_log.warning('read_echo %s=%d/%d failed (%s), skipping it...', sparam, act_slength, slength, str(exc))
		act_slength = act_slength -1
		continue # skip this
		# PAZ - FIXME - allow for incomplete runs
		@@ -742,9 +742,9 @@ def read_xyz(filename):
		detector = parse_detimage(lines)
		data.append(AttrDict(zip(('xyz', 'params', 'tech', 'detector'),
		( xyz , params, tech, detector ))))
		_log.info(r'read %s=%d/%d', sparam, act_length, length)
		_log.info(r'read_xyz %s=%d/%d', sparam, act_length, length)
		except RuntimeError as exc:
		_log.warning('read %s=%d/%d failed (%s), skipping it...', sparam, act_length, length, str(exc))
		_log.warning('read_xyz %s=%d/%d failed (%s), skipping it...', sparam, act_length, length, str(exc))
		act_length = act_length -1
		continue # skip this
		except StopIteration:

pysen/inout/scans.py

+10 −5

Original line number	Diff line number	Diff line
		@@ -173,29 +173,33 @@ class EchoScan(BaseScan):
		ctau = itau
		res = []
		res.append(ipha)

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

		# loop over taus and check that up and down phases are present
		# and number of phases is the same for all taus
		nphases = 0
		ntaus = len(taus)
		updn_present = True
		for t,p in taus:
		has_dn, has_up = False, False
		if DN_IDX in p:
		has_dn = True
		p.remove(DN_IDX)
		has_dn = True
		if UP_IDX in p:
		has_up = True
		p.remove(UP_IDX)
		has_up = True
		if not (has_dn and has_up):
		self.log.warning('%s: up and/or down phase missing for tau=%d',
		self.info['base'], t)
		updn_present = updn_present and has_up and has_dn
		# check number of phases
		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
		return ntaus, nphases, updn_present

		def get_phase_step(self, npha, max_phase_step=180.0):
		"get average phase step and round it to a degree"
		@@ -224,7 +228,7 @@ class EchoScan(BaseScan):
		if not super().read_nexus(nxsfilename, scan_type='echo', **kwargs):
		return False

		ntaus, nphases = self.get_taus_and_phases()
		ntaus, nphases, has_updn = self.get_taus_and_phases()
		avg_step = self.get_phase_step(nphases)
		if phase_step is None:
		phase_step = round(avg_step,0)
		@@ -235,6 +239,7 @@ class EchoScan(BaseScan):

		self.info['nphases'] = nphases
		self.info['phase_step'] = phase_step
		self.info['has_updn'] = has_updn

		# post processing
		self.log.info('%s: found %s tau(s), %d phases/tau, phase_step=%g (deg)',

pysen/inout/writer.py

+8 −2

Original line number	Diff line number	Diff line
		@@ -206,9 +206,15 @@ class EchoWriter(EchoScan):
		out.write(f"scan {echobase}\n")
		out.write( "* presetcounter time\n")
		out.write(f"* preset {preset:.2f}\n")
		if self.info.get('has_updn'):
		out.write(f"* no_of_phases {nphases+PHASE_UP}\n")
		else:
		out.write(f"* no_of_phases {nphases}\n")
		out.write(f"* point_to_down {nphases}\n")
		if self.info.get('has_updn'):
		out.write(f"* point_to_up {nphases+PHASE_DN}\n")
		else:
		out.write(f"* point_to_up {nphases}\n")
		out.write(f"* phase_step {phastep}\n")
		out.write( "eof\n\n")
		return out.getvalue()

pysen/plot/nseplotlib.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -260,7 +260,7 @@ def plot_atari(hdfile, iecho=None, **kwargs):
		ax.axhline(ypix2-1, color='gray')

		ax.text(0.00, 1.01, rf"Q={qave:.3f}$\pm${qvar:.3f} $\AA^{-1}$", transform=ax.transAxes)
		ax.text(0.55, 1.01, rf"$\tau$={tave:.3f}$\pm${tvar:.3f} ns", transform=ax.transAxes)
		ax.text(0.55, 1.01, rf"$\tau$={tave:.3g}$\pm${tvar:.2g} ns", transform=ax.transAxes)

		ax = axes[1,1]
		pha = det [:,ypix1:ypix2,xpix1:xpix2,tbin1:tbin2]
		@@ -308,8 +308,8 @@ def plot_atari(hdfile, iecho=None, **kwargs):
		_amp[0], _amp[1],
		res['average'][0], res['average'][1])
		else:
		res['up'] = average(up),sqrt(sum(up)/len(up))
		res['dn'] = average(dn),sqrt(sum(dn)/len(dn))
		res['up'] = average(up),sqrt(sum(up)/max(1,len(up)))
		res['dn'] = average(dn),sqrt(sum(dn)/max(1,len(dn)))
		fres = 2*res['amplitude'][0]/( res['up'][0] - res['dn'][0] )
		e_fres = fres * res['amplitude'][1]/res['amplitude'][0]
		ax.errorbar(cur[nph:n_idx['up']], dn, fmt='.', color=dcol)
		@@ -323,7 +323,7 @@ def plot_atari(hdfile, iecho=None, **kwargs):
		res['amplitude'][0], res['amplitude'][1],
		res['up'][0], res['up'][1],
		res['dn'][0], res['dn'][1])
		ax.text(0.01, 1.01, _txt, transform=ax.transAxes)
		ax.text(0.50, 1.01, _txt, transform=ax.transAxes, horizontalalignment='center')
		if savefile:
		label=f"tau={tave:.3g}ns"
		outfile =f"{savefile}-{label}"

pysen/revision.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -2,8 +2,8 @@
		PySEN revision module
		"""
		import sys
		__version__ = "2.1.0.dev10"
		__date__ = "Mar 19, 2026"
		__version__ = "2.1.0.dev11"
		__date__ = "Apr 13, 2026"

		def version(full=False):
		"get pysen version number"