Commit 6fa2ad68 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

infer the phase step

parent 93ba1454

pysen/inout/nxs2echo.py

+2 −2
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ from pysen.inout import EchoWriter, make_echofilename 
def main():

    "the main"

    parser = argparse.ArgumentParser()

    parser.set_defaults(ntof=42, npix=32, step=45.0, outdir='.', loglevel=logging.INFO)

    parser.set_defaults(ntof=42, npix=32, step=None, outdir='.', loglevel=logging.INFO)

    parser.add_argument('filename', metavar='file', nargs='+', help='filename to convert')

    parser.add_argument('--outdir', '-o', metavar='out', dest='outdir',

                        help='set output directory (default %(default)s)')
@@ -21,7 +21,7 @@ def main(): 
    parser.add_argument('--ntof', '-T', type=int, dest='ntof',

                        help='set number of tof channels (default %(default)s)')

    parser.add_argument('--step', '-S', type=float, dest='step',

                        help='set precession phase step (default %(default)s)')

                        help='set precession phase step (default: find it from the NeXus file)')

    #

    parser.add_argument('--verbose', '-v', dest='loglevel', action='store_const',

                        const=logging.DEBUG,   help='increase verbosity level')

pysen/inout/scans.py

+28 −6
Original line number Diff line number Diff line
@@ -11,8 +11,6 @@ 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
@@ -119,16 +117,40 @@ class EchoScan(BaseScan): 
                    self.info['base'], t, len(p), nphases)

        return ntaus, nphases



    def get_phase_step(self, phase_step, max_delta=1.0):

        "get average phase step and round it to a degree"

        phasesens   = self.info.get('phasesens')

        nphases     = self.info.get('nphases')

        act_phase_step  = []

        for tau in self.data.values():

            phases = np.asarray([ _pha['phase'] for _pha in tau ])

            phases = phases[:nphases]

            dpha = phases[1:]-phases[:-1]

            act_phase_step.append(list(dpha*phasesens))

        act_phase_step = np.asarray(act_phase_step)

        avg_phase_step = np.average(act_phase_step)

        avg_phase_step = round(avg_phase_step,0)



        if phase_step is None:

            return avg_phase_step



        if abs(avg_phase_step-phase_step)>max_delta:

            self.log.warning("%s: used phase step %g (deg), but actual is %g (deg)",

                            self.info['base'], phase_step, avg_phase_step)

        return phase_step



    def read_nexus(self, nxsfile, **kwargs):

        """read nexus file"""

        kwargs.setdefault('phase_step', DEFAULT_PHASE_STEP)

        phase_step = kwargs.pop('phase_step')

        if not super().read_nexus(nxsfile, scan_type='echo', **kwargs):

            return False

        ntaus, nphases = self.get_taus_and_phases()

        self.info['nphases']    = nphases

        self.log.info('%s: found %s taus, with %d phases in each tau',

            self.info['base'], ntaus, nphases)

        self.info['phase_step'] = self.get_phase_step(phase_step)

        # post processing

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

            self.info['base'], ntaus, nphases, self.info['phase_step'])



        return True



class XYZScan(BaseScan):

pysen/inout/writer.py

+2 −2
Original line number Diff line number Diff line
@@ -147,9 +147,8 @@ class EchoWriter(EchoScan): 
        out.write( "\n")

        return out.getvalue()





    def to_echo(self, outdir='.'):

        "phase point callback"

        "convert read nexus file to .echo file"

        with open(os.path.join(outdir, self.echofile), 'wt', encoding='ascii') as fd:

            #

            self.log.info("%s: creating echo file", self.echofile)
@@ -164,6 +163,7 @@ class EchoWriter(EchoScan): 
            qmin = self.info.get('qmin')

            sample_temp = self.info.get('sample_temp')

            phasesens   = self.info.get('phasesens')



            for it,tau in enumerate(self.data):

                self.log.info("%s: writing tau=%2d", self.echofile, tau)

                #res1   = self.data[tau][ 0] # first phase

pysen/revision.py

+2 −2
Original line number Diff line number Diff line
@@ -3,8 +3,8 @@ PySEN revision module 
"""

import sys

__version__  = "2.0"

__release__  = "b4"

__date__     = "Feb 4, 2025"

__release__  = "b5"

__date__     = "Feb 11, 2025"



def version(full=False):

    "get pysen version number"