Commit 227e49b1 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

bug fixes 

- clarify nseplot help messages
- bugfix in echowriter (missing f-format)
- test fixture fix (timestamps)
parent c5c13ccb

pysen/inout/writer.py

+1 −1
Original line number Diff line number Diff line
@@ -366,7 +366,7 @@ class EchoWriter(EchoScan): 
                fd.write(f"phi =    {phi:g} \n")

                fd.write(f"psi =    {psi:g} \n")

                fd.write(f"q =      {qmin/ANGSTROM:g} /m ")

                fd.write( "( {qmin*sx/ANGSTROM:g}, {qmin*cx/ANGSTROM:g}, 0.0 ) \n")

                fd.write(f"( {qmin*sx/ANGSTROM:g}, {qmin*cx/ANGSTROM:g}, 0.0 ) \n")

                fd.write(f"hkl =    {qmin:g} ( {qmin*sx:g}, {qmin*cx:g}, 0.0 ) \n")

                fd.write(f"fouriertime ............:  {ftau:g} \n")

                fd.write(f"phaseangle sensitivities:  {phasesens:g}     0.000000 deg/a\n")

pysen/physics/nscatt.py

+2 −0
Original line number Diff line number Diff line
@@ -53,7 +53,9 @@ t --> nanoseconds 
import numpy as np



from numpy import pi, cos, exp, sqrt, mgrid, atleast_1d, asarray, sum as npsum, where, expm1

#pylint: disable=no-name-in-module

from scipy.special   import erfc

#pylint: enable=no-name-in-module

from scipy.integrate import quad

from scipy.constants import (Boltzmann as k_B, angstrom as ANGSTROM)

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__  = ".6a"

__date__     = "Aug 27, 2025"

__release__  = ".6"

__date__     = "Sep 2, 2025"



def version(full=False):

    "get pysen version number"

pysen/ui/nseplot.py

+8 −8
Original line number Diff line number Diff line
@@ -40,18 +40,18 @@ def arguments_common(): 
    verbose.add_argument('--verbose', '-v', dest='loglevel', action='count',

                        help='verbose output')

    verbose.add_argument('--quiet',   '-q', dest='loglevel', action='store_const', const=0,

                        help='suppress terminal output')

                        help='succinct output')

    return pars



def arguments_savefig():

def arguments_saveopt():

    "savefig arguments"

    pars = argparse.ArgumentParser(add_help=False)

    pars.set_defaults(savefile=None, savefig=None, outdir='.')

    # save figure/data options

    pars.add_argument('--output-file', '-o', dest='savefile', metavar='file',

                        help='save resulting data (if any) to a file.')

    pars.add_argument('--save-figure', '-S', dest='savefig', metavar='file',

                        help='save the output figure to a file and do not show it.')

    pars.add_argument('--output-data', '-o', dest='savefile', metavar='file',

                        help='write the resulting data (if any) to a file.')

    return pars



def arguments_selection_tof():
@@ -120,7 +120,7 @@ def add_echo_options(subparser, parents=None): 
    pars.add_argument('--only-echo', dest='only_echo', action='store_true',

                       help='show only echo (no up/down)')

    pars.add_argument('--incoherent', '-I', dest='incoherent', action='store_true',

                       help='treat data as from incoherent scatterer')

                       help='assume incoherent scatterer')

    pars.add_argument('--absolute-y', '-Y', dest='absy', metavar='V', type=float,

                       help='use the same vertical scale for all pixels')

    pars.add_argument('--num-pix', '-N', dest='npix', metavar='N', type=int,
@@ -142,9 +142,9 @@ def add_atari_options(subparser, parents=None): 
    pars.add_argument('--only-echo', dest='only_echo', action='store_true',

                      help='show only echo (no up/down)')

    pars.add_argument('--incoherent', '-I', dest='incoherent', action='store_true',

                      help='treat data as from incoherent scatterer')

                      help='assume incoherent scatterer')

    pars.add_argument('--phase0' , dest='phase0', type=float,

                      help='set inital phase for echo fitting (default=%(default)s)')

                      help='set inital phase for echo fitting (default it to read it from the data file)')



def add_old_xyz_options(subparser, parents=None):

    "xyz options"
@@ -367,7 +367,7 @@ def main(): 
                        version='%(prog)s pysen={version}'.format(version=version(full=True)))

    #

    pars_com  = arguments_common()

    pars_fig  = arguments_savefig()

    pars_fig  = arguments_saveopt()

    pars_tof  = arguments_selection_tof()

    pars_pix  = arguments_selection_pix()

    pars_zsc  = arguments_z_scale()

test/test_inout_utils.py

+13 −1
Original line number Diff line number Diff line
@@ -3,8 +3,8 @@ Python unit test cases for pysen.io.utils module 
"""



import unittest

import os

import os.path

#import logging

import gzip

import bz2
@@ -17,6 +17,15 @@ class IOUtilsTestCase(unittest.TestCase): 
    def setUp(self):

        "Setup"



        # make sure that nexus files have correct times

        file0 = os.path.join(TestDataDir,'NSE_15617.nxs.h5')

        atime = os.stat(file0).st_atime

        mtime = os.stat(file0).st_mtime

        for i, fname in enumerate(('NSE_15774.nxs.h5', 'NSE_16247.nxs.h5', 'NSE_16250.nxs.h5')):

            file1 = os.path.join(TestDataDir,fname)

            os.utime(file1, (atime, mtime+(i+1)*600))





    def tearDown(self):

        "Tear-down method"
@@ -101,6 +110,9 @@ class IOUtilsTestCase(unittest.TestCase): 


        # both files exist

        # GO    out=15617 is older than inp=16247

        # make sure that this is true :)





        self.assertFalse(utils.is_file_newer( os.path.join(TestDataDir,'NSE_15617.nxs.h5'),

                                              os.path.join(TestDataDir,'NSE_16247.nxs.h5')))

        # STOP  out=16247 is newer than inp=15617