Commit 813945c4 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

transmission plot bugfix

parent f162deab

misc/fix_nexus_indices.py

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+44 −0
Original line number Diff line number Diff line 
#!/usr/bin/env python



import sys

import os.path

import shutil

import h5py

import numpy as np



filename = sys.argv[1]

cut_index = int(sys.argv[2])

basename = os.path.join('.', os.path.basename(filename))

print(basename, cut_index)



shutil.copy(filename, basename)



hf = h5py.File(basename, mode='r+')



scan_index = hf['/entry/DASlogs/scan_index']

si_values = scan_index['value']

si_times  = scan_index['time']

#

si_ave     = scan_index['average_value']

si_ave_err = scan_index['average_value_error']

si_min     = scan_index['minimum_value']

si_max     = scan_index['maximum_value']



si_values[:cut_index]=0

si_times [:cut_index]=0

for i,(t,v) in enumerate(zip(si_times [cut_index-10:cut_index+10],

                             si_values[cut_index-10:cut_index+10])):

    print(f"{i:8d}, {t:8.2f}, {v:8d}")



si_ave = np.average(si_values)    



scan_index['average_value'][0]        = np.average(si_values)

scan_index['average_value_error'][0]  = np.std(si_values)

scan_index['minimum_value'][0]        = np.min(si_values)

scan_index['maximum_value'][0]        = np.max(si_values)

scan_index['value'][:] = si_values[:]

scan_index['time'][:]  = si_times[:]



hf.close()

misc/fix_nexus_title.py

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+25 −0
Original line number Diff line number Diff line 
#!/usr/bin/env python



import sys

import os.path

import shutil

import h5py

import numpy as np



filename  = sys.argv[1]

new_title = sys.argv[2]

basename = os.path.join('.', os.path.basename(filename))



shutil.copy(filename, basename)



hf = h5py.File(basename, mode='r+')



old_title = hf['/entry/title'][0].decode('ascii')

hf['/entry/title'][0] = new_title.encode('ascii')

print(basename)

print(old_title)

print(new_title)



hf.close()

pysen/plot/qplot.py

+5 −5
Original line number Diff line number Diff line
@@ -432,7 +432,7 @@ def plot_transmission_single(axs, filename, **kwargs): 
    counts  = np.asarray(data["detector array"])

    ecounts = sqrt(counts)

    lmax    = data['wavelength']/ANGSTROM

    sample  = data.get('sample', '')

    sample  = data.get('sample', '').lstrip('_') # remove leading '_'

    proposal = data.get('proposal')

    try:

        prop = proposal.split()
@@ -481,9 +481,9 @@ def plot_transmission(ax0, ax1, filenames, **kwargs): 
    ax0.set_ylabel('Counts/PCharge')

    ax0.grid(True)

    if len(filenames)>5:

        ax0.legend(ncol=2)

        ax0.legend(ncol=2, loc=0)

    else:

        ax0.legend()

        ax0.legend(loc=0)



    if spectrum_only:

        ax0.set_xlabel(r'Neutron Wavelength [$\AA$]')
@@ -503,7 +503,7 @@ def plot_transmission(ax0, ax1, filenames, **kwargs): 
        ax1.errorbar(w, tfac, yerr=efac, fmt='.', color=color, ms=0.01, lw=1.0)

        if polyfit is None:

            ax1.axhline(tavg, color=color, ls='--', lw=0.5)

            out.write("%-20.20s %.4g +/- %.4g\n" % (s, tavg, etavg))

            out.write("%-32.32s %.4g +/- %.4g\n" % (s, tavg, etavg))

        else:

            a = np.polyfit(w, tfac, deg=polyfit)

            ax1.plot(w, np.polyval(a,w), '--',lw=0.5, color=color)
@@ -636,7 +636,7 @@ def action_transmission(filenames, **kwargs): 
                outfiles = convert_files(filename, outdir='.', converter='to_taco')

                new_filenames.extend(outfiles)

            elif filetype == 'application/taco-nse-transmission':

                new_filenames.append(outfiles)

                new_filenames.append(filename)

            else:

                log.warning("File %s is not a transmission file", filename)

                continue

pysen/revision.py

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

import sys

__version__  = "2.1"

__release__  = "b4"

__date__     = "Apr 2, 2025"

__release__  = "b5"

__date__     = "Apr 15, 2025"



def version(full=False):

    "get pysen version number"

test/data/sample1_chol30_pp2p5_bin.dat

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+11395 −0

File added.

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