Skip to main content
  • Home
  • Development
  • Documentation
  • Donate
  • Operational login
  • Browse the archive

swh logo
SoftwareHeritage
Software
Heritage
Archive
Features
  • Search

  • Downloads

  • Save code now

  • Add forge now

  • Help

Revision 384285f1e4152e7b962f0081e629c268bb50d8d7 authored by Jonas on 04 October 2023, 08:33:42 UTC, committed by Jonas on 04 October 2023, 08:33:42 UTC
Add link vide youtube
1 parent ad43f9c
  • Files
  • Changes
  • 1dc96b4
  • /
  • psa_wrapper.py
Raw File Download

To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

  • revision
  • directory
  • content
revision badge
swh:1:rev:384285f1e4152e7b962f0081e629c268bb50d8d7
directory badge
swh:1:dir:1dc96b42fa35ea1865d5fcfe7ecfd14cb2e50ad9
content badge
swh:1:cnt:9d9173b63c4d544dc32af72f5e70ef503b39e9e8

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

  • revision
  • directory
  • content
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
psa_wrapper.py
import subprocess
import os
import numpy
import shutil
import matplotlib
import matplotlib.pyplot as plt


def read_psa_raw_data(filename):
    field_1 = []
    field_2 = []
    with open(filename, 'r') as f:
        for line in f:
            fields = line.strip('\n').split(' ')
            assert len(fields) == 2
            field_1.append(float(fields[0]))
            field_2.append(float(fields[1]))
    return (field_1, field_2)


def psa_wrapper(samples, temp_post_fix = "", points_id=0):
    psabin_path = os.path.join(os.path.dirname(__file__), 'psa_mod/build/psabin')
    temp_path = os.path.join(os.path.dirname(__file__), 'temp' + temp_post_fix)
    if not os.path.exists(temp_path):
        os.makedirs(temp_path)
    print(os.path.curdir, os.path.exists(psabin_path))
    assert os.path.exists(psabin_path) or os.path.exists(psabin_path + '.exe')
    points_name = 'points' + str(points_id) + '_'
    points_path = os.path.join(temp_path, points_name)
    for i in range(len(samples)):
        points = samples[i]
        points_psa_txt = points_path + str(i) + '.txt'
        with open(points_psa_txt, 'w') as f:
            f.write(str(len(points)) + '\n')
            for point in points:
                f.write(str(point[0]) + ' ' + str(point[1]) + '\n')
    average = len(samples) > 1
    flags = ' '
    if average:
        flags +='--avg'
    flags += ' --raw --ani --rp --rdf --spectral '
    if average:
        path_ani = os.path.join(os.path.dirname(__file__), 'avg_ani.txt')
    else:
        path_ani = os.path.join(os.path.dirname(__file__), points_name + '0_ani.txt')
    if os.path.exists(path_ani):
        os.remove(path_ani)
    if average:
        path_rdf = os.path.join(os.path.dirname(__file__), 'avg_rdf.txt')
    else:
        path_rdf = os.path.join(os.path.dirname(__file__), points_name + '0_rdf.txt')
    if os.path.exists(path_rdf):
        os.remove(path_rdf)
    if average:
        path_rp = os.path.join(os.path.dirname(__file__), 'avg_rp.txt')
    else:
        path_rp = os.path.join(os.path.dirname(__file__), points_name + '0_rp.txt')
    if os.path.exists(path_rp):
        os.remove(path_rp)
    if average:
        path_spectral = os.path.join(os.path.dirname(__file__), 'avg_spectral.txt')
    else:
        path_spectral = os.path.join(os.path.dirname(__file__), points_name + '0_spectral.txt')
    if os.path.exists(path_spectral):
        os.remove(path_spectral)
    if average:
        cmd_str = psabin_path + flags + points_path + '*.txt'
    else:
        cmd_str = psabin_path + flags + points_path + '0.txt'
    print(subprocess.run(cmd_str, shell=True))
    # read back data from files
    with open(path_spectral, 'r') as f:
        lines = f.readlines()
        assert len(lines) == 2
        effnyquist = float(lines[0].strip('\n'))
        oscillations = float(lines[1].strip('\n'))
        print("effnyquist = " + str(effnyquist))
        print("oscillations = " + str(oscillations))
    rp_raw_data = read_psa_raw_data(path_rp)
    ani_raw_data = read_psa_raw_data(path_ani)
    rdf_raw_data = read_psa_raw_data(path_rdf)
    os.remove(path_ani)
    os.remove(path_rdf)
    os.remove(path_rp)
    os.remove(path_spectral)
    if not average:
        #os.remove(os.path.join(os.path.dirname(__file__), points_name + '0_spec.png'))
        os.remove(points_path + '0.txt')
    return (
        effnyquist,
        oscillations,
        rp_raw_data,
        ani_raw_data,
        rdf_raw_data,
    )

def plot_data(data, xlabel, ylabel, name, to_pgf=False):
    if to_pgf:
        matplotlib.use("pgf") # for latex (see https://ctan.org/pkg/pgf)
        matplotlib.rcParams.update({
            "pgf.texsystem": "pdflatex",
            'font.family': 'serif',
            'text.usetex': True,
            'pgf.rcfonts': False,
        })
    fig, ax = plt.subplots()
    ax.plot(data[0], data[1], c='k')
    ax.set(xlabel=xlabel, ylabel=ylabel)
    ax.set_xlim(left=0.0)
    if to_pgf:
        fig.savefig(filename + ".pgf")
    else:
        plt.show()

if __name__ == '__main__':
    numpy.random.seed(42)
    samples = []
    num_points = 128
    num_samples = 1
    for i in range(num_samples):
        samples.append(numpy.random.random_sample((num_points, 2)))
    print(len(samples), samples[0].shape)
    (effnyquist, oscillations, data_rp, data_ani, data_rdf) = psa_wrapper(samples)
    plot_data(data_rp, 'Frequency', 'Radial Power', 'plot_rp')
    plot_data(data_ani, 'Frequency', 'Anisotropy', 'plot_ani')
    plot_data(data_rdf, 'Distance', 'RDF', 'plot_rdf')
    # heuristic measure of anisotropy derived from raw data PSA
    print("anisotropy heuristic mean =" + str(numpy.mean(data_ani[1][1:])))
The diff you're trying to view is too large. Only the first 1000 changed files have been loaded.
Showing with 0 additions and 0 deletions (0 / 0 diffs computed)
swh spinner

Computing file changes ...

back to top

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Content policy— Contact— JavaScript license information— Web API