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

https://github.com/hpc-maths/GenEO
21 May 2024, 17:50:58 UTC
  • Code
  • Branches (7)
  • Releases (0)
  • Visits
    • Branches
    • Releases
    • HEAD
    • refs/github-services/pull/1/head
    • refs/github-services/pull/2/head
    • refs/github-services/pull/3/head
    • refs/heads/PCAWG
    • refs/heads/elasticity-x
    • refs/heads/master
    • refs/heads/matis
    No releases to show
  • b13ca60
  • /
  • notebooks
  • /
  • plot.py
Raw File Download Save again
Take a new snapshot of a software origin

If the archived software origin currently browsed is not synchronized with its upstream version (for instance when new commits have been issued), you can explicitly request Software Heritage to take a new snapshot of it.

Use the form below to proceed. Once a request has been submitted and accepted, it will be processed as soon as possible. You can then check its processing state by visiting this dedicated page.
swh spinner

Processing "take a new snapshot" request ...

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.

  • content
  • directory
  • revision
  • snapshot
origin badgecontent badge
swh:1:cnt:d626244f8a6ade39498e51fa13137f8e19d32b05
origin badgedirectory badge
swh:1:dir:2acb7a7e5a469121c98d7affc016b75625702cc9
origin badgerevision badge
swh:1:rev:47b05ef7165f6cee92daa3002503259f0ec84695
origin badgesnapshot badge
swh:1:snp:5600c58bc442523ff2d2f69616f3f4483ec0d504

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.

  • content
  • directory
  • revision
  • snapshot
(requires biblatex-software package)
Generating citation ...
(requires biblatex-software package)
Generating citation ...
(requires biblatex-software package)
Generating citation ...
(requires biblatex-software package)
Generating citation ...
Tip revision: 47b05ef7165f6cee92daa3002503259f0ec84695 authored by gouarin on 28 May 2018, 11:31:32 UTC
fix binder
Tip revision: 47b05ef
plot.py
import vtk
from vtk.util.numpy_support import vtk_to_numpy
import numpy as np
from pythreejs import *
import ipywidgets as widgets
from collections import OrderedDict
from glob import glob

def scalar2rgb(x, cmap='rainbow'):
    import matplotlib.cm, matplotlib.colors
    cNorm = matplotlib.colors.Normalize(vmin=x.min(), vmax=x.max())
    colormap = matplotlib.cm.ScalarMappable(norm=cNorm, cmap=cmap)
    return colormap.to_rgba(x)[..., :3]


def read_data(filename):
    reader = vtk.vtkXMLStructuredGridReader()
    reader.SetFileName(filename)
    reader.Update()
    output = reader.GetOutput()
    data_arrays = output.GetPointData()
    numpy_arrays = [vtk_to_numpy(data_arrays.GetArray(i)) for i in range(data_arrays.GetNumberOfArrays())]
    coords = vtk_to_numpy(output.GetPoints().GetData())
    dim = output.GetDataDimension()
    ncells = reader.GetNumberOfCells()
    elements = np.zeros((ncells, 2 ** dim), dtype=np.uint16)
    for ic in range(ncells):
        c = output.GetCell(ic)
        elements[ic] = [c.GetPointId(ip) for ip in range(c.GetNumberOfPoints())]

    if dim == 2:
        fieldnames = [
         'u', 'v', 'lambda', 'rank']
    else:
        fieldnames = [
         'u', 'v', 'v', 'lambda', 'rank']
    return (
     dim, coords, elements, numpy_arrays, fieldnames)


def read_coarse_vec(filename):
    reader = vtk.vtkXMLStructuredGridReader()
    reader.SetFileName(filename)
    reader.Update()
    output = reader.GetOutput()
    data_arrays = output.GetPointData()
    numpy_arrays = [vtk_to_numpy(data_arrays.GetArray(i)) for i in range(data_arrays.GetNumberOfArrays())]
    return numpy_arrays


def get_faces_and_edges(index):
    if index.shape[1] == 4:
        faces = np.concatenate((index[:, :3], index[:, (0, 2, 3)]))
        edges = np.concatenate((index[:, (0, 1)], index[:, (1, 2)], index[:, (2, 3)], index[:, (3, 0)]))
    else:
        t = ((0, 1, 2), (0, 2, 3), (4, 5, 6), (4, 6, 7), (1, 5, 6), (1, 6, 2), (0, 4, 7),
             (0, 7, 3), (3, 2, 6), (3, 6, 7), (0, 1, 5), (0, 5, 4))
        f = []
        for i in t:
            f.append(index[:, i])

        t = ((0, 1), (1, 2), (2, 3), (3, 0), (4, 5), (5, 6), (6, 7), (7, 4), (0, 4),
             (1, 5), (3, 7), (2, 6))
        e = []
        for i in t:
            e.append(index[:, i])

        faces = np.concatenate(f)
        edges = np.concatenate(e)
    return (faces, edges)


def plot_solution(path, filename):
    coarse_vecs = []
    coarse_files = glob(path + '/coarse_vec*.vts')
    coarse_files.sort()
    for f in coarse_files:
        coarse_vecs.append(read_coarse_vec(f))

    dim, coords, index, numpy_arrays, fieldnames = read_data(path + '/' + filename)
    work = np.zeros_like(coords)
    faces_, edges_ = get_faces_and_edges(index)
    irank = fieldnames.index('rank')
    faces_by_rank = []
    edges_by_rank = []
    for i in range(int(numpy_arrays[irank].max()) + 1):
        mask = numpy_arrays[irank] == i
        ranges = np.arange(mask.size)[mask]
        indices = np.in1d(faces_, ranges)
        indices = np.all(indices.reshape(faces_.shape), axis=1)
        faces_by_rank.append(faces_[indices])
        indices = np.in1d(edges_, ranges)
        indices = np.all(indices.reshape(edges_.shape), axis=1)
        edges_by_rank.append(edges_[indices])

    bcolor = BufferAttribute(array=scalar2rgb(numpy_arrays[0])[faces_],
      normalized=False)
    vertices = BufferAttribute(array=coords[faces_].reshape(-1, 3),
      normalized=False)
    geometry = BufferGeometry(attributes={'position':vertices, 
     'color':bcolor})
    material = MeshBasicMaterial(color='0xffffff', wireframe=True)
    material_color = MeshLambertMaterial(side='DoubleSide',
      color='0xF5F5F5',
      vertexColors='VertexColors',
      transparent=True,
      opacity=0.5)
    mesh_color = Mesh(geometry, material_color)
    edges = BufferAttribute(array=coords[edges_].reshape(-1, 3),
      normalized=False)
    geom_edges = BufferGeometry(attributes={'position': edges})
    material = LineBasicMaterial(color='0xffffff', linewidth=1)
    mesh = LineSegments(geom_edges, material)
    view_width = 600
    view_height = 600
    camera = PerspectiveCamera(fov=50, position=[0, 0, 13], aspect=view_width / view_height)
    ambient_light = AmbientLight()
    scene = Scene()
    scene.add(mesh_color)
    scene.add(mesh)
    scene.add(ambient_light)
    minCoords = coords.min(axis=0)
    maxCoords = coords.max(axis=0)
    midCoords = 0.5 * (minCoords + maxCoords)
    scene.position = tuple(-midCoords)
    scene.background = 'black'
    controller = OrbitControls(controlling=camera)
    if dim == 2:
        controller.enableRotate = False
    renderer = Renderer(camera=camera, scene=scene, controls=[controller], width=view_width,
      height=view_height)
    fields = OrderedDict()
    for v, k in enumerate(fieldnames):
        fields[k] = v

    select = widgets.Dropdown(options=fields,
      value=0,
      description='Fields')
    irank = fieldnames.index('rank')
    domain = OrderedDict({'all': -1})
    for i in range(int(numpy_arrays[irank].max()) + 1):
        domain[('domain {}').format(i)] = i

    select_dom = widgets.Dropdown(options=domain,
      value=-1,
      description='domains')
    coarse_vecs_label = OrderedDict({'none': -1})
    for i in range(len(coarse_vecs)):
        coarse_vecs_label[('coarse vec {}').format(i)] = i

    select_coarse_vecs = widgets.Dropdown(options=coarse_vecs_label,
      value=-1,
      description='coarse vecs')
    show_displacement = widgets.Checkbox(value=False,
      description='Show displacement',
      disabled=False)
    show_mesh = widgets.Checkbox(value=True,
      description='Show mesh',
      disabled=False)
    scale = widgets.IntSlider(value=100,
      min=1,
      max=1000,
      step=1,
      description='Scale factor for coarse vec displacement',
      disabled=False,
      continuous_update=False,
      orientation='horizontal')

    def draw_mesh(change):
        mesh.visible = not mesh.visible

    def update_domain(change):
        rank = select_dom.value
        work[:] = coords
        if show_displacement.value:
            if select_coarse_vecs.value == -1:
                for i in range(dim):
                    work[(..., i)] += numpy_arrays[i]

            else:
                for i in range(dim):
                    work[(..., i)] += scale.value * coarse_vecs[select_coarse_vecs.value][i]

            if rank >= 0:
                new_coords = work[faces_by_rank[rank]].reshape(-1, 3)
                minCoords = new_coords.min(axis=0)
                maxCoords = new_coords.max(axis=0)
                midCoords = 0.5 * (minCoords + maxCoords)
                scene.position = tuple(-midCoords)
                vertices.array = work[faces_by_rank[rank]].reshape(-1, 3)
                bcolor.array = scalar2rgb(numpy_arrays[select.value])[faces_by_rank[rank]]
                edges.array = work[edges_by_rank[rank]].reshape(-1, 3)
            else:
                vertices.array = work[faces_].reshape(-1, 3)
                bcolor.array = scalar2rgb(numpy_arrays[select.value])[faces_]
                edges.array = work[edges_].reshape(-1, 3)
                minCoords = work.min(axis=0)
                maxCoords = work.max(axis=0)
                midCoords = 0.5 * (minCoords + maxCoords)
                scene.position = tuple(-midCoords)

    select.observe(update_domain, names=['value'])
    select_dom.observe(update_domain, names=['value'])
    select_coarse_vecs.observe(update_domain, names=['value'])
    scale.observe(update_domain, names=['value'])
    show_displacement.observe(update_domain, names=['value'])
    show_mesh.observe(draw_mesh, names=['value'])
    show_displacement.value = True
    return widgets.HBox([renderer, widgets.VBox([select, select_dom, select_coarse_vecs, show_displacement, show_mesh, scale])])
# okay decompiling plot.cpython-36.pyc

back to top

Software Heritage — Copyright (C) 2015–2026, 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