Esempio n. 1
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def run_mag_test(fld, title="", show=False):
    vx, vy, vz = fld.component_views()  # pylint: disable=W0612
    vx, vy, vz = fld.component_fields()

    try:
        t0 = time()
        mag_ne = viscid.magnitude(fld, preferred="numexpr", only=False)
        t1 = time()
        logger.info("numexpr mag runtime: %g", t1 - t0)
    except viscid.verror.BackendNotFound:
        xfail("Numexpr is not installed")

    planes = ["z=0", "y=0"]
    nrows = 4
    ncols = len(planes)
    ax = plt.subplot2grid((nrows, ncols), (0, 0))
    ax.axis("equal")

    for ind, p in enumerate(planes):
        plt.subplot2grid((nrows, ncols), (0, ind), sharex=ax, sharey=ax)
        mpl.plot(vx, p, show=False)
        plt.subplot2grid((nrows, ncols), (1, ind), sharex=ax, sharey=ax)
        mpl.plot(vy, p, show=False)
        plt.subplot2grid((nrows, ncols), (2, ind), sharex=ax, sharey=ax)
        mpl.plot(vz, p, show=False)
        plt.subplot2grid((nrows, ncols), (3, ind), sharex=ax, sharey=ax)
        mpl.plot(mag_ne, p, show=False)

    mpl.plt.suptitle(title)
    mpl.auto_adjust_subplots(subplot_params=dict(top=0.9))
    mpl.plt.gcf().set_size_inches(6, 7)

    mpl.plt.savefig(next_plot_fname(__file__))
    if show:
        mpl.mplshow()
Esempio n. 2
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def run_mpl_testA(show=False):
    logger.info("2D cell centered tests")

    x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
    y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
    z = np.array(np.linspace(-1, 1, 2), dtype=dtype)

    fld_s = viscid.empty([x, y, z], center='cell')
    Xcc, Ycc, Zcc = fld_s.get_crds_cc(shaped=True)  # pylint: disable=unused-variable
    fld_s[:, :, :] = np.sin(Xcc) + np.cos(Ycc)

    _, axes = plt.subplots(4, 1, squeeze=False)

    vlt.plot(fld_s, "y=20j", ax=axes[0, 0], show=False, plot_opts="lin_0")
    vlt.plot(fld_s,
             "x=0j:20j,y=0j:5j",
             ax=axes[1, 0],
             earth=True,
             show=False,
             plot_opts="x_-10_0,y_0_7")
    vlt.plot(fld_s, "y=0j", ax=axes[2, 0], show=False, plot_opts="lin_-1_1")
    vlt.plot(fld_s,
             "z=0j,x=-20j:0j",
             ax=axes[3, 0],
             earth=True,
             show=False,
             plot_opts="lin_-5_5")

    plt.suptitle("2d cell centered")
    vlt.auto_adjust_subplots()

    plt.savefig(next_plot_fname(__file__))
    if show:
        vlt.mplshow()
Esempio n. 3
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def run_mpl_testA(show=False):
    logger.info("2D cell centered tests")

    x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
    y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
    z = np.array(np.linspace(-1, 1, 2), dtype=dtype)

    fld_s = viscid.empty([x, y, z], center='cell')
    Xcc, Ycc, Zcc = fld_s.get_crds_cc(shaped=True)  # pylint: disable=unused-variable
    fld_s[:, :, :] = np.sin(Xcc) + np.cos(Ycc)

    nrows = 4
    ncols = 1

    plt.subplot2grid((nrows, ncols), (0, 0))
    mpl.plot(fld_s, "y=20f", show=False, plot_opts="lin_0")
    plt.subplot2grid((nrows, ncols), (1, 0))
    mpl.plot(fld_s, "x=0f:20f,y=0f:5f", earth=True, show=False,
             plot_opts="x_-10_0,y_0_7")
    plt.subplot2grid((nrows, ncols), (2, 0))
    mpl.plot(fld_s, "y=0f", show=False, plot_opts="lin_-1_1")
    plt.subplot2grid((nrows, ncols), (3, 0))
    mpl.plot(fld_s, "z=0f,x=-20f:0f", earth=True, show=False, plot_opts="lin_-5_5")

    mpl.plt.suptitle("2d cell centered")
    mpl.auto_adjust_subplots()

    mpl.plt.savefig(next_plot_fname(__file__))
    if show:
        mpl.mplshow()
Esempio n. 4
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def run_mpl_testB(show=False):
    logger.info("3D node centered tests")

    x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
    y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
    z = np.array(np.linspace(-10, 10, 140), dtype=dtype)

    fld_s = viscid.empty([x, y, z], center='node')
    X, Y, Z = fld_s.get_crds_nc(shaped=True)  # pylint: disable=W0612
    fld_s[:, :, :] = np.sin(X) + np.cos(Y) - np.cos(Z)
    # print("shape: ", fld_s.data.shape)

    nrows = 4
    ncols = 1

    plt.subplot2grid((nrows, ncols), (0, 0))
    mpl.plot(fld_s, "z=0,x=:30", earth=True, plot_opts="lin_0")
    plt.subplot2grid((nrows, ncols), (1, 0))
    mpl.plot(fld_s, "z=0.75f,x=-4:-1,y=-3f:3f", earth=True)
    plt.subplot2grid((nrows, ncols), (2, 0))
    mpl.plot(fld_s, "x=-0.5f:,y=-3f:3f,z=0f", earth=True)
    plt.subplot2grid((nrows, ncols), (3, 0))
    mpl.plot(fld_s, "x=0.0f,y=-5.0f:5.0f", earth=True, plot_opts="log,g")

    mpl.plt.suptitle("3d node centered")
    mpl.auto_adjust_subplots()

    mpl.plt.savefig(next_plot_fname(__file__))
    if show:
        mpl.mplshow()
Esempio n. 5
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def run_div_test(fld, exact, show=False, ignore_inexact=False):
    t0 = time()
    result_numexpr = viscid.div(fld, preferred="numexpr", only=True)
    t1 = time()
    logger.info("numexpr magnitude runtime: %g", t1 - t0)

    result_diff = viscid.diff(result_numexpr, exact[1:-1, 1:-1, 1:-1])
    if not ignore_inexact and not (result_diff.data < 5e-5).all():
        logger.warn("numexpr result is far from the exact result")
    logger.info("min/max(abs(numexpr - exact)): %g / %g",
                np.min(result_diff.data), np.max(result_diff.data))

    planes = ["y=0f", "z=0f"]
    nrows = 2
    ncols = len(planes)
    ax = plt.subplot2grid((nrows, ncols), (0, 0))
    ax.axis("equal")

    for i, p in enumerate(planes):
        plt.subplot2grid((nrows, ncols), (0, i), sharex=ax, sharey=ax)
        mpl.plot(result_numexpr, p, show=False)
        plt.subplot2grid((nrows, ncols), (1, i), sharex=ax, sharey=ax)
        mpl.plot(result_diff, p, show=False)

    if show:
        mpl.mplshow()
Esempio n. 6
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def main():
    parser = argparse.ArgumentParser(description="Test divergence")
    parser.add_argument("--show", "--plot", action="store_true")
    args = vutil.common_argparse(parser)

    dtype = 'float64'

    # use 512 512 256 to inspect memory related things
    x = np.array(np.linspace(-0.5, 0.5, 256), dtype=dtype)
    y = np.array(np.linspace(-0.5, 0.5, 256), dtype=dtype)
    z = np.array(np.linspace(-0.5, 0.5, 64), dtype=dtype)

    v = viscid.empty([x, y, z], name="V", nr_comps=3, center="cell",
                     layout="interlaced")
    exact_cc = viscid.empty([x, y, z], name="exact_cc", center='cell')


    Xcc, Ycc, Zcc = exact_cc.get_crds_cc(shaped=True) #pylint: disable=W0612

    v['x'] = ne.evaluate("(sin(Xcc))")  # + Zcc
    v['y'] = ne.evaluate("(cos(Ycc))")  # + Xcc# + Zcc
    v['z'] = ne.evaluate("-((sin(Zcc)))")  # + Xcc# + Ycc
    exact_cc[:, :, :] = ne.evaluate("cos(Xcc) - sin(Ycc) - cos(Zcc)")

    logger.info("node centered tests")
    v_nc = v.as_centered('node')
    exact_nc = viscid.empty_like(v_nc['x'])
    X, Y, Z = exact_nc.get_crds_nc(shaped=True) #pylint: disable=W0612
    exact_nc[:, :, :] = ne.evaluate("cos(X) - sin(Y) - cos(Z)")
    # FIXME: why is the error so much larger here?
    run_div_test(v_nc, exact_nc, show=args.show, ignore_inexact=True)

    logger.info("cell centered tests")
    v_cc = v_nc.as_centered('cell')
    run_div_test(v_cc, exact_cc, show=args.show)
Esempio n. 7
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def run_mag_test(fld, title="", show=False):
    vx, vy, vz = fld.component_views()  # pylint: disable=W0612
    vx, vy, vz = fld.component_fields()

    try:
        t0 = time()
        mag_ne = viscid.magnitude(fld, preferred="numexpr", only=False)
        t1 = time()
        logger.info("numexpr mag runtime: %g", t1 - t0)
    except viscid.verror.BackendNotFound:
        xfail("Numexpr is not installed")

    planes = ["z=0", "y=0"]
    nrows = 4
    ncols = len(planes)

    _, axes = plt.subplots(nrows, ncols, sharex=True, sharey=True, squeeze=False)

    for ind, p in enumerate(planes):
        vlt.plot(vx, p, ax=axes[0, ind], show=False)
        vlt.plot(vy, p, ax=axes[1, ind], show=False)
        vlt.plot(vz, p, ax=axes[2, ind], show=False)
        vlt.plot(mag_ne, p, ax=axes[3, ind], show=False)

    plt.suptitle(title)
    vlt.auto_adjust_subplots(subplot_params=dict(top=0.9, right=0.9))
    plt.gcf().set_size_inches(6, 7)

    plt.savefig(next_plot_fname(__file__))
    if show:
        vlt.mplshow()
Esempio n. 8
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def run_mag_test(fld, show=False):
    vx, vy, vz = fld.component_views() #pylint: disable=W0612
    vx, vy, vz = fld.component_fields()

    t0 = time()
    mag_ne = viscid.magnitude(fld, preferred="numexpr", only=True)
    t1 = time()
    logger.info("numexpr mag runtime: %g", t1 - t0)
    t0 = time()

    planes = ["z=0", "y=0"]
    nrows = 4
    ncols = len(planes)
    ax = plt.subplot2grid((nrows, ncols), (0, 0))
    ax.axis("equal")

    for ind, p in enumerate(planes):
        plt.subplot2grid((nrows, ncols), (0, ind), sharex=ax, sharey=ax)
        mpl.plot(vx, p, show=False)
        plt.subplot2grid((nrows, ncols), (1, ind), sharex=ax, sharey=ax)
        mpl.plot(vy, p, show=False)
        plt.subplot2grid((nrows, ncols), (2, ind), sharex=ax, sharey=ax)
        mpl.plot(vz, p, show=False)
        plt.subplot2grid((nrows, ncols), (3, ind), sharex=ax, sharey=ax)
        mpl.plot(mag_ne, p, show=False)

    if show:
        mpl.mplshow()
Esempio n. 9
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def run_mpl_testA(show=False):
    logger.info("2D cell centered tests")

    x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
    y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
    z = np.array(np.linspace(-1, 1, 2), dtype=dtype)

    fld_s = viscid.empty([x, y, z], center='cell')
    Xcc, Ycc, Zcc = fld_s.get_crds_cc(shaped=True)  # pylint: disable=unused-variable
    fld_s[:, :, :] = np.sin(Xcc) + np.cos(Ycc)

    _, axes = plt.subplots(4, 1, squeeze=False)

    vlt.plot(fld_s, "y=20j", ax=axes[0, 0], show=False, plot_opts="lin_0")
    vlt.plot(fld_s, "x=0j:20j,y=0j:5j", ax=axes[1, 0], earth=True, show=False,
             plot_opts="x_-10_0,y_0_7")
    vlt.plot(fld_s, "y=0j", ax=axes[2, 0], show=False, plot_opts="lin_-1_1")
    vlt.plot(fld_s, "z=0j,x=-20j:0j", ax=axes[3, 0], earth=True, show=False,
             plot_opts="lin_-5_5")

    plt.suptitle("2d cell centered")
    vlt.auto_adjust_subplots()

    plt.savefig(next_plot_fname(__file__))
    if show:
        vlt.mplshow()
Esempio n. 10
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def run_mpl_testB(show=False):
    logger.info("3D node centered tests")

    x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
    y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
    z = np.array(np.linspace(-10, 10, 140), dtype=dtype)

    fld_s = viscid.empty([x, y, z], center='node')
    X, Y, Z = fld_s.get_crds_nc(shaped=True)  # pylint: disable=W0612
    fld_s[:, :, :] = np.sin(X) + np.cos(Y) - np.cos(Z)
    # print("shape: ", fld_s.data.shape)

    _, axes = plt.subplots(4, 1, squeeze=False)

    vlt.plot(fld_s, "z=0,x=:30", ax=axes[0, 0], earth=True, plot_opts="lin_0")
    vlt.plot(fld_s, "z=0.75j,x=-4:-1,y=-3j:3j", ax=axes[1, 0], earth=True)
    vlt.plot(fld_s, "x=-0.5j:,y=-3j:3j,z=0j", ax=axes[2, 0], earth=True)
    vlt.plot(fld_s, "x=0.0j,y=-5.0j:5.0j", ax=axes[3, 0], earth=True,
             plot_opts="log,g")

    plt.suptitle("3d node centered")
    vlt.auto_adjust_subplots()

    plt.savefig(next_plot_fname(__file__))
    if show:
        vlt.mplshow()
Esempio n. 11
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def run_mpl_testB(show=False):
    logger.info("3D node centered tests")

    x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
    y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
    z = np.array(np.linspace(-10, 10, 140), dtype=dtype)

    fld_s = viscid.empty([x, y, z], center='node')
    X, Y, Z = fld_s.get_crds_nc(shaped=True)  # pylint: disable=W0612
    fld_s[:, :, :] = np.sin(X) + np.cos(Y) - np.cos(Z)
    # print("shape: ", fld_s.data.shape)

    nrows = 4
    ncols = 1

    plt.subplot2grid((nrows, ncols), (0, 0))
    vlt.plot(fld_s, "z=0,x=:30", earth=True, plot_opts="lin_0")
    plt.subplot2grid((nrows, ncols), (1, 0))
    vlt.plot(fld_s, "z=0.75f,x=-4:-1,y=-3f:3f", earth=True)
    plt.subplot2grid((nrows, ncols), (2, 0))
    vlt.plot(fld_s, "x=-0.5f:,y=-3f:3f,z=0f", earth=True)
    plt.subplot2grid((nrows, ncols), (3, 0))
    vlt.plot(fld_s, "x=0.0f,y=-5.0f:5.0f", earth=True, plot_opts="log,g")

    plt.suptitle("3d node centered")
    vlt.auto_adjust_subplots()

    plt.savefig(next_plot_fname(__file__))
    if show:
        vlt.mplshow()
Esempio n. 12
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def _main():
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument("--show", "--plot", action="store_true")
    args = vutil.common_argparse(parser)
    dtype = 'float32'

    x = np.array(np.linspace(-5, 5, 512), dtype=dtype)
    y = np.array(np.linspace(-5, 5, 256), dtype=dtype)
    z = np.array(np.linspace(-5, 5, 256), dtype=dtype)
    v = viscid.empty([x, y, z], name="V", nr_comps=3, center='node',
                     layout='interlaced')
    X, Y, Z = v.get_crds_nc(shaped=True)
    v['x'] = (0.5 * X**2) + (      Y   ) + (0.0 * Z   )
    v['y'] = (0.0 * X   ) + (0.5 * Y**2) + (0.0 * Z   )
    v['z'] = (0.0 * X   ) + (0.0 * Y   ) + (0.5 * Z**2)

    logger.info("Testing node centered magnitudes")
    run_mag_test(v, title="node centered", show=args.show)

    logger.info("Testing cell centered magnitudes")
    v = v.as_centered('cell')
    run_mag_test(v, title="cell centered", show=args.show)

    # print(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024**2)
    # print("ne: ", timereps(10, Div1ne, [vx, vy, vz]))
    # print(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024**2)
    # print("inline: ", timereps(10, Div1inline, [vx, vy, vz]))
    # print(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024**2)

    return 0
Esempio n. 13
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def run_div_test(fld, exact, title='', show=False, ignore_inexact=False):
    t0 = time()
    result_numexpr = viscid.div(fld, preferred="numexpr", only=False)
    t1 = time()
    logger.info("numexpr magnitude runtime: %g", t1 - t0)

    result_diff = viscid.diff(result_numexpr, exact)['x=1:-1, y=1:-1, z=1:-1']
    if not ignore_inexact and not (result_diff.data < 5e-5).all():
        logger.warning("numexpr result is far from the exact result")
    logger.info("min/max(abs(numexpr - exact)): %g / %g",
                np.min(result_diff.data), np.max(result_diff.data))

    planes = ["y=0j", "z=0j"]
    nrows = 2
    ncols = len(planes)
    _, axes = plt.subplots(nrows, ncols, squeeze=False)

    for i, p in enumerate(planes):
        vlt.plot(result_numexpr, p, ax=axes[0, i], show=False)
        vlt.plot(result_diff, p, ax=axes[1, i], show=False)

    plt.suptitle(title)
    vlt.auto_adjust_subplots(subplot_params=dict(top=0.9))

    plt.savefig(next_plot_fname(__file__))
    if show:
        vlt.mplshow()
Esempio n. 14
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def run_mpl_testB(show=False):
    logger.info("3D node centered tests")

    x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
    y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
    z = np.array(np.linspace(-10, 10, 140), dtype=dtype)

    fld_s = viscid.empty([x, y, z], center='node')
    X, Y, Z = fld_s.get_crds_nc(shaped=True)  # pylint: disable=W0612
    fld_s[:, :, :] = np.sin(X) + np.cos(Y) - np.cos(Z)
    # print("shape: ", fld_s.data.shape)

    _, axes = plt.subplots(4, 1, squeeze=False)

    vlt.plot(fld_s, "z=0,x=:30", ax=axes[0, 0], earth=True, plot_opts="lin_0")
    vlt.plot(fld_s, "z=0.75j,x=-4:-1,y=-3j:3j", ax=axes[1, 0], earth=True)
    vlt.plot(fld_s, "x=-0.5j:,y=-3j:3j,z=0j", ax=axes[2, 0], earth=True)
    vlt.plot(fld_s,
             "x=0.0j,y=-5.0j:5.0j",
             ax=axes[3, 0],
             earth=True,
             plot_opts="log,g")

    plt.suptitle("3d node centered")
    vlt.auto_adjust_subplots()

    plt.savefig(next_plot_fname(__file__))
    if show:
        vlt.mplshow()
Esempio n. 15
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def run_div_test(fld, exact, title='', show=False, ignore_inexact=False):
    t0 = time()
    result_numexpr = viscid.div(fld, preferred="numexpr", only=False)
    t1 = time()
    logger.info("numexpr magnitude runtime: %g", t1 - t0)

    result_diff = viscid.diff(result_numexpr, exact)['x=1:-1, y=1:-1, z=1:-1']
    if not ignore_inexact and not (result_diff.data < 5e-5).all():
        logger.warn("numexpr result is far from the exact result")
    logger.info("min/max(abs(numexpr - exact)): %g / %g",
                np.min(result_diff.data), np.max(result_diff.data))

    planes = ["y=0f", "z=0f"]
    nrows = 2
    ncols = len(planes)
    ax = plt.subplot2grid((nrows, ncols), (0, 0))
    ax.axis("equal")

    for i, p in enumerate(planes):
        plt.subplot2grid((nrows, ncols), (0, i), sharex=ax, sharey=ax)
        mpl.plot(result_numexpr, p, show=False)
        plt.subplot2grid((nrows, ncols), (1, i), sharex=ax, sharey=ax)
        mpl.plot(result_diff, p, show=False)

    mpl.plt.suptitle(title)
    mpl.auto_adjust_subplots(subplot_params=dict(top=0.9))

    mpl.plt.savefig(next_plot_fname(__file__))
    if show:
        mpl.mplshow()
Esempio n. 16
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def _main():
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument("--prof", action="store_true")
    parser.add_argument("--show", "--plot", action="store_true")
    args = vutil.common_argparse(parser)

    dtype = 'float64'

    # use 512 512 256 to inspect memory related things
    x = np.array(np.linspace(-0.5, 0.5, 256), dtype=dtype)
    y = np.array(np.linspace(-0.5, 0.5, 256), dtype=dtype)
    z = np.array(np.linspace(-0.5, 0.5, 64), dtype=dtype)

    v = viscid.empty([x, y, z], name="V", nr_comps=3, center="cell",
                     layout="interlaced")
    exact_cc = viscid.empty([x, y, z], name="exact_cc", center='cell')

    Xcc, Ycc, Zcc = exact_cc.get_crds_cc(shaped=True)  # pylint: disable=W0612

    if HAS_NUMEXPR:
        v['x'] = ne.evaluate("(sin(Xcc))")  # + Zcc
        v['y'] = ne.evaluate("(cos(Ycc))")  # + Xcc# + Zcc
        v['z'] = ne.evaluate("-((sin(Zcc)))")  # + Xcc# + Ycc
        exact_cc[:, :, :] = ne.evaluate("cos(Xcc) - sin(Ycc) - cos(Zcc)")
    else:
        v['x'] = (np.sin(Xcc))  # + Zcc
        v['y'] = (np.cos(Ycc))  # + Xcc# + Zcc
        v['z'] = -((np.sin(Zcc)))  # + Xcc# + Ycc
        exact_cc[:, :, :] = np.cos(Xcc) - np.sin(Ycc) - np.cos(Zcc)

    if args.prof:
        print("Without boundaries")
        viscid.timeit(viscid.div, v, bnd=False, timeit_repeat=10,
                      timeit_print_stats=True)
        print("With boundaries")
        viscid.timeit(viscid.div, v, bnd=True, timeit_repeat=10,
                      timeit_print_stats=True)

    logger.info("node centered tests")
    v_nc = v.as_centered('node')
    exact_nc = viscid.empty_like(v_nc['x'])
    X, Y, Z = exact_nc.get_crds_nc(shaped=True)  # pylint: disable=W0612
    if HAS_NUMEXPR:
        exact_nc[:, :, :] = ne.evaluate("cos(X) - sin(Y) - cos(Z)")
    else:
        exact_nc[:, :, :] = np.cos(X) - np.sin(Y) - np.cos(Z)
    # FIXME: why is the error so much larger here?
    run_div_test(v_nc, exact_nc, title='Node Centered', show=args.show,
                 ignore_inexact=True)

    logger.info("cell centered tests")
    v_cc = v_nc.as_centered('cell')
    run_div_test(v_cc, exact_cc, title="Cell Centered", show=args.show)

    return 0
Esempio n. 17
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def make_grid1_cax(ax, position='right', orientation='horizontal', aspect=20.0,
                   fraction=0.05, pad=0.05, shrink=1.0):
    # validate position && orientation
    if orientation == 'vertical':
        if position not in ('left', 'right'):
            raise ValueError("bad position '{0}'".format(position))
    elif orientation == 'horizontal':
        if position not in ('bottom', 'top'):
            raise ValueError("bad position '{0}'".format(position))
    else:
        raise ValueError("bad orientation '{0}'".format(orientation))

    cax = None

    try:
        # prepare axes size given orientation and axes type
        if isinstance(ax, mprojections.polar.PolarAxes):
            kls_x, kls_y = _PolarAxesX, _PolarAxesY
        elif type(ax) in (mprojections.axes.Axes, mprojections.axes.Subplot):
            # note this checks type, not isinstance because all axes derive
            # from axes.Axes, and that's not what we're checking here
            kls_x, kls_y = _AxesX, _AxesY
        else:
            raise _UnexpectedProjection(str(type(ax)))
        size_x = kls_x(ax, aspect=1.0 / aspect)
        size_y = kls_y(ax, aspect=1.0 / aspect)

        # scale the long side by shrink
        if orientation == 'vertical':
            size_y = axes_size.Fraction(1.0 / shrink, size_y)
            width = axes_size.Fraction(fraction, size_x)
            pad_size = axes_size.Fraction(pad, size_x)
        else:
            size_x = axes_size.Fraction(1.0 / shrink, size_x)
            width = axes_size.Fraction(fraction, size_y)
            pad_size = axes_size.Fraction(pad, size_y)

        divider = axes_divider.AxesDivider(ax, xref=size_x, yref=size_y)
        locator = divider.new_locator(nx=0, ny=0)
        ax.set_axes_locator(locator)
        cax = divider.append_axes(position, size=width, pad=pad_size,
                                  axes_class=matplotlib.axes.Axes)
    except _UnexpectedProjection as e:
        logger.info("Viscid can't verify that grid1 axes will "
                    "work to colorbar a {0} axis; falling back to "
                    "default.".format(e.ax_type))
    return cax
Esempio n. 18
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def main():
    parser = argparse.ArgumentParser(description="Load some data files")
    parser.add_argument('files', nargs="*", help='input files')
    args = vutil.common_argparse(parser)

    # print("args", args)
    # logger.error(args)
    # logger.warn(args)
    logger.info("args: {0}".format(args))
    # logger.debug(args)
    print()

    files = readers.load_files(args.files)
    readers.__filebucket__.print_tree()
    print()

    for f in files:
        f.print_tree(depth=-1)
Esempio n. 19
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def main():
    parser = argparse.ArgumentParser(description="Test calc")
    parser.add_argument("--show", "--plot", action="store_true")
    args = vutil.common_argparse(parser)
    dtype = 'float32'

    x = np.array(np.linspace(-5, 5, 512), dtype=dtype)
    y = np.array(np.linspace(-5, 5, 256), dtype=dtype)
    z = np.array(np.linspace(-5, 5, 256), dtype=dtype)
    v = viscid.empty([x, y, z], name="V", nr_comps=3, center='node',
                     layout='interlaced')
    X, Y, Z = v.get_crds_nc(shaped=True)
    v['x'] = 0.5 * X**2 +       Y    + 0.0 * Z
    v['y'] = 0.0 * X    + 0.5 * Y**2 + 0.0 * Z
    v['z'] = 0.0 * X    + 0.0 * Y    + 0.5 * Z**2

    logger.info("Testing node centered magnitudes")
    run_mag_test(v, show=args.show)

    logger.info("Testing cell centered magnitudes")
    v = v.as_centered('cell')
    run_mag_test(v, show=args.show)
Esempio n. 20
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    def _get_imp(self, preferred, only=False):
        if not isinstance(preferred, (list, tuple)):
            if preferred is None:
                preferred = list(self._imps.keys())
            else:
                preferred = [preferred]

        for name in preferred:
            if name in self._imps:
                return self._imps[name]

        msg = "{0} :: {1}".format(self.opname, preferred)
        if only:
            raise verror.BackendNotFound(msg)
        logger.info("No preferred backends available: " + msg)

        for name in self.default_backends:
            if name in self._imps:
                return self._imps[name]

        if len(self._imps) == 0:
            raise verror.BackendNotFound("No backends available")
        return list(self._imps.values())[0]
Esempio n. 21
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    def _get_imp(self, preferred, only=False):
        if not isinstance(preferred, (list, tuple)):
            if preferred is None:
                preferred = list(self._imps.keys())
            else:
                preferred = [preferred]

        for name in preferred:
            if name in self._imps:
                return self._imps[name]

        msg = "{0} :: {1}".format(self.opname, preferred)
        if only:
            raise verror.BackendNotFound(msg)
        logger.info("No preferred backends available: " + msg)

        for name in self.default_backends:
            if name in self._imps:
                return self._imps[name]

        if len(self._imps) == 0:
            raise verror.BackendNotFound("No backends available")
        return list(self._imps.values())[0]
Esempio n. 22
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def run_mpl_testA(show=False):
    logger.info("2D cell centered tests")

    x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
    y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
    z = np.array(np.linspace(-1, 1, 2), dtype=dtype)

    fld_s = viscid.empty([x, y, z], center='cell')
    Xcc, Ycc, Zcc = fld_s.get_crds_cc(shaped=True)  # pylint: disable=unused-variable
    fld_s[:, :, :] = np.sin(Xcc) + np.cos(Ycc)

    nrows = 4
    ncols = 1

    plt.subplot2grid((nrows, ncols), (0, 0))
    vlt.plot(fld_s, "y=20f", show=False, plot_opts="lin_0")
    plt.subplot2grid((nrows, ncols), (1, 0))
    vlt.plot(fld_s,
             "x=0f:20f,y=0f:5f",
             earth=True,
             show=False,
             plot_opts="x_-10_0,y_0_7")
    plt.subplot2grid((nrows, ncols), (2, 0))
    vlt.plot(fld_s, "y=0f", show=False, plot_opts="lin_-1_1")
    plt.subplot2grid((nrows, ncols), (3, 0))
    vlt.plot(fld_s,
             "z=0f,x=-20f:0f",
             earth=True,
             show=False,
             plot_opts="lin_-5_5")

    plt.suptitle("2d cell centered")
    vlt.auto_adjust_subplots()

    plt.savefig(next_plot_fname(__file__))
    if show:
        vlt.mplshow()
Esempio n. 23
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def main():
    parser = argparse.ArgumentParser(description="Streamline a PSC file")
    parser.add_argument("-t", default="2000",
                        help="which time to plot (finds closest)")
    parser.add_argument('infile', nargs=1, help='input file')
    args = vutil.common_argparse(parser)

    # f = readers.load_file("pfd.020000.xdmf")
    # ... or ...
    # using this way of loading files, one probably wants just to give
    # pfd.xdmf to the command line
    f = readers.load_file(args.infile[0])
    f.activate_time(args.t)

    jz = f["jz"]
    # recreate hx as a field of 0 to keep streamlines from moving in
    # that direction
    hx = field.zeros_like(jz, name="hx")
    h1 = field.scalar_fields_to_vector([hx, f["hy"], f["hz"]], name="H",
                                       _force_layout="Interlaced",
                                       forget_source=True)
    e = field.scalar_fields_to_vector([f["ex"], f["ey"], f["ez"]], name="E",
                                      _force_layout="Interlaced",
                                      forget_source=True)

    # plot magnetic fields, just a sanity check
    # ax1 = plt.subplot(211)
    # mpl.plot(f["hy"], flip_plot=True)
    # ax2 = plt.subplot(212, sharex=ax1, sharey=ax1)
    # mpl.plot(f["hz"], flip_plot=True)
    # mpl.mplshow()

    # make a line of 30 seeds straight along the z axis (x, y, z ordered)
    seeds1 = seed.Line((0.0, 0.0, 2.0), (1022.0, 0.0, 0.0), 60)
    # set outer boundary limits for streamlines
    ds = 0.005  # spatial step along the stream line curve
    obound0 = np.array([1, -128, -1000], dtype=h1.dtype)
    obound1 = np.array([1023, 128, 1000], dtype=h1.dtype)
    # calc the streamlines
    lines1, topo1 = streamline.streamlines(h1, seeds1, ds0=ds, maxit=200000,
                                           obound0=obound0, obound1=obound1,
                                           ibound=0.0)
    # run with -v to see this
    logger.info("Topology flags: {0}".format(topo1))

    # rotate plot puts the z axis along the horizontal
    flip_plot = True
    mpl.plot(jz, flip_plot=flip_plot, plot_opts="lin_-.05_.05")
    # mpl.plot_streamlines2d(lines1, "x", flip_plot=flip_plot, color='k')
    plt.xlim([0, 1024])
    plt.ylim([-128, 128])
    plt.show()

    # interpolate e onto each point of the first field line of lines1
    e1 = cycalc.interp_trilin(e, seed.Point(lines1[0]))
    print(e1.shape, lines1[0].shape)
    plt.clf()
    plt.plot(np.linspace(0, ds * e1.shape[0], e1.shape[0]), e1[:, 0])
    plt.xlabel("length along field line")
    plt.ylabel("Ex")
    plt.show()

    return 0
Esempio n. 24
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def _follow_fluid_step(i, dt, grid, root_seeds, plot_function, stream_opts,
                       speed_scale):
    direction = int(dt / np.abs(dt))
    if direction >= 0:
        sl_direction = streamline.DIR_FORWARD
    else:
        sl_direction = streamline.DIR_BACKWARD

    logger.info("working on timestep {0} {1}".format(i, grid.time))
    v = grid["v"]
    logger.debug("finished reading V field")

    logger.debug("calculating new streamline positions")
    flow_lines = calc_streamlines(v,
                                  root_seeds,
                                  output=viscid.OUTPUT_STREAMLINES,
                                  stream_dir=sl_direction,
                                  **stream_opts)[0]

    logger.debug("done with that, now i'm plotting...")
    plot_function(i, grid, v, flow_lines, root_seeds)

    ############################################################
    # now recalculate the seed positions for the next timestep
    logger.debug("finding new seed positions...")
    root_pts = root_seeds.genr_points()
    valid_pt_inds = []
    for i in range(root_pts.shape[1]):
        valid_pt = True

        # get the index of the root point in teh 2d flow line array
        # dist = flow_lines[i] - root_pts[:, [i]]
        # root_ind = np.argmin(np.sum(dist**2, axis=0))
        # print("!!!", root_pts[:, i], "==", flow_lines[i][:, root_ind])
        # interpolate velocity onto teh flow line, and get speed too
        v_interp = cycalc.interp_trilin(v, seed.Point(flow_lines[i]))
        speed = np.sqrt(np.sum(v_interp * v_interp, axis=1))

        # this is a super slopy way to integrate velocity
        # keep marching along the flow line until we get to the next timestep
        t = 0.0
        ind = 0
        if direction < 0:
            flow_lines[i] = flow_lines[i][:, ::-1]
            speed = speed[::-1]

        while t < np.abs(dt):
            ind += 1
            if ind >= len(speed):
                # set valid_pt to True if you want to keep that point for
                # future time steps, but most likely if we're here, the seed
                # has gone out of our region of interest
                ind = len(speed) - 1
                valid_pt = False
                logger.info("OOPS: ran out of streamline, increase "
                            "max_length when tracing flow lines if this "
                            "is unexpected")
                break
            t += stream_opts["ds0"] / (speed_scale * speed[ind])

        root_pts[:, i] = flow_lines[i][:, ind]
        if valid_pt:
            valid_pt_inds.append(i)

    # remove seeds that have flown out of our region of interest
    # (aka, beyond the flow line we drew)
    root_pts = root_pts[:, valid_pt_inds]

    logger.debug("ok, done with all that :)")
    return root_pts
Esempio n. 25
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def _do_multiplot(tind, grid, plot_vars=None, global_popts=None, kwopts=None,
                  share_axes=False, show=False, subplot_params=None,
                  first_run_result=None, first_run=False, **kwargs):
    import matplotlib.pyplot as plt
    from viscid.plot import vpyplot as vlt

    logger.info("Plotting timestep: %d, %g", tind, grid.time)

    if plot_vars is None:
        raise ValueError("No plot_vars given to `_do_multiplot` :(")
    if kwargs:
        logger.info("Unused kwargs: {0}".format(kwargs))

    if kwopts is None:
        kwopts = {}
    transpose = kwopts.get("transpose", False)
    plot_size = kwopts.get("plot_size", None)
    dpi = kwopts.get("dpi", None)
    out_prefix = kwopts.get("out_prefix", None)
    out_format = kwopts.get("out_format", "png")
    selection = kwopts.get("selection", None)
    timeformat = kwopts.get("timeformat", ".02f")
    tighten = kwopts.get("tighten", False)
    # wicked hacky
    # subplot_params = kwopts.get("subplot_params", _subplot_params)

    # nrows = len(plot_vars)
    nrows = len([pv[0] for pv in plot_vars if not pv[0].startswith('^')])
    ncols = 1
    if transpose:
        nrows, ncols = ncols, nrows

    if nrows == 0:
        logger.warn("I have no variables to plot")
        return

    fig = plt.gcf()
    if plot_size is not None:
        fig.set_size_inches(*plot_size, forward=True)
    if dpi is not None:
        fig.set_dpi(dpi)

    shareax = None

    this_row = -1
    for i, fld_meta in enumerate(plot_vars):
        if not fld_meta[0].startswith('^'):
            this_row += 1
            same_axis = False
        else:
            same_axis = True

        fld_name_meta = fld_meta[0].lstrip('^')
        fld_name_split = fld_name_meta.split(',')
        if '=' in fld_name_split[0]:
            # if fld_name is actually an equation, assume
            # there's no slice, and commas are part of the
            # equation
            fld_name = ",".join(fld_name_split)
            fld_slc = ""
        else:
            fld_name = fld_name_split[0]
            fld_slc = ",".join(fld_name_split[1:])
        if selection is not None:
            # fld_slc += ",{0}".format(selection)
            if fld_slc != "":
                fld_slc = ",".join([fld_slc, selection])
            else:
                fld_slc = selection
        if fld_slc.strip() == "":
            fld_slc = None

        # print("fld_time:", fld.time)
        if this_row < 0:
            raise ValueError("first plot can't begin with a +")
        row = this_row
        col = 0
        if transpose:
            row, col = col, row
        if not same_axis:
            ax = plt.subplot2grid((nrows, ncols), (row, col),
                                  sharex=shareax, sharey=shareax)
        if i == 0 and share_axes:
            shareax = ax

        if "plot_opts" not in fld_meta[1]:
            fld_meta[1]["plot_opts"] = global_popts
        elif global_popts is not None:
            fld_meta[1]["plot_opts"] = "{0},{1}".format(
                fld_meta[1]["plot_opts"], global_popts)

        with grid.get_field(fld_name, slc=fld_slc) as fld:
            vlt.plot(fld, masknan=True, **fld_meta[1])
        # print("fld cache", grid[fld_meta[0]]._cache)

    if timeformat and timeformat.lower() != "none":
        plt.suptitle(grid.format_time(timeformat))

    # for adjusting subplots / tight_layout and applying the various
    # hacks to keep plots from dancing around in movies
    if not subplot_params and first_run_result:
        subplot_params = first_run_result
    if tighten:
        tighten = dict(rect=[0, 0.03, 1, 0.90])
    ret = vlt.auto_adjust_subplots(tight_layout=tighten,
                                   subplot_params=subplot_params)
    if not first_run:
        ret = None

    if out_prefix:
        plt.savefig("{0}_{1:06d}.{2}".format(out_prefix, tind + 1, out_format))
    if show:
        plt.show()
    plt.clf()

    return ret
Esempio n. 26
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def _follow_fluid_step(i, dt, grid, root_seeds, plot_function, stream_opts,
                       speed_scale):
    direction = int(dt / np.abs(dt))
    if direction >= 0:
        sl_direction = streamline.DIR_FORWARD
    else:
        sl_direction = streamline.DIR_BACKWARD

    logger.info("working on timestep {0} {1}".format(i, grid.time))
    v = grid["v"]
    logger.debug("finished reading V field")

    logger.debug("calculating new streamline positions")
    flow_lines = calc_streamlines(v, root_seeds,
                                  output=viscid.OUTPUT_STREAMLINES,
                                  stream_dir=sl_direction,
                                  **stream_opts)[0]

    logger.debug("done with that, now i'm plotting...")
    plot_function(i, grid, v, flow_lines, root_seeds)

    ############################################################
    # now recalculate the seed positions for the next timestep
    logger.debug("finding new seed positions...")
    root_pts = root_seeds.genr_points()
    valid_pt_inds = []
    for i in range(root_pts.shape[1]):
        valid_pt = True

        # get the index of the root point in teh 2d flow line array
        # dist = flow_lines[i] - root_pts[:, [i]]
        # root_ind = np.argmin(np.sum(dist**2, axis=0))
        # print("!!!", root_pts[:, i], "==", flow_lines[i][:, root_ind])
        # interpolate velocity onto teh flow line, and get speed too
        v_interp = cycalc.interp_trilin(v, seed.Point(flow_lines[i]))
        speed = np.sqrt(np.sum(v_interp * v_interp, axis=1))

        # this is a super slopy way to integrate velocity
        # keep marching along the flow line until we get to the next timestep
        t = 0.0
        ind = 0
        if direction < 0:
            flow_lines[i] = flow_lines[i][:, ::-1]
            speed = speed[::-1]

        while t < np.abs(dt):
            ind += 1
            if ind >= len(speed):
                # set valid_pt to True if you want to keep that point for
                # future time steps, but most likely if we're here, the seed
                # has gone out of our region of interest
                ind = len(speed) - 1
                valid_pt = False
                logger.info("OOPS: ran out of streamline, increase "
                            "max_length when tracing flow lines if this "
                            "is unexpected")
                break
            t += stream_opts["ds0"] / (speed_scale * speed[ind])

        root_pts[:, i] = flow_lines[i][:, ind]
        if valid_pt:
            valid_pt_inds.append(i)

    # remove seeds that have flown out of our region of interest
    # (aka, beyond the flow line we drew)
    root_pts = root_pts[:, valid_pt_inds]

    logger.debug("ok, done with all that :)")
    return root_pts
Esempio n. 27
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def _do_multiplot(tind, grid, plot_vars=None, global_popts=None, kwopts=None,
                  share_axes=False, show=False, subplot_params=None,
                  first_run_result=None, first_run=False, **kwargs):
    import matplotlib.pyplot as plt
    from viscid.plot import mpl

    logger.info("Plotting timestep: %d, %g", tind, grid.time)

    if plot_vars is None:
        raise ValueError("No plot_vars given to vlab._do_multiplot :(")
    if kwargs:
        logger.info("Unused kwargs: {0}".format(kwargs))

    if kwopts is None:
        kwopts = {}
    transpose = kwopts.get("transpose", False)
    plot_size = kwopts.get("plot_size", None)
    dpi = kwopts.get("dpi", None)
    out_prefix = kwopts.get("out_prefix", None)
    out_format = kwopts.get("out_format", "png")
    selection = kwopts.get("selection", None)
    timeformat = kwopts.get("timeformat", ".02f")
    tighten = kwopts.get("tighten", False)
    # wicked hacky
    # subplot_params = kwopts.get("subplot_params", _subplot_params)

    # nrows = len(plot_vars)
    nrows = len([pv[0] for pv in plot_vars if not pv[0].startswith('^')])
    ncols = 1
    if transpose:
        nrows, ncols = ncols, nrows

    if nrows == 0:
        logger.warn("I have no variables to plot")
        return

    fig = plt.gcf()
    if plot_size is not None:
        fig.set_size_inches(*plot_size, forward=True)
    if dpi is not None:
        fig.set_dpi(dpi)

    shareax = None

    this_row = -1
    for i, fld_meta in enumerate(plot_vars):
        if not fld_meta[0].startswith('^'):
            this_row += 1
            same_axis = False
        else:
            same_axis = True

        fld_name_meta = fld_meta[0].lstrip('^')
        fld_name_split = fld_name_meta.split(',')
        if '=' in fld_name_split[0]:
            # if fld_name is actually an equation, assume
            # there's no slice, and commas are part of the
            # equation
            fld_name = ",".join(fld_name_split)
            fld_slc = ""
        else:
            fld_name = fld_name_split[0]
            fld_slc = ",".join(fld_name_split[1:])
        if selection is not None:
            # fld_slc += ",{0}".format(selection)
            if fld_slc != "":
                fld_slc = ",".join([fld_slc, selection])
            else:
                fld_slc = selection
        if fld_slc.strip() == "":
            fld_slc = None

        # print("fld_time:", fld.time)
        if this_row < 0:
            raise ValueError("first plot can't begin with a +")
        row = this_row
        col = 0
        if transpose:
            row, col = col, row
        if not same_axis:
            ax = plt.subplot2grid((nrows, ncols), (row, col),
                                  sharex=shareax, sharey=shareax)
        if i == 0 and share_axes:
            shareax = ax

        if not "plot_opts" in fld_meta[1]:
            fld_meta[1]["plot_opts"] = global_popts
        elif global_popts is not None:
            fld_meta[1]["plot_opts"] = "{0},{1}".format(
                fld_meta[1]["plot_opts"], global_popts)

        with grid.get_field(fld_name, slc=fld_slc) as fld:
            mpl.plot(fld, masknan=True, **fld_meta[1])
        # print("fld cache", grid[fld_meta[0]]._cache)

    if timeformat and timeformat.lower() != "none":
        plt.suptitle(grid.format_time(timeformat))

    # for adjusting subplots / tight_layout and applying the various
    # hacks to keep plots from dancing around in movies
    if not subplot_params and first_run_result:
        subplot_params = first_run_result
    if tighten:
        tighten = dict(rect=[0, 0.03, 1, 0.90])
    ret = mpl.auto_adjust_subplots(tight_layout=tighten,
                                   subplot_params=subplot_params)
    if not first_run:
        ret = None

    if out_prefix:
        plt.savefig("{0}_{1:06d}.{2}".format(out_prefix, tind + 1, out_format))
    if show:
        plt.show()
    plt.clf()

    return ret