diff --git a/examples/tutorials/plot_custom_emissivity.py b/examples/tutorials/plot_custom_emissivity.py new file mode 100644 index 000000000..349aa3d45 --- /dev/null +++ b/examples/tutorials/plot_custom_emissivity.py @@ -0,0 +1,91 @@ +""" +Computing a camera image with custom emissivity +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +This tutorial defines an emissivity that varies in space and computes the signal +received by a camera using this emissivity. +""" + +############################################################################### +# We start by loading a built-in `tofu` configuration and define a 2D camera. + +import matplotlib.pyplot as plt +import numpy as np +import tofu as tf + +configB2 = tf.geom.utils.create_config("B2") + +cam2d = tf.geom.utils.create_CamLOS2D( + config=configB2, + P=[3.4, 0, 0], + N12=100, + F=0.1, + D12=0.1, + angs=[np.pi, np.pi/6, 0], + Name="", + Exp="", + Diag="", +) + +############################################################################### +# Now, we define an emissivity function that depends on r and z coordinates. +# We can plot its profile in the (0, X, Z) plane. + +def emissivity(pts, t=None, vect=None): + """Custom emissivity as a function of geometry. + + :param pts: ndarray of shape (3, n_points) (each column is a xyz coordinate) + :param t: optional, time parameter to add a time dependency to the + emissivity function + :param vect: + :return: + - emissivity -- 2D array holding the emissivity for each point in the + input grid + """ + r, z = np.hypot(pts[0, :], pts[1, :]), pts[2, :] + e = np.exp(-(r - 2.4) ** 2 / 0.2 ** 2 - z ** 2 / 0.4 ** 2) + if t is not None: + e = np.cos(np.atleast_1d(t))[:, None] * e[None, :] + else: + # as stated in documentation of calc_signal, e.ndim must be 2 + e = np.reshape(e, (1, -1)) + return e + + +y = np.linspace(2, 3, num=90) +z = np.linspace(-0.5, 0.5, num=100) +Y, Z = np.meshgrid(y, z) +X = np.zeros_like(Y) +pts = np.c_[X.ravel(), Y.ravel(), Z.ravel()].T +emissivity_vals = emissivity(pts) +emissivity_vals = emissivity_vals.reshape(X.shape) + + +def project_to_2D(xyz): + """Projection to (0, X, Z) plane.""" + return xyz[0], xyz[2] + + +fig, ax = plt.subplots() +ax.pcolormesh(Y, Z, emissivity_vals) +ax.set_xlabel('y') +ax.set_ylabel('z') +configB2.plot(lax=ax, proj='cross') +cam_center, = ax.plot(*project_to_2D(cam2d._dgeom['pinhole']), '*', ms=20) +ax.legend(handles=[cam_center], labels=['camera pinhole'], loc='upper right') + +############################################################################### +# Finally, we compute an image using the 2D camera and this emissivity. +# If we provide a time vector, the field will vary in a cosinusoidal fashion +# (see above definition) across time. + +time_vector = np.linspace(0, 2 * np.pi, num=100) + +sig, units = cam2d.calc_signal(emissivity, + res=0.01, + reflections=False, + newcalc=True, + plot=False, + t=time_vector) +sig.plot(ntMax=1) +plt.show() diff --git a/tofu/data/_plot.py b/tofu/data/_plot.py index 67a885884..d99cb0abe 100644 --- a/tofu/data/_plot.py +++ b/tofu/data/_plot.py @@ -374,7 +374,7 @@ def _DataCam12D_plot(lData, key=None, nchMax=_nchMax, ntMax=_ntMax, lt = [dd.t for dd in lData] nt = lData[0].nt if nt == 1: - Dt = [t[0]-0.001,t[0]+0.001] + Dt = [lt[0][0]-0.001, lt[0][0]+0.001] else: Dt = np.array([[np.nanmin(t), np.nanmax(t)] for t in lt]) Dt = [np.min(Dt[:,0]), np.max(Dt[:,1])] diff --git a/tofu/utils.py b/tofu/utils.py index 38a54167a..f727a83ca 100644 --- a/tofu/utils.py +++ b/tofu/utils.py @@ -546,7 +546,7 @@ def _get_load_npzmat_dict(out, pfe, mode='npz', exclude_keys=[]): if out[k].ndim == 1: dout[k] = out[k].tolist() else: - dout[k] = np.squeeze(out[k],axis=0).tolist() + dout[k] = np.atleast_1d(np.squeeze(out[k],axis=0)).tolist() if type(dout[k][0]) is str: dout[k] = [kk.strip() for kk in dout[k]] else: @@ -555,7 +555,7 @@ def _get_load_npzmat_dict(out, pfe, mode='npz', exclude_keys=[]): dout[k] = tuple(dout[k]) elif typ=='ndarray': if mode == 'mat': - dout[k] = np.squeeze(out[k]) + dout[k] = np.atleast_1d(np.squeeze(out[k])) if dout[k].shape == (0,0): dout[k] = dout[k].ravel() else: @@ -2484,11 +2484,15 @@ def func(li, val=val, n1=n1, n2=n2): else: assert type(val) is np.ndarray - val = val.squeeze() + # val = np.atleast_1d(val.squeeze()) ndim = val.ndim - assert ndim >= len(lrids) - assert len(lrids) >= ninds - assert ndim >= ninds + c0 = ndim >= len(lrids) and len(lrids) >= ninds and ndim >= ninds + if not c0: + msg = "Wrong dimension / shape / references!\n" + msg += " val.ndim : {}\n".format(ndim) + msg += " lrids : {}\n".format(str(lrids)) + msg += " len(linds): {}\n".format(ninds) + raise Exception(msg) if ndim == ninds: if ndim == 1: @@ -2566,13 +2570,17 @@ def func(val, ind0=None, refb=refb): return np.nanargmin(np.abs(ref-val[1])) else: - refb = 0.5*(ref[1:]+ref[:-1]) - if Type == 'x': - def func(val, ind0=None, refb=refb): - return np.digitize([val[0]], refb)[0] + if ref.size == 1: + def func(val, ind0=None): + return 0 else: - def func(val, ind0=None, refb=refb): - return np.digitize([val[1]], refb)[0] + refb = 0.5*(ref[1:]+ref[:-1]) + if Type == 'x': + def func(val, ind0=None, refb=refb): + return np.digitize([val[0]], refb)[0] + else: + def func(val, ind0=None, refb=refb): + return np.digitize([val[1]], refb)[0] elif indother is None: assert ref.ndim == 2 if np.any(np.isnan(ref)): diff --git a/tofu/version.py b/tofu/version.py index 3a178e146..1fc557b2f 100644 --- a/tofu/version.py +++ b/tofu/version.py @@ -1,2 +1,2 @@ # Do not edit, pipeline versioning governed by git tags! -__version__ = '1.4.1-190-gd25622d' +__version__ = '1.4.1-217-g754c8bb'