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Merged
Didou09 merged 6 commits into from
Nov 19, 2019
Merged

[bug fix #255] found bug #257

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11ab20c
[bug fix #255] found bug
lasofivec Nov 18, 2019
a667bec
[bf #255] added doc for ani/vect definition
lasofivec Nov 19, 2019
fcc95f0
[pep8] changes for flake
lasofivec Nov 19, 2019
820e73f
[doc] typo corrections
lasofivec Nov 19, 2019
6b2afd4
[bf #255] ani=None by default
lasofivec Nov 19, 2019
8ab1c43
[bf-#255] Fixed unit tests for tutorials
Nov 19, 2019
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5 changes: 4 additions & 1 deletion examples/tutorials/tuto_plot_custom_emissivity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,13 +31,15 @@
# 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:
:param vect: optional, ndarray of shape (3, n_points), if anisotropic
emissivity, unit direction vectors (X,Y,Z)
:return:
- emissivity -- 2D array holding the emissivity for each point in the
input grid
Expand Down Expand Up @@ -88,6 +90,7 @@ def project_to_2D(xyz):
method="sum",
newcalc=True,
plot=False,
ani=False,
t=time_vector)

sig.plot(ntMax=1)
Expand Down
36 changes: 19 additions & 17 deletions tofu/geom/_GG.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -2860,7 +2860,6 @@ def LOS_calc_signal(func, double[:,::1] ray_orig, double[:,::1] ray_vdir, res,
cdef double[1] loc_eff_res
cdef double[::1] reseff_mv
cdef double[::1] res_mv
cdef double[::1,:] sig_mv
cdef double[:,::1] val_mv
cdef double[:,::1] pts_mv
cdef double[:,::1] usbis_mv
Expand Down Expand Up @@ -2928,7 +2927,6 @@ def LOS_calc_signal(func, double[:,::1] ray_orig, double[:,::1] ray_vdir, res,
n_imode = _st.get_nb_imode(imode)
# Initialization result
sig = np.empty((nt, nlos), dtype=float, order='F')
sig_mv = sig
# If the resolution is the same for every LOS, we create a tab
if res_is_list :
res_arr = np.asarray(res)
Expand Down Expand Up @@ -3025,11 +3023,12 @@ def LOS_calc_signal(func, double[:,::1] ray_orig, double[:,::1] ray_vdir, res,
pts, usbis = _st.call_get_sample_single_ani(lims[0, ii],
lims[1, ii],
res_mv[ii],
n_dmode, n_imode,
n_dmode,
n_imode,
&loc_eff_res[0],
&nb_rows[0],
ray_orig[:,ii:ii+1],
ray_vdir[:,ii:ii+1])
ray_orig[:, ii:ii+1],
ray_vdir[:, ii:ii+1])
# loop over time for calling and integrating
for jj in range(nt):
val = func(pts, t=ltime[jj], vect=-usbis, **fkwdargs)
Expand Down Expand Up @@ -3129,7 +3128,7 @@ def LOS_calc_signal(func, double[:,::1] ray_orig, double[:,::1] ray_vdir, res,
ray_orig[:, ii:ii+1],
ray_vdir[:, ii:ii+1])
val_2d = func(pts, t=t, vect=-usbis, **fkwdargs)
sig_mv[:, ii] = np.sum(val_2d, axis=-1)*loc_eff_res[0]
sig[:, ii] = np.sum(val_2d, axis=-1)*loc_eff_res[0]
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@lasofivec lasofivec Nov 19, 2019

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@Didou09 :

Could you find the reason why an error was thrown with vect=None ? It should not

It doesn't anymore. Here is the only real change in this PR, that fixes the bug.

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@lasofivec lasofivec Nov 19, 2019

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PS: if you see line 3319, it only happened if ani=True, minimize=hybrid, method=sum, and if you see line 2863 I took out the variable which was no longer need and verified all loops to see that this error was nowhere else.

elif n_imode == 1: # simpson integration mode
for ii in range(nlos):
pts, usbis = _st.call_get_sample_single_ani(lims[0, ii],
Expand Down Expand Up @@ -3162,39 +3161,42 @@ def LOS_calc_signal(func, double[:,::1] ray_orig, double[:,::1] ray_vdir, res,
# -- not anisotropic -----------------------------------------------
if n_imode == 0: # "sum" integration mode
for ii in range(nlos):
pts = _st.call_get_sample_single(lims[0,ii], lims[1,ii],
pts = _st.call_get_sample_single(lims[0, ii],
lims[1, ii],
res_mv[ii],
n_dmode, n_imode,
&loc_eff_res[0],
&nb_rows[0],
ray_orig[:,ii:ii+1],
ray_vdir[:,ii:ii+1])
ray_orig[:, ii:ii+1],
ray_vdir[:, ii:ii+1])
val_2d = func(pts, t=t, **fkwdargs)
sig[:, ii] = np.sum(val_2d,axis=-1)*loc_eff_res[0]
sig[:, ii] = np.sum(val_2d, axis=-1)*loc_eff_res[0]
elif n_imode == 1: # "simpson" integration mode
for ii in range(nlos):
pts = _st.call_get_sample_single(lims[0,ii], lims[1,ii],
pts = _st.call_get_sample_single(lims[0, ii],
lims[1, ii],
res_mv[ii],
n_dmode, n_imode,
&loc_eff_res[0],
&nb_rows[0],
ray_orig[:,ii:ii+1],
ray_vdir[:,ii:ii+1])
ray_orig[:, ii:ii+1],
ray_vdir[:, ii:ii+1])
val = func(pts, t=t, **fkwdargs)
sig[:, ii] = scpintg.simps(val, x=None, axis=-1,
dx=loc_eff_res[0])
elif n_imode == 2: # "romberg" integration mode
for ii in range(nlos):
pts = _st.call_get_sample_single(lims[0,ii], lims[1,ii],
pts = _st.call_get_sample_single(lims[0, ii],
lims[1, ii],
res_mv[ii],
n_dmode, n_imode,
&loc_eff_res[0],
&nb_rows[0],
ray_orig[:,ii:ii+1],
ray_vdir[:,ii:ii+1])
ray_orig[:, ii:ii+1],
ray_vdir[:, ii:ii+1])
val = func(pts, t=t, **fkwdargs)
sig[:, ii] = scpintg.romb(val, show=False, axis=1,
dx=loc_eff_res[0])
dx=loc_eff_res[0])
return sig


Expand Down
18 changes: 12 additions & 6 deletions tofu/geom/_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5789,7 +5789,9 @@ def check_ff(self, ff, t=None, ani=None):
+ "\t\t\t - vect is a (3, npts) np.ndarray\n"
+ "\t\t\t - vect contains the (x, y, z) coordinates "
+ "of the units vectors of the photon emission directions"
+ "for each pts. Used for anisotropic emissivity.\n"
+ "for each pts. Present only for anisotropic emissivity, "
+ "unless specifically indicated otherwise "
+ "(with ani=False in LOS_calc_signal).\n"
+ "\t\t\tDoes not affect the outpout shape (still (nt, npts))")

# .. Checking basic definition of function ..........................
Expand Down Expand Up @@ -6005,11 +6007,6 @@ def calc_signal(
=> the method returns W/m2 (resp. W/m2/sr)
The line is sampled using :meth:`~tofu.geom.LOS.get_sample`,

The integral can be computed using three different methods:
- 'sum': A numpy.sum() on the local values (x segments lengths)
- 'simps': using :meth:`scipy.integrate.simps`
- 'romb': using :meth:`scipy.integrate.romb`

Except func, arguments common to :meth:`~tofu.geom.LOS.get_sample`

Parameters
Expand All @@ -6024,6 +6021,15 @@ def calc_signal(
- vect: None / (3,N) np.ndarray, unit direction vectors (X,Y,Z)
Should return at least:
- val : (N,) np.ndarray, local emissivity values
method : string, the integral can be computed using 3 different methods
- 'sum': A numpy.sum() on the local values (x segments) DEFAULT
- 'simps': using :meth:`scipy.integrate.simps`
- 'romb': using :meth:`scipy.integrate.romb`
minimize : string, method to minimize for computation optimization
- "calls": minimal number of calls to `func` (default)
- "memory": slowest method, to use only if "out of memory" error
- "hybrid": mix of before-mentioned methods.


Returns
-------
Expand Down
6 changes: 4 additions & 2 deletions tofu/tests/tests09_tutorials/tests01_runall.py
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Original file line number Diff line number Diff line change
Expand Up @@ -154,8 +154,10 @@ def _test_tuto(cls, tuto=None, pathtuto=_HERE, root=_TFROOT):
out = subprocess.run(cmd, shell=True, check=False,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
if 'error' in out.stderr.decode().lower():
error = out.stderr.decode()
ls = out.stderr.decode().split('\n')
if any(['Error' in ss and not 'ModuleNotFoundError' in ss
for ss in ls]):
error = '\n'.join(ls)
except Exception as err:
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error = err

Expand Down