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Merged
Didou09 merged 22 commits into from
Nov 17, 2019
Merged

Bug fixes in calc_signal and get_sample #249

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9813371
[debugging] added prints for Issue247
lasofivec Nov 13, 2019
28c5c1f
[debugging] k coeffs from get sample ok, not pts reconstruction
lasofivec Nov 13, 2019
8fcd989
[debugging] found bug in los get_sample
lasofivec Nov 13, 2019
d290787
[debugging] found bug in los integration
lasofivec Nov 13, 2019
4654415
[debugging] cleaning code
lasofivec Nov 13, 2019
9b7c9ef
[debugging] took out c code for maintainability
lasofivec Nov 13, 2019
fcb5b33
[Issue247] cleaning, reverting some changes
lasofivec Nov 13, 2019
0f27f15
[Issue247] found bug in hybird and memory minimization methods
lasofivec Nov 14, 2019
03b8cfb
[Issue247] Added np.allclose() test in tests01_geom.tests03_core.Test…
Nov 15, 2019
83bb165
[Issue247] Removed CamLOS2D and 'rel' cases from tests01_geom.tests03…
Nov 15, 2019
8a0924e
[Issue247] Added tests09_tutorials for running tutorials
Nov 15, 2019
7cd3e3c
[Issue247] PEP8 compliance 1
Nov 15, 2019
57e9d6a
[Issue247] PEP8 compliance 2
Nov 15, 2019
56df4eb
[Issue247] PEP8 compliance 3
Nov 15, 2019
23539c9
[Issue247] PEP8 compliance 4
Nov 15, 2019
f855d29
[Issue247] Fixed tests, but test files generated not yet deleted
Nov 17, 2019
48cd492
[Issue247] Fixed unit tests and removed saved files automatically
Nov 17, 2019
fdc6fa0
[Issue247] Trting to remove Config print in unit tests tests01_geom/t…
Nov 17, 2019
bb8ce2d
[Issue247] Renamed tutorials and copied in tests folder to easily run…
Nov 17, 2019
2254e7f
[Issue247] Fixed tests again
Nov 17, 2019
4760fd3
[Issue247] One last print of Config left in unit tests, can't find it
Nov 17, 2019
ed51236
[Issue247] PEP8 compliance
Nov 17, 2019
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0 examples/tutorials/plot_basic_tutorial.py → examples/tutorials/tuto_plot_basic.py
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File renamed without changes.
8 changes: 7 additions & 1 deletion examples/tutorials/plot_create_geometry.py → ...es/tutorials/tuto_plot_create_geometry.py
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Expand Up @@ -9,6 +9,12 @@
import matplotlib.pyplot as plt
import tofu.geom as tfg

import os
import tofu as tf
print(os.getcwd())
print(tf.__version__)
print(tf.__path__)

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@lasofivec lasofivec Nov 19, 2019

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Not sure why these lines were added. I didn't reviewed the last version of this PR, but if you agree @Didou09 I will revert these lines.
Furthermore, the renaming of the files means that the doc construction will fail, see sphinx-gallery's doc. I'm working on making the necessary changes on another branch

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@Didou09 Didou09 Nov 19, 2019

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These lines were added for debugging, I forgot to remove them, yes you can delete them


###############################################################################
# Creating an empty Vessel
Expand Down Expand Up @@ -86,7 +92,7 @@

# Plot the polygon by default in two projections (cross-section and horizontal)
# and return the list of axes
Lax = ves.plot(element="P")
lax = ves.plot(element="P")


###############################################################################
Expand Down
5 changes: 4 additions & 1 deletion examples/tutorials/plot_custom_emissivity.py → .../tutorials/tuto_plot_custom_emissivity.py
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Expand Up @@ -84,8 +84,11 @@ def project_to_2D(xyz):
sig, units = cam2d.calc_signal(emissivity,
res=0.01,
reflections=False,
minimize="hybrid",
method="sum",
newcalc=True,
plot=False,
t=time_vector)

sig.plot(ntMax=1)
plt.show()
plt.show(block=False)
148 changes: 71 additions & 77 deletions tofu/geom/_GG.pyx
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16 changes: 0 additions & 16 deletions tofu/geom/_basic_geom_tools.pxd
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Expand Up @@ -18,15 +18,6 @@ from cpython.array cimport array, clone
cdef double _VSMALL
cdef double _SMALL

cdef extern from "_fast_sum.c":
void sum_rows_blocks(double *orig, double *out, int n_rows, int n_cols) nogil

cdef extern from "_fast_sum.c":
void sum_par_mat(double *orig, double *out, int n_rows, int n_cols) nogil

cdef extern from "_fast_sum.c":
double sum_par_one_row(double *orig, int n_rows) nogil

# ==============================================================================
# == Redifinition of functions
# ==============================================================================
Expand Down Expand Up @@ -107,11 +98,4 @@ cdef void compute_diff_div(const double[:, ::1] vec1,
# ==============================================================================
# == Matrix sum (np.sum)
# ==============================================================================
cdef void sum_by_rows(double *orig, double *out,
int n_rows, int n_cols) nogil

cdef void sum_naive_rows(double* orig, double* out,
int n_rows, int n_cols) nogil
cdef double sum_naive(double* orig, int n_cols) nogil

cdef long sum_naive_int(long* orig, int n_cols) nogil
17 changes: 0 additions & 17 deletions tofu/geom/_basic_geom_tools.pyx
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Expand Up @@ -370,23 +370,6 @@ cdef inline void sum_by_rows(double *orig, double *out,


# ...........
cdef inline void sum_naive_rows(double* orig, double* out,
int n_rows, int n_cols) nogil:
cdef int ii, jj
for ii in prange(n_rows):
out[ii] = 0
for jj in range(n_cols):
out[ii] += orig[ii*n_cols + jj]

return


cdef inline double sum_naive(double* orig, int n_cols) nogil:
cdef int ii
cdef double out = 0.
for ii in prange(n_cols):
out += orig[ii]
return out

cdef inline long sum_naive_int(long* orig, int n_cols) nogil:
cdef int ii
Expand Down
9 changes: 4 additions & 5 deletions tofu/geom/_core.py
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Expand Up @@ -5886,7 +5886,7 @@ def calc_signal(
self,
func,
t=None,
ani=None,
ani=False,
fkwdargs={},
Brightness=True,
res=None,
Expand Down Expand Up @@ -5981,6 +5981,7 @@ def calc_signal(
num_threads=num_threads,
Test=True,
)

c0 = (
reflections
and self._dgeom["dreflect"] is not None
Expand Down Expand Up @@ -6013,11 +6014,11 @@ def calc_signal(
)

# Integrate
# Creating the arrays with null everywhere..........
if s.ndim == 2:
sig = np.full((s.shape[0], self.nRays), np.nan)
else:
sig = np.full((1, self.nRays), np.nan)

if t is None or len(t) == 1:
sig[0, indok] = s
else:
Expand All @@ -6033,6 +6034,7 @@ def calc_signal(
compact=True,
pts=True,
)

if ani:
nbrep = np.r_[
indpts[0], np.diff(indpts), pts.shape[1] - indpts[-1]
Expand All @@ -6045,13 +6047,11 @@ def calc_signal(
# This is the slowest step (~3.8 s with res=0.02
# and interferometer)
val = func(pts, t=t, vect=vect)

# Integrate
if val.ndim == 2:
sig = np.full((val.shape[0], self.nRays), np.nan)
else:
sig = np.full((1, self.nRays), np.nan)

indpts = np.r_[0, indpts, pts.shape[1]]
for ii in range(0, self.nRays):
sig[:, ii] = (
Expand All @@ -6061,7 +6061,6 @@ def calc_signal(
)
* reseff[ii]
)

# Format output
return self._calc_signal_postformat(
sig,
Expand Down
56 changes: 0 additions & 56 deletions tofu/geom/_fast_sum.c
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43 changes: 14 additions & 29 deletions tofu/geom/_sampling_tools.pxd
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Expand Up @@ -81,16 +81,20 @@ cdef call_get_sample_single_ani(double los_kmin, double los_kmax,
int n_dmode, int n_imode,
double[1] eff_res,
long[1] nb_rows,
double[:,::1] ray_orig,
double[:,::1] ray_vdir)

cdef cnp.ndarray[double,ndim=2,mode='c'] call_get_sample_single(double los_kmin, double los_kmax,
double resol,
int n_dmode, int n_imode,
double[1] eff_res,
long[1] nb_rows,
double[:,::1] ray_orig,
double[:,::1] ray_vdir)
double[:, ::1] ray_orig,
double[:, ::1] ray_vdir)

cdef cnp.ndarray[double,
ndim=2,
mode='c'] call_get_sample_single(double los_kmin,
double los_kmax,
double resol,
int n_dmode,
int n_imode,
double[1] eff_res,
long[1] nb_rows,
double[:, ::1] ray_orig,
double[:, ::1] ray_vdir)

cdef int los_get_sample_core_const_res(int nlos,
double* los_lim_min,
Expand Down Expand Up @@ -124,22 +128,3 @@ cdef void los_get_sample_pts(int nlos,
double* coeff_ptr,
long* los_ind,
int num_threads) nogil

# -- Integrations utility function ---------------------------------------------
cdef void integrate_sum_nlos(int nlos, int nt,
double[:,::1] val_2d,
double[::1,:] sig_mv,
long* ind_arr,
double* reseff_arr,
int num_threads) nogil

cdef void integrate_c_sum_mat(double[:,::1] val_mv,
double* sig,
int nrows, int ncols,
double loc_eff_res,
int num_threads) nogil

cdef double integrate_c_sum_vec(double* val_mv,
int nza,
double loc_eff_res,
int num_threads) nogil
82 changes: 10 additions & 72 deletions tofu/geom/_sampling_tools.pyx
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Expand Up @@ -456,6 +456,7 @@ cdef inline void middle_rule_abs_s2(int nlos,
loc_x = los_kmin[0]
middle_rule_single(num_raf, loc_x, loc_resol,
&los_coeffs[first_index])

# filling tab...... CANNOT BE PARALLEL !!
for ii in range(1, nlos):
num_raf = ind_cum[ii]
Expand Down Expand Up @@ -505,8 +506,6 @@ cdef inline void middle_rule_abs_var_s1(int nlos,
return




cdef inline void middle_rule_abs_var_s2(int nlos,
double* los_kmin,
double* los_kmax,
Expand Down Expand Up @@ -561,7 +560,6 @@ cdef inline void middle_rule_abs_var(int nlos,
middle_rule_abs_var_s2(nlos, los_kmin, los_kmax,
eff_resolution, los_coeffs,
los_ind, los_nraf, num_threads)

# ...
free(los_nraf)
return
Expand Down Expand Up @@ -1301,7 +1299,8 @@ cdef inline call_get_sample_single_ani(double los_kmin, double los_kmax,
# computing points
usbis = np.repeat(ray_vdir, sz_coeff, axis=1)
ksbis = np.asarray(<double[:sz_coeff]>los_coeffs[0])
pts = ray_orig + ksbis[None,:] * usbis
pts = ray_orig + ksbis[None, :] * usbis
# freeing memory used
if los_coeffs != NULL:
if los_coeffs[0] != NULL:
free(los_coeffs[0])
Expand Down Expand Up @@ -1458,7 +1457,7 @@ cdef inline void los_get_sample_core_var_res(int nlos,
return


# # -- utility for calc signal ---------------------------------------------------
# -- utility for calc signal ---------------------------------------------------
cdef inline void los_get_sample_pts(int nlos,
double* ptx,
double* pty,
Expand All @@ -1482,9 +1481,9 @@ cdef inline void los_get_sample_pts(int nlos,
loc_vy = ray_vdir[1,0]
loc_vz = ray_vdir[2,0]
for ii in range(los_ind[0]):
ptx[ii] = loc_ox + coeff_ptr[ii] + loc_vx
pty[ii] = loc_oy + coeff_ptr[ii] + loc_vy
ptz[ii] = loc_oz + coeff_ptr[ii] + loc_vz
ptx[ii] = loc_ox + coeff_ptr[ii] * loc_vx
pty[ii] = loc_oy + coeff_ptr[ii] * loc_vy
ptz[ii] = loc_oz + coeff_ptr[ii] * loc_vz
usx[ii] = loc_vx
usy[ii] = loc_vy
usz[ii] = loc_vz
Expand All @@ -1497,71 +1496,10 @@ cdef inline void los_get_sample_pts(int nlos,
loc_vy = ray_vdir[1,jj]
loc_vz = ray_vdir[2,jj]
for ii in range(los_ind[jj-1], los_ind[jj]):
ptx[ii] = loc_ox + coeff_ptr[ii] + loc_vx
pty[ii] = loc_oy + coeff_ptr[ii] + loc_vy
ptz[ii] = loc_oz + coeff_ptr[ii] + loc_vz
ptx[ii] = loc_ox + coeff_ptr[ii] * loc_vx
pty[ii] = loc_oy + coeff_ptr[ii] * loc_vy
ptz[ii] = loc_oz + coeff_ptr[ii] * loc_vz
usx[ii] = loc_vx
usy[ii] = loc_vy
usz[ii] = loc_vz
return


# -- calling sampling and intergrating with sum --------------------------------
cdef inline void integrate_sum_nlos(int nlos, int nt,
double[:,::1] val_2d,
double[::1,:] sig_mv,
long* ind_arr,
double* reseff_arr,
int num_threads) nogil:
cdef int ii, jj
cdef int jjp1
jj = 0
jjp1 = ind_arr[0]
integrate_c_sum_mat(val_2d[:,jj:jjp1],
&sig_mv[0,0],
nt, jjp1 - jj,
reseff_arr[0], num_threads)
with nogil, parallel(num_threads=num_threads):
for ii in prange(1,nlos):
# sig[:,ii] = np.sum(val_2d[:,indbis[ii]:indbis[ii+1]],
# axis=-1)*reseff_mv[ii]
jj = ind_arr[ii-1]
jjp1 = ind_arr[ii]
integrate_c_sum_mat(val_2d[:,jj:jjp1],
&sig_mv[0,ii],
nt, jjp1 - jj,
reseff_arr[ii], num_threads)
return

cdef inline void integrate_c_sum_mat(double[:,::1] val_mv,
double* sig,
int nrows, int ncols,
double loc_eff_res,
int num_threads) nogil:
cdef double* vsum
cdef int jj
# ...
vsum = <double*>malloc(nrows*sizeof(double))
_bgt.sum_rows_blocks(&val_mv[0,0], &vsum[0],
nrows, ncols)
# _bgt.sum_by_rows(val_mv, &vsum[0],
# nrows, ncols)
# _bgt.sum_naive_rows(val_mv, &vsum[0],
# nrows, ncols)
# _bgt.sum_par_mat(val_mv, &vsum[0],
# nrows, ncols)
for jj in range(nrows):
sig[jj] = vsum[jj] * loc_eff_res
free(vsum)
return


cdef inline double integrate_c_sum_vec(double* val_mv,
int nsz,
double loc_eff_res,
int num_threads) nogil:
cdef double vsum
cdef int jj
# ...
vsum = _bgt.sum_par_one_row(val_mv, nsz)
return vsum * loc_eff_res
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