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Faster los calc signal sum calls for newcalc=False #308

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Merged
lasofivec merged 3 commits into from
Jan 6, 2020
Merged

Faster los calc signal sum calls for newcalc=False #308

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4a7a4e6
[FasterLOSCalcSumCalls] Replace loop on partial sum by ufinc np.add.r…
Dec 2, 2019
e9af491
[(FasterLOSCalcSignalSumCalls] Corrected tests
Dec 2, 2019
5d7d5f1
[FasterLOSCalcSignalSumCalls] PEP8 Compliance
Dec 2, 2019
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1 change: 1 addition & 0 deletions tofu/data/_comp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -413,6 +413,7 @@ def func(pts, vect=None, t=None, ntall=ntall,
shapeval = list(pts.shape)
shapeval[0] = ntall if t is None else t.size
val = np.full(tuple(shapeval), fill_value)

if t is None:
for ii in range(0,ntall):
val[ii,...] = mplTriLinInterp(mpltri,
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12 changes: 8 additions & 4 deletions tofu/data/_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3677,11 +3677,15 @@ def _get_indtu(t=None, tall=None, tbinall=None,
# Get indt (t with respect to tbinall)
indt, indtu = None, None
if t is not None:
indt = np.digitize(t, tbinall)
indtu = np.unique(indt)
if len(t) == len(tall) and np.allclose(t, tall):
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@Didou09 Didou09 Dec 2, 2019

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handle trivial case first, particularly suited for cases with t.size = 1

indt = np.arange(0, tall.size)
indtu = indt
else:
indt = np.digitize(t, tbinall)
indtu = np.unique(indt)
# Update
tall = tall[indtu]

# Update
tall = tall[indtu]
if idref1d is not None:
assert indtr1 is not None
indtr1 = indtr1[indtu]
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59 changes: 21 additions & 38 deletions tofu/geom/_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6025,7 +6025,7 @@ def calc_signal(
reflections=True,
coefs=None,
ind=None,
out=object,
returnas=object,
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@Didou09 Didou09 Dec 2, 2019

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much more explicit variable name, especially since we tend to use 'out' to store temporary output inside functions.
It as the case in the other method by the way (calc_signal_from_Plasma2D()), out was redefined at line 6254

plot=True,
dataname=None,
fs=None,
Expand Down Expand Up @@ -6086,7 +6086,7 @@ def calc_signal(
# Format input

indok, Ds, us, DL, E = self._calc_signal_preformat(
ind=ind, DL=DL, out=out, Brightness=Brightness
ind=ind, DL=DL, out=returnas, Brightness=Brightness
)

if Ds is None:
Expand Down Expand Up @@ -6180,19 +6180,9 @@ def calc_signal(
# 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] = (
np.nansum(
val[:, indpts[ii]:indpts[ii + 1]],
axis=-1
)
* reseff[ii]
)
sig = np.add.reduceat(val, np.r_[0, indpts],
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@Didou09 Didou09 Dec 2, 2019

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More concise and numerically faster, only advantages :-)
Usable in _GG.LOS_calc_signal(method='sum', minimize='calls') ?
Usable elsewhere ?

Compatible with parallelization ?

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@lasofivec lasofivec Jan 6, 2020

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nope, only functions that don't require gil can be parallelized, calling numpy functions requires the gil, so it is not possible. This is why it wasn't parallelized with newcalc=True

axis=-1)*reseff[None, :]

# Format output
return self._calc_signal_postformat(
sig,
Expand All @@ -6202,7 +6192,7 @@ def calc_signal(
E=E,
units=units,
plot=plot,
out=out,
out=returnas,
fs=fs,
dmargin=dmargin,
wintit=wintit,
Expand Down Expand Up @@ -6236,7 +6226,7 @@ def calc_signal_from_Plasma2D(
reflections=True,
coefs=None,
ind=None,
out=object,
returnas=object,
plot=True,
dataname=None,
fs=None,
Expand All @@ -6250,7 +6240,7 @@ def calc_signal_from_Plasma2D(

# Format input
indok, Ds, us, DL, E = self._calc_signal_preformat(
ind=ind, out=out, t=t, Brightness=Brightness
ind=ind, out=returnas, t=t, Brightness=Brightness
)

if Ds is None:
Expand All @@ -6262,12 +6252,12 @@ def calc_signal_from_Plasma2D(
# Get time vector
if t is None:
out = plasma2d._checkformat_qr12RPZ(
quant=quant,
ref1d=ref1d,
ref2d=ref2d,
q2dR=q2dR,
q2dPhi=q2dPhi,
q2dZ=q2dZ,
quant=quant,
ref1d=ref1d,
ref2d=ref2d,
q2dR=q2dR,
q2dPhi=q2dPhi,
q2dZ=q2dZ,
)
t = plasma2d._get_tcom(*out[:4])[0]
else:
Expand Down Expand Up @@ -6368,6 +6358,8 @@ def funcbis(*args, **kwdargs):
indpts[0], np.diff(indpts), pts.shape[1] - indpts[-1]
]
vect = np.repeat(self.u, nbrep, axis=1)
if fill_value is None:
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@Didou09 Didou09 Dec 2, 2019

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Avoid nans, they are not handled by np.add.reduceat() => we set fill_value to 0 instead in this case (if not forced by the user)

fill_value = 0.

# Get quantity values at ptsRZ
# This is the slowest step (~3.8 s with res=0.02
Expand All @@ -6388,19 +6380,10 @@ def funcbis(*args, **kwdargs):
fill_value=fill_value,
)

# 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] = (
np.nansum(val[:, indpts[ii]:indpts[ii + 1]],
axis=-1)
* reseff[ii]
)
# Integrate using ufunc reduceat for speed
# (cf. https://stackoverflow.com/questions/59079141)
sig = np.add.reduceat(val, np.r_[0, indpts],
axis=-1)*reseff[None, :]

# Format output
# this is the secod slowest step (~0.75 s)
Expand All @@ -6412,7 +6395,7 @@ def funcbis(*args, **kwdargs):
E=E,
units=units,
plot=plot,
out=out,
out=returnas,
fs=fs,
dmargin=dmargin,
wintit=wintit,
Expand Down
2 changes: 1 addition & 1 deletion tofu/tests/tests01_geom/tests03_core.py
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Expand Up @@ -874,7 +874,7 @@ def ffT(Pts, t=None, vect=None):
resMode=rm,
method=dm, minimize=mmz,
ind=ind,
plot=False, out=np.ndarray,
plot=False, returnas=np.ndarray,
fs=(12, 6), connect=connect)
sig, units = out
assert not np.all(np.isnan(sig)), str(ii)
Expand Down
2 changes: 1 addition & 1 deletion tofu/tests/tests02_data/tests03_core.py
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Expand Up @@ -475,7 +475,7 @@ def setup_class(cls, nch=30, nt=50, SavePath='./', verb=False):
lData = [None for ii in range(0,len(lc))]
for ii in range(0,len(lc)):
sig = lc[ii].calc_signal(emiss, t=t, res=0.01, method=lm[ii],
plot=False, out=np.ndarray)[0]
plot=False, returnas=np.ndarray)[0]
sig = sig[:,:,None]*flamb[None,None,:]
cla = eval('tfd.DataCam%sDSpectral'%('2' if lc[ii]._is2D() else '1'))
data = cla(data=sig, Name='All', Diag='Test',
Expand Down