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Merged
lasofivec merged 6 commits into from
Nov 25, 2019
Merged

[Issue215] fixed #279

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b97c0f0
[Issue215] Fixed interpolation bug, original quantity was called with…
Nov 22, 2019
9a53486
[Issue215] PEP8 Compliance 1
Nov 22, 2019
114b865
[Issue215] PEP8 Compliance 2
Nov 22, 2019
134fc3f
[Issue215] PEP8 Compliance 3
Nov 22, 2019
32e0627
[Issue215] PEP8 Compliance 4
Nov 22, 2019
dc8b1ae
[Issue215] PEP8 Compliance 5
Nov 22, 2019
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127 changes: 74 additions & 53 deletions tofu/data/_comp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -424,11 +424,13 @@ def func(pts, vect=None, t=None, ntall=ntall,
tbinall=tbinall,
idref1d=idref1d,
idref2d=idref2d)[1:-2]
for ii in range(0,ntall):
for ii in range(0, ntall):
ind = indt == indtu[ii]
val[ind,...] = mplTriLinInterp(mpltri,
vquant[indtq[ii],:],
trifinder=trifind)(r,z).filled(fill_value)
val[ind, ...] = mplTriLinInterp(
mpltri,
vquant[indtq[indtu[ii]], :],
trifinder=trifind
)(r, z).filled(fill_value)
return val, t

# --------------------
Expand Down Expand Up @@ -456,9 +458,10 @@ def func(pts, vect=None, t=None, ntall=ntall,
tbinall=tbinall,
idref1d=idref1d,
idref2d=idref2d)[1:-2]
for ii in range(0,ntall):
for ii in range(0, ntall):
ind = indt == indtu[ii]
val[ind,indok] = vquant[indtq[ii],indpts[indok]]
val[ind, indok] = vquant[indtq[indtu[ii]],
indpts[indok]]
return val, t


Expand Down Expand Up @@ -492,30 +495,34 @@ def func(pts, vect=None, t=None, ntall=ntall,

# interpolate 1d
# This is reasonable (~0.15 s)
val[ii,...] = scpinterp.interp1d(vr1[indtr1[ii],:],
vquant[indtq[ii],:],
kind='linear',
bounds_error=False,
fill_value=fill_value)(np.asarray(vii))
val[ii, ...] = scpinterp.interp1d(
vr1[indtr1[ii], :],
vquant[indtq[ii], :],
kind='linear',
bounds_error=False,
fill_value=fill_value
)(np.asarray(vii))
t = tall
else:
out = plasma._get_indtu(t=t, tall=tall, tbinall=tbinall,
idref1d=idref1d, idref2d=idref2d,
indtr1=indtr1, indtr2=indtr2)[1:]
ntall, indt, indtu, indtr1, indtr2 = out
for ii in range(0,ntall):
for ii in range(0, ntall):
# get ref values for mapping
vii = mplTriLinInterp(mpltri,
vr2[indtr2[ii],:],
trifinder=trifind)(r,z)
vr2[indtr2[ii], :],
trifinder=trifind)(r, z)

# interpolate 1d
ind = indt == indtu[ii]
val[ind,...] = scpinterp.interp1d(vr1[indtr1[ii],:],
vquant[indtq[ii],:],
kind='linear',
bounds_error=False,
fill_value=fill_value)(np.asarray(vii))
val[ind, ...] = scpinterp.interp1d(
vr1[indtr1[indtu[ii]], :],
vquant[indtq[indtu[ii]], :],
kind='linear',
bounds_error=False,
fill_value=fill_value
)(np.asarray(vii))
val[np.isnan(val)] = fill_value

return val, t
Expand All @@ -538,11 +545,13 @@ def func(pts, vect=None, t=None, ntall=ntall,
if t is None:
for ii in range(0,ntall):
# interpolate 1d
val[ii,indok] = scpinterp.interp1d(vr1[indtr1[ii],:],
vquant[indtq[ii],:],
kind='linear',
bounds_error=False,
fill_value=fill_value)(vr2[indtr2[ii],indpts[indok]])
val[ii, indok] = scpinterp.interp1d(
vr1[indtr1[ii], :],
vquant[indtq[ii], :],
kind='linear',
bounds_error=False,
fill_value=fill_value
)(vr2[indtr2[ii], indpts[indok]])
t = tall
else:
out = plasma._get_indtu(t=t, tall=tall, tbinall=tbinall,
Expand All @@ -552,11 +561,13 @@ def func(pts, vect=None, t=None, ntall=ntall,
for ii in range(0,ntall):
# interpolate 1d
ind = indt == indtu[ii]
val[ind,indok] = scpinterp.interp1d(vr1[indtr1[ii],:],
vquant[indtq[ii],:],
kind='linear',
bounds_error=False,
fill_value=fill_value)(vr2[indtr2[ii],indpts[indok]])
val[ind, indok] = scpinterp.interp1d(
vr1[indtr1[indtu[ii]], :],
vquant[indtq[indtu[ii]], :],
kind='linear',
bounds_error=False,
fill_value=fill_value
)(vr2[indtr2[ii], indpts[indok]])
return val, t
return func

Expand Down Expand Up @@ -610,34 +621,42 @@ def func(pts, vect=None, t=None, ntall=ntall,
for ii in range(0,ntall):
valR[ii,...] = mplTriLinInterp(mpltri,
vq2dR[indtq[ii],:],
trifinder=trifind)(r,z)
trifinder=trifind)(r, z)
valPhi[ii,...] = mplTriLinInterp(mpltri,
vq2dPhi[indtq[ii],:],
trifinder=trifind)(r,z)
trifinder=trifind)(r, z)
valZ[ii,...] = mplTriLinInterp(mpltri,
vq2dZ[indtq[ii],:],
trifinder=trifind)(r,z)
trifinder=trifind)(r, z)
t = tall
else:
ntall, indt, indtu = plasma._get_indtu(t=t, tall=tall,
tbinall=tbinall)[1:4]
for ii in range(0,ntall):
ind = indt == indtu[ii]
valR[ind,...] = mplTriLinInterp(mpltri,
vq2dR[indtq[ii],:],
trifinder=trifind)(r,z)
valPhi[ind,...] = mplTriLinInterp(mpltri,
vq2dPhi[indtq[ii],:],
trifinder=trifind)(r,z)
valZ[ind,...] = mplTriLinInterp(mpltri,
vq2dZ[indtq[ii],:],
trifinder=trifind)(r,z)
valR[ind, ...] = mplTriLinInterp(
mpltri,
vq2dR[indtq[indtu[ii]], :],
trifinder=trifind
)(r, z)
valPhi[ind, ...] = mplTriLinInterp(
mpltri,
vq2dPhi[indtq[indtu[ii]], :],
trifinder=trifind
)(r, z)
valZ[ind, ...] = mplTriLinInterp(
mpltri,
vq2dZ[indtq[indtu[ii]], :],
trifinder=trifind
)(r, z)


if Type == 'sca':
val = valR*vR[None,:] + valPhi*vPhi[None,:] + valZ*vZ[None,:]
val = (valR*vR[None, :] + valPhi*vPhi[None, :]
+ valZ*vZ[None, :])
elif Type == 'abs(sca)':
val = np.abs(valR*vR[None,:] + valPhi*vPhi[None,:] + valZ*vZ[None,:])
val = np.abs(valR*vR[None, :] + valPhi*vPhi[None, :]
+ valZ*vZ[None, :])

val[np.isnan(val)] = fill_value
return val, t
Expand Down Expand Up @@ -668,28 +687,30 @@ def func(pts, vect=None, t=None, ntall=ntall,
valZ = np.full(tuple(shapeval), fill_value)

# Interpolate
indpts = trifind(r,z)
indpts = trifind(r, z)
if t is None:
for ii in range(0,ntall):
valR[ii,...] = vq2dR[indtq[ii],indpts]
valPhi[ii,...] = vq2dPhi[indtq[ii],indpts]
valZ[ii,...] = vq2dZ[indtq[ii],indpts]
valR[ii, ...] = vq2dR[indtq[ii], indpts]
valPhi[ii, ...] = vq2dPhi[indtq[ii], indpts]
valZ[ii, ...] = vq2dZ[indtq[ii], indpts]
t = tall
else:
ntall, indt, indtu = plasma._get_indtu(t=t, tall=tall,
tbinall=tbinall,
idref1d=idref1d,
idref2d=idref2d)[1:]
for ii in range(0,ntall):
for ii in range(0, ntall):
ind = indt == indtu[ii]
valR[ind,...] = vq2dR[indtq[ii],indpts]
valPhi[ind,...] = vq2dPhi[indtq[ii],indpts]
valZ[ind,...] = vq2dZ[indtq[ii],indpts]
valR[ind, ...] = vq2dR[indtq[indtu[ii]], indpts]
valPhi[ind, ...] = vq2dPhi[indtq[indtu[ii]], indpts]
valZ[ind, ...] = vq2dZ[indtq[indtu[ii]], indpts]

if Type == 'sca':
val = valR*vR[None,:] + valPhi*vPhi[None,:] + valZ*vZ[None,:]
val = (valR*vR[None, :] + valPhi*vPhi[None, :]
+ valZ*vZ[None, :])
elif Type == 'abs(sca)':
val = np.abs(valR*vR[None,:] + valPhi*vPhi[None,:] + valZ*vZ[None,:])
val = np.abs(valR*vR[None, :] + valPhi*vPhi[None, :]
+ valZ*vZ[None, :])
val[np.isnan(val)] = fill_value
return val, t
return func
2 changes: 1 addition & 1 deletion tofu/version.py
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
# Do not edit, pipeline versioning governed by git tags!
__version__ = '1.4.2-alpha2-13-g7db6643'
__version__ = '1.4.2-alpha2-20-gb97c0f0'