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ift
NIFTy
Commits
19ece6ba
Commit
19ece6ba
authored
Jun 23, 2020
by
Martin Reinecke
Browse files
Merge branch 'adjust_gridder' into 'NIFTy_7'
Switch to ducc0.wgridder See merge request
!549
parents
990befe7
e615e0b5
Pipeline
#77433
passed with stages
in 25 minutes and 35 seconds
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7
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View file @
19ece6ba
...
...
@@ -13,7 +13,6 @@ RUN apt-get update && apt-get install -y \
python3-mpi4py python3-matplotlib \
# more optional NIFTy dependencies
&& pip3 install ducc0 \
&& pip3 install git+https://gitlab.mpcdf.mpg.de/ift/nifty_gridder.git \
&& pip3 install jupyter \
&& rm -rf /var/lib/apt/lists/*
...
...
README.md
View file @
19ece6ba
...
...
@@ -50,9 +50,7 @@ Installation
Optional dependencies:
-
[
DUCC0
](
https://gitlab.mpcdf.mpg.de/mtr/ducc
)
for faster FFTs, spherical
harmonic transforms, and non-uniform Fourier transforms
-
[
nifty_gridder
](
https://gitlab.mpcdf.mpg.de/ift/nifty_gridder
)
(
for
radio
interferometry responses)
harmonic transforms, and radio interferometry gridding support
-
[
mpi4py
](
https://mpi4py.scipy.org
)
(
for
MPI-parallel execution)
-
[
matplotlib
](
https://matplotlib.org/
)
(
for
field plotting)
...
...
@@ -86,10 +84,6 @@ If this library is present, NIFTy will detect it automatically and prefer
DUCC's FFT is compiled with optimizations for the host CPU and can provide
significantly faster transforms.
Support for the radio interferometry gridder is added via:
pip3 install --user git+https://gitlab.mpcdf.mpg.de/ift/nifty_gridder.git
MPI support is added via:
sudo apt-get install python3-mpi4py
...
...
demos/bench_gridder.py
deleted
100644 → 0
View file @
990befe7
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Copyright(C) 2019-2020 Max-Planck-Society
# Author: Martin Reinecke
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
from
time
import
time
import
matplotlib.pyplot
as
plt
import
numpy
as
np
import
nifty7
as
ift
def
main
():
N0s
,
a0s
,
b0s
,
c0s
=
[],
[],
[],
[]
for
ii
in
range
(
10
,
26
):
nu
=
1024
nv
=
1024
N
=
int
(
2
**
ii
)
print
(
'N = {}'
.
format
(
N
))
rng
=
ift
.
random
.
current_rng
()
uv
=
rng
.
uniform
(
-
.
5
,
.
5
,
(
N
,
2
))
vis
=
rng
.
normal
(
0.
,
1.
,
N
)
+
1j
*
rng
.
normal
(
0.
,
1.
,
N
)
uvspace
=
ift
.
RGSpace
((
nu
,
nv
))
visspace
=
ift
.
UnstructuredDomain
(
N
)
img
=
rng
.
standard_normal
((
nu
,
nv
))
img
=
ift
.
makeField
(
uvspace
,
img
)
t0
=
time
()
GM
=
ift
.
GridderMaker
(
uvspace
,
eps
=
1e-7
,
uv
=
uv
)
vis
=
ift
.
makeField
(
visspace
,
vis
)
op
=
GM
.
getFull
().
adjoint
t1
=
time
()
op
(
img
).
val
t2
=
time
()
op
.
adjoint
(
vis
).
val
t3
=
time
()
print
(
t2
-
t1
,
t3
-
t2
)
N0s
.
append
(
N
)
a0s
.
append
(
t1
-
t0
)
b0s
.
append
(
t2
-
t1
)
c0s
.
append
(
t3
-
t2
)
print
(
'Measure rest operator'
)
sc
=
ift
.
StatCalculator
()
op
=
GM
.
getRest
().
adjoint
for
_
in
range
(
10
):
t0
=
time
()
res
=
op
(
img
)
sc
.
add
(
time
()
-
t0
)
print
(
'FFT shape'
,
res
.
shape
)
plt
.
scatter
(
N0s
,
a0s
,
label
=
'Gridder mr'
)
plt
.
legend
()
# no idea why this is necessary, but if it is omitted, the range is wrong
plt
.
ylim
(
min
(
a0s
),
max
(
a0s
))
plt
.
ylabel
(
'time [s]'
)
plt
.
title
(
'Initialization'
)
plt
.
loglog
()
plt
.
savefig
(
'bench0.png'
)
plt
.
close
()
plt
.
scatter
(
N0s
,
b0s
,
color
=
'k'
,
marker
=
'^'
,
label
=
'Gridder mr times'
)
plt
.
scatter
(
N0s
,
c0s
,
color
=
'k'
,
label
=
'Gridder mr adjoint times'
)
plt
.
axhline
(
sc
.
mean
,
label
=
'FFT'
)
plt
.
axhline
(
sc
.
mean
+
np
.
sqrt
(
sc
.
var
))
plt
.
axhline
(
sc
.
mean
-
np
.
sqrt
(
sc
.
var
))
plt
.
legend
()
plt
.
ylabel
(
'time [s]'
)
plt
.
title
(
'Apply'
)
plt
.
loglog
()
plt
.
savefig
(
'bench1.png'
)
plt
.
close
()
if
__name__
==
'__main__'
:
main
()
docs/source/installation.rst
View file @
19ece6ba
...
...
@@ -23,10 +23,6 @@ If this library is present, NIFTy will detect it automatically and prefer
DUCC's FFT is compiled with optimizations for the host CPU and can provide
significantly faster transforms.
Support for the radio interferometry gridder is added via::
pip3 install --user git+https://gitlab.mpcdf.mpg.de/ift/nifty_gridder.git
MPI support is added via::
sudo apt-get install python3-mpi4py
...
...
src/__init__.py
View file @
19ece6ba
...
...
@@ -86,7 +86,7 @@ from .library.light_cone_operator import LightConeOperator
from
.library.wiener_filter_curvature
import
WienerFilterCurvature
from
.library.adjust_variances
import
(
make_adjust_variances_hamiltonian
,
do_adjust_variances
)
from
.library.gridder
import
Gridder
Maker
from
.library.gridder
import
Gridder
from
.library.correlated_fields
import
CorrelatedFieldMaker
from
.
import
extra
...
...
src/library/gridder.py
View file @
19ece6ba
...
...
@@ -24,88 +24,42 @@ from ..operators.linear_operator import LinearOperator
from
..sugar
import
makeDomain
,
makeField
class
Gridder
Maker
(
object
):
def
__init__
(
self
,
dirty_domain
,
uv
,
eps
=
2e-1
3
):
import
nifty_gridder
dirty_domain
=
makeDomain
(
dirty_domain
)
if
(
len
(
dirty_domain
)
!=
1
or
not
isinstance
(
dirty_domain
[
0
],
RGSpace
)
or
not
len
(
dirty_domain
.
shape
)
==
2
):
raise
ValueError
(
"need
dirty_domain
with exactly one 2D RGSpace"
)
class
Gridder
(
LinearOperator
):
def
__init__
(
self
,
target
,
uv
,
eps
=
2e-1
0
,
nthreads
=
1
):
self
.
_capability
=
self
.
TIMES
|
self
.
ADJOINT_TIMES
self
.
_target
=
makeDomain
(
target
)
if
(
len
(
self
.
_target
)
!=
1
or
not
isinstance
(
self
.
_target
[
0
],
RGSpace
)
or
not
len
(
self
.
_target
.
shape
)
==
2
):
raise
ValueError
(
"need
target
with exactly one 2D RGSpace"
)
if
uv
.
ndim
!=
2
:
raise
ValueError
(
"uv must be a 2D array"
)
if
uv
.
shape
[
1
]
!=
2
:
raise
ValueError
(
"second dimension of uv must have length 2"
)
dstx
,
dsty
=
dirty_domain
[
0
].
distances
# wasteful hack to adjust to shape required by nifty_gridder
uvw
=
np
.
empty
((
uv
.
shape
[
0
],
3
),
dtype
=
np
.
float64
)
uvw
[:,
0
:
2
]
=
uv
uvw
[:,
2
]
=
0.
# Scale uv such that 0<uv<=1 which is assumed by nifty_gridder
uvw
[:,
0
]
=
uvw
[:,
0
]
*
dstx
uvw
[:,
1
]
=
uvw
[:,
1
]
*
dsty
speedOfLight
=
299792458.
bl
=
nifty_gridder
.
Baselines
(
uvw
,
np
.
array
([
speedOfLight
]))
nxdirty
,
nydirty
=
dirty_domain
.
shape
gconf
=
nifty_gridder
.
GridderConfig
(
nxdirty
,
nydirty
,
eps
,
1.
,
1.
)
nu
,
nv
=
gconf
.
Nu
(),
gconf
.
Nv
()
self
.
_idx
=
nifty_gridder
.
getIndices
(
bl
,
gconf
,
np
.
zeros
((
uv
.
shape
[
0
],
1
),
dtype
=
np
.
bool
))
self
.
_bl
=
bl
du
,
dv
=
1.
/
(
nu
*
dstx
),
1.
/
(
nv
*
dsty
)
grid_domain
=
RGSpace
([
nu
,
nv
],
distances
=
[
du
,
dv
],
harmonic
=
True
)
self
.
_rest
=
_RestOperator
(
dirty_domain
,
grid_domain
,
gconf
)
self
.
_gridder
=
RadioGridder
(
grid_domain
,
bl
,
gconf
,
self
.
_idx
)
def
getGridder
(
self
):
return
self
.
_gridder
def
getRest
(
self
):
return
self
.
_rest
def
getFull
(
self
):
return
self
.
getRest
()
@
self
.
_gridder
def
ms2vis
(
self
,
x
):
return
self
.
_bl
.
ms2vis
(
x
,
self
.
_idx
)
class
_RestOperator
(
LinearOperator
):
def
__init__
(
self
,
dirty_domain
,
grid_domain
,
gconf
):
self
.
_domain
=
makeDomain
(
grid_domain
)
self
.
_target
=
makeDomain
(
dirty_domain
)
self
.
_gconf
=
gconf
self
.
_capability
=
self
.
TIMES
|
self
.
ADJOINT_TIMES
def
apply
(
self
,
x
,
mode
):
self
.
_check_input
(
x
,
mode
)
res
=
x
.
val
if
mode
==
self
.
TIMES
:
res
=
self
.
_gconf
.
grid2dirty
(
res
)
else
:
res
=
self
.
_gconf
.
dirty2grid
(
res
)
return
makeField
(
self
.
_tgt
(
mode
),
res
)
class
RadioGridder
(
LinearOperator
):
def
__init__
(
self
,
grid_domain
,
bl
,
gconf
,
idx
):
self
.
_domain
=
DomainTuple
.
make
(
UnstructuredDomain
((
bl
.
Nrows
())))
self
.
_target
=
DomainTuple
.
make
(
grid_domain
)
self
.
_bl
=
bl
self
.
_gconf
=
gconf
self
.
_idx
=
idx
self
.
_capability
=
self
.
TIMES
|
self
.
ADJOINT_TIMES
UnstructuredDomain
((
uv
.
shape
[
0
])))
# wasteful hack to adjust to shape required by ducc0.wgridder
self
.
_uvw
=
np
.
empty
((
uv
.
shape
[
0
],
3
),
dtype
=
np
.
float64
)
self
.
_uvw
[:,
0
:
2
]
=
uv
self
.
_uvw
[:,
2
]
=
0.
self
.
_eps
=
float
(
eps
)
self
.
_nthreads
=
int
(
nthreads
)
def
apply
(
self
,
x
,
mode
):
import
nifty_gridder
self
.
_check_input
(
x
,
mode
)
speedOfLight
=
299792458.
freq
=
np
.
array
([
speedOfLight
])
x
=
x
.
val
nxdirty
,
nydirty
=
self
.
_target
[
0
].
shape
nu
,
nv
=
max
(
2
*
nxdirty
,
16
),
max
(
2
*
nydirty
,
16
)
dstx
,
dsty
=
self
.
_target
[
0
].
distances
from
ducc0.wgridder
import
ms2dirty
,
dirty2ms
if
mode
==
self
.
TIMES
:
x
=
self
.
_bl
.
ms2vis
(
x
.
val
.
reshape
((
-
1
,
1
)),
self
.
_idx
)
res
=
nifty_gridder
.
vis2grid
(
self
.
_bl
,
self
.
_gconf
,
self
.
_idx
,
x
)
res
=
ms2dirty
(
self
.
_uvw
,
freq
,
x
.
reshape
((
-
1
,
1
)),
None
,
nxdirty
,
nydirty
,
dstx
,
dsty
,
nu
,
nv
,
self
.
_eps
,
False
,
self
.
_nthreads
,
0
)
else
:
res
=
nifty_gridder
.
grid2vis
(
self
.
_bl
,
self
.
_gc
on
f
,
self
.
_idx
,
x
.
val
)
res
=
self
.
_bl
.
vis2ms
(
res
,
self
.
_idx
)
.
reshape
((
-
1
,))
res
=
dirty2ms
(
self
.
_uvw
,
freq
,
x
,
N
on
e
,
dstx
,
dsty
,
nu
,
nv
,
self
.
_eps
,
False
,
self
.
_nthreads
,
0
)
res
=
res
.
reshape
((
-
1
,))
return
makeField
(
self
.
_tgt
(
mode
),
res
)
test/test_operators/test_nft.py
View file @
19ece6ba
...
...
@@ -46,10 +46,9 @@ def test_gridding(nu, nv, N, eps):
dstx
,
dsty
=
dom
.
distances
uv
[:,
0
]
=
uv
[:,
0
]
/
dstx
uv
[:,
1
]
=
uv
[:,
1
]
/
dsty
GM
=
ift
.
Gridder
Maker
(
dom
,
uv
=
uv
,
eps
=
eps
)
Op
=
ift
.
Gridder
(
dom
,
uv
=
uv
,
eps
=
eps
)
vis2
=
ift
.
makeField
(
ift
.
UnstructuredDomain
(
vis
.
shape
),
vis
)
Op
=
GM
.
getFull
()
pynu
=
Op
(
vis2
).
val
# DFT
x
,
y
=
np
.
meshgrid
(
...
...
@@ -72,8 +71,7 @@ def test_cartesian():
tmp
=
np
.
vstack
([
uu
[
None
,
:],
vv
[
None
,
:]])
uv
=
np
.
transpose
(
tmp
,
(
2
,
1
,
0
)).
reshape
(
-
1
,
2
)
GM
=
ift
.
GridderMaker
(
dom
,
uv
=
uv
)
op
=
GM
.
getFull
().
adjoint
op
=
ift
.
Gridder
(
dom
,
uv
=
uv
).
adjoint
fld
=
ift
.
from_random
(
dom
,
'normal'
)
arr
=
fld
.
val
...
...
@@ -95,16 +93,9 @@ def test_cartesian():
def
test_build
(
nu
,
nv
,
N
,
eps
):
dom
=
ift
.
RGSpace
([
nu
,
nv
])
uv
=
ift
.
random
.
current_rng
().
random
((
N
,
2
))
-
0.5
GM
=
ift
.
GridderMaker
(
dom
,
uv
=
uv
,
eps
=
eps
)
R0
=
GM
.
getGridder
()
R1
=
GM
.
getRest
()
R
=
R1
@
R0
RF
=
GM
.
getFull
()
RF
=
ift
.
Gridder
(
dom
,
uv
=
uv
,
eps
=
eps
)
# Consistency checks
flt
=
np
.
float64
cmplx
=
np
.
complex128
ift
.
extra
.
check_linear_operator
(
R0
,
cmplx
,
flt
,
only_r_linear
=
True
)
ift
.
extra
.
check_linear_operator
(
R1
,
flt
,
flt
)
ift
.
extra
.
check_linear_operator
(
R
,
cmplx
,
flt
,
only_r_linear
=
True
)
ift
.
extra
.
check_linear_operator
(
RF
,
cmplx
,
flt
,
only_r_linear
=
True
)
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