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ift
NIFTy
Commits
996ea442
Commit
996ea442
authored
May 16, 2017
by
Jakob Knollmueller
Browse files
Wiener Filter advanced
parents
4cb89177
1cb43f82
Pipeline
#12518
passed with stage
in 6 minutes and 12 seconds
Changes
17
Pipelines
1
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.gitlab-ci.yml
View file @
996ea442
...
...
@@ -13,7 +13,7 @@ before_script:
-
apt-get update
-
>
apt-get install -y build-essential python python-pip python-dev git
autoconf gsl-bin libgsl-dev wget python-numpy
cython
autoconf gsl-bin libgsl-dev wget python-numpy
-
pip install --upgrade -r ci/requirements_base.txt
-
chmod +x ci/*.sh
...
...
Makefile
deleted
100644 → 0
View file @
4cb89177
# This Makefile implements common tasks needed by developers
# A list of implemented rules can be obtained by the command "make help"
.DEFAULT_GOAL
=
build
.PHONY .SILENT
:
help
help
:
echo
echo
" Implemented targets:"
echo
echo
" build build pypmc for python2 and python3"
echo
" buildX build pypmc for pythonX only where X is one of {2,3}"
echo
" build-sdist build pypmc from the dist directory (python 2 and 3)"
echo
" build-sdistX build pypmc from the dist directory (pythonX, X in {2,3})"
echo
" check use nosetests to test pypmc with python 2.7 and 3"
echo
" checkX use nosetests to test pypmc with python 2.7 or 3,"
echo
" where X is one of {2,3}"
echo
" check-fast use nosetests to run only quick tests of pypmc"
echo
" using nosetests-2.7 and nosetests3"
echo
" check-sdist use nosetests-2.7 and nosetests3 to test the distribution"
echo
" generated by 'make sdist'"
echo
" check-sdistX use nosetests-2.7 or nosetests3 to test the distribution"
echo
" generated by 'make sdist', where X is one of {2,3}"
echo
" clean delete compiled and temporary files"
echo
" coverage produce and show a code coverage report"
echo
" Note: Cython modules cannot be analyzed"
echo
" distcheck runs 'check', check-sdist', 'run-examples' and"
echo
" opens a browser with the built documentation"
echo
" doc build the html documentation using sphinx"
echo
" doc-pdf build the pdf documentation using sphinx"
echo
" help show this message"
echo
" run-examples run all examples using python 2 and 3"
echo
" sdist make a source distribution"
echo
" show-todos show todo marks in the source code"
echo
.PHONY
:
clean
clean
:
#remove build doc
rm
-rf
./doc/_build
#remove .pyc files created by python 2.7
rm
-f
./*.pyc
find
-P
.
-name
'*.pyc'
-delete
#remove .pyc files crated by python 3
rm
-rf
./__pycache__
find
-P
.
-name
__pycache__
-delete
#remove build folder in root directory
rm
-rf
./build
#remove cythonized C source and object files
find
-P
.
-name
'*.c'
-delete
#remove variational binaries only if command line argument specified
find
-P
.
-name
'*.so'
-delete
#remove backup files
find
-P
.
-name
'*~'
-delete
#remove files created by coverage
rm
-f
.coverage
rm
-rf
coverage
# remove egg info
rm
-rf
pypmc.egg-info
# remove downloaded seutptools
rm
-f
setuptools-3.3.zip
# remove dist/
rm
-rf
dist
.PHONY
:
build
build
:
build2
.PHONY
:
build2
build2
:
python2 setup.py build_ext
--inplace
.PHONY
:
check
:
check2
.PHONY
:
check2
check2
:
build2
@
# run tests
nosetests-2.7
--processes
=
-1
--process-timeout
=
60
# run tests in parallel
mpirun
-n
2
nosetests-2.7
.PHONY
:
check-fast
check-fast
:
build
nosetests-2.7
-a
'!slow'
--processes
=
-1
--process-timeout
=
60
nosetests3
-a
'!slow'
--processes
=
-1
--process-timeout
=
60
.PHONY
:
.build-system-default
.build-system-default
:
python setup.py build_ext
--inplace
.PHONY
:
doc
doc
:
.build-system-default
cd
doc
&&
make html
.PHONY
:
doc-pdf
doc-pdf
:
.build-system-default
cd
doc
;
make latexpdf
.PHONY
:
run-examples
run-examples
:
build
cd
examples
;
\
for
file
in
$
$(ls)
;
do
\
echo
running
$
${file}
with python2
&&
\
python2
$
${file}
&&
\
echo
running
$
${file}
with python3
&&
\
python3
$
${file}
&&
\
\
# execute with mpirun if mpi4py appears in the file
\
if
grep
-Fq
'mpi4py'
$
${file}
;
then
\
echo
"
$
${file}
"
is mpi parallelized
&&
\
echo
running
$
${file}
in
parallel with python2
&&
\
mpirun
-n
2 python2
$
${file}
&&
\
echo
running
$
${file}
in
parallel with python3
&&
\
mpirun
-n
2 python3
$
${file}
;
\
fi
\
;
\
done
.PHONY
:
sdist
sdist
:
python setup.py sdist
.PHONY
:
build-sdist
build-sdist
:
build-sdist2 build-sdist3
./dist/pypmc*/NUL
:
sdist
cd
dist
&&
tar
xaf
*
.tar.gz
&&
cd
*
.PHONY
:
build-sdist2
build-sdist2
:
./dist/pypmc*/NUL
cd
dist/pypmc
*
&&
python2 setup.py build
.PHONY
:
build-sdist3
build-sdist3
:
./dist/pypmc*/NUL
cd
dist/pypmc
*
&&
python3 setup.py build
.PHONY
:
check-sdist
check-sdist
:
check-sdist2 check-sdist3
.PHONY
:
check-sdist2
check-sdist2
:
build-sdist2
cd
dist/
*
/build/lib
*
2.7
&&
\
nosetests-2.7
--processes
=
-1
--process-timeout
=
60
&&
\
mpirun
-n
2 nosetests-2.7
.PHONY
:
check-sdist3
check-sdist3
:
build-sdist3
cd
dist/
*
/build/lib
*
3.
*
&&
\
nosetests3
--processes
=
-1
--process-timeout
=
60
&&
\
mpirun
-n
2 nosetests3
.PHONY
:
distcheck
distcheck
:
check check-sdist doc
@
# execute "run-examples" after all other recipes makes are done
make run-examples
xdg-open link_to_documentation
.PHONY
:
show-todos
grep_cmd
=
ack-grep
-i
--no-html
--no-cc
[
^
"au""sphinx.ext."
]
todo
show-todos
:
@
# suppress errors here
@
# note that no todo found is considered as error
$(grep_cmd)
doc
;
\
$(grep_cmd)
pypmc
;
\
$(grep_cmd)
examples
;
echo
\
.PHONY
:
coverage
coverage
:
.build-system-default
rm
-rf
coverage
nosetests
--with-coverage
--cover-package
=
nifty
--cover-html
--cover-html-dir
=
coverage
xdg-open coverage/index.html
PKG-INFO
deleted
100644 → 0
View file @
4cb89177
Metadata-Version: 1.0
Name: ift_nifty
Version: 1.0.6
Summary: Numerical Information Field Theory
Home-page: http://www.mpa-garching.mpg.de/ift/nifty/
Author: Theo Steininger
Author-email: theos@mpa-garching.mpg.de
License: GPLv3
Description: UNKNOWN
Platform: UNKNOWN
README.md
View file @
996ea442
...
...
@@ -15,7 +15,7 @@ Summary
a versatile library designed to enable the development of signal
inference algorithms that operate regardless of the underlying spatial
grid and its resolution. Its object-oriented framework is written in
Python, although it accesses libraries written in
Cython,
C++
,
and C for
Python, although it accesses libraries written in C++ and C for
efficiency.
NIFTY offers a toolkit that abstracts discretized representations of
...
...
@@ -71,7 +71,6 @@ Installation
-
[
Python
](
http://www.python.org/
)
(
v2.7.x
)
-
[
NumPy
](
http://www.numpy.org/
)
-
[
Cython
](
http://cython.org/
)
### Download
...
...
@@ -95,7 +94,7 @@ Starting with a fresh Ubuntu installation move to a folder like
-
Using pip install numpy etc...:
sudo pip install numpy
cython
sudo pip install numpy
-
Install pyHealpix:
...
...
@@ -147,10 +146,9 @@ MacPorts, missing ones need to be installed manually. It may also be
mentioned that one should only use one package manager, as multiple ones
may cause trouble.
-
Install
basic packages numpy and cython
:
-
Install
numpy
:
sudo port install py27-numpy
sudo port install py27-cython
-
Install pyHealpix:
...
...
ci/requirements.txt
View file @
996ea442
numpy
cython
mpi4py
matplotlib
plotly
...
...
nifty/operators/__init__.py
View file @
996ea442
...
...
@@ -24,7 +24,7 @@ from diagonal_operator import DiagonalOperator
from
endomorphic_operator
import
EndomorphicOperator
from
smoothing_operator
import
SmoothingOperator
from
smoothing_operator
import
*
from
fft_operator
import
*
...
...
nifty/operators/linear_operator/linear_operator.py
View file @
996ea442
...
...
@@ -75,7 +75,8 @@ class LinearOperator(Loggable, object):
def
__init__
(
self
,
default_spaces
=
None
):
self
.
default_spaces
=
default_spaces
def
_parse_domain
(
self
,
domain
):
@
staticmethod
def
_parse_domain
(
domain
):
return
utilities
.
parse_domain
(
domain
)
@
abc
.
abstractproperty
...
...
nifty/operators/response_operator/response_operator.py
View file @
996ea442
...
...
@@ -6,6 +6,7 @@ from nifty.operators.smoothing_operator import SmoothingOperator
from
nifty.operators.composed_operator
import
ComposedOperator
from
nifty.operators.diagonal_operator
import
DiagonalOperator
class
ResponseOperator
(
LinearOperator
):
""" NIFTy ResponseOperator (example)
...
...
@@ -80,27 +81,22 @@ class ResponseOperator(LinearOperator):
shape_target
=
np
.
append
(
shape_target
,
self
.
_domain
[
ii
].
shape
)
self
.
_target
=
self
.
_parse_domain
(
FieldArray
(
shape_target
))
self
.
_sigma
=
sigma
self
.
_exposure
=
exposure
self
.
_kernel
=
len
(
self
.
_domain
)
*
[
None
]
for
ii
in
xrange
(
len
(
self
.
_kernel
)):
self
.
_kernel
[
ii
]
=
SmoothingOperator
(
self
.
_domain
[
ii
],
sigma
=
self
.
_sigma
[
ii
])
self
.
_composed_kernel
=
ComposedOperator
(
self
.
_kernel
)
self
.
_exposure_op
=
len
(
self
.
_domain
)
*
[
None
]
if
len
(
self
.
_exposure_op
)
!=
len
(
self
.
_kernel
):
raise
ValueError
(
"Definition of kernel and exposure do not suit "
"each other"
)
else
:
for
ii
in
xrange
(
len
(
self
.
_exposure_op
)):
self
.
_exposure_op
[
ii
]
=
DiagonalOperator
(
self
.
_domain
[
ii
],
diagonal
=
self
.
_exposure
[
ii
])
self
.
_composed_exposure
=
ComposedOperator
(
self
.
_exposure_op
)
kernel_smoothing
=
len
(
self
.
_domain
)
*
[
None
]
kernel_exposure
=
len
(
self
.
_domain
)
*
[
None
]
if
len
(
sigma
)
!=
len
(
exposure
):
raise
ValueError
(
"Length of smoothing kernel and length of"
"exposure do not match"
)
for
ii
in
xrange
(
len
(
kernel_smoothing
)):
kernel_smoothing
[
ii
]
=
SmoothingOperator
(
self
.
_domain
[
ii
],
sigma
=
sigma
[
ii
])
kernel_exposure
[
ii
]
=
DiagonalOperator
(
self
.
_domain
[
ii
],
diagonal
=
exposure
[
ii
])
self
.
_composed_kernel
=
ComposedOperator
(
kernel_smoothing
)
self
.
_composed_exposure
=
ComposedOperator
(
kernel_exposure
)
@
property
def
domain
(
self
):
...
...
nifty/operators/smoothing_operator/__init__.py
View file @
996ea442
...
...
@@ -16,4 +16,4 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
smoothing_operator
import
SmoothingOperator
from
.
smoothing_operator
import
SmoothingOperator
nifty/operators/smoothing_operator/direct_smoothing_operator.py
0 → 100644
View file @
996ea442
# -*- coding: utf8 -*-
import
numpy
as
np
from
d2o
import
STRATEGIES
from
.smoothing_operator
import
SmoothingOperator
class
DirectSmoothingOperator
(
SmoothingOperator
):
def
__init__
(
self
,
domain
,
sigma
,
log_distances
=
False
,
default_spaces
=
None
):
super
(
DirectSmoothingOperator
,
self
).
__init__
(
domain
,
sigma
,
log_distances
,
default_spaces
)
self
.
effective_smoothing_width
=
3.01
def
_precompute
(
self
,
x
,
sigma
,
dxmax
=
None
):
""" Does precomputations for Gaussian smoothing on a 1D irregular grid.
Parameters
----------
x: 1D floating point array or list containing the individual grid
positions. Points must be given in ascending order.
sigma: The sigma of the Gaussian with which the function living on x
should be smoothed, in the same units as x.
dxmax: (optional) The maximum distance up to which smoothing is
performed, in the same units as x. Default is 3.01*sigma.
Returns
-------
ibegin: integer array of the same size as x
ibegin[i] is the minimum grid index to consider when computing the
smoothed value at grid index i
nval: integer array of the same size as x
nval[i] is the number of indices to consider when computing the
smoothed value at grid index i.
wgt: list with the same number of entries as x
wgt[i] is an array with nval[i] entries containing the
normalized smoothing weights.
"""
if
dxmax
is
None
:
dxmax
=
self
.
effective_smoothing_width
*
sigma
x
=
np
.
asarray
(
x
)
ibegin
=
np
.
searchsorted
(
x
,
x
-
dxmax
)
nval
=
np
.
searchsorted
(
x
,
x
+
dxmax
)
-
ibegin
wgt
=
[]
expfac
=
1.
/
(
2.
*
sigma
*
sigma
)
for
i
in
range
(
x
.
size
):
t
=
x
[
ibegin
[
i
]:
ibegin
[
i
]
+
nval
[
i
]]
-
x
[
i
]
t
=
np
.
exp
(
-
t
*
t
*
expfac
)
t
*=
1.
/
np
.
sum
(
t
)
wgt
.
append
(
t
)
return
ibegin
,
nval
,
wgt
def
_apply_kernel_along_array
(
self
,
power
,
startindex
,
endindex
,
distances
,
smooth_length
,
smoothing_width
,
ibegin
,
nval
,
wgt
):
if
smooth_length
==
0.0
:
return
power
[
startindex
:
endindex
]
p_smooth
=
np
.
zeros
(
endindex
-
startindex
,
dtype
=
power
.
dtype
)
for
i
in
xrange
(
startindex
,
endindex
):
imin
=
max
(
startindex
,
ibegin
[
i
])
imax
=
min
(
endindex
,
ibegin
[
i
]
+
nval
[
i
])
p_smooth
[
imin
:
imax
]
+=
(
power
[
i
]
*
wgt
[
i
][
imin
-
ibegin
[
i
]:
imax
-
imin
+
ibegin
[
i
]])
return
p_smooth
def
_apply_along_axis
(
self
,
axis
,
arr
,
startindex
,
endindex
,
distances
,
smooth_length
,
smoothing_width
):
nd
=
arr
.
ndim
if
axis
<
0
:
axis
+=
nd
if
(
axis
>=
nd
):
raise
ValueError
(
"axis must be less than arr.ndim; axis=%d, rank=%d."
%
(
axis
,
nd
))
ibegin
,
nval
,
wgt
=
self
.
_precompute
(
distances
,
smooth_length
,
smooth_length
*
smoothing_width
)
ind
=
np
.
zeros
(
nd
-
1
,
dtype
=
np
.
int
)
i
=
np
.
zeros
(
nd
,
dtype
=
object
)
shape
=
arr
.
shape
indlist
=
np
.
asarray
(
range
(
nd
))
indlist
=
np
.
delete
(
indlist
,
axis
)
i
[
axis
]
=
slice
(
None
,
None
)
outshape
=
np
.
asarray
(
shape
).
take
(
indlist
)
i
.
put
(
indlist
,
ind
)
Ntot
=
np
.
product
(
outshape
)
holdshape
=
outshape
slicedArr
=
arr
[
tuple
(
i
.
tolist
())]
res
=
self
.
_apply_kernel_along_array
(
slicedArr
,
startindex
,
endindex
,
distances
,
smooth_length
,
smoothing_width
,
ibegin
,
nval
,
wgt
)
outshape
=
np
.
asarray
(
arr
.
shape
)
outshape
[
axis
]
=
endindex
-
startindex
outarr
=
np
.
zeros
(
outshape
,
dtype
=
arr
.
dtype
)
outarr
[
tuple
(
i
.
tolist
())]
=
res
k
=
1
while
k
<
Ntot
:
# increment the index
ind
[
nd
-
1
]
+=
1
n
=
-
1
while
(
ind
[
n
]
>=
holdshape
[
n
])
and
(
n
>
(
1
-
nd
)):
ind
[
n
-
1
]
+=
1
ind
[
n
]
=
0
n
-=
1
i
.
put
(
indlist
,
ind
)
slicedArr
=
arr
[
tuple
(
i
.
tolist
())]
res
=
self
.
_apply_kernel_along_array
(
slicedArr
,
startindex
,
endindex
,
distances
,
smooth_length
,
smoothing_width
,
ibegin
,
nval
,
wgt
)
outarr
[
tuple
(
i
.
tolist
())]
=
res
k
+=
1
return
outarr
def
_smooth
(
self
,
x
,
spaces
,
inverse
):
# infer affected axes
# we rely on the knowledge, that `spaces` is a tuple with length 1.
affected_axes
=
x
.
domain_axes
[
spaces
[
0
]]
if
len
(
affected_axes
)
>
1
:
raise
ValueError
(
"By this implementation only one-dimensional "
"spaces can be smoothed directly."
)
affected_axis
=
affected_axes
[
0
]
distance_array
=
x
.
domain
[
spaces
[
0
]].
get_distance_array
(
distribution_strategy
=
'not'
)
distance_array
=
distance_array
.
get_local_data
(
copy
=
False
)
if
self
.
log_distances
:
np
.
log
(
distance_array
,
out
=
distance_array
)
# collect the local data + ghost cells
local_data_Q
=
False
if
x
.
distribution_strategy
==
'not'
:
local_data_Q
=
True
elif
x
.
distribution_strategy
in
STRATEGIES
[
'slicing'
]:
# infer the local start/end based on the slicing information of
# x's d2o. Only gets non-trivial for axis==0.
if
0
!=
affected_axis
:
local_data_Q
=
True
else
:
start_index
=
x
.
val
.
distributor
.
local_start
start_distance
=
distance_array
[
start_index
]
augmented_start_distance
=
\
(
start_distance
-
self
.
effective_smoothing_width
*
self
.
sigma
)
augmented_start_index
=
\
np
.
searchsorted
(
distance_array
,
augmented_start_distance
)
true_start
=
start_index
-
augmented_start_index
end_index
=
x
.
val
.
distributor
.
local_end
end_distance
=
distance_array
[
end_index
-
1
]
augmented_end_distance
=
\
(
end_distance
+
self
.
effective_smoothing_width
*
self
.
sigma
)
augmented_end_index
=
\
np
.
searchsorted
(
distance_array
,
augmented_end_distance
)
true_end
=
true_start
+
x
.
val
.
distributor
.
local_length
augmented_slice
=
slice
(
augmented_start_index
,
augmented_end_index
)
augmented_data
=
x
.
val
.
get_data
(
augmented_slice
,
local_keys
=
True
,
copy
=
False
)
augmented_data
=
augmented_data
.
get_local_data
(
copy
=
False
)
augmented_distance_array
=
distance_array
[
augmented_slice
]
else
:
raise
ValueError
(
"Direct smoothing not implemented for given"
"distribution strategy."
)
if
local_data_Q
:
# if the needed data resides on the nodes already, the necessary
# are the same; no matter what the distribution strategy was.
augmented_data
=
x
.
val
.
get_local_data
(
copy
=
False
)
augmented_distance_array
=
distance_array
true_start
=
0
true_end
=
x
.
shape
[
affected_axis
]
# perform the convolution along the affected axes
# currently only one axis is supported
data_axis
=
affected_axes
[
0
]
if
inverse
:
true_sigma
=
1.
/
self
.
sigma
else
:
true_sigma
=
self
.
sigma
local_result
=
self
.
_apply_along_axis
(
data_axis
,
augmented_data
,
startindex
=
true_start
,
endindex
=
true_end
,
distances
=
augmented_distance_array
,
smooth_length
=
true_sigma
,
smoothing_width
=
self
.
effective_smoothing_width
)
result
=
x
.
copy_empty
()
result
.
val
.
set_local_data
(
local_result
,
copy
=
False
)
return
result
nifty/operators/smoothing_operator/fft_smoothing_operator.py
0 → 100644
View file @
996ea442
# -*- coding: utf-8 -*-
import
numpy
as
np
from
nifty.operators.fft_operator
import
FFTOperator
from
.smoothing_operator
import
SmoothingOperator
class
FFTSmoothingOperator
(
SmoothingOperator
):
def
_smooth
(
self
,
x
,
spaces
,
inverse
):
Transformator
=
FFTOperator
(
x
.
domain
[
spaces
[
0
]])
# transform to the (global-)default codomain and perform all remaining
# steps therein
transformed_x
=
Transformator
(
x
,
spaces
=
spaces
)
codomain
=
transformed_x
.
domain
[
spaces
[
0
]]
coaxes
=
transformed_x
.
domain_axes
[
spaces
[
0
]]
# create the kernel using the knowledge of codomain about itself
axes_local_distribution_strategy
=
\
transformed_x
.
val
.
get_axes_local_distribution_strategy
(
axes
=
coaxes
)
kernel
=
codomain
.
get_distance_array
(
distribution_strategy
=
axes_local_distribution_strategy
)
if
self
.
log_distances
:
kernel
.
apply_scalar_function
(
np
.
log
,
inplace
=
True
)
kernel
.
apply_scalar_function
(
codomain
.
get_fft_smoothing_kernel_function
(
self
.
sigma
),
inplace
=
True
)
# now, apply the kernel to transformed_x
# this is done node-locally utilizing numpys reshaping in order to
# apply the kernel to the correct axes
local_transformed_x
=
transformed_x
.
val
.
get_local_data
(
copy
=
False
)
local_kernel
=
kernel
.
get_local_data
(
copy
=
False
)
reshaper
=
[
transformed_x
.
shape
[
i
]
if
i
in
coaxes
else
1
for
i
in
xrange
(
len
(
transformed_x
.
shape
))]
local_kernel
=
np
.
reshape
(
local_kernel
,
reshaper
)
# apply the kernel
if
inverse
:
local_transformed_x
/=
local_kernel
else
:
local_transformed_x
*=
local_kernel
transformed_x
.
val
.
set_local_data
(
local_transformed_x
,
copy
=
False
)
smoothed_x
=
Transformator
.
adjoint_times
(
transformed_x
,
spaces
=
spaces
)
result
=
x
.
copy_empty
()
result
.
set_val
(
smoothed_x
,
copy
=
False
)
return
result
nifty/operators/smoothing_operator/smooth_util.pyx
deleted
100644 → 0
View file @
4cb89177
#cython: nonecheck=False
#cython: boundscheck=True