Commit 996ea442 authored by Jakob Knollmueller's avatar Jakob Knollmueller
Browse files

Wiener Filter advanced

parents 4cb89177 1cb43f82
Pipeline #12518 passed with stage
in 6 minutes and 12 seconds
...@@ -13,7 +13,7 @@ before_script: ...@@ -13,7 +13,7 @@ before_script:
- apt-get update - apt-get update
- > - >
apt-get install -y build-essential python python-pip python-dev git 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 - pip install --upgrade -r ci/requirements_base.txt
- chmod +x ci/*.sh - chmod +x ci/*.sh
......
# 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
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
...@@ -15,7 +15,7 @@ Summary ...@@ -15,7 +15,7 @@ Summary
a versatile library designed to enable the development of signal a versatile library designed to enable the development of signal
inference algorithms that operate regardless of the underlying spatial inference algorithms that operate regardless of the underlying spatial
grid and its resolution. Its object-oriented framework is written in 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. efficiency.
NIFTY offers a toolkit that abstracts discretized representations of NIFTY offers a toolkit that abstracts discretized representations of
...@@ -71,7 +71,6 @@ Installation ...@@ -71,7 +71,6 @@ Installation
- [Python](http://www.python.org/) (v2.7.x) - [Python](http://www.python.org/) (v2.7.x)
- [NumPy](http://www.numpy.org/) - [NumPy](http://www.numpy.org/)
- [Cython](http://cython.org/)
### Download ### Download
...@@ -95,7 +94,7 @@ Starting with a fresh Ubuntu installation move to a folder like ...@@ -95,7 +94,7 @@ Starting with a fresh Ubuntu installation move to a folder like
- Using pip install numpy etc...: - Using pip install numpy etc...:
sudo pip install numpy cython sudo pip install numpy
- Install pyHealpix: - Install pyHealpix:
...@@ -147,10 +146,9 @@ MacPorts, missing ones need to be installed manually. It may also be ...@@ -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 mentioned that one should only use one package manager, as multiple ones
may cause trouble. may cause trouble.
- Install basic packages numpy and cython: - Install numpy:
sudo port install py27-numpy sudo port install py27-numpy
sudo port install py27-cython
- Install pyHealpix: - Install pyHealpix:
......
numpy numpy
cython
mpi4py mpi4py
matplotlib matplotlib
plotly plotly
......
...@@ -24,7 +24,7 @@ from diagonal_operator import DiagonalOperator ...@@ -24,7 +24,7 @@ from diagonal_operator import DiagonalOperator
from endomorphic_operator import EndomorphicOperator from endomorphic_operator import EndomorphicOperator
from smoothing_operator import SmoothingOperator from smoothing_operator import *
from fft_operator import * from fft_operator import *
......
...@@ -75,7 +75,8 @@ class LinearOperator(Loggable, object): ...@@ -75,7 +75,8 @@ class LinearOperator(Loggable, object):
def __init__(self, default_spaces=None): def __init__(self, default_spaces=None):
self.default_spaces = default_spaces self.default_spaces = default_spaces
def _parse_domain(self, domain): @staticmethod
def _parse_domain(domain):
return utilities.parse_domain(domain) return utilities.parse_domain(domain)
@abc.abstractproperty @abc.abstractproperty
......
...@@ -6,6 +6,7 @@ from nifty.operators.smoothing_operator import SmoothingOperator ...@@ -6,6 +6,7 @@ from nifty.operators.smoothing_operator import SmoothingOperator
from nifty.operators.composed_operator import ComposedOperator from nifty.operators.composed_operator import ComposedOperator
from nifty.operators.diagonal_operator import DiagonalOperator from nifty.operators.diagonal_operator import DiagonalOperator
class ResponseOperator(LinearOperator): class ResponseOperator(LinearOperator):
""" NIFTy ResponseOperator (example) """ NIFTy ResponseOperator (example)
...@@ -80,27 +81,22 @@ class ResponseOperator(LinearOperator): ...@@ -80,27 +81,22 @@ class ResponseOperator(LinearOperator):
shape_target = np.append(shape_target, self._domain[ii].shape) shape_target = np.append(shape_target, self._domain[ii].shape)
self._target = self._parse_domain(FieldArray(shape_target)) self._target = self._parse_domain(FieldArray(shape_target))
self._sigma = sigma
self._exposure = exposure kernel_smoothing = len(self._domain)*[None]
kernel_exposure = len(self._domain)*[None]
self._kernel = len(self._domain)*[None]
if len(sigma)!= len(exposure):
for ii in xrange(len(self._kernel)): raise ValueError("Length of smoothing kernel and length of"
self._kernel[ii] = SmoothingOperator(self._domain[ii], "exposure do not match")
sigma=self._sigma[ii])
for ii in xrange(len(kernel_smoothing)):
self._composed_kernel = ComposedOperator(self._kernel) kernel_smoothing[ii] = SmoothingOperator(self._domain[ii],
sigma=sigma[ii])
self._exposure_op = len(self._domain)*[None] kernel_exposure[ii] = DiagonalOperator(self._domain[ii],
if len(self._exposure_op) != len(self._kernel): diagonal=exposure[ii])
raise ValueError("Definition of kernel and exposure do not suit "
"each other") self._composed_kernel = ComposedOperator(kernel_smoothing)
else: self._composed_exposure = ComposedOperator(kernel_exposure)
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)
@property @property
def domain(self): def domain(self):
......
...@@ -16,4 +16,4 @@ ...@@ -16,4 +16,4 @@
# You should have received a copy of the GNU General Public License # You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>. # along with this program. If not, see <http://www.gnu.org/licenses/>.
from smoothing_operator import SmoothingOperator from .smoothing_operator import SmoothingOperator
# -*- 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
# -*- 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)