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Commit 223f71e3 authored by Theo Steininger's avatar Theo Steininger
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Merge branch 'master' into field_docu

parents 4bd83702 23cbce7a
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.gitlab-ci.yml
View file @ 223f71e3
......@@ -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 @ 4bd83702
# 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 @ 4bd83702
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
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......@@ -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 @ 223f71e3
numpy
cython
mpi4py
matplotlib
plotly
......
demos/wiener_filter.py
View file @ 223f71e3
......@@ -11,16 +11,36 @@ rank = comm.rank
if __name__ == "__main__":
distribution_strategy = 'not'
#Setting up physical constants
#total length of Interval or Volume the field lives on, e.g. in meters
L = 2.
#typical distance over which the field is correlated (in same unit as L)
correlation_length = 0.1
#variance of field in position space sqrt(<|s_x|^2>) (in unit of s)
field_variance = 2.
#smoothing length that response (in same unit as L)
response_sigma = 0.1
#defining resolution (pixels per dimension)
N_pixels = 512
#Setting up derived constants
k_0 = 1./correlation_length
#note that field_variance**2 = a*k_0/4. for this analytic form of power
#spectrum
a = field_variance**2/k_0*4.
pow_spec = (lambda k: a / (1 + k/k_0) ** 4)
pixel_width = L/N_pixels
# Setting up the geometry
s_space = RGSpace([512, 512])
s_space = RGSpace([N_pixels, N_pixels], distances = pixel_width)
fft = FFTOperator(s_space)
h_space = fft.target[0]
p_space = PowerSpace(h_space, distribution_strategy=distribution_strategy)
# Creating the mock data
pow_spec = (lambda k: 42 / (k + 1) ** 3)
S = create_power_operator(h_space, power_spectrum=pow_spec,
distribution_strategy=distribution_strategy)
......@@ -30,7 +50,7 @@ if __name__ == "__main__":
sh = sp.power_synthesize(real_signal=True)
ss = fft.inverse_times(sh)
R = SmoothingOperator(s_space, sigma=0.1)
R = SmoothingOperator(s_space, sigma=response_sigma)
signal_to_noise = 1
N = DiagonalOperator(s_space, diagonal=ss.var()/signal_to_noise, bare=True)
......
demos/wiener_filter_harmonic - Kopie.py 0 → 100644
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from nifty import *
from mpi4py import MPI
import plotly.offline as py
import plotly.graph_objs as go
comm = MPI.COMM_WORLD
rank = comm.rank
def plot_maps(x, name):
trace = [None]*len(x)
keys = x.keys()
field = x[keys[0]]
domain = field.domain[0]
shape = len(domain.shape)
max_n = domain.shape[0]*domain.distances[0]
step = domain.distances[0]
x_axis = np.arange(0, max_n, step)
if shape == 1:
for ii in xrange(len(x)):
trace[ii] = go.Scatter(x= x_axis, y=x[keys[ii]].val.get_full_data(), name=keys[ii])
fig = go.Figure(data=trace)
py.plot(fig, filename=name)
elif shape == 2:
for ii in xrange(len(x)):
py.plot([go.Heatmap(z=x[keys[ii]].val.get_full_data().real)], filename=keys[ii])
else:
raise TypeError("Only 1D and 2D field plots are supported")
def plot_power(x, name):
layout = go.Layout(
xaxis=dict(
type='log',
autorange=True
),
yaxis=dict(
type='log',
autorange=True
)
)
trace = [None]*len(x)
keys = x.keys()
field = x[keys[0]]
domain = field.domain[0]
x_axis = domain.kindex
for ii in xrange(len(x)):
trace[ii] = go.Scatter(x= x_axis, y=x[keys[ii]].val.get_full_data(), name=keys[ii])
fig = go.Figure(data=trace, layout=layout)
py.plot(fig, filename=name)
np.random.seed(42)
if __name__ == "__main__":
distribution_strategy = 'not'
# setting spaces
npix = np.array([500]) # number of pixels
total_volume = 1. # total length
# setting signal parameters
lambda_s = .05 # signal correlation length
sigma_s = 10. # signal variance
#setting response operator parameters
length_convolution = .025
exposure = 1.
# calculating parameters
k_0 = 4. / (2 * np.pi * lambda_s)
a_s = sigma_s ** 2. * lambda_s * total_volume
# creation of spaces
# x1 = RGSpace([npix,npix], distances=total_volume / npix,
# zerocenter=False)
# k1 = RGRGTransformation.get_codomain(x1)
x1 = HPSpace(32)
k1 = HPLMTransformation.get_codomain(x1)
p1 = PowerSpace(harmonic_partner=k1, logarithmic=False)
# creating Power Operator with given spectrum
spec = (lambda k: a_s / (1 + (k / k_0) ** 2) ** 2)
p_field = Field(p1, val=spec)
S_op = create_power_operator(k1, spec)
# creating FFT-Operator and Response-Operator with Gaussian convolution
Fft_op = FFTOperator(domain=x1, target=k1,
domain_dtype=np.float64,
target_dtype=np.complex128)
R_op = ResponseOperator(x1, sigma=[length_convolution],
exposure=[exposure])
# drawing a random field
sk = p_field.power_synthesize(real_signal=True, mean=0.)
s = Fft_op.adjoint_times(sk)
signal_to_noise = 1
N_op = DiagonalOperator(R_op.target, diagonal=s.var()/signal_to_noise, bare=True)
n = Field.from_random(domain=R_op.target,
random_type='normal',
std=s.std()/np.sqrt(signal_to_noise),
mean=0.)
d = R_op(s) + n
# Wiener filter
j = Fft_op.times(R_op.adjoint_times(N_op.inverse_times(d)))
D = HarmonicPropagatorOperator(S=S_op, N=N_op, R=R_op)
mk = D(j)
m = Fft_op.adjoint_times(mk)
# z={}
# z["signal"] = s
# z["reconstructed_map"] = m
# z["data"] = d
# z["lambda"] = R_op(s)
# z["j"] = j
#
# plot_maps(z, "Wiener_filter.html")
demos/wiener_filter_harmonic.py 0 → 100644
View file @ 223f71e3
from nifty import *
from mpi4py import MPI
import plotly.offline as py
import plotly.graph_objs as go
comm = MPI.COMM_WORLD
rank = comm.rank
def plot_maps(x, name):
trace = [None]*len(x)
keys = x.keys()
field = x[keys[0]]
domain = field.domain[0]
shape = len(domain.shape)
max_n = domain.shape[0]*domain.distances[0]
step = domain.distances[0]
x_axis = np.arange(0, max_n, step)
if shape == 1:
for ii in xrange(len(x)):
trace[ii] = go.Scatter(x= x_axis, y=x[keys[ii]].val.get_full_data(), name=keys[ii])
fig = go.Figure(data=trace)
py.plot(fig, filename=name)
elif shape == 2:
for ii in xrange(len(x)):
py.plot([go.Heatmap(z=x[keys[ii]].val.get_full_data())], filename=keys[ii])
else:
raise TypeError("Only 1D and 2D field plots are supported")
def plot_power(x, name):
layout = go.Layout(
xaxis=dict(
type='log',
autorange=True
),
yaxis=dict(
type='log',
autorange=True
)
)
trace = [None]*len(x)
keys = x.keys()
field = x[keys[0]]
domain = field.domain[0]
x_axis = domain.kindex
for ii in xrange(len(x)):
trace[ii] = go.Scatter(x= x_axis, y=x[keys[ii]].val.get_full_data(), name=keys[ii])
fig = go.Figure(data=trace, layout=layout)
py.plot(fig, filename=name)
np.random.seed(42)
if __name__ == "__main__":
distribution_strategy = 'not'
# setting spaces
npix = np.array([500]) # number of pixels
total_volume = 1. # total length
# setting signal parameters
lambda_s = .05 # signal correlation length
sigma_s = 10. # signal variance
#setting response operator parameters
length_convolution = .025
exposure = 1.
# calculating parameters
k_0 = 4. / (2 * np.pi * lambda_s)
a_s = sigma_s ** 2. * lambda_s * total_volume
# creation of spaces
# x1 = RGSpace([npix,npix], distances=total_volume / npix,
# zerocenter=False)
# k1 = RGRGTransformation.get_codomain(x1)
x1 = HPSpace(64)
k1 = HPLMTransformation.get_codomain(x1)
p1 = PowerSpace(harmonic_partner=k1, logarithmic=False)
# creating Power Operator with given spectrum
spec = (lambda k: a_s / (1 + (k / k_0) ** 2) ** 2)
p_field = Field(p1, val=spec)
S_op = create_power_operator(k1, spec)
# creating FFT-Operator and Response-Operator with Gaussian convolution
# adjust dtype_target probperly
Fft_op = FFTOperator(domain=x1, target=k1,
domain_dtype=np.float64,
target_dtype=np.float64)
R_op = ResponseOperator(x1, sigma=[length_convolution],
exposure=[exposure])
# drawing a random field
sk = p_field.power_synthesize(real_power=True, mean=0.)
s = Fft_op.adjoint_times(sk)
signal_to_noise = 1
N_op = DiagonalOperator(R_op.target, diagonal=s.var()/signal_to_noise, bare=True)
n = Field.from_random(domain=R_op.target,
random_type='normal',
std=s.std()/np.sqrt(signal_to_noise),
mean=0)
d = R_op(s) + n
# Wiener filter
j = Fft_op.times(R_op.adjoint_times(N_op.inverse_times(d)))
D = HarmonicPropagatorOperator(S=S_op, N=N_op, R=R_op)
mk = D(j)
m = Fft_op.adjoint_times(mk)
# z={}
# z["signal"] = s
# z["reconstructed_map"] = m
# z["data"] = d
# z["lambda"] = R_op(s)
#
# plot_maps(z, "Wiener_filter.html")
demos/wiener_filter_unit.py 0 → 100644
View file @ 223f71e3
from nifty import *
from mpi4py import MPI
import plotly.offline as py
import plotly.graph_objs as go
comm = MPI.COMM_WORLD
rank = comm.rank
def plot_maps(x, name):
trace = [None]*len(x)
keys = x.keys()
field = x[keys[0]]
domain = field.domain[0]
shape = len(domain.shape)
max_n = domain.shape[0]*domain.distances[0]
step = domain.distances[0]
x_axis = np.arange(0, max_n, step)
if shape == 1:
for ii in xrange(len(x)):
trace[ii] = go.Scatter(x= x_axis, y=x[keys[ii]].val.get_full_data(), name=keys[ii])
fig = go.Figure(data=trace)
py.plot(fig, filename=name)
elif shape == 2:
for ii in xrange(len(x)):
py.plot([go.Heatmap(z=x[keys[ii]].val.get_full_data())], filename=keys[ii])
else:
raise TypeError("Only 1D and 2D field plots are supported")
def plot_power(x, name):
layout = go.Layout(
xaxis=dict(
type='log',
autorange=True
),
yaxis=dict(
type='log',