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ift
NIFTy
Commits
a0e370b0
Commit
a0e370b0
authored
Jan 07, 2019
by
Martin Reinecke
Browse files
merge NIFTy_5
parents
4404fc4a
bd9f4a4e
Changes
108
Hide whitespace changes
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.gitlab-ci.yml
View file @
a0e370b0
...
...
@@ -34,32 +34,24 @@ build_docker_from_cache:
-
docker build -t $CONTAINER_TEST_IMAGE .
-
docker push $CONTAINER_TEST_IMAGE
test
_python2_with_coverage
:
test
:
stage
:
test
variables
:
OMPI_MCA_btl_vader_single_copy_mechanism
:
none
script
:
-
mpiexec -n 2 --bind-to none pytest -q test
-
pytest -q --cov=nifty5 test
-
mpiexec -n 2 --bind-to none pytest
-3
-q test
-
pytest
-3
-q --cov=nifty5 test
-
>
python -m coverage report --omit "*plotting*,*distributed_do*"
python
3
-m coverage report --omit "*plotting*,*distributed_do*"
-
>
python -m coverage report --omit "*plotting*,*distributed_do*" | grep TOTAL | awk '{ print "TOTAL: "$4; }'
test_python3
:
stage
:
test
variables
:
OMPI_MCA_btl_vader_single_copy_mechanism
:
none
script
:
-
pytest-3 -q
-
mpiexec -n 2 --bind-to none pytest-3 -q
python3 -m coverage report --omit "*plotting*,*distributed_do*" | grep TOTAL | awk '{ print "TOTAL: "$4; }'
pages
:
stage
:
release
before_script
:
-
ls
script
:
-
python setup.py install --user -f
-
python
3
setup.py install --user -f
-
sh docs/generate.sh
-
mv docs/build/ public/
artifacts
:
...
...
@@ -69,7 +61,6 @@ pages:
-
NIFTy_4
before_script
:
-
python setup.py install --user -f
-
python3 setup.py install --user -f
run_ipynb
:
...
...
@@ -80,7 +71,6 @@ run_ipynb:
run_getting_started_1
:
stage
:
demo_runs
script
:
-
python demos/getting_started_1.py
-
python3 demos/getting_started_1.py
-
mpiexec -n 2 --bind-to none python3 demos/getting_started_1.py 2> /dev/null
artifacts
:
...
...
@@ -90,7 +80,6 @@ run_getting_started_1:
run_getting_started_2
:
stage
:
demo_runs
script
:
-
python demos/getting_started_2.py
-
python3 demos/getting_started_2.py
-
mpiexec -n 2 --bind-to none python3 demos/getting_started_2.py 2> /dev/null
artifacts
:
...
...
@@ -100,7 +89,6 @@ run_getting_started_2:
run_getting_started_3
:
stage
:
demo_runs
script
:
-
python demos/getting_started_3.py
-
python3 demos/getting_started_3.py
artifacts
:
paths
:
...
...
@@ -109,7 +97,6 @@ run_getting_started_3:
run_bernoulli
:
stage
:
demo_runs
script
:
-
python demos/bernoulli_demo.py
-
python3 demos/bernoulli_demo.py
artifacts
:
paths
:
...
...
@@ -118,7 +105,6 @@ run_bernoulli:
run_curve_fitting
:
stage
:
demo_runs
script
:
-
python demos/polynomial_fit.py
-
python3 demos/polynomial_fit.py
artifacts
:
paths
:
...
...
Dockerfile
View file @
a0e370b0
...
...
@@ -5,27 +5,23 @@ RUN apt-get update && apt-get install -y \
git \
# Packages needed for NIFTy
libfftw3-dev \
python python-pip python-dev python-future python-scipy cython \
python3 python3-pip python3-dev python3-future python3-scipy cython3 \
# Documentation build dependencies
python-sphinx python-sphinx-rtd-theme python-numpydoc \
python
3
-sphinx python
3
-sphinx-rtd-theme python
3
-numpydoc \
# Testing dependencies
python-nose python-coverage python-parameterized python-pytest python-pytest-cov \
python3-nose python3-coverage python3-parameterized python3-pytest python3-pytest-cov \
python3-coverage python3-parameterized python3-pytest python3-pytest-cov \
# Optional NIFTy dependencies
openmpi-bin libopenmpi-dev
python-mpi4py
python3-mpi4py \
openmpi-bin libopenmpi-dev python3-mpi4py \
# Packages needed for NIFTy
&& pip install pyfftw \
&& pip3 install pyfftw \
# Optional NIFTy dependencies
&& pip install git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git \
&& pip3 install git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git \
# Testing dependencies
&& rm -rf /var/lib/apt/lists/*
# Needed for demos to be running
RUN
apt-get update
&&
apt-get
install
-y
python-matplotlib
python3-matplotlib
\
&&
python3
-m
pip
install
--upgrade
pip
&&
python3
-m
pip
install
jupyter
&&
python
-m
pip
install
--upgrade
pip
&&
python
-m
pip
install
jupyter
\
RUN
apt-get update
&&
apt-get
install
-y
python3-matplotlib
\
&&
python3
-m
pip
install
--upgrade
pip
&&
python3
-m
pip
install
jupyter
\
&&
rm
-rf
/var/lib/apt/lists/
*
# Set matplotlib backend
...
...
README.md
View file @
a0e370b0
...
...
@@ -37,7 +37,7 @@ Installation
### Requirements
-
[
Python
](
https://www.python.org/
)
(
v2.7
.x
or
3.5.x
)
-
[
Python
3
](
https://www.python.org/
)
(
3.5
.x
or
later
)
-
[
SciPy
](
https://www.scipy.org/
)
-
[
pyFFTW
](
https://pypi.python.org/pypi/pyFFTW
)
...
...
@@ -61,8 +61,8 @@ distributions, the "apt" lines will need slight changes.
NIFTy5 and its mandatory dependencies can be installed via:
sudo apt-get install git libfftw3-dev python python-pip python-dev
pip install --user git+https://gitlab.mpcdf.mpg.de/ift/NIFTy.git@NIFTy_5
sudo apt-get install git libfftw3-dev python
3
python
3
-pip python
3
-dev
pip
3
install --user git+https://gitlab.mpcdf.mpg.de/ift/NIFTy.git@NIFTy_5
(Note: If you encounter problems related to
`pyFFTW`
, make sure that you are
using a pip-installed
`pyFFTW`
package. Unfortunately, some distributions are
...
...
@@ -71,35 +71,26 @@ with the installed `FFTW3` libraries.)
Plotting support is added via:
pip install --user matplotlib
pip
3
install --user matplotlib
Support for spherical harmonic transforms is added via:
pip install --user git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
pip
3
install --user git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
MPI support is added via:
sudo apt-get install openmpi-bin libopenmpi-dev
pip install --user mpi4py
### Installation for Python 3
If you want to run NIFTy with Python 3, you need to make the following changes
to the instructions above:
-
in all
`apt-get`
commands, replace
`python-*`
by
`python3-*`
-
in all
`pip`
commands, replace
`pip`
by
`pip3`
pip3 install --user mpi4py
### Running the tests
In oder to run the tests one needs two additional packages:
pip install --user nose parameterized coverage
sudo apt-get install python3-coverage python3-parameterized python3-pytest python3-pytest-cov
Afterwards the tests (including a coverage report) can be run using the
following command in the repository root:
nosetests -x --with-coverage --cover-html --cover-package
=nifty5
pytest-3 --cov
=nifty5
test
### First Steps
...
...
@@ -108,7 +99,7 @@ For a quick start, you can browse through the [informal
introduction
](
http://ift.pages.mpcdf.de/NIFTy/code.html
)
or
dive into NIFTy by running one of the demonstrations, e.g.:
python demos/getting_started_1.py
python
3
demos/getting_started_1.py
### Acknowledgement
...
...
demos/bernoulli_demo.py
View file @
a0e370b0
...
...
@@ -11,7 +11,7 @@
# 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) 2013-201
8
Max-Planck-Society
# Copyright(C) 2013-201
9
Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
...
...
demos/getting_started_1.py
View file @
a0e370b0
...
...
@@ -11,7 +11,7 @@
# 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) 2013-201
8
Max-Planck-Society
# Copyright(C) 2013-201
9
Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
...
...
@@ -101,12 +101,18 @@ if __name__ == '__main__':
# Masking operator to model that parts of the field have not been observed
mask
=
ift
.
Field
.
from_global_data
(
position_space
,
mask
)
Mask
=
ift
.
DiagonalOperator
(
mask
)
<<<<<<<
HEAD
# The response operator consists out of
# - an harmonic transform (to get to image space)
# - the application of the mask
# - the removal of geometric information
=======
# Operators can be composed either with paranthesis
>>>>>>>
NIFTy_5
R
=
GR
(
Mask
(
HT
))
# or with @
R
=
GR
@
Mask
@
HT
data_space
=
GR
.
target
...
...
@@ -119,10 +125,17 @@ if __name__ == '__main__':
MOCK_NOISE
=
N
.
draw_sample
()
data
=
R
(
MOCK_SIGNAL
)
+
MOCK_NOISE
<<<<<<<
HEAD
# Build inverse propagator D and information source j
D_inv
=
R
.
adjoint
(
N
.
inverse
(
R
))
+
S
.
inverse
j
=
R
.
adjoint_times
(
N
.
inverse_times
(
data
))
# Make D_inv invertible (via Conjugate Gradient)
=======
# Build propagator D and information source j
j
=
R
.
adjoint_times
(
N
.
inverse_times
(
data
))
D_inv
=
R
.
adjoint
@
N
.
inverse
@
R
+
S
.
inverse
# Make it invertible
>>>>>>>
NIFTy_5
IC
=
ift
.
GradientNormController
(
iteration_limit
=
500
,
tol_abs_gradnorm
=
1e-3
)
D
=
ift
.
InversionEnabler
(
D_inv
,
IC
,
approximation
=
S
.
inverse
).
inverse
...
...
demos/getting_started_2.py
View file @
a0e370b0
...
...
@@ -11,7 +11,7 @@
# 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) 2013-201
8
Max-Planck-Society
# Copyright(C) 2013-201
9
Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
...
...
demos/getting_started_3.py
View file @
a0e370b0
...
...
@@ -11,7 +11,7 @@
# 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) 2013-201
8
Max-Planck-Society
# Copyright(C) 2013-201
9
Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
...
...
demos/plot_test.py
View file @
a0e370b0
# 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) 2013-2019 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
import
nifty5
as
ift
import
numpy
as
np
...
...
demos/polynomial_fit.py
View file @
a0e370b0
# 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) 2013-2019 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
import
matplotlib.pyplot
as
plt
import
numpy
as
np
...
...
docs/source/conf.py
View file @
a0e370b0
...
...
@@ -52,9 +52,6 @@ extensions = [
'numpydoc'
,
'sphinx.ext.autosummary'
,
'sphinx.ext.napoleon'
,
# 'sphinx.ext.coverage',
# 'sphinx.ext.todo',
# 'sphinx.ext.mathjax',
'sphinx.ext.imgmath'
,
'sphinx.ext.viewcode'
]
...
...
@@ -75,7 +72,7 @@ master_doc = 'index'
# General information about the project.
project
=
u
'NIFTy5'
copyright
=
u
'2013-201
8
, Max-Planck-Society'
copyright
=
u
'2013-201
9
, Max-Planck-Society'
author
=
u
'Theo Steininger / Martin Reinecke'
# The version info for the project you're documenting, acts as replacement for
...
...
@@ -94,20 +91,10 @@ release = u'5.0.0'
# Usually you set "language" from the command line for these cases.
language
=
None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns
=
[]
# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
...
...
@@ -122,12 +109,6 @@ add_module_names = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style
=
'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos
=
True
...
...
@@ -149,175 +130,27 @@ html_theme_options = {
html_theme_path
=
[
sphinx_rtd_theme
.
get_html_theme_path
()]
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo
=
'nifty_logo_black.png'
# The name of an image file (relative to this directory) to use as a favicon of
# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path
=
[]
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
html_last_updated_fmt
=
'%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# If false, no module index is generated.
html_domain_indices
=
False
# If false, no index is generated.
html_use_index
=
False
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
html_show_sourcelink
=
False
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
#html_search_language = 'en'
# A dictionary with options for the search language support, empty by default.
# Now only 'ja' uses this config value
#html_search_options = {'type': 'default'}
# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#html_search_scorer = 'scorer.js'
# Output file base name for HTML help builder.
htmlhelp_basename
=
'NIFTydoc'
# -- Options for LaTeX output ---------------------------------------------
#latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
# Latex figure (float) alignment
#'figure_align': 'htbp',
#}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
#latex_documents = [
# (master_doc, 'NIFTy.tex', u'NIFTy Documentation',
# u'NIFTy', 'manual'),
#]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
# If true, show URL addresses after external links.
#latex_show_urls = False
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
#man_pages = [
# (master_doc, 'nifty', u'NIFTy Documentation',
# [author], 1)
#]
# If true, show URL addresses after external links.
#man_show_urls = False
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
#texinfo_documents = [
# (master_doc, 'NIFTy', u'NIFTy Documentation',
# author, 'NIFTy', 'One line description of project.',
# 'Miscellaneous'),
#]
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# If false, no module index is generated.
#texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
# Example configuration for intersphinx: refer to the Python standard library.
#intersphinx_mapping = {'https://docs.python.org/': None}
docs/source/installation.rst
View file @
a0e370b0
...
...
@@ -7,8 +7,8 @@ distributions, the "apt" lines will need slight changes.
NIFTy5 and its mandatory dependencies can be installed via::
sudo apt-get install git libfftw3-dev python python-pip python-dev
pip install --user git+https://gitlab.mpcdf.mpg.de/ift/NIFTy.git@NIFTy_
4
sudo apt-get install git libfftw3-dev python
3
python
3
-pip python
3
-dev
pip
3
install --user git+https://gitlab.mpcdf.mpg.de/ift/NIFTy.git@NIFTy_
5
(Note: If you encounter problems related to `pyFFTW`, make sure that you are
using a pip-installed `pyFFTW` package. Unfortunately, some distributions are
...
...
@@ -17,22 +17,13 @@ with the installed `FFTW3` libraries.)
Plotting support is added via::
pip install --user matplotlib
pip
3
install --user matplotlib
Support for spherical harmonic transforms is added via::
pip install --user git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
pip
3
install --user git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
MPI support is added via::
sudo apt-get install openmpi-bin libopenmpi-dev
pip install --user mpi4py
Installation for Python 3
-------------------------
If you want to run NIFTy with Python 3, you need to make the following changes
to the instructions above:
- in all `apt-get` commands, replace `python-*` by `python3-*`
- in all `pip` commands, replace `pip` by `pip3`
pip3 install --user mpi4py
nifty5/compat.py
deleted
100644 → 0
View file @
4404fc4a
from
__future__
import
absolute_import
,
division
,
print_function
from
builtins
import
(
ascii
,
bytes
,
chr
,
dict
,
filter
,
hex
,
input
,
map
,
next
,
oct
,
open
,
pow
,
range
,
round
,
super
,
zip
)
from
functools
import
reduce
nifty5/data_objects/distributed_do.py
View file @
a0e370b0
...
...
@@ -11,19 +11,15 @@
# 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) 2013-201
8
Max-Planck-Society
# Copyright(C) 2013-201
9
Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from
__future__
import
absolute_import
,
division
,
print_function
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
import
sys
from
functools
import
reduce
import
numpy
as
np
from
mpi4py
import
MPI
from
..compat
import
*
from
.random
import
Random
__all__
=
[
"ntask"
,
"rank"
,
"master"
,
"local_shape"
,
"data_object"
,
"full"
,
...
...
nifty5/data_objects/numpy_do.py
View file @
a0e370b0
...
...
@@ -11,10 +11,9 @@
# 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) 2013-201
8
Max-Planck-Society
# Copyright(C) 2013-201
9
Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
# Data object module for NIFTy that uses simple numpy ndarrays.
...
...
nifty5/data_objects/random.py
View file @
a0e370b0
...
...
@@ -11,17 +11,12 @@
# 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) 2013-201
8
Max-Planck-Society
# Copyright(C) 2013-201
9
Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from
__future__
import
absolute_import
,
division
,
print_function
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
import
numpy
as
np
from
..compat
import
*
class
Random
(
object
):
@
staticmethod
...
...
nifty5/dobj.py
View file @
a0e370b0
...
...
@@ -11,14 +11,9 @@
# 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) 2013-201
8
Max-Planck-Society
# Copyright(C) 2013-201
9
Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from
__future__
import
absolute_import
,
division
,
print_function