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Commit b9a36665 authored by Daniel Boeckenhoff's avatar Daniel Boeckenhoff
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merged with actual tensors library

parent 6d6de152
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setup.py
View file @ b9a36665
......@@ -8,7 +8,7 @@ from setuptools import setup, find_packages
setup(
name='tfields',
version='0.1.0',
version='1.1.0.dev1',
description='numpy + sympy implementation of tensor fields with attached coordinate systems',
author='Daniel Boeckenhoff',
author_email='dboe@ipp.mpg.de',
......@@ -17,9 +17,9 @@ setup(
test_require=['doctest'],
url='https://gitlab.mpcdf.mpg.de/dboe/tfields',
# install_requires=['numpy', 'scipy'],
entry_points={
'console_scripts': ['tfields = tfields.__main__']
},
# entry_points={
# 'console_scripts': ['tfields = tfields.__main__']
# },
classifiers=[
# How mature is this project? Common values are
# 3 - Alpha
......@@ -43,7 +43,14 @@ setup(
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6'
]
],
python_requires='>=2.7',
keywords="tensors coordinate trafo sympy numpy",
project_urls={
'Documentation': 'https://packaging.python.org/tutorials/distributing-packages/',
'Source': 'https://gitlab.mpcdf.mpg.de/dboe/tfields/',
'Tracker': 'https://github.com/pypa/sampleproject/issues',
}
)
......
tfields/__init__.py
View file @ b9a36665
from . import bases
from . import core
from . import bases
# __all__ = ['core', 'points3D']
from .core import Tensors, TensorFields, TensorMaps
from .mask import getMask
# from .points3D import Points3D
if __name__ == '__main__':
import doctest
doctest.testmod(optionflags=doctest.ELLIPSIS)
from .mask import getMask
tfields/bases.py
View file @ b9a36665
"""
Tools for sympy coordinate transformation
"""
import tfields as tf
import tfields
import numpy as np
import sympy
import sympy.diffgeom
......@@ -70,7 +70,7 @@ cartesian.connect_to(spherical,
def getCoordSystem(base):
if isinstance(base, string_types):
base = getattr(tf.bases, base)
base = getattr(tfields.bases, base)
if not isinstance(base, sympy.diffgeom.CoordSystem):
raise TypeError("Wrong type of coordSystem base.")
return base
......@@ -95,18 +95,18 @@ def lambdifiedTrafo(baseOld, baseNew):
Examples:
>>> import numpy as np
>>> import tfields as tf
>>> import tfields
Transform cartestian to cylinder or spherical
>>> a = np.array([[3,4,0]])
>>> trafo = tf.bases.lambdifiedTrafo(tf.bases.cartesian,
... tf.bases.cylinder)
>>> trafo = tfields.bases.lambdifiedTrafo(tfields.bases.cartesian,
... tfields.bases.cylinder)
>>> new = np.concatenate([trafo(*coords).T for coords in a])
>>> assert new[0, 0] == 5
>>> trafo = tf.bases.lambdifiedTrafo(tf.bases.cartesian,
... tf.bases.spherical)
>>> trafo = tfields.bases.lambdifiedTrafo(tfields.bases.cartesian,
... tfields.bases.spherical)
>>> new = np.concatenate([trafo(*coords).T for coords in a])
>>> assert new[0, 0] == 5
......@@ -125,9 +125,9 @@ def transform(array, baseOld, baseNew):
Transform cylinder to spherical. No connection is defined so routing via
cartesian
>>> import numpy as np
>>> from tfields.bases import transform
>>> import tfields
>>> b = np.array([[5, np.arctan(4. / 3), 0]])
>>> newB = transform(b, 'cylinder', 'spherical')
>>> newB = tfields.bases.transform(b, 'cylinder', 'spherical')
>>> assert newB[0, 0] == 5
>>> assert round(newB[0, 1], 10) == round(b[0, 1], 10)
......@@ -142,13 +142,13 @@ def transform(array, baseOld, baseNew):
return transform(tmpArray, baseTmp, baseNew)
raise ValueError("Trafo not found.")
trafo = tf.bases.lambdifiedTrafo(baseOld, baseNew)
trafo = tfields.bases.lambdifiedTrafo(baseOld, baseNew)
with warnings.catch_warnings():
warnings.filterwarnings('ignore', message="invalid value encountered in double_scalars")
new = np.concatenate([trafo(*coords).T for coords in array])
return new
if __name__ == '__main__':
if __name__ == '__main__': # pragma: no cover
import doctest
doctest.testmod()
tfields/core.py
View file @ b9a36665
import tfields
import tfields.bases
import numpy as np
from contextlib import contextmanager
from collections import Counter
......@@ -50,7 +49,7 @@ class AbstractNdarray(np.ndarray):
__slotDtypes__ = []
__slotSetters__ = []
def __new__(cls, array, **kwargs):
def __new__(cls, array, **kwargs): # pragma: no cover
raise NotImplementedError("{clsType} type must implement '__new__'"
.format(clsType=type(cls)))
......@@ -102,6 +101,7 @@ class AbstractNdarray(np.ndarray):
Examples:
>>> from tempfile import NamedTemporaryFile
>>> import pickle
>>> import tfields
Build a dummy scalar field
>>> from tfields import Tensors, TensorFields
......@@ -204,6 +204,15 @@ class Tensors(AbstractNdarray):
...
ValueError: Incorrect dimension: 3 given, 2 demanded.
The dimension argument (dim) becomes necessary if you want to initialize
an empty array
>>> _ = Tensors([]) # doctest: +ELLIPSIS
Traceback (most recent call last):
...
ValueError: Empty tensors need dimension parameter 'dim'.
>>> Tensors([], dim=7)
Tensors([], shape=(0, 7), dtype=float64)
"""
__slots__ = ['coordSys']
__slotDefaults__ = ['cartesian']
......@@ -230,13 +239,7 @@ class Tensors(AbstractNdarray):
''' process empty inputs '''
if len(tensors) == 0:
if dim is not None:
if issubclass(type(tensors), cls):
if not tensors.dim == dim:
raise ValueError("Tensor dimension and "
"requested dimension are "
"not the same.")
else:
tensors = np.empty((0, dim))
tensors = np.empty((0, dim))
else:
raise ValueError("Empty tensors need dimension "
"parameter 'dim'.")
......@@ -396,7 +399,7 @@ class Tensors(AbstractNdarray):
self.coordSys = coordSys
@contextmanager
def tempCoordSys(self, coordSys=None):
def tempCoordSys(self, coordSys):
"""
Temporarily change the coordSys to another coordSys and change it back at exit
This method is for cleaner code only.
......@@ -404,6 +407,7 @@ class Tensors(AbstractNdarray):
Args:
see coordinateTransform
Examples:
>>> import tfields
>>> p = tfields.Tensors([[1,2,3]], coordSys=tfields.bases.SPHERICAL)
>>> with p.tempCoordSys(tfields.bases.CYLINDER):
... assert p.coordSys == tfields.bases.CYLINDER
......@@ -411,9 +415,7 @@ class Tensors(AbstractNdarray):
"""
baseBefore = self.coordSys
if coordSys is None:
yield
elif baseBefore == coordSys:
if baseBefore == coordSys:
yield
else:
self.coordinateTransform(coordSys)
......@@ -459,7 +461,7 @@ class TensorFields(Tensors):
super(TensorFields, self).coordinateTransform(coordSys)
for field in self.fields:
field.coordinateTransform(coordSys)
class TensorMaps(TensorFields):
"""
......@@ -487,19 +489,8 @@ class TensorMaps(TensorFields):
__slots__ = ['coordSys', 'fields', 'maps']
__slotDtypes__ = [None, None, int]
# @classmethod
# def _updateSlotKwargs(cls, kwargs, skipCache=True):
# maps = kwargs.pop('maps', None)
# # Add maps
# if maps is not None:
# maps = np.empty((0, 3), dtype=int)
# kwargs['maps'] = maps
# super(TensorMaps, cls)._updateSlotKwargs(kwargs, skipCache=skipCache)
if __name__ == '__main__':
if __name__ == '__main__': # pragma: no cover
import doctest
doctest.testmod()
# doctest.run_docstring_examples(TensorMaps, globals())
tfields/mask.py
View file @ b9a36665
......@@ -15,6 +15,8 @@ logger = loggingTools.Logger(__name__)
def getMask(array, cutExpression=None, coords=None):
"""
Linking sympy and numpy by retrieving a mask according to the cutExpression
Args:
array (numpy ndarray)
cutExpression (sympy logical expression)
......@@ -27,21 +29,22 @@ def getMask(array, cutExpression=None, coords=None):
>>> x, y, z = sympy.symbols('x y z')
>>> a = np.array([[1., 2., 3.], [4., 5., 6.], [1, 2, -6], [-5, -5, -5], [1,0,-1], [0,1,-1]])
>>> tfields.getMask(a, x > 0)
array([ True, True, True, False, True, False], dtype=bool)
>>> assert np.array_equal(tfields.getMask(a, x > 0),
... np.array([ True, True, True, False, True, False]))
And combination
>>> tfields.getMask(a, (x > 0) & (y < 3))
array([ True, False, True, False, True, False], dtype=bool)
>>> assert np.array_equal(tfields.getMask(a, (x > 0) & (y < 3)),
... np.array([True, False, True, False, True, False]))
Or combination
>>> tfields.getMask(a, (x > 0) | (y > 3))
array([ True, True, True, False, True, False], dtype=bool)
>>> assert np.array_equal(tfields.getMask(a, (x > 0) | (y > 3)),
... np.array([True, True, True, False, True, False]))
If array of other shape than (?, 3) is given, the coords need to be specified
>>> a0, a1 = sympy.symbols('a0 a1')
>>> tfields.getMask([[0., 1.], [-1, 3]], a1 > 2, coords=[a0, a1])
array([False, True], dtype=bool)
>>> assert np.array_equal(tfields.getMask([[0., 1.], [-1, 3]], a1 > 2,
... coords=[a0, a1]),
... np.array([False, True], dtype=bool))
"""
if isinstance(array, list):
......@@ -63,11 +66,11 @@ def getMask(array, cutExpression=None, coords=None):
cutExpression,
modules={'&': np.logical_and, '|': np.logical_or})
mask = np.array([preMask(*x) for x in array])
mask = np.array([preMask(*x) for x in array], dtype=bool)
return mask
if __name__ == '__main__':
if __name__ == '__main__': # pragma: no cover
import doctest
doctest.testmod()
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