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Commit 8521b7e0 authored by dboe's avatar dboe
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removed all relative imports in favour of absolute

parent 78b25499
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Makefile
View file @ 8521b7e0
......@@ -32,6 +32,8 @@ clean:
rm -rf .tox
rm -rf .pytest_cache
rm -rf *.egg-info
rm -rf */__pycache__
rm -rf */**/__pycache__
pre-commit clean
publish:
......
tests/test_mesh3D.py
View file @ 8521b7e0
......@@ -5,7 +5,7 @@ import unittest
import sympy # NOQA: F401
import os
import sys
from .test_core import TensorMaps_Check
from tests.test_core import TensorMaps_Check
THIS_DIR = os.path.dirname(
os.path.realpath(os.path.join(os.getcwd(), os.path.expanduser(__file__))))
sys.path.append(os.path.normpath(os.path.join(THIS_DIR)))
......
tfields/__init__.py
View file @ 8521b7e0
......@@ -4,19 +4,14 @@ __author__ = """Daniel Böckenhoff"""
__email__ = "dboe@ipp.mpg.de"
__version__ = "0.3.2"
from . import core # NOQA
from . import bases # NOQA
from . import lib # NOQA
# methods:
from .core import dim, rank # NOQA
from .mask import evalf # NOQA
from .lib import * # NOQA
from tfields.core import dim, rank # NOQA
from tfields.mask import evalf # NOQA
# classes:
from .core import Tensors, TensorFields, TensorMaps, Container, Maps # NOQA
from .points3D import Points3D # NOQA
from .mesh3D import Mesh3D # NOQA
from .triangles3D import Triangles3D # NOQA
from .planes3D import Planes3D # NOQA
from .bounding_box import Node # NOQA
from tfields.core import Tensors, TensorFields, TensorMaps, Container, Maps # NOQA
from tfields.points3D import Points3D # NOQA
from tfields.mesh3D import Mesh3D # NOQA
from tfields.triangles3D import Triangles3D # NOQA
from tfields.planes3D import Planes3D # NOQA
from tfields.bounding_box import Node # NOQA
tfields/bases/__init__.py
View file @ 8521b7e0
......@@ -7,7 +7,7 @@ Mail: daniel.boeckenhoff@ipp.mpg.de
part of tfields library
Tools for sympy coordinate transformation
"""
from .bases import * # NOQA
from . import manifold_3 # NOQA
from .manifold_3 import CARTESIAN, CYLINDER, SPHERICAL # NOQA
from .manifold_3 import cartesian, cylinder, spherical # NOQA
from tfields.bases.bases import get_coord_system, get_coord_system_name, lambdified_trafo, transform # NOQA
from tfields.bases import manifold_3 # NOQA
from tfields.bases.manifold_3 import CARTESIAN, CYLINDER, SPHERICAL # NOQA
from tfields.bases.manifold_3 import cartesian, cylinder, spherical # NOQA
tfields/bases/bases.py
View file @ 8521b7e0
......@@ -51,7 +51,7 @@ def get_coord_system_name(base):
return str(base)
def lambdifiedTrafo(base_old, base_new):
def lambdified_trafo(base_old, base_new):
"""
Args:
base_old (sympy.CoordSystem)
......@@ -64,13 +64,13 @@ def lambdifiedTrafo(base_old, base_new):
Transform cartestian to cylinder or spherical
>>> a = np.array([[3,4,0]])
>>> trafo = tfields.bases.lambdifiedTrafo(tfields.bases.cartesian,
... tfields.bases.cylinder)
>>> trafo = tfields.bases.lambdified_trafo(tfields.bases.cartesian,
... tfields.bases.cylinder)
>>> new = np.concatenate([trafo(*coords).T for coords in a])
>>> assert new[0, 0] == 5
>>> trafo = tfields.bases.lambdifiedTrafo(tfields.bases.cartesian,
... tfields.bases.spherical)
>>> trafo = tfields.bases.lambdified_trafo(tfields.bases.cartesian,
... tfields.bases.spherical)
>>> new = np.concatenate([trafo(*coords).T for coords in a])
>>> assert new[0, 0] == 5
......@@ -128,17 +128,17 @@ def transform(array, base_old, base_new):
raise ValueError("Trafo not found.")
# very fast trafos in numpy only
shortTrafo = None
short_trafo = None
try:
shortTrafo = getattr(base_old, 'to_{base_new.name}'.format(**locals()))
short_trafo = getattr(base_old, 'to_{base_new.name}'.format(**locals()))
except AttributeError:
pass
if shortTrafo:
shortTrafo(array)
if short_trafo:
short_trafo(array)
return
# trafo via lambdified sympy expressions
trafo = tfields.bases.lambdifiedTrafo(base_old, base_new)
trafo = tfields.bases.lambdified_trafo(base_old, base_new)
with warnings.catch_warnings():
warnings.filterwarnings('ignore', message="invalid value encountered in double_scalars")
array[:] = np.concatenate([trafo(*coords).T for coords in array])
......
tfields/bases/manifold_3.py
View file @ 8521b7e0
import tfields
import sympy
import sympy.diffgeom
import numpy as np
import warnings
......@@ -59,7 +60,7 @@ def cartesian_to_cylinder(array):
array[:, 1] = np.sign(y_vals) * np.arccos(x_vals / array[:, 0])
np.seterr(divide='warn', invalid='warn')
array[:, 1][problem_phi_indices] = np.pi
tfields.convert_nan(array, 0.) # for cases like cartesian 0, 0, 1
tfields.lib.util.convert_nan(array, 0.) # for cases like cartesian 0, 0, 1
cartesian.to_cylinder = cartesian_to_cylinder
......@@ -139,7 +140,7 @@ def cartesian_to_spherical(array):
array[:, 1] = np.sign(array[:, 1]) * np.arccos(array[:, 0] / np.sqrt(xy))
array[:, 1][problemPhiIndices] = np.pi
tfields.convert_nan(array, 0.) # for cases like cartesian 0, 0, 1
tfields.lib.util.convert_nan(array, 0.) # for cases like cartesian 0, 0, 1
# array[:,1] = np.arctan2(array[:,1], array[:,0]) # phi for phi between 0, 2pi
# r
......
tfields/core.py
View file @ 8521b7e0
......@@ -2516,7 +2516,7 @@ class TensorMaps(TensorFields):
inst = self
if duplicates:
inst = self.copy()
duplicates = tfields.duplicates(self, axis=0)
duplicates = tfields.lib.util.duplicates(self, axis=0)
for tensor_index, duplicate_index in zip(
range(self.shape[0]), duplicates
):
......@@ -2527,7 +2527,8 @@ class TensorMaps(TensorFields):
for f in range(len(self.maps[map_dim])): # face index
mp = np.array(self.maps[map_dim], dtype=int)
if tensor_index in mp[f]:
index = tfields.index(mp[f], tensor_index)
index = tfields.lib.util.index(mp[f],
tensor_index)
inst.maps[map_dim][f][index] = duplicate_index
return inst.removed(stale_mask)
......
tfields/lib/__init__.py
View file @ 8521b7e0
......@@ -7,112 +7,8 @@ Mail: daniel.boeckenhoff@ipp.mpg.de
Collection of additional numpy functions
part of tfields library
"""
import numpy as np
def convert_nan(array, value=0.):
"""
Replace all occuring NaN values by value
"""
nanIndices = np.isnan(array)
array[nanIndices] = value
def view1D(ar):
"""
https://stackoverflow.com/a/44999009/ @Divakar
"""
ar = np.ascontiguousarray(ar)
voidDt = np.dtype((np.void, ar.dtype.itemsize * ar.shape[1]))
return ar.view(voidDt).ravel()
def argsort_unique(idx):
"""
https://stackoverflow.com/a/43411559/ @Divakar
"""
n = idx.size
sidx = np.empty(n, dtype=int)
sidx[idx] = np.arange(n)
return sidx
def duplicates(ar, axis=None):
"""
View1D version of duplicate search
Speed up version after
https://stackoverflow.com/questions/46284660 \
/python-numpy-speed-up-2d-duplicate-search/46294916#46294916
Args:
ar (array_like): array
other args: see np.isclose
Examples:
>>> import tfields
>>> import numpy as np
>>> a = np.array([[1, 0, 0], [1, 0, 0], [2, 3, 4]])
>>> tfields.duplicates(a, axis=0)
array([0, 0, 2])
An empty sequence will not throw errors
>>> assert np.array_equal(tfields.duplicates([], axis=0), [])
Returns:
list of int: int is pointing to first occurence of unique value
"""
if len(ar) == 0:
return np.array([])
if axis != 0:
raise NotImplementedError()
sidx = np.lexsort(ar.T)
b = ar[sidx]
groupIndex0 = np.flatnonzero((b[1:] != b[:-1]).any(1)) + 1
groupIndex = np.concatenate(([0], groupIndex0, [b.shape[0]]))
ids = np.repeat(range(len(groupIndex) - 1), np.diff(groupIndex))
sidx_mapped = argsort_unique(sidx)
ids_mapped = ids[sidx_mapped]
grp_minidx = sidx[groupIndex[:-1]]
out = grp_minidx[ids_mapped]
return out
def index(ar, entry, rtol=0, atol=0, equal_nan=False, axis=None):
"""
Examples:
>>> import tfields
>>> a = np.array([[1, 0, 0], [1, 0, 0], [2, 3, 4]])
>>> tfields.index(a, [2, 3, 4], axis=0)
2
>>> a = np.array([[1, 0, 0], [2, 3, 4]])
>>> tfields.index(a, 4)
5
Returns:
list of int: indices of point occuring
"""
if axis is None:
ar = ar.flatten()
elif axis != 0:
raise NotImplementedError()
for i, part in enumerate(ar):
isclose = np.isclose(part, entry, rtol=rtol, atol=atol,
equal_nan=equal_nan)
if axis is not None:
isclose = isclose.all()
if isclose:
return i
if __name__ == '__main__':
import doctest
doctest.testmod()
else:
from . import grid # NOQA
from .grid import igrid # NOQA
from . import stats # NOQA
from .stats import mode, median, mean # NOQA
from . import symbolics # NOQA
from . import sets # NOQA
from . import util # NOQA
from tfields.lib import grid # NOQA
from tfields.lib import stats # NOQA
from tfields.lib import symbolics # NOQA
from tfields.lib import sets # NOQA
from tfields.lib import util # NOQA
tfields/lib/grid.py
View file @ 8521b7e0
......@@ -54,9 +54,9 @@ def igrid(*base_vectors, **kwargs):
Initilaize using the mgrid notation
>>> import tfields
>>> import numpy as np
>>> assert np.array_equal(tfields.igrid((0, 1, 2j),
... (3, 4, 2j),
... (6, 7, 2j)),
>>> assert np.array_equal(tfields.lib.grid.igrid((0, 1, 2j),
... (3, 4, 2j),
... (6, 7, 2j)),
... [[ 0., 3., 6.],
... [ 0., 3., 7.],
... [ 0., 4., 6.],
......@@ -66,8 +66,9 @@ def igrid(*base_vectors, **kwargs):
... [ 1., 4., 6.],
... [ 1., 4., 7.]])
>>> assert np.array_equal(tfields.igrid([3, 4], np.linspace(0, 1, 2),
... (6, 7, 2),
>>> assert np.array_equal(tfields.lib.grid.igrid([3, 4],
... np.linspace(0, 1, 2),
... (6, 7, 2),
... iter_order=[1, 0, 2]),
... [[ 3., 0., 6.],
... [ 3., 0., 7.],
......@@ -77,10 +78,10 @@ def igrid(*base_vectors, **kwargs):
... [ 3., 1., 7.],
... [ 4., 1., 6.],
... [ 4., 1., 7.]])
>>> assert np.array_equal(tfields.igrid(np.linspace(0, 1, 2),
... np.linspace(3, 4, 2),
... np.linspace(6, 7, 2),
... iter_order=[2, 0, 1]),
>>> assert np.array_equal(tfields.lib.grid.igrid(np.linspace(0, 1, 2),
... np.linspace(3, 4, 2),
... np.linspace(6, 7, 2),
... iter_order=[2, 0, 1]),
... [[ 0., 3., 6.],
... [ 0., 4., 6.],
... [ 1., 3., 6.],
......@@ -131,12 +132,13 @@ def base_vectors(array, rtol=None, atol=None):
Examples:
>>> import tfields
>>> grid = tfields.igrid((3, 5, 5j))
>>> grid = tfields.lib.grid.igrid((3, 5, 5j))
>>> tfields.lib.grid.base_vectors(grid[:, 0])
(3.0, 5.0, 5j)
>>> grid2 = tfields.igrid((3, 5, 5j),
... (1, 2, 2j))
>>> grid_circle = tfields.igrid(*tfields.lib.grid.base_vectors(grid2))
>>> grid2 = tfields.lib.grid.igrid((3, 5, 5j),
... (1, 2, 2j))
>>> grid_circle = tfields.lib.grid.igrid(
... *tfields.lib.grid.base_vectors(grid2))
>>> assert tfields.Tensors(grid_circle).equal(grid2)
"""
......
tfields/lib/util.py
View file @ 8521b7e0
......@@ -3,6 +3,7 @@ Various utility functions
"""
import itertools
from six import string_types
import numpy as np
def pairwise(iterable):
......@@ -113,6 +114,102 @@ def multi_sort(array, *others, **kwargs):
return tuple(cast_type(x) for x in zip(*method(zip(array, *others), **kwargs)))
def convert_nan(ar, value=0.):
"""
Replace all occuring NaN values by value
"""
nanIndices = np.isnan(ar)
ar[nanIndices] = value
def view1D(ar):
"""
Delete duplicate columns of the input array
https://stackoverflow.com/a/44999009/ @Divakar
"""
ar = np.ascontiguousarray(ar)
voidDt = np.dtype((np.void, ar.dtype.itemsize * ar.shape[1]))
return ar.view(voidDt).ravel()
def argsort_unique(idx):
"""
https://stackoverflow.com/a/43411559/ @Divakar
"""
n = idx.size
sidx = np.empty(n, dtype=int)
sidx[idx] = np.arange(n)
return sidx
def duplicates(ar, axis=None):
"""
View1D version of duplicate search
Speed up version after
https://stackoverflow.com/questions/46284660 \
/python-numpy-speed-up-2d-duplicate-search/46294916#46294916
Args:
ar (array_like): array
other args: see np.isclose
Examples:
>>> import tfields
>>> import numpy as np
>>> a = np.array([[1, 0, 0], [1, 0, 0], [2, 3, 4]])
>>> tfields.lib.util.duplicates(a, axis=0)
array([0, 0, 2])
An empty sequence will not throw errors
>>> assert np.array_equal(tfields.lib.util.duplicates([], axis=0), [])
Returns:
list of int: int is pointing to first occurence of unique value
"""
if len(ar) == 0:
return np.array([])
if axis != 0:
raise NotImplementedError()
sidx = np.lexsort(ar.T)
b = ar[sidx]
groupIndex0 = np.flatnonzero((b[1:] != b[:-1]).any(1)) + 1
groupIndex = np.concatenate(([0], groupIndex0, [b.shape[0]]))
ids = np.repeat(range(len(groupIndex) - 1), np.diff(groupIndex))
sidx_mapped = argsort_unique(sidx)
ids_mapped = ids[sidx_mapped]
grp_minidx = sidx[groupIndex[:-1]]
out = grp_minidx[ids_mapped]
return out
def index(ar, entry, rtol=0, atol=0, equal_nan=False, axis=None):
"""
Examples:
>>> import tfields
>>> a = np.array([[1, 0, 0], [1, 0, 0], [2, 3, 4]])
>>> tfields.lib.util.index(a, [2, 3, 4], axis=0)
2
>>> a = np.array([[1, 0, 0], [2, 3, 4]])
>>> tfields.lib.util.index(a, 4)
5
Returns:
list of int: indices of point occuring
"""
if axis is None:
ar = ar.flatten()
elif axis != 0:
raise NotImplementedError()
for i, part in enumerate(ar):
isclose = np.isclose(part, entry, rtol=rtol, atol=atol,
equal_nan=equal_nan)
if axis is not None:
isclose = isclose.all()
if isclose:
return i
if __name__ == '__main__':
import doctest
doctest.testmod()
tfields/mesh3D.py
View file @ 8521b7e0
......@@ -380,8 +380,8 @@ class Mesh3D(tfields.TensorMaps):
"""
vertices = tfields.Tensors.grid(*base_vectors, **kwargs)
base_vectors = tfields.grid.ensure_complex(*base_vectors)
base_vectors = tfields.grid.to_base_vectors(*base_vectors)
base_vectors = tfields.lib.grid.ensure_complex(*base_vectors)
base_vectors = tfields.lib.grid.to_base_vectors(*base_vectors)
fix_coord = None
for coord in range(3):
if len(base_vectors[coord]) > 1:
......@@ -446,8 +446,8 @@ class Mesh3D(tfields.TensorMaps):
if not len(base_vectors) == 3:
raise AttributeError("3 base_vectors vectors required")
base_vectors = tfields.grid.ensure_complex(*base_vectors)
base_vectors = tfields.grid.to_base_vectors(*base_vectors)
base_vectors = tfields.lib.grid.ensure_complex(*base_vectors)
base_vectors = tfields.lib.grid.to_base_vectors(*base_vectors)
indices = [0, -1]
coords = range(3)
......
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