From 03cc96cdee50a177389cfe9af9f2ce99c6c00d57 Mon Sep 17 00:00:00 2001
From: "Boeckenhoff, Daniel (dboe)" <daniel.boeckenhoff@ipp.mpg.de>
Date: Tue, 7 Aug 2018 09:57:58 +0200
Subject: [PATCH] before publishing. especially saving npz neat now
---
tfields/__init__.py | 2 +-
tfields/bases/bases.py | 4 ++--
tfields/core.py | 16 +++++++++++-----
tfields/lib/util.py | 8 +++++---
tfields/plotting/__init__.py | 4 ++--
tfields/plotting/mpl.py | 23 +++++++++++++++--------
tfields/triangles3D.py | 3 +--
7 files changed, 37 insertions(+), 23 deletions(-)
diff --git a/tfields/__init__.py b/tfields/__init__.py
index 6565cde..4771b49 100644
--- a/tfields/__init__.py
+++ b/tfields/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.1.0.dev5'
+__version__ = '0.1.0.dev6'
__author__ = "Daniel Boeckenhoff"
__email__ = "daniel.boeckenhoff@ipp.mpg.de"
diff --git a/tfields/bases/bases.py b/tfields/bases/bases.py
index c94ef72..d27f4d9 100644
--- a/tfields/bases/bases.py
+++ b/tfields/bases/bases.py
@@ -42,13 +42,13 @@ def get_coord_system_name(base):
str: name of base
"""
if isinstance(base, sympy.diffgeom.CoordSystem):
- base = str(getattr(base, 'name'))
+ base = getattr(base, 'name')
# if not (isinstance(base, string_types) or base is None):
# baseType = type(base)
# raise ValueError("Coordinate system must be string_type."
# " Retrieved value '{base}' of type {baseType}."
# .format(**locals()))
- return base
+ return str(base)
def lambdifiedTrafo(base_old, base_new):
diff --git a/tfields/core.py b/tfields/core.py
index 3931d67..f4a931d 100644
--- a/tfields/core.py
+++ b/tfields/core.py
@@ -277,9 +277,11 @@ class AbstractNdarray(np.ndarray):
>>> _ = out_file_maps.seek(0)
>>> m1 = tfields.TensorMaps.load(out_file_maps.name)
>>> assert m.equal(m1)
+ >>> assert m.maps[0].dtype == m1.maps[0].dtype
"""
- np.savez(path, **self._as_dict())
+ content_dict = self._as_dict()
+ np.savez(path, **content_dict)
@classmethod
def _load_npz(cls, path, **load_kwargs):
@@ -454,7 +456,10 @@ class Tensors(AbstractNdarray):
dtype = tensors.dtype
else:
if dtype is None:
- dtype = np.float64
+ if hasattr(tensors, 'dtype'):
+ dtype = tensors.dtype
+ else:
+ dtype = np.float64
''' demand iterable structure '''
try:
@@ -980,7 +985,7 @@ class Tensors(AbstractNdarray):
"""
coords = sympy.symbols('x y z')
with self.tmp_transform(coord_sys or self.coord_sys):
- mask = tfields.evalf(self, expression, coords=coords)
+ mask = tfields.evalf(np.array(self), expression, coords=coords)
return mask
def cut(self, expression, coord_sys=None):
@@ -1087,7 +1092,7 @@ class Tensors(AbstractNdarray):
return d[d > 0].reshape(d.shape[0], - 1).min(axis=1)
except MemoryError:
min_dists = np.empty(self.shape[0])
- for i, point in enumerate(other):
+ for i, point in enumerate(np.array(other)):
d = self.distances([point], **kwargs)
min_dists[i] = d[d > 0].reshape(-1).min()
return min_dists
@@ -1762,7 +1767,7 @@ class TensorMaps(TensorFields):
indices = np.array(range(len(self)))
keep_indices = indices[mask]
if isinstance(keep_indices, int):
- keep_indices = [keep_indices]
+ keep_indices = np.array([keep_indices])
delete_indices = set(indices.flat).difference(set(keep_indices.flat))
masks = []
@@ -1832,5 +1837,6 @@ class TensorMaps(TensorFields):
if __name__ == '__main__': # pragma: no cover
import doctest
doctest.testmod()
+ # doctest.run_docstring_examples(Tensors._save_npz, globals())
# doctest.run_docstring_examples(TensorMaps.cut, globals())
# doctest.run_docstring_examples(AbstractNdarray._save_npz, globals())
diff --git a/tfields/lib/util.py b/tfields/lib/util.py
index 66e3926..41a8ffc 100644
--- a/tfields/lib/util.py
+++ b/tfields/lib/util.py
@@ -57,10 +57,12 @@ def flatten(seq, container=None, keep_types=None):
def multi_sort(array, *others, **kwargs):
"""
- Sort both lists with list 1
+ Sort all given lists parralel with array sorting, ie rearrange the items in
+ the other lists in the same way, you rearrange them for array due to array
+ sorting
Args:
- array
- *others
+ array (list)
+ *others (list)
**kwargs:
method (function): sorting function. Default is 'sorted'
...: further arguments are passed to method. Default rest is
diff --git a/tfields/plotting/__init__.py b/tfields/plotting/__init__.py
index 23014fd..77d5d65 100644
--- a/tfields/plotting/__init__.py
+++ b/tfields/plotting/__init__.py
@@ -206,12 +206,12 @@ class PlotOptions(object):
else:
return self.pop(attr, default)
- def retrieveChain(self, *args, **kwargs):
+ def retrieve_chain(self, *args, **kwargs):
default = kwargs.pop('default', None)
keep = kwargs.pop('keep', True)
if len(args) > 1:
return self.retrieve(args[0],
- self.retrieveChain(*args[1:],
+ self.retrieve_chain(*args[1:],
default=default,
keep=keep),
keep=keep)
diff --git a/tfields/plotting/mpl.py b/tfields/plotting/mpl.py
index 1d39712..4cdb794 100644
--- a/tfields/plotting/mpl.py
+++ b/tfields/plotting/mpl.py
@@ -191,6 +191,8 @@ def plot_mesh(vertices, faces, **kwargs):
vmin
vmax
"""
+ vertices = np.array(vertices)
+ faces = np.array(faces)
if faces.shape[0] == 0:
warnings.warn("No faces to plot")
return None
@@ -201,9 +203,9 @@ def plot_mesh(vertices, faces, **kwargs):
full = True
mesh = tfields.Mesh3D(vertices, faces=faces)
xAxis, yAxis, zAxis = po.getXYZAxis()
- facecolors = po.retrieveChain('facecolors', 'color',
- default=0,
- keep=False)
+ facecolors = po.retrieve_chain('facecolors', 'color',
+ default=0,
+ keep=False)
if full:
# implementation that will sort the triangles by zAxis
centroids = mesh.centroids()
@@ -212,8 +214,13 @@ def plot_mesh(vertices, faces, **kwargs):
axesIndices.pop(axesIndices.index(yAxis))
zAxis = axesIndices[0]
zs = centroids[:, zAxis]
- zs, faces, facecolors = tfields.lib.util.multi_sort(zs, faces,
- facecolors)
+ try:
+ iter(facecolors)
+ zs, faces, facecolors = tfields.lib.util.multi_sort(zs, faces,
+ facecolors)
+ except TypeError:
+ zs, faces = tfields.lib.util.multi_sort(zs, faces)
+
nFacesInitial = len(faces)
else:
# cut away "back sides" implementation
@@ -246,9 +253,9 @@ def plot_mesh(vertices, faces, **kwargs):
artist = plot_array(vertices, **d)
elif po.dim == 3:
label = po.pop('label', None)
- color = po.retrieveChain('color', 'c', 'facecolors',
- default='grey',
- keep=False)
+ color = po.retrieve_chain('color', 'c', 'facecolors',
+ default='grey',
+ keep=False)
color = po.formatColors(color,
fmt='rgba',
length=len(faces))
diff --git a/tfields/triangles3D.py b/tfields/triangles3D.py
index 2134f91..54fbba7 100644
--- a/tfields/triangles3D.py
+++ b/tfields/triangles3D.py
@@ -488,7 +488,6 @@ class Triangles3D(tfields.TensorFields):
not invertable matrices the you will always get False
>>> m3 = tfields.Mesh3D([[0,0,0], [2,0,0], [4,0,0], [0,1,0]],
... faces=[[0, 1, 2], [0, 1, 3]]);
- >>> import pytest
>>> mask = m3.triangles()._in_triangles(np.array([0.2, 0.2, 0]), delta=0.3)
>>> assert np.array_equal(mask,
... np.array([False, True], dtype=bool))
@@ -550,7 +549,7 @@ class Triangles3D(tfields.TensorFields):
For Example, if you want to know the number of points in one
face, just do:
- >> tris.in_triangles(poits).sum(axis=0)
+ >> tris.in_triangles(poits).sum(axis=0)[face_index]
"""
if self.ntriangles() == 0:
--
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