From 9bc2a23f709c19adc2d7c49638ff627a39bae4cc Mon Sep 17 00:00:00 2001
From: "Boeckenhoff, Daniel (dboe)" <daniel.boeckenhoff@ipp.mpg.de>
Date: Fri, 3 Aug 2018 18:43:37 +0200
Subject: [PATCH] np.savez implemented generally for all sub types of Tensors
---
setup.py | 2 +
tfields/__init__.py | 2 +-
tfields/bases/bases.py | 5 +-
tfields/core.py | 127 +++++++++++++++++++++++++++++++++-------
tfields/mesh3D.py | 3 +-
tfields/plotting/mpl.py | 9 ++-
tfields/triangles3D.py | 4 ++
7 files changed, 122 insertions(+), 30 deletions(-)
diff --git a/setup.py b/setup.py
index aa93c74..33fce85 100644
--- a/setup.py
+++ b/setup.py
@@ -31,6 +31,8 @@ setup(
'sympy',
'scipy',
'pathlib',
+ 'six',
+ 'matplotlib',
],
entry_points={
'console_scripts': ['tfields = tfields.__main__:runDoctests']
diff --git a/tfields/__init__.py b/tfields/__init__.py
index 9518a8e..6565cde 100644
--- a/tfields/__init__.py
+++ b/tfields/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.1.0.dev4'
+__version__ = '0.1.0.dev5'
__author__ = "Daniel Boeckenhoff"
__email__ = "daniel.boeckenhoff@ipp.mpg.de"
diff --git a/tfields/bases/bases.py b/tfields/bases/bases.py
index f66b21f..c94ef72 100644
--- a/tfields/bases/bases.py
+++ b/tfields/bases/bases.py
@@ -22,8 +22,9 @@ def get_coord_system(base):
Return:
sympy.diffgeom.get_coord_system
"""
- if isinstance(base, string_types):
- base = getattr(tfields.bases, base)
+ if (isinstance(base, string_types)
+ or (isinstance(base, np.ndarray) and base.dtype.kind in {'U', 'S'})):
+ base = getattr(tfields.bases, str(base))
if not isinstance(base, sympy.diffgeom.CoordSystem):
bse_tpe = type(base)
expctd_tpe = type(sympy.diffgeom.CoordSystem)
diff --git a/tfields/core.py b/tfields/core.py
index 6075736..8c08e3d 100644
--- a/tfields/core.py
+++ b/tfields/core.py
@@ -115,6 +115,8 @@ class AbstractNdarray(np.ndarray):
def __reduce__(self):
"""
important for pickling
+ see https://stackoverflow.com/questions/26598109/
+ preserve-custom-attributes-when-pickling-subclass-of-numpy-array
Examples:
>>> from tempfile import NamedTemporaryFile
>>> import pickle
@@ -127,13 +129,13 @@ class AbstractNdarray(np.ndarray):
>>> scalarField = TensorFields(vectors, scalars, coord_sys='cylinder')
Save it and restore it
- >>> outFile = NamedTemporaryFile(suffix='.pickle')
+ >>> out_file = NamedTemporaryFile(suffix='.pickle')
>>> pickle.dump(scalarField,
- ... outFile)
- >>> _ = outFile.seek(0)
+ ... out_file)
+ >>> _ = out_file.seek(0)
- >>> sf = pickle.load(outFile)
+ >>> sf = pickle.load(out_file)
>>> sf.coord_sys == 'cylinder'
True
>>> sf.fields[0][2] == 2.
@@ -250,26 +252,34 @@ class AbstractNdarray(np.ndarray):
Args:
path (open file or str/unicode): destination to save file to.
Examples:
+ Build some dummies:
>>> import tfields
>>> from tempfile import NamedTemporaryFile
- >>> outFile = NamedTemporaryFile(suffix='.npz')
+ >>> out_file = NamedTemporaryFile(suffix='.npz')
>>> p = tfields.Points3D([[1., 2., 3.], [4., 5., 6.], [1, 2, -6]])
- >>> p.save(outFile.name)
- >>> _ = outFile.seek(0)
- >>> p1 = tfields.Points3D.load(outFile.name)
+
+ >>> scalars = tfields.Tensors([0, 1, 2])
+ >>> vectors = tfields.Tensors([[0, 0, 0], [0, 0, 1], [0, -1, 0]])
+ >>> maps = [tfields.TensorFields([[0, 1, 2], [0, 1, 2]], [42, 21]),
+ ... tfields.TensorFields([[1], [2]], [-42, -21])]
+ >>> m = tfields.TensorMaps(vectors, scalars,
+ ... maps=maps)
+
+ Simply give the file name to save
+ >>> p.save(out_file.name)
+ >>> _ = out_file.seek(0)
+ >>> p1 = tfields.Points3D.load(out_file.name)
>>> assert p.equal(p1)
- """
- kwargs = {}
- for attr in self._iter_slots():
- if not hasattr(self, attr):
- # attribute in __slots__ not found.
- warnings.warn("When saving instance of class {0} Attribute {1} not set."
- "This Attribute is not saved.".format(self.__class__, attr), Warning)
- else:
- kwargs[attr] = getattr(self, attr)
+ The fully nested structure of a TensorMaps object is reconstructed
+ >>> out_file_maps = NamedTemporaryFile(suffix='.npz')
+ >>> m.save(out_file_maps.name)
+ >>> _ = out_file_maps.seek(0)
+ >>> m1 = tfields.TensorMaps.load(out_file_maps.name)
+ >>> assert m.equal(m1)
- np.savez(path, self, **kwargs)
+ """
+ np.savez(path, **self._as_dict())
@classmethod
def _load_npz(cls, path, **load_kwargs):
@@ -278,10 +288,82 @@ class AbstractNdarray(np.ndarray):
Given a path to a npz file, construct the object
"""
np_file = np.load(path, **load_kwargs)
- keys = np_file.keys()
- bulk = np_file['arr_0']
- data_kwargs = {key: np_file[key] for key in keys if key not in ['arr_0']}
- return cls.__new__(cls, bulk, **data_kwargs)
+ return cls._from_dict(**np_file)
+
+ def _as_dict(self):
+ """
+ Recursively walk trough all __slots__ and describe all elements
+ """
+ d = {}
+ d['bulk'] = np.array(self)
+ d['bulk_type'] = self.__class__.__name__
+ for attr in self._iter_slots():
+ value = getattr(self, attr)
+ if isinstance(value, list):
+ if len(value) == 0:
+ d[attr] = None
+ if all([isinstance(part, AbstractNdarray) for part in value]):
+ for i, part in enumerate(value):
+ part_dict = part._as_dict()
+ for part_attr, part_value in part_dict.items():
+ d["{attr}::{i}::{part_attr}".format(**locals())] = part_value
+ continue
+ if isinstance(value, AbstractNdarray):
+ value = value._as_dict()
+ d[attr] = value
+ return d
+
+ @classmethod
+ def _from_dict(cls, **d):
+ """
+ Opposite of _as_dict
+ """
+ list_dict = {}
+ kwargs = {}
+ '''
+ De-Flatten the first layer of lists
+ '''
+ for key in sorted(d.keys()):
+ if '::' in key:
+ splits = key.split('::')
+ attr, _, end = key.partition('::')
+ if attr not in list_dict:
+ list_dict[attr] = {}
+
+ index, _, end = end.partition('::')
+ if not index.isdigit():
+ raise ValueError("None digit index given")
+ index = int(index)
+ if index not in list_dict[attr]:
+ list_dict[attr][index] = {}
+ list_dict[attr][index][end] = d[key]
+ else:
+ kwargs[key] = d[key]
+
+ '''
+ Build the lists (recursively)
+ '''
+ for key in list_dict.keys():
+ sub_dict = list_dict[key]
+ list_dict[key] = []
+ for index in sorted(sub_dict.keys()):
+ bulk_type = sub_dict[index].get('bulk_type')
+ bulk_type = getattr(tfields, bulk_type.tolist())
+ list_dict[key].append(bulk_type._from_dict(**sub_dict[index]))
+
+ '''
+ Build the normal way
+ '''
+ bulk = kwargs.pop('bulk')
+ bulk_type = kwargs.pop('bulk_type')
+ obj = cls.__new__(cls, bulk, **kwargs)
+
+ '''
+ Set list attributes
+ '''
+ for attr, list_value in list_dict.items():
+ setattr(obj, attr, list_value)
+ return obj
class Tensors(AbstractNdarray):
@@ -1753,3 +1835,4 @@ if __name__ == '__main__': # pragma: no cover
import doctest
doctest.testmod()
# doctest.run_docstring_examples(TensorFields.__getitem__, globals())
+ # doctest.run_docstring_examples(AbstractNdarray._save_npz, globals())
diff --git a/tfields/mesh3D.py b/tfields/mesh3D.py
index 8d17498..b23c5b3 100644
--- a/tfields/mesh3D.py
+++ b/tfields/mesh3D.py
@@ -200,8 +200,7 @@ class Mesh3D(tfields.TensorMaps):
>>> m1 = tfields.Mesh3D.load(outFile.name)
>>> bool(np.all(m == m1))
True
- >>> m1.faces
- array([[0, 1, 2]])
+ >>> assert np.array_equal(m1.faces, np.array([[0, 1, 2]]))
"""
def __new__(cls, tensors, *fields, **kwargs):
diff --git a/tfields/plotting/mpl.py b/tfields/plotting/mpl.py
index 3367fbf..1d39712 100644
--- a/tfields/plotting/mpl.py
+++ b/tfields/plotting/mpl.py
@@ -121,7 +121,10 @@ def save(path, *fmts, **kwargs):
if first_label:
if not extra_artists:
extra_artists = []
- extra_artists.append(first_label)
+ if isinstance(first_label, list):
+ extra_artists.extend(first_label)
+ else:
+ extra_artists.append(first_label)
kwargs['bbox_extra_artists'] = kwargs.pop('bbox_extra_artists',
extra_artists)
@@ -564,7 +567,7 @@ def autoscale_3d(axis, array=None, xLim=None, yLim=None, zLim=None):
axis.set_zlim([zMin, zMax])
-def set_legend(axis, artists):
+def set_legend(axis, artists, **kwargs):
"""
Convenience method to set a legend from multiple artists to an axis.
"""
@@ -574,7 +577,7 @@ def set_legend(axis, artists):
handles.append(artist[0])
else:
handles.append(artist)
- axis.legend(handles=handles)
+ return axis.legend(handles=handles, **kwargs)
def set_colorbar(axis, artist, label=None, divide=True, **kwargs):
diff --git a/tfields/triangles3D.py b/tfields/triangles3D.py
index c9f22f5..bf24ae5 100644
--- a/tfields/triangles3D.py
+++ b/tfields/triangles3D.py
@@ -544,6 +544,10 @@ class Triangles3D(tfields.TensorFields):
there is just one True for each points index
triangle indices can have multiple true values
+ For Example, if you want to know the number of points in one
+ face, just do:
+ >> tris.in_triangles(poits).sum(axis=0)
+
"""
if self.ntriangles() == 0:
return np.empty((tensors.shape[0], 0), dtype=bool)
--
GitLab