def _getitems(self, indices=None, axis=0, indexing=None, tol=None, broadcast=None, keepdims=False):
# first find the index for the shared axes
tuple_indices = self._get_indices(indices, axis=axis, tol=tol, keepdims=keepdims, indexing=indexing)
# then index all arrays, one after the other
newdata = self.__class__()
# then apply take in 'position' mode
newdata = self.__class__()
axes_dict = {ax.name:ax[ix] for ix, ax in zip(tuple_indices, self.axes) if not np.isscalar(ix)}
indices_dict = {ax.name:ix for ix, ax in zip(tuple_indices, self.axes)}
# loop over variables
for k in self.keys():
v = self[k]
# loop over axes to index on
for axis in kw_indices.keys():
if np.ndim(v) == 0 or axis not in v.dims:
if raise_error:
raise ValueError("{} does not have dimension {} ==> set raise_error=False to keep this variable unchanged".format(k, axis))
else:
continue
# slice along one axis
v = v.take({axis:kw_indices[axis]}, indexing='position')
newdata[k] = v
return newdata
def _check_axis_values(values, dtype=None):
""" convert Axis type to have "object" instead of string
"""
try:
values = np.asarray(values, dtype=dtype)
except Exception as error:
raise TypeError(error.message + "\n==> axis values could not be converted to numpy array")
# Treat the particular case of a sequence of sequences, leads to a 2-D array
# ==> convert to a list of tuples
if values.ndim == 2:
try:
val = np.empty(values.shape[0], dtype=object)
val[:] = list(zip(*values.T.tolist())) # pass a list of tuples
values = val
except:
pass
if values.ndim != 1:
raise ValueError("an Axis object can only be 1-D, got ndim={}".format(values.ndim))
if values.dtype.kind in ("S", "U"):
values = np.asarray(values, dtype=object)
return values
def _set_dims(self, newdims):
if not np.iterable(newdims):
raise TypeError("new dims must be iterable")
if not isinstance(newdims, dict):
if len(newdims) != len(self.dims):
raise ValueError("dimensions number mismatch")
newdims = dict(zip(self.dims, newdims))
for old in newdims.keys():
self.axes[old].name = newdims[old]
def _get_values(self):
# Each element of the new axis is a tuple, which makes a 2-D numpy array
if len(self.axes) == 1:
return self.axes[0].values
aval = _flatten(*[ax.values for ax in self.axes])
val = np.empty(aval.shape[0], dtype=object)
val[:] = list(zip(*aval.T.tolist())) # pass a list of tuples
return val
def from_arrays(cls, arrays, dims=None):
""" list of np.ndarrays and dims
"""
assert np.iterable(arrays) and (dims is None or len(dims) == len(arrays)), "invalid input arrays={}, dims={}".format(arrays, dims)
# default names
if dims is None:
dims = ["x{}".format(i) for i in range(len(arrays))]
return cls(list(zip(dims, arrays)))
def _flatten(*list_of_arrays):
""" flatten a list of arrays ax1, ax2, ... to a list of tuples [(ax1[0], ax2[0], ax3[0]..), (ax1[0], ax2[0], ax3[1]..), ...]
"""
assert len(list_of_arrays) > 0, "empty axis"
if len(list_of_arrays) == 1:
return list_of_arrays[0]
kwargs = dict(indexing="ij")
grd = np.meshgrid(*list_of_arrays, **kwargs)
array_of_tuples = np.array(list(zip(*[g.ravel() for g in grd])))
assert array_of_tuples.shape[1] == len(list_of_arrays), "pb when reshaping: {} and {}".format(array_of_tuples.shape, len(list_of_arrays))
assert array_of_tuples.shape[0] == np.prod([x.size for x in list_of_arrays]), "pb when reshaping: {} and {}".format(array_of_tuples.shape, np.prod([x.size for x in list_of_arrays]))
return array_of_tuples
def _get_axes_info(self, axes):
""" return axis (dimension) positions AND names from a sequence of axis (dimension) positions OR names
Parameters
----------
axes : sequence of str or int, representing axis (dimension)
names or positions, possibly mixed up.
Returns
-------
pos : list of `int` indicating dimension's rank in the array
names : list of dimension names
"""
pos, names = zip(*[self._get_axis_info(x) for x in axes])
return pos, names
def getaxes_broadcast(obj, indices):
""" broadcast array-indices & integers, numpy's classical
Examples
--------
>>> import dimarray as da
>>> a = da.zeros(shape=(3,4,5,6))
>>> a.take((slice(None),[0, 1],slice(None),2), broadcast=True).shape
(2, 3, 5)
>>> a.take((slice(None),[0, 1],2,slice(None)), broadcast=True).shape
(3, 2, 6)
"""
from dimarray import Axis, Axes
# new axes: broacast indices (should do the same as above, since integers are just broadcast)
indices2 = broadcast_indices(indices)
# assert np.all(newval == obj.values[indices2])
# make a multi-axis with tuples
is_array2 = np.array([np.iterable(ix) for ix in indices2])
nb_array2 = is_array2.sum()
# If none or one array is present, easy
if nb_array2 <= 1:
newaxes = [obj.axes[i][ix] for i, ix in enumerate(indices) if not np.isscalar(ix)] # indices or indices2, does not matter
# else, finer check needed
else:
# same stats but on original indices
is_array = np.array([np.iterable(ix) for ix in indices])
array_ix_pos = np.where(is_array)[0]
# Determine where the axis will be inserted
# - need to consider the integers as well (broadcast as arrays)
# - if two indexed dimensions are not contiguous, new axis placed at first position...
# obj = zeros((3,4,5,6))
# obj[:,[1,2],:,0].shape ==> (2, 3, 5)
# obj[:,[1,2],0,:].shape ==> (3, 2, 6)
array_ix_pos2 = np.where(is_array2)[0]
if np.any(np.diff(array_ix_pos2) > 1): # that mean, if two indexed dimensions are not contiguous
insert = 0
else:
insert = array_ix_pos2[0]
# Now determine axis value
# ...if originally only one array was provided, use these values correspondingly
if len(array_ix_pos) == 1:
i = array_ix_pos[0]
values = obj.axes[i].values[indices[i]]
name = obj.axes[i].name
# ...else use a list of tuples
else:
values = list(zip(*[obj.axes[i].values[indices2[i]] for i in array_ix_pos]))
name = ",".join([obj.axes[i].name for i in array_ix_pos])
broadcastaxis = Axis(values, name)
newaxes = Axes()
for i, ax in enumerate(obj.axes):
# axis is already part of the broadcast axis: skip
if is_array2[i]:
continue
else:
newaxis = ax[indices2[i]]
## do not append axis if scalar
#if np.isscalar(newaxis):
# continue
newaxes.append(newaxis)
# insert the right new axis at the appropriate position
newaxes.insert(insert, broadcastaxis)
return newaxes
def todict(self):
return odict(zip(self.keys(), self.values()))