def _rmatvec(self, x):
x = da.reshape(x, self.dims_fft)
if self.chunks[1] is not None:
x = x.rechunk(self.chunks[1])
y = sqrt(np.prod(self.nffts)) * da.fft.ifft2(
x, s=self.nffts, axes=(self.dirs[0], self.dirs[1]))
y = da.take(y, np.arange(self.dims[self.dirs[0]]), axis=self.dirs[0])
y = da.take(y, np.arange(self.dims[self.dirs[1]]), axis=self.dirs[1])
y = y.ravel()
return y
def __getitem__(self, index):
batch = self.labels.iloc[index * self.batch_size:(index + 1) *
self.batch_size]
optical_flow = da.take(self.optical_flow,
batch['frame'].values,
axis=0).compute()
segments = da.take(self.segments, batch['frame'].values,
axis=0).compute()
frames = np.concatenate(
[optical_flow, np.expand_dims(segments, 4)], axis=3)
return frames, batch['speed'].values
def all(self):
labels = self.labels.sort_values('frame')
with dask.config.set(pool=ThreadPool(8)):
print 'load dask array...'
optical_flow = da.take(self.optical_flow,
labels['frame'].values,
axis=0).compute()
segments = da.take(self.segments, labels['frame'].values,
axis=0).compute()
frames = np.concatenate(
[optical_flow, np.expand_dims(segments, 4)], axis=3)
return frames, labels['speed'].values
def coarsen_destagger_dask(x, blocks, stagger=None, mode='wrap'):
"""
Examples
--------
>>> x = da.arange(6, chunks=6)
>>> xc = coarsen_destagger_dask(x, {0: 2}, stagger=0)
>>> xc.compute()
array([ 1. , 3. , 3.5])
>>> x = da.from_array(x, chunks=x.shape)
>>> xc = coarsen_destagger_dask(x, {0: 2}, stagger=0)
>>> xc.compute()
array([ 1. , 3. , 3.5])
"""
output_numpy = False
try:
x._keys
except AttributeError:
output_numpy = True
x = da.from_array(x, x.shape)
xcoarse = coarsen_centered_np(x, blocks)
# TODO refactor this code to another function
if stagger is not None:
blk = {key: val
for key, val in blocks.items()
if key != stagger}
left_inds = np.arange(0, x.shape[stagger], blocks[stagger])
left = da.coarsen(np.sum, da.take(x, left_inds, stagger), blk)
n = left.shape[stagger]
# handle boundary conditions
if mode == 'wrap':
bc = da.take(left, [0], axis=stagger)
elif mode == 'clip':
bc = da.take(left, [-1], axis=stagger)
else:
raise ValueError(f"Unknown boundary `mode` given: {mode}")
right = da.take(left, np.arange(1, n), axis=stagger)
right = da.concatenate((right, bc), axis=stagger)
xcoarse = xcoarse + (right - left)/2
n = np.prod(list(blocks.values()))
ans = xcoarse/n
if output_numpy:
return ans.compute()
else:
return ans
def _rmatvec(self, x):
if self.reshape:
x = da.reshape(x, self.dims_fft)
if self.chunks[1] is not None:
x = x.rechunk(self.chunks[1])
if not self.reshape:
if self.real:
y = sqrt(self.nfft) * da.fft.irfft(x, n=self.nfft, axis=-1)
y = da.real(y)
else:
y = sqrt(self.nfft) * da.fft.ifft(x, n=self.nfft, axis=-1)
if self.nfft != self.dims[self.dir]:
y = y[:self.dims[self.dir]]
if self.fftshift:
y = da.fft.fftshift(y)
else:
if self.real:
y = sqrt(self.nfft) * da.fft.irfft(
x, n=self.nfft, axis=self.dir)
y = da.real(y)
else:
y = sqrt(self.nfft) * da.fft.ifft(
x, n=self.nfft, axis=self.dir)
if self.nfft != self.dims[self.dir]:
y = da.take(y,
np.arange(0, self.dims[self.dir]),
axis=self.dir)
if self.fftshift:
y = da.fft.fftshift(y, axes=self.dir)
y = y.ravel()
y = y.astype(self.dtype)
return y
def test_take_dask_from_numpy():
x = np.arange(5).astype('f8')
y = da.from_array(np.array([1, 2, 3, 3, 2 ,1]), chunks=3)
z = da.take(x * 2, y)
assert z.chunks == y.chunks
assert eq(z, np.array([2., 4., 6., 6., 4., 2.]))
def test_take_dask_from_numpy():
x = np.arange(5).astype('f8')
y = da.from_array(np.array([1, 2, 3, 3, 2, 1]), chunks=3)
z = da.take(x * 2, y)
assert z.chunks == y.chunks
assert_eq(z, np.array([2., 4., 6., 6., 4., 2.]))
def _matvec(self, x):
if not self.inplace:
x = x.copy()
if not self.reshape:
y = x[self.iava]
else:
x = da.reshape(x, self.dims)
y = da.take(x, self.iava, axis=self.dir)
return y
def predict(self, X):
if len(self.estimators) == 1:
preds = self.estimators[0].predict(X)
else:
preds = self.proba2predict(self.predict_proba(X))
if self.task != 'regression' and self.classes_ is not None:
preds = da.take(np.array(self.classes_), preds, axis=0)
return preds
def _ifftshift(x, axes=None):
"""Similar to numpy.fft.ifttshift but based on dask.array"""
if axes is None:
axes = list(range(x.ndim))
elif isinstance(axes, integer_types):
axes = (axes, )
for k in axes:
n = x.shape[k]
p2 = n - (n + 1) // 2
mylist = np.concatenate((np.arange(p2, n), np.arange(p2)))
x = da.take(x, mylist, k)
return x
def _dask_oindex(x, indices):
"""Perform outer indexing on dask array `x`, one dimension at a time.
It is assumed that `indices` is suitably normalised (no ellipsis, etc.)
"""
axis = 0
for index in indices:
x = da.take(x, index, axis=axis)
# If axis wasn't dropped by a scalar index:
if not isinstance(index, Integral):
axis += 1
return x
def dataset(self):
with self._lock:
if self._dataset is None:
try:
dataset = self._orig_dataset[self.keep]
except NotImplementedError:
# Dask does not like multiple boolean indices: go one dim at a time
dataset = self._orig_dataset
for dim, keep_per_dim in enumerate(self.keep):
dataset = da.take(dataset, keep_per_dim, axis=dim)
for transform in self.transforms:
dataset = transform(dataset)
self._dataset = dataset
self._orig_dataset = None
return self._dataset
def test_take():
x = np.arange(400).reshape((20, 20))
a = da.from_array(x, chunks=(5, 5))
assert_eq(np.take(x, 3, axis=0), da.take(a, 3, axis=0))
assert_eq(np.take(x, [3, 4, 5], axis=-1), da.take(a, [3, 4, 5], axis=-1))
with pytest.raises(ValueError):
da.take(a, 3, axis=2)
assert same_keys(da.take(a, [3, 4, 5], axis=-1), da.take(a, [3, 4, 5], axis=-1))
def test_take():
x = np.arange(400).reshape((20, 20))
a = da.from_array(x, chunks=(5, 5))
assert_eq(np.take(x, 3, axis=0), da.take(a, 3, axis=0))
assert_eq(np.take(x, [3, 4, 5], axis=-1), da.take(a, [3, 4, 5], axis=-1))
with pytest.raises(ValueError):
da.take(a, 3, axis=2)
assert same_keys(da.take(a, [3, 4, 5], axis=-1),
da.take(a, [3, 4, 5], axis=-1))
def take(self, indices, axis=None):
out = da.take(self, indices, axis=axis)
if len(out.shape) == len(self.shape):
out = view_subclass(out, type(self))
return out
def take_array(arr, indices, axis=None):
if DaskToolBox.exist_dask_object(arr, indices):
return da.take(arr, indices=indices, axis=axis)
else:
return np.take(arr, indices=indices, axis=axis)
def select_indices(a, indices, *, axis=0):
a = ensure_dask_array(a)
indices = ensure_dask_or_numpy_array(indices)
return da.take(a, indices, axis=axis)
for cross_id in xids:
print("processing", cross_id, "...")
par_ix = xdf.query('cross == @cross_id').query(
'role == "parent"').index.values
pro_ix = xdf.query('cross == @cross_id').query(
'role == "progeny"').index.values
if par_ix.size != 2:
print("Must be two parents: {0} found".format(par_ix.size))
continue
# grab genotypes of cross and AD
pr_gt = x_gt.take(par_ix, axis=1)
pg_gt = x_gt.take(pro_ix, axis=1)
pr_ad = da.take(x_ad, par_ix, axis=1)
# count hom refs and alts of parents
hom_alt_sum = pr_gt.is_hom_alt().sum(axis=1).compute()
hom_ref_sum = pr_gt.is_hom_ref().sum(axis=1).compute()
# identify discordance
mat_discords, mat_cov = compute_discords(pr_gt[:, 0], pr_ad[:, 0])
pat_discords, pat_cov = compute_discords(pr_gt[:, 1], pr_ad[:, 1])
# identify high coverage sites
loc_high_cov = (mat_cov >= 30) & (pat_cov >= 30)
loc_no_discords = (mat_discords + pat_discords) == 0
loc_sufficient_calls = pg_gt.count_called(axis=1).compute() >= 10
loc_all_filters = (loc_high_cov & loc_sufficient_calls) & loc_no_discords
def take(self, indices, axis=None):
out = da.take(self, indices, axis=axis)
if len(out.shape) == len(self.shape):
out = view_subclass(out, type(self))
return out
