def isel(self, indexers: Mapping[Axes, Union[int, tuple]]):
"""Given a dictionary mapping the index name to either a value or a range represented as a
tuple, return an Imagestack with each dimension indexed by position accordingly
Parameters
----------
indexers : Dict[Axes, (int/tuple)]
A dictionary of dim:index where index is the value or range to index the dimension
Examples
--------
Create an Imagestack using the ``synthetic_stack`` method
>>> from starfish import ImageStack
>>> from starfish.types import Axes
>>> stack = ImageStack.synthetic_stack(5, 5, 15, 200, 200)
>>> stack
<starfish.ImageStack (r: 5, c: 5, z: 15, y: 200, x: 200)>
>>> stack.isel({Axes.ROUND: (1, None), Axes.CH: 0, Axes.ZPLANE: 0})
<starfish.ImageStack (r: 4, c: 1, z: 1, y: 200, x: 200)>
>>> stack.isel({Axes.ROUND: 0, Axes.CH: 0, Axes.ZPLANE: 1,
...Axes.Y: 100, Axes.X: (None, 100)})
<starfish.ImageStack (r: 1, c: 1, z: 1, y: 1, x: 100)>
and the imagestack's physical coordinates
xarray also indexed and recalculated according to the x,y slicing.
Returns
-------
ImageStack :
a new image stack indexed by given value or range.
"""
stack = deepcopy(self)
selector = indexing_utils.convert_to_selector(indexers)
stack._data._data = indexing_utils.index_keep_dimensions(self.xarray, selector, by_pos=True)
return stack
def get_partial(self, indexers: Mapping[Axes, Union[int, slice, Sequence]]):
"""
Slice the codebook data according to the provided indexing parameters. Used in a composite
codebook scenario.
Parameters
----------
indexers : Mapping[Axes, Union[int, Sequence]]
A dictionary of dim:index where index is the value, values or range to index the
dimension
"""
selector = indexing_utils.convert_to_selector(indexers)
return indexing_utils.index_keep_dimensions(self, indexers=selector)
def sel(self, indexers: Mapping[Axes, Union[int, slice, Sequence]]):
"""Given a dictionary mapping the index name to either a value or a range represented as a
tuple, return an Imagestack with each dimension indexed accordingly
Parameters
----------
indexers : Mapping[Axes, Union[int, Union[int, Sequence]]
A dictionary of dim:index where index is the value, values, or range to index the
dimension
Examples
--------
Create an Imagestack :py:func:`~starfish.imagestack.imagestack.ImageStack.synthetic_stack`
>>> from starfish import ImageStack
>>> from starfish.core.imagestack.test.factories import synthetic_stack
>>> from starfish.types import Axes
>>> stack = synthetic_stack(5, 5, 15, 200, 200)
>>> stack
<starfish.ImageStack (r: 5, c: 5, z: 15, y: 200, x: 200)>
>>> stack.sel({Axes.ROUND: (1, None), Axes.CH: 0, Axes.ZPLANE: 0})
<starfish.ImageStack (r: 4, c: 1, z: 1, y: 200, x: 200)>
>>> stack.sel({Axes.ROUND: 0, Axes.CH: 0, Axes.ZPLANE: 1,
...Axes.Y: 100, Axes.X: (None, 100)})
<starfish.ImageStack (r: 1, c: 1, z: 1, y: 1, x: 100)>
and the imagestack's physical coordinates
xarray also indexed and recalculated according to the x,y slicing.
Returns
-------
ImageStack :
a new image stack indexed by given value or range.
"""
self._ensure_data_loaded()
stack = deepcopy(self)
selector = indexing_utils.convert_to_selector(indexers)
stack._data = indexing_utils.index_keep_dimensions(
self.xarray, selector)
return stack
def get_slice(
self, selector: Mapping[Axes, Union[int, slice]]
) -> Tuple[np.ndarray, Sequence[Axes]]:
"""
Given a dictionary mapping the index name to either a value or a slice range, return a
numpy array representing the slice, and a list of the remaining axes beyond the normal x-y
tile.
Examples
--------
Slicing with a scalar
>>> from starfish import ImageStack
>>> from starfish.core.imagestack.test.factories import synthetic_stack
>>> from starfish.core.types import Axes
>>> stack = synthetic_stack(3, 4, 5, 20, 10)
>>> stack.shape
OrderedDict([(<Axes.ROUND: 'r'>, 3),
(<Axes.CH: 'c'>, 4),
(<Axes.ZPLANE: 'z'>, 5),
('y', 20),
('x', 10)])
>>> stack.axis_labels(Axes.ROUND)
[0, 1, 2]
>>> stack.axis_labels(Axes.CH)
[0, 1, 2, 3]
>>> stack.axis_labels(Axes.ZPLANE)
[2, 3, 4, 5, 6]
>>> data, axes = stack.get_slice({Axes.ZPLANE: 6})
>>> data.shape
(3, 4, 20, 10)
>>> axes
[<Axes.ROUND: 'r'>, <Axes.CH: 'c'>]
Slicing with a range
>>> from starfish import ImageStack
>>> from starfish.core.imagestack.test.factories import synthetic_stack
>>> from starfish.core.types import Axes
>>> stack = synthetic_stack(3, 4, 5, 20, 10)
>>> stack.shape
OrderedDict([(<Axes.ROUND: 'r'>, 3),
(<Axes.CH: 'c'>, 4),
(<Axes.ZPLANE: 'z'>, 5),
('y', 20),
('x', 10)])
>>> stack.axis_labels(Axes.ROUND)
[0, 1, 2]
>>> stack.axis_labels(Axes.CH)
[0, 1, 2, 3]
>>> stack.axis_labels(Axes.ZPLANE)
[2, 3, 4, 5, 6]
>>> data, axes = stack.get_slice({Axes.ZPLANE: 5, Axes.CH: slice(2, 4)})
>>> data.shape
(3, 2, 20, 10)
>>> axes
[<Axes.ROUND: 'r'>, <Axes.CH: 'c'>]
"""
formatted_indexers = indexing_utils.convert_to_selector(selector)
_, axes = self._build_slice_list(selector)
result = self._data.sel(formatted_indexers).values
if result.dtype != np.float32:
warnings.warn(
f"Non-float32 dtype: {result.dtype} detected. Data has likely been set using "
f"private attributes of ImageStack. ImageStack only supports float data in the "
f"range [0, 1]. Many algorithms will not function properly if provided other "
f"DataTypes. See: http://scikit-image.org/docs/dev/user_guide/data_types.html"
)
return result, axes
