Mechanism to reduce multiple masks into one

starfish/core/morphology/Filter/__init__.py

@@ -2,6 +2,7 @@
 BinaryMaskCollection."""
 from ._base import FilterAlgorithm
 from .map import Map
+from .reduce import Reduce
 
 # autodoc's automodule directive only captures the modules explicitly listed in __all__.
 all_filters = {

starfish/core/morphology/Filter/reduce.py

@@ -0,0 +1,94 @@
+from typing import Callable, Optional, Tuple, Union
+
+import numpy as np
+
+from starfish.core.morphology.binary_mask import BinaryMaskCollection
+from starfish.core.types import FunctionSource, FunctionSourceBundle
+from ._base import FilterAlgorithm
+
+
+class Reduce(FilterAlgorithm):
+    """
+    Reduce takes masks from one ``BinaryMaskCollection`` and reduces it down to a single mask by
+    applying a specified function.  That mask is then returned as a new ``BinaryMaskCollection``.
+
+    An initial value is used to start the reduction process.  The first call to the function will be
+    called with ``initial`` and ``M0`` and produce ``R0``.  The second call to the function will be
+    called with ``R0`` and ``M1`` and produce ``R1``.
+
+    Parameters
+    ----------
+    func : Union[str, FunctionSourceBundle]
+        Function to reduce the tiles in the input.
+
+        If this value is a string, then the python package is :py:attr:`FunctionSource.np`.
+
+        If this value is a ``FunctionSourceBundle``, then the python package and module name is
+        obtained from the bundle.
+    initial : Union[np.ndarray, Callable[[Tuple[int, ...]], np.ndarray]]
+        An initial array that is the same shape as an uncropped mask, or a callable that accepts the
+        shape of an uncropped mask as its parameter and produces an initial array.
+
+    Examples
+    --------
+    Applying a logical 'AND' across all the masks in a collection.
+        >>> from starfish.core.morphology.binary_mask.test import factories
+        >>> from starfish.morphology import Filter
+        >>> from starfish.types import FunctionSource
+        >>> import numpy as np
+        >>> from skimage.morphology import disk
+        >>> binary_mask_collection = factories.binary_mask_collection_2d()
+        >>> initial_mask_producer = lambda shape: np.ones(shape=shape)
+        >>> ander = Filter.Reduce(FunctionSource.np("logical_and"), initial_mask_producer)
+        >>> anded = anded.run(binary_mask_collection)
+
+    See Also
+    --------
+    starfish.core.types.Axes
+
+    """
+
+    def __init__(
+        self,
+            func: Union[str, FunctionSourceBundle],
+            initial: Union[np.ndarray, Callable[[Tuple[int, ...]], np.ndarray]],
+            *func_args,
+            **func_kwargs,
+    ) -> None:
+        if isinstance(func, str):
+            self._func = FunctionSource.np(func)
+        elif isinstance(func, FunctionSourceBundle):
+            self._func = func
+        self._initial = initial
+        self._func_args = func_args
+        self._func_kwargs = func_kwargs
+
+    def run(
+            self,
+            binary_mask_collection: BinaryMaskCollection,
+            n_processes: Optional[int] = None,
+            *args,
+            **kwargs
+    ) -> BinaryMaskCollection:
+        """Map from input to output by applying a specified function to the input.
+
+        Parameters
+        ----------
+        binary_mask_collection : BinaryMaskCollection
+            BinaryMaskCollection to be filtered.
+        n_processes : Optional[int]
+            The number of processes to use for apply. If None, uses the output of os.cpu_count()
+            (default = None).
+
+        Returns
+        -------
+        BinaryMaskCollection
+            Return the results of filter as a new BinaryMaskCollection.
+        """
+
+        # Apply the reducing function
+        return binary_mask_collection._reduce(
+            self._func.resolve(),
+            self._initial,
+            *self._func_args,
+            **self._func_kwargs)

starfish/core/morphology/Filter/test/test_reduce.py

@@ -0,0 +1,29 @@
+import numpy as np
+
+from starfish.core.morphology.binary_mask.test.factories import binary_mask_collection_2d
+from ..reduce import Reduce
+
+
+def test_reduce():
+    def make_initial(shape):
+        constant_initial = np.zeros(shape=shape, dtype=np.bool)
+        constant_initial[0, 0] = 1
+        return constant_initial
+
+    input_mask_collection = binary_mask_collection_2d()
+    filt = Reduce("logical_xor", make_initial)
+    output_mask_collection = filt.run(input_mask_collection)
+
+    assert len(output_mask_collection) == 1
+    uncropped_output = output_mask_collection.uncropped_mask(0)
+    assert np.array_equal(
+        np.asarray(uncropped_output),
+        np.array(
+            [[False, True, True, True, True, True],
+             [False, False, False, False, False, False],
+             [False, False, False, False, False, False],
+             [False, False, False, True, True, True],
+             [False, False, False, True, True, False],
+             ],
+            dtype=np.bool,
+        ))

starfish/core/morphology/binary_mask/binary_mask.py

@@ -579,6 +579,61 @@ def _apply_single_mask(
             None
         )
 
+    def _reduce(
+            self,
+            function: Callable,
+            initial: Union[np.ndarray, Callable[[Tuple[int, ...]], np.ndarray]],
+            *args,
+            **kwargs
+    ) -> "BinaryMaskCollection":
+        """Given a function that takes two ndarray and outputs another, apply that function to all
+        the masks in this collection to form a new collection.  Each time, the function is called
+        with the result of the previous call to the method and the next uncropped mask.  The first
+        time the function is called, the first argument is provided by ``initial``, which is either
+        an array sized to match the uncropped mask, or a callable that takes a single parameter,
+        which is the shape of the array to be produced.
+
+        Parameters
+        ----------
+        function : Callable[[np.ndarray, np.ndarray], np.ndarray]
+            A function that should produce an accumulated result when given an accumulated result
+            and a mask array.  The shape of the inputs and the outputs should be identical.
+        initial : Union[np.ndarray, Callable[[Tuple[int, ...]], np.ndarray]]
+            An initial array that is the same shape as an uncropped mask, or a callable that accepts
+            the shape of an uncropped mask as its parameter and produces an initial array.
+
+        Examples
+        --------
+        Applying a logical 'AND' across all the masks.
+            >>> import numpy as np
+            >>> from starfish.core.morphology.binary_mask.test import factories
+            >>> binary_mask_collection = factories.binary_mask_collection_2d()
+            >>> anded_mask_collection = binary_mask_collection._reduce(
+                np.logical_and, np.ones(shape=(5, 6), dtype=np.bool))
+
+        Applying a logical 'AND' across all the masks, without hard-coding the size of the array.
+            >>> import numpy as np
+            >>> from starfish.core.morphology.binary_mask.test import factories
+            >>> binary_mask_collection = factories.binary_mask_collection_2d()
+            >>> anded_mask_collection = binary_mask_collection._reduce(
+                np.logical_and, lambda shape: np.ones(shape=shape, dtype=np.bool))
+        """
+        if callable(initial):
+            shape = tuple(len(self._pixel_ticks[axis])
+                          for axis, _ in zip(*_get_axes_names(len(self._pixel_ticks))))
+            result = initial(shape)
+        else:
+            result = initial
+        for ix in range(len(self)):
+            result = function(result, self.uncropped_mask(ix).values, *args, **kwargs)
+
+        return BinaryMaskCollection.from_binary_arrays_and_ticks(
+            [result],
+            self._pixel_ticks,
+            self._physical_ticks,
+            self._log,
+        )
+
 
 # these need to be at the end to avoid recursive imports
 from . import _io  # noqa

starfish/core/morphology/binary_mask/test/test_binary_mask.py

@@ -185,3 +185,45 @@ def test_apply():
 
     assert np.array_equal(region_1[Axes.Y.value], [2, 3, 4])
     assert np.array_equal(region_1[Axes.X.value], [2, 3, 4, 5])
+
+
+def test_reduce():
+    def make_initial(shape):
+        constant_initial = np.zeros(shape=shape, dtype=np.bool)
+        constant_initial[0, 0] = 1
+        return constant_initial
+
+    input_mask_collection = binary_mask_collection_2d()
+
+    constant_initial = make_initial((5, 6))
+    xored_binary_mask_constant_initial = input_mask_collection._reduce(
+        np.logical_xor, constant_initial)
+    assert len(xored_binary_mask_constant_initial) == 1
+    uncropped_output = xored_binary_mask_constant_initial.uncropped_mask(0)
+    assert np.array_equal(
+        np.asarray(uncropped_output),
+        np.array(
+            [[False, True, True, True, True, True],
+             [False, False, False, False, False, False],
+             [False, False, False, False, False, False],
+             [False, False, False, True, True, True],
+             [False, False, False, True, True, False],
+             ],
+            dtype=np.bool,
+        ))
+
+    xored_binary_mask_programmatic_initial = input_mask_collection._reduce(
+        np.logical_xor, make_initial)
+    assert len(xored_binary_mask_programmatic_initial) == 1
+    uncropped_output = xored_binary_mask_programmatic_initial.uncropped_mask(0)
+    assert np.array_equal(
+        np.asarray(uncropped_output),
+        np.array(
+            [[False, True, True, True, True, True],
+             [False, False, False, False, False, False],
+             [False, False, False, False, False, False],
+             [False, False, False, True, True, True],
+             [False, False, False, True, True, False],
+             ],
+            dtype=np.bool,
+        ))