dacapo.experiments.datasplits.datasets.arrays.logical_or_array

Classes

LogicalOrArray

Array that computes the logical OR of the instances in a list of source arrays.

Module Contents

class dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray(array_config)

Array that computes the logical OR of the instances in a list of source arrays.

name

str The name of the array

source_array

Array The source array from which to take the logical OR

axes()

() -> List[str] Get the axes of the array

dims()

() -> int Get the number of dimensions of the array

voxel_size()

() -> Coordinate Get the voxel size of the array

roi()

() -> Roi Get the region of interest of the array

writable()

() -> bool Get whether the array is writable

dtype()

() -> type Get the data type of the array

num_channels()

() -> int Get the number of channels in the array

data()

() -> np.ndarray Get the data of the array

attrs()

() -> dict Get the attributes of the array

__getitem__()

(roi: Roi) -> np.ndarray Get the data of the array in the region of interest

_can_neuroglance()

() -> bool Get whether the array can be visualized in neuroglance

_neuroglancer_source()

() -> dict Get the neuroglancer source of the array

_neuroglancer_layer()

() -> Tuple[neuroglancer.Layer, dict] Get the neuroglancer layer of the array

_source_name()

() -> str Get the name of the source array

Notes

The LogicalOrArray class is used to create a LogicalOrArray. The LogicalOrArray class is a subclass of the Array class.

name

property axes

Get the axes of the array

Returns:

The axes of the array

Return type:

List[str]

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.axes
['x', 'y', 'z']

Notes

The axes method is used to get the axes of the array. The axes are the dimensions of the array.

property dims: int

Get the number of dimensions of the array

Returns:

The number of dimensions of the array

Return type:

int

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.dims
3

Notes

The dims method is used to get the number of dimensions of the array. The number of dimensions is the number of axes of the array.

property voxel_size: funlib.geometry.Coordinate

Get the voxel size of the array

Returns:

The voxel size of the array

Return type:

Coordinate

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.voxel_size
Coordinate(x=1.0, y=1.0, z=1.0)

Notes

The voxel_size method is used to get the voxel size of the array. The voxel size is the size of a voxel in the array.

property roi: funlib.geometry.Roi

Get the region of interest of the array

Returns:

The region of interest of the array

Return type:

Roi

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.roi
Roi(offset=(0, 0, 0), shape=(10, 10, 10))

Notes

The roi method is used to get the region of interest of the array. The region of interest is the shape and offset of the array.

property writable: bool

Get whether the array is writable

Returns:

Whether the array is writable

Return type:

bool

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.writable
False

Notes

The writable method is used to get whether the array is writable. An array is writable if it can be modified.

property dtype

Get the data type of the array

Returns:

The data type of the array

Return type:

type

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.dtype
<class 'numpy.uint8'>

Notes

The dtype method is used to get the data type of the array. The data type is the type of the data in the array.

property num_channels

Get the number of channels in the array

Returns:

The number of channels in the array

Return type:

int

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.num_channels
1

Notes

The num_channels method is used to get the number of channels in the array. The number of channels is the number of channels in the array.

property data

Get the data of the array

Returns:

The data of the array

Return type:

np.ndarray

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.data
array([[[1, 1, 1, ..., 1, 1, 1],
        [1, 1, 1, ..., 1, 1, 1],
        [1, 1, 1, ..., 1, 1, 1],
        ...,
        [1, 1, 1, ..., 1, 1, 1],
        [1, 1, 1, ..., 1, 1, 1],
        [1, 1, 1, ..., 1, 1, 1]]], dtype=uint8)

Notes

The data method is used to get the data of the array. The data is the content of the array.

property attrs

Get the attributes of the array

Returns:

The attributes of the array

Return type:

dict

Raises:

ValueError – If the array is not writable

Examples

>>> array_config = MergeInstancesArrayConfig(
...     name="logical_or",
...     source_array_configs=[
...         ArrayConfig(
...             name="mask1",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask1",
...                 mask_id=1,
...             ),
...         ),
...         ArrayConfig(
...             name="mask2",
...             array_type=MaskArray,
...             source_array_config=MaskArrayConfig(
...                 name="mask2",
...                 mask_id=2,
...             ),
...         ),
...     ],
... )
>>> array = array_config.create_array()
>>> array.attrs
{'name': 'logical_or'}

Notes

The attrs method is used to get the attributes of the array. The attributes are the metadata of the array.