dacapo.experiments.datasplits.datasets.arrays.numpy_array

Classes

NumpyArray

This is just a wrapper for a numpy array to make it fit the DaCapo Array interface.

Module Contents

class dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray(array_config)

This is just a wrapper for a numpy array to make it fit the DaCapo Array interface.

data: The numpy array.

dtype: The data type of the numpy array.

roi: The region of interest of the numpy array.

voxel_size: The voxel size of the numpy array.

axes: The axes of the numpy array.

from_gp_array(): Create a NumpyArray from a Gunpowder Array.

from_np_array(): Create a NumpyArray from a numpy array.

Note

This class is a subclass of Array.

property attrs

Returns the attributes of the array.

Returns:: The attributes of the array.
Return type:: dict
Raises:: ValueError – If the array does not have attributes.

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.attrs
{}

Note

This method is a property. It returns the attributes of the array.

classmethod from_gp_array(array: gunpowder.Array)

Create a NumpyArray from a Gunpowder Array.

Parameters:: array (gp.Array) – The Gunpowder Array.
Returns:: The NumpyArray.
Return type:: NumpyArray
Raises:: ValueError – If the array does not have a data type.

Examples

>>> array = gp.Array(data=np.zeros((2, 3, 4)), spec=gp.ArraySpec(roi=Roi((0, 0, 0), (2, 3, 4)), voxel_size=Coordinate((1, 1, 1))))
>>> array = NumpyArray.from_gp_array(array)
>>> array.data
array([[[0., 0., 0., 0.],
        [0., 0., 0., 0.],
        [0., 0., 0., 0.]],

            [[0., 0., 0., 0.],
            [0., 0., 0., 0.],
            [0., 0., 0., 0.]]])

Note

This method creates a NumpyArray from a Gunpowder Array.

classmethod from_np_array(array: numpy.ndarray, roi, voxel_size, axes)

Create a NumpyArray from a numpy array.

Parameters:

array (np.ndarray) – The numpy array.
roi (Roi) – The region of interest of the array.
voxel_size (Coordinate) – The voxel size of the array.
axes (List[str]) – The axes of the array.

Returns:

The NumpyArray.

Return type:

NumpyArray

Raises:

ValueError – If the array does not have a data type.

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.data
array([[[0., 0., 0., 0.],
        [0., 0., 0., 0.],
        [0., 0., 0., 0.]],

         [[0., 0., 0., 0.],
          [0., 0., 0., 0.],
          [0., 0., 0., 0.]]])

Note

This method creates a NumpyArray from a numpy array.

property axes

Returns the axes of the array.

Returns:: The axes of the array.
Return type:: List[str]
Raises:: ValueError – If the array does not have axes.

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.axes
['z', 'y', 'x']

Note

This method is a property. It returns the axes of the array.

property dims

Returns the number of dimensions of the array.

Returns:: The number of dimensions of the array.
Return type:: int
Raises:: ValueError – If the array does not have a dimension.

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.dims
3

Note

This method is a property. It returns the number of dimensions of the array.

property voxel_size

Returns the voxel size of the array.

Returns:: The voxel size of the array.
Return type:: Coordinate

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.voxel_size
Coordinate((1, 1, 1))

Note

This method is a property. It returns the voxel size of the array.

property roi

Returns the region of interest of the array.

Returns:: The region of interest of the array.
Return type:: Roi

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.roi
Roi((0, 0, 0), (2, 3, 4))

Note

This method is a property. It returns the region of interest of the array.

property writable: bool

Returns whether the array is writable.

Returns:: Whether the array is writable.
Return type:: bool
Raises:: ValueError – If the array is not writable.

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.writable
True

Note

This method is a property. It returns whether the array is writable.

property data

Returns the numpy array.

Returns:: The numpy array.
Return type:: np.ndarray

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.data
array([[[0., 0., 0., 0.],
        [0., 0., 0., 0.],
        [0., 0., 0., 0.]],

       [[0., 0., 0., 0.],
        [0., 0., 0., 0.],
        [0., 0., 0., 0.]]])

Note

This method is a property. It returns the numpy array.

property dtype

Returns the data type of the array.

Returns:: The data type of the array.
Return type:: np.dtype
Raises:: ValueError – If the array does not have a data type.

Examples

>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.dtype
dtype('float64')

Note

This method is a property. It returns the data type of the array.

property num_channels

Returns the number of channels in the array.

Returns:: The number of channels in the array.
Return type:: int
Raises:: ValueError – If the array does not have a channel dimension.

Examples

>>> array = NumpyArray.from_np_array(np.zeros((1, 2, 3, 4)), Roi((0, 0, 0), (1, 2, 3)), Coordinate((1, 1, 1)), ["b", "c", "z", "y", "x"])
>>> array.num_channels
1
>>> array = NumpyArray.from_np_array(np.zeros((2, 3, 4)), Roi((0, 0, 0), (2, 3, 4)), Coordinate((1, 1, 1)), ["z", "y", "x"])
>>> array.num_channels
Traceback (most recent call last):
...
ValueError: Array does not have a channel dimension.

Note

This method is a property. It returns the number of channels in the array.