dacapo.experiments.datasplits.datasets.arrays.merge_instances_array
===================================================================

.. py:module:: dacapo.experiments.datasplits.datasets.arrays.merge_instances_array


Classes
-------

.. autoapisummary::

   dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray


Module Contents
---------------

.. py:class:: MergeInstancesArray(array_config)



   This array merges multiple source arrays into a single array by summing them. This is useful for merging
   instance segmentation arrays into a single array. NeuoGlancer will display each instance as a different color.

   .. attribute:: name

      str
      The name of the array

   .. attribute:: source_array_configs

      List[ArrayConfig]
      A list of source arrays to merge

   .. method:: __getitem__(roi

      Roi) -> np.ndarray
      Returns a numpy array with the requested region of interest

   .. method:: _can_neuroglance() -> bool

      
      Returns True if the array can be visualized in neuroglancer

   .. method:: _neuroglancer_source() -> str

      
      Returns the source name for the array in neuroglancer

   .. method:: _neuroglancer_layer() -> Tuple[neuroglancer.SegmentationLayer, Dict[str, Any]]

      
      Returns a neuroglancer layer and its configuration

   .. method:: _source_name() -> str

      
      Returns the source name for the array

   .. note::

      This array is not writable
      Source arrays must have the same shape.


   .. py:attribute:: name


   .. py:property:: axes
      Returns the axes of the array

      :returns: The axes of the array
      :rtype: List[str]

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      axes = array.axes
      ```

      .. note:: This example shows how to get the axes of the array


   .. py:property:: dims
      :type: int

      Returns the number of dimensions of the array

      :returns: The number of dimensions of the array
      :rtype: int

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      dims = array.dims
      ```

      .. note:: This example shows how to get the number of dimensions of the array


   .. py:property:: voxel_size
      :type: funlib.geometry.Coordinate

      Returns the voxel size of the array

      :returns: The voxel size of the array
      :rtype: Coordinate

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      voxel_size = array.voxel_size
      ```

      .. note:: This example shows how to get the voxel size of the array


   .. py:property:: roi
      :type: funlib.geometry.Roi

      Returns the region of interest of the array

      :returns: The region of interest of the array
      :rtype: Roi

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      roi = array.roi
      ```

      .. note:: This example shows how to get the region of interest of the array


   .. py:property:: writable
      :type: bool

      Returns True if the array is writable, False otherwise

      :returns: True if the array is writable, False otherwise
      :rtype: bool

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      writable = array.writable
      ```

      .. note:: This example shows how to check if the array is writable


   .. py:property:: dtype
      Returns the data type of the array

      :returns: The data type of the array
      :rtype: np.dtype

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      dtype = array.dtype
      ```

      .. note:: This example shows how to get the data type of the array


   .. py:property:: num_channels
      Returns the number of channels of the array

      :returns: The number of channels of the array
      :rtype: int

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      num_channels = array.num_channels
      ```

      .. note:: This example shows how to get the number of channels of the array


   .. py:property:: data
      Returns the data of the array

      :returns: The data of the array
      :rtype: np.ndarray

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      data = array.data
      ```

      .. note:: This example shows how to get the data of the array


   .. py:property:: attrs
      Returns the attributes of the array

      :returns: The attributes of the array
      :rtype: Dict[str, Any]

      :raises ValueError: If the source arrays have different shapes

      .. rubric:: Example

      ```python
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArray
      from dacapo.experiments.datasplits.datasets.arrays import MergeInstancesArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
      from dacapo.experiments.datasplits.datasets.arrays import ArrayType
      from funlib.geometry import Coordinate, Roi
      array_config = MergeInstancesArrayConfig(
          name="array",
          source_array_configs=[
              ArrayConfig(
                  name="array1",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array1.h5",
              ),
              ArrayConfig(
                  name="array2",
                  array_type=ArrayType.INSTANCE_SEGMENTATION,
                  path="path/to/array2.h5",
              ),
          ],
      )
      array = MergeInstancesArray(array_config)
      attributes = array.attrs
      ```

      .. note:: This example shows how to get the attributes of the array