TraitMatrix#

class pybrops.core.mat.TraitMatrix.TraitMatrix[source]#

Bases: SortableMatrix

An abstract class for matrix wrapper objects with trait metadata.

The purpose of this abstract class is to provide base functionality for:

trait metadata manipulation routines.
trait manipulation routines.

Methods

`adjoin`	Add additional elements to the end of the Matrix along an axis.
`adjoin_trait`	Add additional elements to the end of the Matrix along the trait axis.
`append`	Append values to the Matrix.
`append_trait`	Append values to the TraitMatrix along the trait axis.
`concat`	Concatenate matrices together along an axis.
`concat_trait`	Concatenate list of Matrix together along the trait axis.
`copy`	Make a shallow copy of the Matrix.
`deepcopy`	Make a deep copy of the Matrix.
`delete`	Delete sub-arrays along an axis.
`delete_trait`	Delete sub-arrays along the trait axis.
`from_hdf5`	Read an object from an HDF5 file.
`incorp`	Incorporate values along the given axis before the given indices.
`incorp_trait`	Incorporate values along the trait axis before the given indices.
`insert`	Insert values along the given axis before the given indices.
`insert_trait`	Insert values along the trait axis before the given indices.
`lexsort`	Perform an indirect stable sort using a sequence of keys.
`lexsort_trait`	Perform an indirect stable sort using a sequence of keys along the trait axis.
`remove`	Remove sub-arrays along an axis.
`remove_trait`	Remove sub-arrays along the trait axis.
`reorder`	Reorder elements of the Matrix using an array of indices.
`reorder_trait`	Reorder elements of the Matrix along the trait axis using an array of indices.
`select`	Select certain values from the matrix.
`select_trait`	Select certain values from the Matrix along the trait axis.
`sort`	Sort slements of the Matrix using a sequence of keys.
`sort_trait`	Sort slements of the Matrix along the trait axis using a sequence of keys.
`to_hdf5`	Write an object to an HDF5 file.

Attributes

`mat`	Pointer to raw matrix object.
`mat_ndim`	Number of dimensions of the raw matrix.
`mat_shape`	Shape of the raw matrix.
`ntrait`	Number of traits.
`trait`	Trait label.
`trait_axis`	Axis along which traits are stored.

abstract __add__(value)#

Elementwise add matrices

Parameters:: value (object) – Object which to add.
Returns:: out – An object resulting from the addition.
Return type:: object

abstract __mul__(value)#

Elementwise multiply matrices

Parameters:: value (object) – Object which to multiply.
Returns:: out – An object resulting from the multiplication.
Return type:: object

abstract adjoin(values, axis, **kwargs)#

Add additional elements to the end of the Matrix along an axis.

Parameters:

values (Matrix or numpy.ndarray) – Values are appended to append to the Matrix.
axis (int) – The axis along which values are adjoined.
kwargs (dict) – Additional keyword arguments.

Returns:

out – A copy of mat with values appended to axis. Note that adjoin does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract adjoin_trait(values, trait, **kwargs)[source]#

Add additional elements to the end of the Matrix along the trait axis.

Parameters:

values (Matrix, numpy.ndarray) – Values are appended to adjoin to the Matrix.
trait (numpy.ndarray) – Trait names to adjoin to the TraitMatrix.
kwargs (dict) – Additional keyword arguments.

Returns:

out – A copy of the TraitMatrix with values appended to axis. Note that adjoin does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract append(values, axis, **kwargs)#

Append values to the Matrix.

Parameters:

values (Matrix, numpy.ndarray) – Values are appended to append to the matrix.
axis (int) – The axis along which values are appended.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract append_trait(values, trait, **kwargs)[source]#

Append values to the TraitMatrix along the trait axis.

Parameters:

values (Matrix, numpy.ndarray) – Values are appended to append to the TraitMatrix.
trait (numpy.ndarray) – Trait names to append to the TraitMatrix.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract classmethod concat(mats, axis, **kwargs)#

Concatenate matrices together along an axis.

Parameters:

mats (Sequence of Matrix) – List of Matrix to concatenate. The matrices must have the same shape, except in the dimension corresponding to axis.
axis (int) – The axis along which the arrays will be joined.
kwargs (dict) – Additional keyword arguments

Returns:

out – The concatenated matrix. Note that concat does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract classmethod concat_trait(mats, **kwargs)[source]#

Concatenate list of Matrix together along the trait axis.

Parameters:

mats (Sequence of TraitMatrix) – List of TraitMatrix to concatenate. The matrices must have the same shape, except in the dimension corresponding to axis.
kwargs (dict) – Additional keyword arguments

Returns:

out – The concatenated TraitMatrix. Note that concat does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract copy()#

Make a shallow copy of the Matrix.

Returns:: out – A shallow copy of the original Matrix.
Return type:: Matrix

abstract deepcopy(memo)#

Make a deep copy of the Matrix.

Parameters:: memo (dict) – Dictionary of memo metadata.
Returns:: out – A deep copy of the original Matrix.
Return type:: Matrix

abstract delete(obj, axis, **kwargs)#

Delete sub-arrays along an axis.

Parameters:

obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.
axis (int) – The axis along which to delete the subarray defined by obj.
kwargs (dict) – Additional keyword arguments.

Returns:

out – A Matrix with deleted elements. Note that concat does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract delete_trait(obj, **kwargs)[source]#

Delete sub-arrays along the trait axis.

Parameters:

obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.
kwargs (dict) – Additional keyword arguments.

Returns:

out – A TraitMatrix with deleted elements. Note that concat does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract classmethod from_hdf5(filename, groupname)#

Read an object from an HDF5 file.

Parameters:

filename (str, Path, h5py.File) – If str, an HDF5 file name from which to read. If Path, an HDF5 file name from which to read. If h5py.File, an opened HDF5 file from which to read.
groupname (str, None) – If str, an HDF5 group name under which object data is stored. If None, object is read from base HDF5 group.

Returns:

out – An object read from an HDF5 file.

Return type:

HDF5InputOutput

abstract incorp(obj, values, axis, **kwargs)#

Incorporate values along the given axis before the given indices.

Parameters:

obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is incorporated.
values (numpy.ndarray) – Values to incorporate into the matrix.
axis (int) – The axis along which values are incorporated.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract incorp_trait(obj, values, trait, **kwargs)[source]#

Incorporate values along the trait axis before the given indices.

Parameters:

obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is incorporated.
values (Matrix, numpy.ndarray) – Values to incorporate into the matrix.
trait (numpy.ndarray) – Trait names to incorporate into the Matrix.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract insert(obj, values, axis, **kwargs)#

Insert values along the given axis before the given indices.

Parameters:

obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is inserted.
values (ArrayLike) – Values to insert into the matrix.
axis (int) – The axis along which values are inserted.
kwargs (dict) – Additional keyword arguments.

Returns:

out – A Matrix with values inserted. Note that insert does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract insert_trait(obj, values, trait, **kwargs)[source]#

Insert values along the trait axis before the given indices.

Parameters:

obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is inserted.
values (Matrix, numpy.ndarray) – Values to insert into the matrix.
trait (numpy.ndarray) – Trait names to insert into the TraitMatrix.
kwargs (dict) – Additional keyword arguments.

Returns:

out – A TraitMatrix with values inserted. Note that insert does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract lexsort(keys, axis, **kwargs)#

Perform an indirect stable sort using a sequence of keys.

Parameters:

keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.
axis (int) – Axis to be indirectly sorted.
kwargs (dict) – Additional keyword arguments.

Returns:

indices – Array of indices that sort the keys along the specified axis.

Return type:

A (N,) ndarray of ints

abstract lexsort_trait(keys, **kwargs)[source]#

Perform an indirect stable sort using a sequence of keys along the trait axis.

Parameters:

keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.
kwargs (dict) – Additional keyword arguments.

Returns:

indices – Array of indices that sort the keys along the specified axis.

Return type:

A (N,) ndarray of ints

abstract property mat: object#: Pointer to raw matrix object.

abstract property mat_ndim: int#: Number of dimensions of the raw matrix.

abstract property mat_shape: tuple#: Shape of the raw matrix.

abstract property ntrait: int#: Number of traits.

abstract remove(obj, axis, **kwargs)#

Remove sub-arrays along an axis.

Parameters:

obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.
axis (int) – The axis along which to remove the subarray defined by obj.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract remove_trait(obj, **kwargs)[source]#

Remove sub-arrays along the trait axis.

Parameters:

obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract reorder(indices, axis, **kwargs)#

Reorder elements of the Matrix using an array of indices. Note this modifies the Matrix in-place.

Parameters:

indices (A (N,) ndarray of ints, Sequence of ints) – Array of indices that reorder the matrix along the specified axis.
axis (int) – Axis to be reordered.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract reorder_trait(indices, **kwargs)[source]#

Reorder elements of the Matrix along the trait axis using an array of indices. Note this modifies the Matrix in-place.

Parameters:

indices (A (N,) ndarray of ints, Sequence of ints) – Array of indices that reorder the matrix along the specified axis.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract select(indices, axis, **kwargs)#

Select certain values from the matrix.

Parameters:

indices (ArrayLike (Nj, ...)) – The indices of the values to select.
axis (int) – The axis along which values are selected.
kwargs (dict) – Additional keyword arguments.

Returns:

out – The output matrix with values selected. Note that select does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract select_trait(indices, **kwargs)[source]#

Select certain values from the Matrix along the trait axis.

Parameters:

indices (ArrayLike (Nj, ...)) – The indices of the values to select.
kwargs (dict) – Additional keyword arguments.

Returns:

out – The output TraitMatrix with values selected. Note that select does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract sort(keys, axis, **kwargs)#

Sort slements of the Matrix using a sequence of keys. Note this modifies the Matrix in-place.

Parameters:

keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.
axis (int) – Axis to be indirectly sorted.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract sort_trait(keys, **kwargs)[source]#

Sort slements of the Matrix along the trait axis using a sequence of keys. Note this modifies the Matrix in-place.

Parameters:

keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.
kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract to_hdf5(filename, groupname, overwrite)#

Write an object to an HDF5 file.

Parameters:

filename (str, Path, h5py.File) – If str, an HDF5 file name to which to write. If Path, an HDF5 file path to which to write. If h5py.File, an opened HDF5 file to which to write.
groupname (str, None) – If str, an HDF5 group name under which object data is stored. If None, object is written to the base HDF5 group.
overwrite (bool) – Whether to overwrite values in an HDF5 file if a field already exists.

Return type:

None

abstract property trait: object#: Trait label.

abstract property trait_axis: int#: Axis along which traits are stored.