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DenseSquareMatrix#

class pybrops.core.mat.DenseSquareMatrix.DenseSquareMatrix(mat, **kwargs)[source]#

Bases: DenseMatrix, SquareMatrix

A concrete class for dense square matrices. A “square matrix” is defined as a matrix that has the same axis metadata associated with two or more axes. For example:

This is a square matrix since metadata applies to axes 0 and 1:
       taxa
     +-------+
taxa | (n,n) |
     +-------+

This is not a square matrix since unique metadata applies to each axis:
       vrnt
     +-------+
taxa | (n,p) |  Where: n == p
     +-------+

The purpose of this concrete class is to implement base functionality for:

  1. Square matrix axis metadata.

  2. Determination of square matrix conformity.

Constructor for the concrete class DenseSquareMatrix.

Parameters:

kwargs (dict) – Used for cooperative inheritance. Dictionary passing unused arguments to the parent class constructor.

Methods

adjoin

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

concat

Concatenate matrices together along an axis.

copy

Make a shallow copy of the Matrix.

deepcopy

Make a deep copy of the Matrix.

delete

Delete sub-arrays along an axis.

from_hdf5

Read DenseMatrix from an HDF5 file.

insert

Insert values along the given axis before the given indices.

is_square

Determine whether the axis lengths for the square axes are identical.

select

Select certain values from the matrix.

to_hdf5

Write GenotypeMatrix to an HDF5 file.

Attributes

mat

Pointer to raw numpy.ndarray object.

mat_ndim

Number of dimensions of the raw numpy.ndarray.

mat_shape

Shape of the raw numpy.ndarray.

nsquare

Number of axes that are square.

square_axes

Axis indices for axes that are square.

square_axes_len

Axis lengths for axes that are square.
__add__(value)#

Elementwise add matrices

Parameters:

value (object) – Object which to add.

Returns:

out – An object resulting from the addition.

Return type:

object

__mul__(value)#

Elementwise multiply matrices

Parameters:

value (object) – Object which to multiply.

Returns:

out – An object resulting from the multiplication.

Return type:

object

adjoin(values, axis=-1, **kwargs)#

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

Parameters:

  • values (DenseMatrix, numpy.ndarray) – Values are appended to append to the Matrix.

  • axis (int) – The axis along which values are appended.

  • 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:

DenseMatrix

static concat(mats, axis, **kwargs)#

Concatenate matrices together along an axis.

Parameters:

  • mats (ArrayLike of DenseMatrix) – 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 – A concatenated DenseMatrix. Note that concat does not occur in-place: a new DenseMatrix is allocated and filled.

Return type:

Matrix

copy()#

Make a shallow copy of the Matrix.

Returns:

out – A shallow copy of the original DenseMatrix.

Return type:

DenseMatrix

deepcopy(memo=None)#

Make a deep copy of the Matrix.

Parameters:

memo (dict) – Dictionary of memo metadata.

Returns:

out – A deep copy of the original DenseMatrix.

Return type:

DenseMatrix

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

Return type:

DenseMatrix

classmethod from_hdf5(filename, groupname=None)#

Read DenseMatrix from an HDF5 file.

Parameters:

  • filename (str, Path, h5py.File) – If str or Path, an HDF5 file name from which to read. File is closed after reading. If h5py.File, an opened HDF5 file from which to read. File is not closed after reading.

  • groupname (str, None) – If str, an HDF5 group name under which DenseMatrix data is stored. If None, DenseMatrix is read from base HDF5 group.

Returns:

out – A dense matrix read from file.

Return type:

DenseMatrix

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 (Matrix, numpy.ndarray) – 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

is_square()[source]#

Determine whether the axis lengths for the square axes are identical.

Returns:

out – True if all square axes are the same length. False if not all square axes are the same length.

Return type:

bool

property mat: ndarray#

Pointer to raw numpy.ndarray object.

property mat_ndim: int#

Number of dimensions of the raw numpy.ndarray.

property mat_shape: tuple#

Shape of the raw numpy.ndarray.

property nsquare: int#

Number of axes that are square.

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 – A DenseMatrix with values selected. Note that select does not occur in-place: a new DenseMatrix is allocated and filled.

Return type:

DenseMatrix

property square_axes: tuple#

Axis indices for axes that are square.

property square_axes_len: tuple#

Axis lengths for axes that are square.

to_hdf5(filename, groupname=None, overwrite=True)#

Write GenotypeMatrix to an HDF5 file.

Parameters:

  • filename (str, Path, h5py.File) – If str, an HDF5 file name to which to write. File is closed after writing. If h5py.File, an opened HDF5 file to which to write. File is not closed after writing.

  • groupname (str, None) – If str, an HDF5 group name under which the DenseMatrix data is stored. If None, the DenseMatrix 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

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