wepy.boundary_conditions.boundary module

Abstract base class and null boundary condition class for conveniently making compliant boundary condition classes for use in wepy.

class wepy.boundary_conditions.boundary.BoundaryConditions(**kwargs)[source]

Bases: object

Abstract base class for conveniently making compliant boundary condition classes.

Includes empty record group definitions and useful getters for those.

Null constructor accepts and ignores any key word arguments.

BC_FIELDS = ()

String names of fields produced in this record group.

Boundary condition (BC) records are typically used to report on changes to the state of the BC object.

Notes

These fields are not critical to the proper functioning of the rest of the wepy framework and can be modified freely.

However, reporters specific to this boundary condition probably will make use of these records.

BC_SHAPES = ()

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

BC_DTYPES = ()

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

BC_RECORD_FIELDS = ()

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

WARPING_FIELDS = ('walker_idx', 'target_idx', 'weight')

String names of fields produced in this record group.

Warping records are typically used to report whenever a walker satisfied the boundary conditions and was warped and had its state changed.

Warning

Be careful when modifying these fields as they may be integrated with other wepy framework features. Namely recognition of discontinuous warping events for making contiguous trajectories from cloning and merging lineages.

The behavior of whether or not a warping event is discontinuous is given by a BoundaryCondition class’s warping_discontinuity which likely depends on the existence of particular fields.

WARPING_SHAPES = ((1,), (1,), (1,))

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

WARPING_DTYPES = (<class 'int'>, <class 'int'>, <class 'float'>)

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

WARPING_RECORD_FIELDS = ('walker_idx', 'target_idx', 'weight')

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

PROGRESS_FIELDS = ()

String names of fields produced in this record group.

Progress records are typically used to report on measures of walkers at each cycle.

Notes

These fields are not critical to the proper functioning of the rest of the wepy framework and can be modified freely.

However, reporters specific to this boundary condition probably will make use of these records.

PROGRESS_SHAPES = ()

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

PROGRESS_DTYPES = ()

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

PROGRESS_RECORD_FIELDS = ()

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

bc_field_names()[source]

Access the class level FIELDS constant for this record group.

bc_field_shapes()[source]

Access the class level SHAPES constant for this record group.

bc_field_dtypes()[source]

Access the class level DTYPES constant for this record group.

bc_fields()[source]

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

bc_record_field_names()[source]

Access the class level RECORD_FIELDS constant for this record group.

warping_field_names()[source]

Access the class level FIELDS constant for this record group.

warping_field_shapes()[source]

Access the class level SHAPES constant for this record group.

warping_field_dtypes()[source]

Access the class level DTYPES constant for this record group.

warping_fields()[source]

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

warping_record_field_names()[source]

Access the class level RECORD_FIELDS constant for this record group.

progress_field_names()[source]

Access the class level FIELDS constant for this record group.

progress_field_shapes()[source]

Access the class level SHAPES constant for this record group.

progress_field_dtypes()[source]

Access the class level DTYPES constant for this record group.

progress_fields()[source]

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

progress_record_field_names()[source]

Access the class level RECORD_FIELDS constant for this record group.

warp_walkers(walkers, cycle)[source]

Apply boundary condition logic to walkers.

If walkers satisfy the boundary conditions then they will be ‘warped’ and have a corresponding state change take place. Each event recorded is returned as a single dictionary-style record in ‘warp_data’ list. These records correspond to the ‘WARPING’ record group.

Additional data calculated on walkers may be returned in the single ‘progress_data’ dictionary-style record, which corresponds to the ‘PROGRESS’ record group.

Any changes to the internal state of the boundary condition object (e.g. modification of parameters) should be recorded in at least one dictionary-style record in the ‘bc_data’ list. This corresponds to the ‘BC’ record group.

Parameters

  • walkers (list of walkers) – A list of objects implementing the Walker interface

  • cycle (int) – The index of the cycle this is for. Used to generate proper records.

Returns

  • new_walkers (list of walkers) – A list of objects implementing the Walker interface, that have had boundary condition logic applied.

  • warp_data (list of dict of str : value) – A list of dictionary style records for each warping event that occured.

  • bc_data (list of dict of str : value) – A list of dictionary style records for each boundary condition state change event record that occured.

  • progress_data (dict of str : list of value) – Dictionary style progress records. The values should be lists corresponding to each walker.

classmethod warping_discontinuity(warping_record)[source]

Given a warping record returns either True for a discontiuity occured or False if a discontinuity did not occur.

Parameters

warping_record (tuple) – A tuple record of type ‘WARPING’

Returns

is_discontinuous – True if discontinuous warping record False if continuous.

Return type

bool

class wepy.boundary_conditions.boundary.NoBC(**kwargs)[source]

Bases: wepy.boundary_conditions.boundary.BoundaryConditions

Boundary conditions class that does nothing.

You may use this class as a stub in order to have an boundary condition class. However, this is not necessary since boundary conditions are optional in the sim_manager anyhow.

Null constructor accepts and ignores any key word arguments.

warp_walkers(walkers, cycle)[source]

Apply boundary condition logic to walkers, of which there is none.

Simply returns all walkers provided with empty records data since there is nothing to do.

Parameters

  • walkers (list of walkers) – A list of objects implementing the Walker interface

  • cycle (int) – The index of the cycle this is for. Used to generate proper records.

Returns

  • new_walkers (list of walkers) – A list of objects implementing the Walker interface, that have had boundary condition logic applied.

  • warp_data (list of dict of str : value) – A list of dictionary style records for each warping event that occured.

  • bc_data (list of dict of str : value) – A list of dictionary style records for each boundary condition state change event record that occured.

  • progress_data (dict of str : list of value) – Dictionary style progress records. The values should be lists corresponding to each walker.

BC_DTYPES = ()

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

BC_FIELDS = ()

String names of fields produced in this record group.

Boundary condition (BC) records are typically used to report on changes to the state of the BC object.

Notes

These fields are not critical to the proper functioning of the rest of the wepy framework and can be modified freely.

However, reporters specific to this boundary condition probably will make use of these records.

BC_RECORD_FIELDS = ()

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

BC_SHAPES = ()

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

PROGRESS_DTYPES = ()

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

PROGRESS_FIELDS = ()

String names of fields produced in this record group.

Progress records are typically used to report on measures of walkers at each cycle.

Notes

These fields are not critical to the proper functioning of the rest of the wepy framework and can be modified freely.

However, reporters specific to this boundary condition probably will make use of these records.

PROGRESS_RECORD_FIELDS = ()

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

PROGRESS_SHAPES = ()

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

WARPING_DTYPES = (<class 'int'>, <class 'int'>, <class 'float'>)

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

WARPING_FIELDS = ('walker_idx', 'target_idx', 'weight')

String names of fields produced in this record group.

Warping records are typically used to report whenever a walker satisfied the boundary conditions and was warped and had its state changed.

Warning

Be careful when modifying these fields as they may be integrated with other wepy framework features. Namely recognition of discontinuous warping events for making contiguous trajectories from cloning and merging lineages.

The behavior of whether or not a warping event is discontinuous is given by a BoundaryCondition class’s warping_discontinuity which likely depends on the existence of particular fields.

WARPING_RECORD_FIELDS = ('walker_idx', 'target_idx', 'weight')

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

WARPING_SHAPES = ((1,), (1,), (1,))

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

bc_field_dtypes()

Access the class level DTYPES constant for this record group.

bc_field_names()

Access the class level FIELDS constant for this record group.

bc_field_shapes()

Access the class level SHAPES constant for this record group.

bc_fields()

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

bc_record_field_names()

Access the class level RECORD_FIELDS constant for this record group.

progress_field_dtypes()

Access the class level DTYPES constant for this record group.

progress_field_names()

Access the class level FIELDS constant for this record group.

progress_field_shapes()

Access the class level SHAPES constant for this record group.

progress_fields()

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

progress_record_field_names()

Access the class level RECORD_FIELDS constant for this record group.

classmethod warping_discontinuity(warping_record)[source]

Given a warping record returns either True for a discontiuity occured or False if a discontinuity did not occur.

Parameters

warping_record (tuple) – A tuple record of type ‘WARPING’

Returns

is_discontinuous – True if discontinuous warping record False if continuous.

Return type

bool

warping_field_dtypes()

Access the class level DTYPES constant for this record group.

warping_field_names()

Access the class level FIELDS constant for this record group.

warping_field_shapes()

Access the class level SHAPES constant for this record group.

warping_fields()

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

warping_record_field_names()

Access the class level RECORD_FIELDS constant for this record group.

class wepy.boundary_conditions.boundary.RandomBC(**kwargs)[source]

Bases: wepy.boundary_conditions.boundary.BoundaryConditions

Boundary conditions that randomly warps both continuously and discontinuously.

Can be used with any system as it won’t actually mutate states.

Null constructor accepts and ignores any key word arguments.

WARPING_DTYPES = (<class 'int'>, <class 'int'>, <class 'float'>)

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

WARPING_FIELDS = ('walker_idx', 'target_idx', 'weight')

String names of fields produced in this record group.

Warping records are typically used to report whenever a walker satisfied the boundary conditions and was warped and had its state changed.

Warning

Be careful when modifying these fields as they may be integrated with other wepy framework features. Namely recognition of discontinuous warping events for making contiguous trajectories from cloning and merging lineages.

The behavior of whether or not a warping event is discontinuous is given by a BoundaryCondition class’s warping_discontinuity which likely depends on the existence of particular fields.

WARPING_RECORD_FIELDS = ('walker_idx', 'target_idx', 'weight')

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

WARPING_SHAPES = ((1,), (1,), (1,))

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

bc_field_dtypes()

Access the class level DTYPES constant for this record group.

bc_field_names()

Access the class level FIELDS constant for this record group.

bc_field_shapes()

Access the class level SHAPES constant for this record group.

bc_fields()

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

bc_record_field_names()

Access the class level RECORD_FIELDS constant for this record group.

progress_field_dtypes()

Access the class level DTYPES constant for this record group.

progress_field_names()

Access the class level FIELDS constant for this record group.

progress_field_shapes()

Access the class level SHAPES constant for this record group.

progress_fields()

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

progress_record_field_names()

Access the class level RECORD_FIELDS constant for this record group.

classmethod warping_discontinuity(warping_record)

Given a warping record returns either True for a discontiuity occured or False if a discontinuity did not occur.

Parameters

warping_record (tuple) – A tuple record of type ‘WARPING’

Returns

is_discontinuous – True if discontinuous warping record False if continuous.

Return type

bool

warping_field_dtypes()

Access the class level DTYPES constant for this record group.

warping_field_names()

Access the class level FIELDS constant for this record group.

warping_field_shapes()

Access the class level SHAPES constant for this record group.

warping_fields()

Returns a list of zipped field specs.

Returns

record_specs – A list of the specs for each field, a spec is a tuple of type (field_name, shape_spec, dtype_spec)

Return type

list of tuple

warping_record_field_names()

Access the class level RECORD_FIELDS constant for this record group.

BC_FIELDS = ('ping',)

String names of fields produced in this record group.

Boundary condition (BC) records are typically used to report on changes to the state of the BC object.

Notes

These fields are not critical to the proper functioning of the rest of the wepy framework and can be modified freely.

However, reporters specific to this boundary condition probably will make use of these records.

BC_SHAPES = ((1,),)

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

BC_DTYPES = (<class 'int'>,)

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

BC_RECORD_FIELDS = ('ping',)

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

PROGRESS_FIELDS = ('weight',)

String names of fields produced in this record group.

Progress records are typically used to report on measures of walkers at each cycle.

Notes

These fields are not critical to the proper functioning of the rest of the wepy framework and can be modified freely.

However, reporters specific to this boundary condition probably will make use of these records.

PROGRESS_SHAPES = (Ellipsis,)

Numpy-style shapes of all fields produced in records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A tuple of ints that specify the shape of the field element array.

  2. Ellipsis, indicating that the field is variable length and limited to being a rank one array (e.g. (3,) or (1,)).

  3. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

Note that the shapes must be tuple and not simple integers for rank-1 arrays.

Option B will result in the special h5py datatype ‘vlen’ and should not be used for large datasets for efficiency reasons.

PROGRESS_DTYPES = (<class 'float'>,)

Specifies the numpy dtypes to be used for records.

There should be the same number of elements as there are in the corresponding ‘FIELDS’ class constant.

Each entry should either be:

  1. A numpy.dtype object.

  1. None, indicating that the first instance of this field will not be known until runtime. Any field that is returned by a record producing method will automatically interpreted as None if not specified here.

PROGRESS_RECORD_FIELDS = ('weight',)

Optional, names of fields to be selected for truncated representation of the record group.

These entries should be strings that are previously contained in the ‘FIELDS’ class constant.

While strictly no constraints on to which fields can be added here you should only choose those fields whose features could fit into a plaintext csv or similar format.

DISCONTINUITY_TARGET_IDXS = (0,)
warp_walkers(walkers, cycle)[source]

Apply boundary condition logic to walkers.

If walkers satisfy the boundary conditions then they will be ‘warped’ and have a corresponding state change take place. Each event recorded is returned as a single dictionary-style record in ‘warp_data’ list. These records correspond to the ‘WARPING’ record group.

Additional data calculated on walkers may be returned in the single ‘progress_data’ dictionary-style record, which corresponds to the ‘PROGRESS’ record group.

Any changes to the internal state of the boundary condition object (e.g. modification of parameters) should be recorded in at least one dictionary-style record in the ‘bc_data’ list. This corresponds to the ‘BC’ record group.

Parameters

  • walkers (list of walkers) – A list of objects implementing the Walker interface

  • cycle (int) – The index of the cycle this is for. Used to generate proper records.

Returns

  • new_walkers (list of walkers) – A list of objects implementing the Walker interface, that have had boundary condition logic applied.

  • warp_data (list of dict of str : value) – A list of dictionary style records for each warping event that occured.

  • bc_data (list of dict of str : value) – A list of dictionary style records for each boundary condition state change event record that occured.

  • progress_data (dict of str : list of value) – Dictionary style progress records. The values should be lists corresponding to each walker.