Module Reference

pyms3d_core.select_device(device: int = 0) → str

Select hardware device to run the computations on. 0 for GPU, 1 for CPU, leave unspecified for auto. This must be called before any other function.

class pyms3d_core.MsComplex

Bases: MsComplexBase

asc(self: pyms3d_core.pyms3d_core.MsComplex, cp: int) → numpy.ndarray[numpy.int32]

List of ascending cps connected to a critical point

asc_geom(self: pyms3d_core.pyms3d_core.MsComplex, cp: int, hversion: int = -1, ToPts: bool = True) → numpy.ndarray

Ascending manifold geometry of the given critical point

Parameters:

• cp – the critical point id

• hversion – desired hierarchical version. -1 indicates current version.

• ToPts – convert the geometry data to point indices.

Returns: If ToPts False, returns a list of cellids. If ToPts True, returned shape depends on the index of cp as follows:

• CP Index 0: Returns a list of size NC of point indices in Primal grid

• CP Index 1: Returns a list of size NC’ x 4 of point indices in Dual grid

• CP Index 2: Returns a list of size NC’ x 2 of point indices in Dual grid

Where NC is the number of cells in the ascending mfold of cp, and NC’ is the number of cells in the ascending mfold of cp whose dual points are inside the Primal grid.

canc_pairs(self: pyms3d_core.pyms3d_core.MsComplex) → numpy.ndarray[numpy.int32]

get all cancellation pairs

collect_geom(self: pyms3d_core.pyms3d_core.MsComplex, dir: int = 2, dim: int = -1) → None

Collect the geometry of all surviving critical points

Parameters:

• dir – Geometry type dir=0 –> Descending dir=1 –> Ascending dir=2 –> Both (default)

• dim – Critical point type dim=-1 –> All (default) dim=0,1,2,3 –> Minima, 1-saddle,2-saddle,Maxima

Note

Call only after the compute function is called.

compute_arr(self: pyms3d_core.pyms3d_core.MsComplex, arr: numpy.ndarray) → None

Compute the MsComplex from a 3D numpy array

compute_bin(self: pyms3d_core.pyms3d_core.MsComplex, filepath: str, dims 3-tuple: tuple) → None

Compute the MsComplex from a raw/bin file

cp_cellid(self: pyms3d_core.pyms3d_core.MsComplex, cp: int) → tuple

Cell id of the critical cell associated with the critical point

cp_detail_string(self: pyms3d_core.pyms3d_core.MsComplexBase, cp: int) → str

Get a string with detailed information about the critical point

cp_func(self: pyms3d_core.pyms3d_core.MsComplexBase, cp: int) → float

Function value at the critical point

cp_index(self: pyms3d_core.pyms3d_core.MsComplexBase, cp: int) → int

Morse index at the critical point

cp_pairid(self: pyms3d_core.pyms3d_core.MsComplexBase, cp: int) → int

Index of the paired critical point (-1 if unpaired)

cp_vertid(self: pyms3d_core.pyms3d_core.MsComplex, cp: int) → tuple

Vertex id of the critical cell associated with the critical point

cps(self: pyms3d_core.pyms3d_core.MsComplex, dim: int = -1) → numpy.ndarray

Returns a list of surviving critical points based on dimension

cps_cellid(self: pyms3d_core.pyms3d_core.MsComplex) → numpy.ndarray[numpy.int16]

Get cell ids of all critical points

cps_func(self: pyms3d_core.pyms3d_core.MsComplex) → numpy.ndarray[numpy.float32]

Get function values of all critical points

cps_index(self: pyms3d_core.pyms3d_core.MsComplex) → numpy.ndarray[numpy.int8]

Get Morse indices of all critical points

cps_pairid(self: pyms3d_core.pyms3d_core.MsComplex) → numpy.ndarray[numpy.int32]

Get cancellation pair ids of all critical points

cps_vertid(self: pyms3d_core.pyms3d_core.MsComplex) → numpy.ndarray[numpy.int16]

Get maximal vertex ids of all critical points

dbg_serialize(self: pyms3d_core.pyms3d_core.MsComplex) → dict

Serialize the internal state for debugging

des(self: pyms3d_core.pyms3d_core.MsComplex, cp: int) → numpy.ndarray[numpy.int32]

List of descending cps connected to a critical point

des_geom(self: pyms3d_core.pyms3d_core.MsComplex, cp: int, hversion: int = -1, ToPts: bool = True) → numpy.ndarray

Descending manifold geometry of the given critical point

Parameters:

• cp – the critical point id

• hversion – desired hierarchical version. -1 indicates current version.

• ToPts – convert the geometry data to point indices.

Returns: If ToPts False, returns a list of cellids. If ToPts True, returned shape depends on the index of cp as follows:

• CP Index 0: Returns a list of size NC of point indices in Primal grid

• CP Index 1: Returns a list of size NC’ x 4 of point indices in Dual grid

• CP Index 2: Returns a list of size NC’ x 2 of point indices in Dual grid

Where NC is the number of cells in the descending mfold of cp, and NC’ is the number of cells in the descending mfold of cp whose dual points are inside the Primal grid.

dual_points(self: pyms3d_core.pyms3d_core.MsComplex) → numpy.ndarray[numpy.float32]

Get dual grid point coordinates

load(self: pyms3d_core.pyms3d_core.MsComplex, filepath: str) → None

Load mscomplex from file

num_cps(self: pyms3d_core.pyms3d_core.MsComplexBase) → int

Number of Critical Points

primal_points(self: pyms3d_core.pyms3d_core.MsComplex) → numpy.ndarray[numpy.float32]

Get primal grid point coordinates

save(self: pyms3d_core.pyms3d_core.MsComplex, filepath: str) → None

Save mscomplex to file

simplify_pers(self: pyms3d_core.pyms3d_core.MsComplexBase, thresh: float = 1.0, is_nrm: bool = True, nmax: int = 0, nmin: int = 0) → None

Simplify the Morse-Smale complex using topological persistence.

Parameters:

• thresh – Persistence threshold.

• is_nrm – Indicates if the threshold is normalized to [0,1]. If false, the threshold is in the scale of the input function.

• nmax – Number of maxima/minima that should be retained. Set to 0 to ignore.

• nmin – Number of maxima/minima that should be retained. Set to 0 to ignore.

Note

Any combination of the above criteria may be set. Simplification will stop when any of the criteria is reached. Call only after the compute function is called.

vert_func(self: pyms3d_core.pyms3d_core.MsComplex, x: int, y: int, z: int) → float

Scalar value at vertex coordinate

vert_funcs(self: pyms3d_core.pyms3d_core.MsComplex, arg0: int, arg1: int, arg2: int) → numpy.ndarray[numpy.float32]

Scalar value at all vertices