:param name: Name of the Data Function.
:type name: str
+
+ :raises DataFunctionError: If a name is not provided.
"""
def __init__(self, name=None):
@@ -128,11 +130,11 @@ Source code for spatialpy.core.datafunction
"""
This method must be overridden by the DataFunction subclass.
- NOTE: The spatial location is evaulated at t=0 and is not
- reevaluated as the fluid domain moves over time.
+ NOTE: The spatial location is evaulated at t=0 and is not \
+ re-evaluated as the fluid domain moves over time.
- :param point: The x,y,z position
- :type point: vector of 3 doubles
+ :param point: The x, y, z position.
+ :type point: float[3]
:returns: Value of function at this spatial location.
:rtype: float
diff --git a/docs/build/html/_modules/spatialpy/core/domain.html b/docs/build/html/_modules/spatialpy/core/domain.html
index 1e734839..7b608992 100644
--- a/docs/build/html/_modules/spatialpy/core/domain.html
+++ b/docs/build/html/_modules/spatialpy/core/domain.html
@@ -130,13 +130,13 @@ Source code for spatialpy.core.domain
:type numpoints: int
:param xlim: Range of domain along x-axis
- :type xlim: tuple(float)
+ :type xlim: float(2)
:param ylim: Range of domain along y-axis
- :type ylim: tuple(float)
+ :type ylim: float(2)
:param zlim: Range of domain along z-axis
- :type zlim: tuple(float)
+ :type zlim: float(2)
:param rho: Background density for the system
:type rho: float
@@ -148,7 +148,7 @@ Source code for spatialpy.core.domain
:type P0: float
:param gravity: Acceleration of gravity for the system.
- :type species: float
+ :type gravity: float[3]
"""
def __init__(self, numpoints, xlim, ylim, zlim, rho0=1.0, c0=10, P0=None, gravity=None):
self.vertices = numpy.zeros((numpoints, 3), dtype=float)
@@ -225,10 +225,10 @@ Source code for spatialpy.core.domain
[docs] def compile_prep(self):
"""
- Generate the domain list of type ids and check for invalid type_ids and rho values
+ Generate the domains list of type ids and check for invalid type_ids and rho values
in preperation of compiling the simulation files.
- :raises DomainError: If a type_id is not set or rh for a particle is 0.
+ :raises DomainError: If a type_id is not set or rho=0 for a particle.
"""
if self.type_id.tolist().count(None) > 0:
raise DomainError(f"Particles must be assigned a type_id.")
@@ -243,7 +243,7 @@ Source code for spatialpy.core.domain
Add a single point particle to the domain space.
:param point: Spatial coordinate vertices of point to be added
- :type point: tuple(float, float, float) or tuple(float, float)
+ :type point: float(3)
:param vol: Default volume of particle to be added
:type vol: float
@@ -251,19 +251,19 @@ Source code for spatialpy.core.domain
:param mass: Default mass of particle to be added
:type mass: float
- :param type_id: Particle type ID of particle to be created
+ :param type_id: Particle type ID of particle to be craddedeated
:type type_id: str | int
- :param nu: Default viscosity of particle to be created
+ :param nu: Default viscosity of particle to be added
:type nu: float
:param fixed: True if particle is spatially fixed, else False
:type fixed: bool
- :param c: Default artificial speed of sound of particle to be created
+ :param c: Default artificial speed of sound of particle to be added
:type c: float
- :param rho: Default density of particle to be created
+ :param rho: Default density of particle to be added
:type rho: float
:raises DomainError: Type_id is 0 or type_id contains an invalid character.
@@ -297,9 +297,9 @@ Source code for spatialpy.core.domain
"""
Add a type definition to the domain. By default, all regions are set to type 0.
- :param geometry_ivar: an instance of a 'spatialpy.Geometry' subclass. The 'inside()' method
+ :param geometry_ivar: an instance of a :py:class:`spatialpy.core.geometry.Geometry` subclass. The 'inside()' method
of this object will be used to assign properties to points.
- :type geometry_ivar: spatialpy.Geometry.Geometry
+ :type geometry_ivar: spatialpy.core.geometry.Geometry
:param type_id: The identifier for this type.
:type type_id: str | int
@@ -363,9 +363,9 @@ Source code for spatialpy.core.domain
"""
Fill a geometric shape with particles.
- :param geometry_ivar: an instance of a 'spatialpy.Geometry' subclass. The 'inside()' method
+ :param geometry_ivar: an instance of a :py:class:`spatialpy.core.geometry.Geometry` subclass. The 'inside()' method
of this object will be used to create add the particles.
- :type geometry_ivar: spatialpy.geometry.Geometry
+ :type geometry_ivar: spatialpy.core.geometry.Geometry
:param deltax: Distance between particles on the x-axis.
:type deltax: float
@@ -394,8 +394,7 @@ Source code for spatialpy.core.domain
:param zmax: Maximum z value of the bounding box (defaults to Domain.zlim[1]).
:type zmax: float
- :param kwargs: Key word arguments for Domain.add_point.
- :type kwargs: dict
+ :param \**kwargs: Additional keyword arguments passed to :py:meth:`Domain.add_point`.
:returns: The number of particles that were created within this geometry.
:rtype: int
@@ -509,10 +508,10 @@ Source code for spatialpy.core.domain
Get distance between 2 domain vertices.
:param start: Starting point
- :type start: tuple(float, float, float) or tuple(float, float)
+ :type start: float(3)
:param end: Ending point
- :type end: tuple(float, float, float) or tuple(float, float)
+ :type end: float(2)
:returns: a distance measurement between start and end point
:rtype: float
@@ -524,10 +523,10 @@ Source code for spatialpy.core.domain
Find the nearest vertex of a given point in the domain.
:param point: Target source point
- :type point: tuple(float, float, float) or tuple(float, float)
+ :type point: float(3)
:returns: The coordinates of the nearest vertex to the source point.
- :rtype: tuple(float, float, float) or tuple(float, float)
+ :rtype: float(3)
"""
min_dist = None
min_vtx = None
@@ -745,7 +744,7 @@ Source code for spatialpy.core.domain
:type filename: str
:returns: SpatialPy Domain object created from xml mesh.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
root = ET.parse(filename).getroot()
if not root.tag == 'dolfin':
@@ -798,7 +797,7 @@ Source code for spatialpy.core.domain
:type mesh_obj: meshio.Mesh
:returns: SpatialPy Domain object created from the meshio object
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
# create domain object
xlim = (min(mesh_obj.points[:, 0]), max(mesh_obj.points[:, 0]))
@@ -808,11 +807,13 @@ Source code for spatialpy.core.domain
#vertices
obj.vertices = mesh_obj.points
# triangles
- if 'triangle' in mesh_obj.cells:
- obj.triangles = mesh_obj.cells['triangle']
+ triangles = list(filter(lambda cell: cell.type == "triangle", mesh_obj.cells))
+ if triangles:
+ obj.triangles = triangles[0].data
#tetrahedrons
- if 'tetra' in mesh_obj.cells:
- obj.tetrahedrons = mesh_obj.cells['tetra']
+ tetras = list(filter(lambda cell: cell.type == "tetra", mesh_obj.cells))
+ if tetras:
+ obj.tetrahedrons = tetras[0].data
# volume
obj.calculate_vol()
if not numpy.count_nonzero(obj.vol):
@@ -833,18 +834,14 @@ Source code for spatialpy.core.domain
:type filename: str
:returns: SpatialPy Domain object created from the mesh file.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
- try:
- import pygmsh # pylint: disable=import-outside-toplevel
- except ImportError as err:
- raise DomainError("The python package 'pygmsh' is not installed.") from err
try:
import meshio # pylint: disable=import-outside-toplevel
except ImportError as err:
raise DomainError("The python package 'meshio' is not installed.") from err
- return cls.import_meshio_object(meshio.msh_io.read(filename))
+ return cls.import_meshio_object(meshio.read(filename))
[docs] def read_stochss_subdomain_file(self, filename, type_ids=None):
"""
@@ -884,7 +881,7 @@ Source code for spatialpy.core.domain
:type filename: str
:returns: SpatialPy Domain object created from StochSS domain.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
try:
with open(filename, "r", encoding="utf-8") as domain_file:
@@ -920,13 +917,13 @@ Source code for spatialpy.core.domain
Create a filled 3D domain
:param xlim: highest and lowest coordinate in the x dimension
- :type xlim: tuple(float, float)
+ :type xlim: float(2)
:param ylim: highest and lowest coordinate in the y dimension
- :type ylim: tuple(float, float)
+ :type ylim: float(2)
:param zlim: highest and lowest coordinate in the z dimension
- :type zlim: tuple(float, float)
+ :type zlim: float(2)
:param nx: number of particle spacing in the x dimension
:type nx: int
@@ -950,22 +947,15 @@ Source code for spatialpy.core.domain
:type c: float
:param rho: default density of particles to be created.
- :type rho:
+ :type rho: float
:param fixed: spatially fixed flag of particles to be created. Defaults to false.
:type fixed: bool
- :param rho0: background density for the system. Defaults to 1.0
- :type rho0: float
-
- :param c0: speed of sound for the system. Defaults to 10
- :type c0: float
-
- :param P0: background pressure for the system. Defaults to 10
- :type P0: float
-
+ :param \**kwargs: Additional keyword arguments passed to :py:class:`Domain`.
+
:returns: Uniform 3D SpatialPy Domain object.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
# Create domain object
numberparticles = nx * ny * nz
@@ -992,10 +982,10 @@ Source code for spatialpy.core.domain
Create a filled 2D domain
:param xlim: highest and lowest coordinate in the x dimension
- :type xlim: tuple(float, float)
+ :type xlim: float(2)
:param ylim: highest and lowest coordinate in the y dimension
- :type ylim: tuple(float, float)
+ :type ylim: float(2)
:param nx: number of particle spacing in the x dimension
:type nx: int
@@ -1016,22 +1006,15 @@ Source code for spatialpy.core.domain
:type c: float
:param rho: default density of particles to be created.
- :type rho:
+ :type rho: float
:param fixed: spatially fixed flag of particles to be created. Defaults to false.
:type fixed: bool
- :param rho0: background density for the system. Defaults to 1.0
- :type rho0: float
-
- :param c0: speed of sound for the system. Defaults to 10
- :type c0: float
-
- :param P0: background pressure for the system. Defaults to 10
- :type P0: float
+ :param \**kwargs: Additional keyword arguments passed to :py:class:`Domain`.
:returns: Uniform 2D SpatialPy Domain object.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
# Create domain object
numberparticles = nx * ny
diff --git a/docs/build/html/_modules/spatialpy/core/geometry.html b/docs/build/html/_modules/spatialpy/core/geometry.html
index bbdc26dc..8ca065ff 100644
--- a/docs/build/html/_modules/spatialpy/core/geometry.html
+++ b/docs/build/html/_modules/spatialpy/core/geometry.html
@@ -150,7 +150,7 @@ Source code for spatialpy.core.geometry
[docs]class GeometryExterior(Geometry):
"""
Mark particles that are on the edge of the domain.
- only works for meshes that define triangles and tetrahedrons.
+ only works for domains that define triangles and tetrahedrons.
"""
[docs] def inside(self, point, on_boundary):
"""
@@ -168,7 +168,7 @@ Source code for spatialpy.core.geometry
[docs]class GeometryInterior(Geometry):
"""
Mark particles that are not on the edge of the domain.
- Only works for meshes that define triangles and tetrahedrons.
+ Only works for domains that define triangles and tetrahedrons.
"""
[docs] def inside(self, point, on_boundary):
"""
diff --git a/docs/build/html/_modules/spatialpy/core/initialcondition.html b/docs/build/html/_modules/spatialpy/core/initialcondition.html
index 13d3e41e..9dc0c791 100644
--- a/docs/build/html/_modules/spatialpy/core/initialcondition.html
+++ b/docs/build/html/_modules/spatialpy/core/initialcondition.html
@@ -116,11 +116,14 @@ Source code for spatialpy.core.initialcondition
<
"""
Class used to defined initial conditions in SpatialPy.
SubClasses must implement the 'apply(model)' method, which
- direction modifies the model.u0[species,voxel] matrix.
+ direction modifies the model.u0[species, voxel] matrix.
"""
[docs] def apply(self, model):
"""
Set the initial condition of the species to the count.
+
+ :param model: Model contianing the target species.
+ :type model: spatialpy.core.model.Model
"""
raise InitialConditionError("spatialpy.InitialCondition subclasses must implement apply()")
@@ -129,7 +132,7 @@ Source code for spatialpy.core.initialcondition
<
Class used to defined the place initial condition in SpatialPy.
:param species: The species to set the initial condition.
- :type species: spayialpy.species.Species
+ :type species: spatialpy.core.species.Species
:param count: The initial condition for the target species.
:type count: int
@@ -151,7 +154,7 @@ Source code for spatialpy.core.initialcondition
<
Set the initial condition of the species to the count at the location.
:param model: Model contianing the target species.
- :type model: spatialpy.model.Model
+ :type model: spatialpy.core.model.Model
"""
spec_name = self.species.name
spec_ndx = None
@@ -167,7 +170,7 @@ Source code for spatialpy.core.initialcondition
<
Class used to defined the uniform initial condition in SpatialPy.
:param species: The species to set the initial condition.
- :type species: spayialpy.species.Species
+ :type species: spatialpy.core.species.Species
:param count: The initial condition for the target species.
:type count: int
@@ -194,7 +197,7 @@ Source code for spatialpy.core.initialcondition
<
Set 'count' of 'species' in over the list of types (all types if None).
:param model: Model contianing the target species.
- :type model: spatialpy.model.Model
+ :type model: spatialpy.core.model.Model
"""
spec_name = self.species.name
spec_ndx = None
@@ -219,7 +222,7 @@ Source code for spatialpy.core.initialcondition
<
Class used to defined the scatter initial condition in SpatialPy.
:param species: The species to set the initial condition.
- :type species: spayialpy.species.Species
+ :type species: spatialpy.core.species.Species
:param count: The initial condition for the target species.
:type count: int
@@ -246,7 +249,7 @@ Source code for spatialpy.core.initialcondition
<
Scatter 'count' of 'species' randomly over the list of types (all types if None).
:param model: Model contianing the target species.
- :type model: spatialpy.model.Model
+ :type model: spatialpy.core.model.Model
"""
spec_name = self.species.name
spec_ndx = None
diff --git a/docs/build/html/_modules/spatialpy/core/model.html b/docs/build/html/_modules/spatialpy/core/model.html
index 5f5db543..6e155948 100644
--- a/docs/build/html/_modules/spatialpy/core/model.html
+++ b/docs/build/html/_modules/spatialpy/core/model.html
@@ -125,8 +125,8 @@ Source code for spatialpy.core.model
"""
SpatialPy model to StochSS converter
- :param spatailpy_model: SpatialPy model to be converted to StochSS
- :type spatialpy_model: spatialpy.Model
+ :param spatialpy_model: SpatialPy model to be converted to StochSS
+ :type spatialpy_model: spatialpy.core.model.Model
:param filename: Path to the exported stochss model
:type filename: str
@@ -422,12 +422,12 @@ Source code for spatialpy.core.model
Adds a species, or list of species to the model. Will return the added object upon success.
:param obj: The species or list of species to be added to the model object.
- :type obj: spatialpy.Model.Species | list(spatialpy.Model.Species
+ :type obj: spatialpy.core.species.Species | list(spatialpy.core.species.Species
:returns: Species object which was added to the model.
- :rtype: spatialpy.Species | list(spatialpy.Species)
+ :rtype: spatialpy.core.species.Species | list(spatialpy.core.species.Species)
- :raises ModelError: If obj is not a spatialpy.Species
+ :raises ModelError: If obj is not a spatialpy.core.species.Species
"""
from spatialpy.core.species import Species # pylint: disable=import-outside-toplevel
if isinstance(obj, list):
@@ -452,7 +452,7 @@ Source code for spatialpy.core.model
Remove a Species from model.listOfSpecies.
:param obj: Species object to be removed
- :type obj: spatialpy.Model.Species
+ :type obj: spatialpy.core.species.Species
"""
self.listOfSpecies.pop(obj) # raises key error if param is missing
@@ -482,7 +482,7 @@ Source code for spatialpy.core.model
:type sname: str
:returns: The Species objected represented by given 'sname'
- :rtype: spatialpy.Model.Species
+ :rtype: spatialpy.core.species.Species
:raises ModelError: if the model does not contain the requested species
"""
@@ -510,12 +510,12 @@ Source code for spatialpy.core.model
Parameter object or a list of Parameter objects.
:param params: Parameter object or list of Parameters to be added.
- :type params: spatialpy.Model.Parameter | list(spatialpy.Model.Parameter)
+ :type params: spatialpy.core.parameter.Parameter | list(spatialpy.core.parameter.Parameter)
:returns: Parameter object which has been added to the model.
- :rtype: spatialpy.Parameter | list(spatialpy.Parameter)
+ :rtype: spatialpy.core.parameter.Parameter | list(spatialpy.core.parameter.Parameter)
- :raises ModelError: if obj is not a spatialpy.Parameter
+ :raises ModelError: if obj is not a spatialpy.core.parameter.Parameter
"""
from spatialpy.core.parameter import Parameter # pylint: disable=import-outside-toplevel
if isinstance(params,list):
@@ -542,7 +542,7 @@ Source code for spatialpy.core.model
Remove a Parameter from model.listOfParameters.
:param obj: Parameter object to be removed
- :type obj: spatialpy.Model.Parameter
+ :type obj: spatialpy.core.parameter.Parameter
"""
self.listOfParameters.pop(obj)
@@ -559,11 +559,11 @@ Source code for spatialpy.core.model
"""
Return the Parameter object from model associated with 'pname'
- :param pname: Name of parameter to be removed
- :type pname: spatialpy.Model.Parameter
+ :param pname: Name of parameter to be returned
+ :type pname: str
:returns: The Parameter object represented in the model by 'pname'
- :rtype: Spatialpy.Model.Parameter
+ :rtype: Spatialpy.core.parameter.Parameter
:raises ModelError: No parameter named {pname}
"""
@@ -592,12 +592,12 @@ Source code for spatialpy.core.model
or a dict with name, instance pairs.
:param reacs: Reaction or list of Reactions to be added.
- :type reacs: spatialpy.Model.Reaction | list(spatialpy.Model.Reaction)
+ :type reacs: spatialpy.core.reaction.Reaction | list(spatialpy.core.reaction.Reaction)
:returns: The Reaction object(s) added to the model
- :rtype: spatialpy.Model.Reaction
+ :rtype: spatialpy.core.reaction.Reaction | list(spatialpy.core.reaction.Reaction)
- :raises ModelError: Invalid input/reaction to add_reaction()
+ :raises ModelError: if obj is not a spatialpy.core.reaction.Reaction
"""
from spatialpy.core.reaction import Reaction # pylint: disable=import-outside-toplevel
if isinstance(reacs, list):
@@ -622,7 +622,7 @@ Source code for spatialpy.core.model
Remove reaction from model.listOfReactions
:param obj: Reaction to be removed.
- :type obj: spatialpy.Model.Reaction
+ :type obj: spatialpy.core.reaction.Reaction
"""
self.listOfReactions.pop(obj)
@@ -648,11 +648,11 @@ Source code for spatialpy.core.model
"""
Retrieve a reaction object from the model by name
- :param rname: name of Reaction to retrieve
+ :param rname: name of the reaction to be returned
:type rname: str
:returns: The Reaction Object in the model represented by 'rname'
- :rtype: spatialpy.Model.Reaction
+ :rtype: spatialpy.core.reaction.Reaction
:raises ModelError: Could not find reaction
"""
@@ -689,7 +689,7 @@ Source code for spatialpy.core.model
:type profile: bool
:returns: A SpatialPy Result object containing simulation data.
- :rtype: spatialpy.Result.Result
+ :rtype: spatialpy.core.result.Result
"""
from spatialpy.solvers.solver import Solver # pylint: disable=import-outside-toplevel
@@ -701,7 +701,7 @@ Source code for spatialpy.core.model
[docs] def set_timesteps(self, output_interval, num_steps, timestep_size=None):
- """"
+ """
Set the simlation time span parameters.
:param output_interval: size of each output timestep in seconds
@@ -761,7 +761,7 @@ Source code for spatialpy.core.model
Add a spatial domain to the model
:param domain: The Domain object to be added to the model
- :type domain: spatialpy.Domain.Domain
+ :type domain: spatialpy.core.domain.Domain
:raises ModelError: Invalid Domain object
"""
@@ -774,15 +774,15 @@ Source code for spatialpy.core.model
[docs] def add_data_function(self, data_function):
"""
Add a scalar spatial function to the simulation. This is useful if you have a
- spatially varying in put to your model. Argument is a instances of subclass of the
- spatialpy.DataFunction class. It must implement a function 'map(x)' which takes a
- the spatial positon 'x' as an array, and it returns a float value.
+ spatially varying input to your model. Argument is a instances of subclass of the
+ spatialpy.DataFunction class. It must implement a function 'map(point)' which takes a
+ the spatial positon 'point' as an array, and it returns a float value.
:param data_function: Data function to be added.
:type data_function: spatialpy.DataFunction
:returns: DataFunction object(s) added tothe model.
- :rtype: spatialpy.DataFunction | list(spatialpy.DataFunction)
+ :rtype: spatialpy.core.datafunction.DataFunction | list(spatialpy.core.datafunction.DataFunction)
:raises ModelError: Invalid DataFunction
"""
@@ -804,16 +804,16 @@ Source code for spatialpy.core.model
Add an initial condition object to the initialization of the model.
:param init_cond: Initial condition to be added
- :type init_cond: spatialpy.InitialCondition.InitialCondition
+ :type init_cond: spatialpy.core.initialcondition.InitialCondition
"""
self.listOfInitialConditions.append(init_cond)
[docs] def add_boundary_condition(self, bound_cond):
"""
- Add an BoundaryCondition object to the model.
+ Add an boundary condition object to the model.
:param bound_cond: Boundary condition to be added
- :type bound_cond: spatialpy.BoundaryCondition
+ :type bound_cond: spatialpy.core.boundarycondition.BoundaryCondition
"""
bound_cond.model = self
self.listOfBoundaryConditions.append(bound_cond)
diff --git a/docs/build/html/_modules/spatialpy/core/reaction.html b/docs/build/html/_modules/spatialpy/core/reaction.html
index 3525a238..3c4d5a34 100644
--- a/docs/build/html/_modules/spatialpy/core/reaction.html
+++ b/docs/build/html/_modules/spatialpy/core/reaction.html
@@ -135,7 +135,7 @@ Source code for spatialpy.core.reaction
:type propensity_function: str
:param rate: if mass action, rate is a reference to a parameter instance.
- :type rate: spatialpy.model.Parameter
+ :type rate: spatialpy.core.parameter.Parameter
:param annotation: Description of the reaction (meta)
:type annotation: str
@@ -270,8 +270,8 @@ Source code for spatialpy.core.reaction
"""
Add a product to this reaction
- :param S: Species object to be produced by the reaction
- :type S: spatialpy.Model.Species
+ :param species: Species object to be produced by the reaction
+ :type species: spatialpy.core.species.Species
:param stoichiometry: Stoichiometry of this product.
:type stoichiometry: int
@@ -288,7 +288,7 @@ Source code for spatialpy.core.reaction
Add a reactant to this reaction
:param species: reactant Species object
- :type species: spatialpy.Model.Species
+ :type species: spatialpy.core.species.Species
:param stoichiometry: Stoichiometry of this participant reactant
:type stoichiometry: int
@@ -316,7 +316,7 @@ Source code for spatialpy.core.reaction
Deferred object initialization, called by model.add_reaction().
:param model: Target SpatialPy Model for annotation.
- :type model: spatialpy.Model
+ :type model: spatialpy.core.model.Model
"""
self.ode_propensity_function = self.propensity_function
diff --git a/docs/build/html/_modules/spatialpy/core/result.html b/docs/build/html/_modules/spatialpy/core/result.html
index 4256e5b5..aa473c0b 100644
--- a/docs/build/html/_modules/spatialpy/core/result.html
+++ b/docs/build/html/_modules/spatialpy/core/result.html
@@ -405,25 +405,25 @@ Source code for spatialpy.core.result
one or all timepoints. Returns a numpy array containing the species population/concentration values.
:param species: A species in string or dictionary form to retreive information about
- :type species: str | dict
+ :type species: str | spatialpy.core.species.Species
:param timepoints: A time point where the information should be retreived from.
If 'timepoints' is None (default), a matrix of dimension:
(number of timepoints) x (number of voxels) is returned.
If an integer value is given, that value is used to index into the timespan, and that time point is returned
- as a 1D array with size (number of voxel).
- :type timepoints: int (default None)
+ as a 1D array with size (number of voxel). Defaults to None
+ :type timepoints: int
:param concentration: Whether or not the species is a concentration (True) or population (False)
If concentration is False (default), the integer, raw, trajectory data is returned.
- If set to True, the concentration (=copy_number/volume) is returned.
- :type concentration: bool (default False)
+ If set to True, the concentration (=copy_number/volume) is returned. Defaults to False
+ :type concentration: bool
- :param deterministic: Whether or not the species is deterministic (True) or stochastic (False)
- :type deterministic: bool (default False)
+ :param deterministic: Whether or not the species is deterministic (True) or stochastic (False). Defaults to False
+ :type deterministic: bool
- :param debug: Whether or not debug information should be printed
- :type debug: bool (default False)
+ :param debug: Whether or not debug information should be printed. Defaults to False
+ :type debug: bool
:returns: A numpy array containing population/concentration values for target species across specified
timepoints. Defaults to all timepoints.
@@ -433,7 +433,7 @@ Source code for spatialpy.core.result
"""
num_voxel = self.model.domain.get_num_voxels()
- if isinstance(species,str):
+ if isinstance(species, str):
spec_name = species
else:
spec_name = species.name
@@ -497,11 +497,13 @@ Source code for spatialpy.core.result
:param deterministic: Whether or not to plot the data as deterministic
:type deterministic: bool
- :param width: Width in pixels of output plot box
- :type width: int (default 500)
+ :param width: Width in pixels of output plot box or for matplotlib inches of output plot box. \
+ Defaults to 500 (Plotly) or 6.4 (MatPlotLib)
+ :type width: int
- :param height: Height in pixels of output plot box
- :type height: int (default 500)
+ :param height: Height in pixels of output plot box or for matplotlib inches of output plot box. \
+ Defaults to 500 (Plotly) or 4.8 (MatPlotLib)
+ :type height: int
:param colormap: colormap to use. Plotly specification, valid values: "Plotly3","Jet","Blues","YlOrRd",
"PuRd","BuGn","YlOrBr","PuBuGn","BuPu","YlGnBu", "PuBu","GnBu","YlGn","Greens","Reds",
@@ -543,7 +545,7 @@ Source code for spatialpy.core.result
:returns: A dictionary containing data for a plotly figure of species output trajectory
:rtype: dict
- :raises ResultsError: unable to plot species for given time
+ :raises ResultError: unable to plot species for given time
"""
time_index_list = self.get_timespan()
@@ -671,7 +673,14 @@ Source code for spatialpy.core.result
given, that value is used to index into the timespan, and that time point is returned \
as a 1D array with size (number of voxel).
- :param property_name: A string describing the property to be returned.
+ :param property_name: A string describing the property to be returned. Can be one of: {
+ 'v' : velocity,
+ 'rho': density,
+ 'mass': mass,
+ 'id': type_id,
+ 'type': type as str,
+ 'bvf_phi': boundary volume fraction,
+ 'nu': viscosity}
:type property_name: str
:param timepoints: timespan index to be returned. Default is None
@@ -680,7 +689,7 @@ Source code for spatialpy.core.result
:returns: a numpy array of target property values across timepoints, defaults to all timepoints.
:rtype: numpy.ndarray
- :raises ResultsError: Could not get data for given timepoints.
+ :raises ResultError: Could not get data for given timepoints.
"""
l_time = len(self.get_timespan()) - 1
@@ -732,11 +741,13 @@ Source code for spatialpy.core.result
:param p_ndx: The property index of the results to be plotted
:type p_ndx: int
- :param width: Width in pixels of output plot box or for matplotlib inches of output plot box
- :type width: int (default 500)
+ :param width: Width in pixels of output plot box or for matplotlib inches of output plot box. \
+ Defaults to 500 (Plotly) or 6.4 (MatPlotLib)
+ :type width: int
- :param height: Height in pixels of output plot box or for matplotlib inches of output plot box
- :type height: int (default 500)
+ :param height: Height in pixels of output plot box or for matplotlib inches of output plot box. \
+ Defaults to 500 (Plotly) or 4.8 (MatPlotLib)
+ :type height: int
:param colormap: colormap to use. Plotly specification, valid values: "Plotly3","Jet","Blues","YlOrRd",
"PuRd","BuGn","YlOrBr","PuBuGn","BuPu","YlGnBu", "PuBu","GnBu","YlGn","Greens","Reds",
@@ -928,9 +939,9 @@ Source code for spatialpy.core.result
The columns of modelname_mesh.csv are: 'Voxel ID', 'X', 'Y', 'Z', 'Type', 'Volume', 'Mass', 'Viscosity'
The columns of modelname_species_S.csv: 'Time', 'Voxel 0', Voxel 1', ... 'Voxel N'.
- :type folder_name: str (default current working directory)
- :param folder_name: A path where the vtk files will be written, created if non-existant.
- If no path is provided current working directory is used.
+ :type folder_name: str
+ :param folder_name: A path where the vtk files will be written, created if non-existant. \
+ Defaults current working directory
"""
if not folder_name:
folder_name = os.path.abspath(os.getcwd())
@@ -959,13 +970,13 @@ Source code for spatialpy.core.result
for voxel in range(num_vox):
writer.writerow([voxel] + data[:,voxel].tolist())
-[docs] def export_to_vtk(self, timespan, folder_name=None):
+ def __export_to_vtk(self, timespan, folder_name=None):
"""
Write the trajectory to a collection of vtk files.
The exported data is #molecules/volume, where the volume unit is implicit from the mesh dimension.
Not currently implemented.
"""
- raise ResultError("Not implemented.")
+ raise ResultError("Not implemented.")
diff --git a/docs/build/html/_modules/spatialpy/core/species.html b/docs/build/html/_modules/spatialpy/core/species.html
index 0de7a3d4..8429f830 100644
--- a/docs/build/html/_modules/spatialpy/core/species.html
+++ b/docs/build/html/_modules/spatialpy/core/species.html
@@ -121,7 +121,7 @@ Source code for spatialpy.core.species
:param diffusion_coefficient: Non-constant coefficient of diffusion for Species.
:type diffusion_coefficient: float
- :param restrict_to: Set the diffusion coefficient to zero for 'species' in all types not in 'listOfTypes'.
+ :param restrict_to: Set the diffusion coefficient to zero for 'species' in all types not in 'listOfTypes'. \
This effectively restricts the movement of 'species' to the types specified in 'listOfTypes'.
:type restrict_to: int, str, list of ints or list of strs
"""
@@ -164,7 +164,7 @@ Source code for spatialpy.core.species
:param diffusion_coefficient: Non-constant coefficient of diffusion for Species.
:type diffusion_coefficient: float
- :raises SpeciesError: If diffusion_coefficient is negative.
+ :raises SpeciesError: If diffusion_coefficient is negative or not a valid type.
"""
if not (isinstance(diffusion_coefficient, (Parameter, float, int)) or \
type(diffusion_coefficient).__name__ == 'Parameter'):
diff --git a/docs/build/html/_modules/spatialpy/solvers/solver.html b/docs/build/html/_modules/spatialpy/solvers/solver.html
index c4967386..5c84fcbc 100644
--- a/docs/build/html/_modules/spatialpy/solvers/solver.html
+++ b/docs/build/html/_modules/spatialpy/solvers/solver.html
@@ -142,7 +142,7 @@ Source code for spatialpy.solvers.solver
SpatialPy solver object.
:param model: Target model of solver simulation.
- :type model: spatialpy.Model.Model
+ :type model: spatialpy.core.model.Model
:param debug_level: Target level of debugging.
:type debug_level: int
diff --git a/docs/build/html/_modules/spatialpy/stochss/stochss_export.html b/docs/build/html/_modules/spatialpy/stochss/stochss_export.html
index bb8ca688..cead8e00 100644
--- a/docs/build/html/_modules/spatialpy/stochss/stochss_export.html
+++ b/docs/build/html/_modules/spatialpy/stochss/stochss_export.html
@@ -293,13 +293,17 @@ Source code for spatialpy.stochss.stochss_export
"""
SpatialPy model to StochSS converter
- Args:
- spatialpy_model : spatialpy.Model
- SpatialPy model to be converted to StochSS
- filename : str
- Path to the exported stochss model
- return_stochss_model : bool
- Whether or not to return the model
+ :param model: SpatialPy model to be converted to StochSS.
+ :type model: spatialpy.core.model.Model
+
+ :param filename: Path to the exported stochss model.
+ :type filename: str
+
+ :param return_stochss_model: Whether or not to return the model.
+ :type return_stochss_model: bool
+
+ :returns: StochSS model dict if return_stochss_model is True else path to StochSS model file.
+ :rtype: dict | str
"""
_ = model.compile_prep()
if path is None:
diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
index ef9b1b78..33060207 100644
--- a/docs/build/html/_sources/index.rst.txt
+++ b/docs/build/html/_sources/index.rst.txt
@@ -20,7 +20,7 @@ The latest version of SpatialPy can be found on `PyPI `_ for more information on how to build and simulate your models with SpatialPy. For an example of how to use SpatialPy to simulate a spatial stochastic reaction-diffusion system, see the `3D Cylinder Demo `_. We also provide examples of how to use SpatialPy to simulate physics (`Gravity Demo `_) and fluid flow (`Weir Model `_).
+See our `Example Notebook - Start Here `_ for more information on how to build and simulate your models with SpatialPy. For an example of how to use SpatialPy to simulate a spatial stochastic reaction-diffusion system, see the `3D Cylinder Demo `_. We also provide examples of how to use SpatialPy to simulate physics (`Gravity Demo `_) and fluid flow (`Weir Model `_).
Reporting Issues
diff --git a/docs/build/html/classes/spatialpy.core.html b/docs/build/html/classes/spatialpy.core.html
index a5249b96..0b5b39b2 100644
--- a/docs/build/html/classes/spatialpy.core.html
+++ b/docs/build/html/classes/spatialpy.core.html
@@ -128,7 +128,7 @@ Submodulesobject
Set spatial regions of the domain where a property of
particles are held constant (updated each simulation step)
-
+
- Conditions (one or more of the following must be set):
xmin, xmax: (float) min or max value in the x dimension
ymin, ymax: (float) min or max value in the y dimension
Submodules
@@ -154,17 +151,9 @@ Submodules
-- Parameters
-
+target (str) – Set target to properties, can be ‘nu’ ‘rho’ or ‘v’ or species name If species name, determinstic must also be set to True/False.
value (float or float[3]) – Value property will take in region defined by the conditions
model (spatialpy.Model.Model) – Target model of boundary condition
model (spatialpy.core.model.Model) – Target model of boundary condition
@@ -257,18 +246,18 @@ SubmodulesParameters
name (str) – Name of the Data Function.
- Raises
+DataFunctionError – If a name is not provided.
+
-
map(point)[source]¶
This method must be overridden by the DataFunction subclass.
-
-- NOTE: The spatial location is evaulated at t=0 and is not
reevaluated as the fluid domain moves over time.
-
+NOTE: The spatial location is evaulated at t=0 and is not re-evaluated as the fluid domain moves over time.
- Parameters
-point (vector of 3 doubles) – The x,y,z position
+point (float[3]) – The x, y, z position.
- Returns
Value of function at this spatial location.
@@ -305,13 +294,13 @@ SubmodulesParameters
numpoints (int) – Total number of spatial domain points
xlim (tuple(float)) – Range of domain along x-axis
ylim (tuple(float)) – Range of domain along y-axis
zlim (tuple(float)) – Range of domain along z-axis
xlim (float(2)) – Range of domain along x-axis
ylim (float(2)) – Range of domain along y-axis
zlim (float(2)) – Range of domain along z-axis
rho (float) – Background density for the system
c0 (float) – Speed of sound for the system
P0 (float) – Background pressure for the system
gravity – Acceleration of gravity for the system.
gravity (float[3]) – Acceleration of gravity for the system.
@@ -322,14 +311,14 @@ Submodules
- Parameters
-point (tuple(float, float, float) or tuple(float, float)) – Spatial coordinate vertices of point to be added
point (float(3)) – Spatial coordinate vertices of point to be added
vol (float) – Default volume of particle to be added
mass (float) – Default mass of particle to be added
type_id (str | int) – Particle type ID of particle to be created
nu (float) – Default viscosity of particle to be created
type_id (str | int) – Particle type ID of particle to be craddedeated
nu (float) – Default viscosity of particle to be added
fixed (bool) – True if particle is spatially fixed, else False
c (float) – Default artificial speed of sound of particle to be created
rho (float) – Default density of particle to be created
c (float) – Default artificial speed of sound of particle to be added
rho (float) – Default density of particle to be added
- Raises
@@ -350,13 +339,13 @@ Submodules
- Parameters
-point (tuple(float, float, float) or tuple(float, float)) – Target source point
+point (float(3)) – Target source point
- Returns
The coordinates of the nearest vertex to the source point.
- Return type
-tuple(float, float, float) or tuple(float, float)
+float(3)
@@ -364,11 +353,11 @@ Submodules
compile_prep()[source]¶
-Generate the domain list of type ids and check for invalid type_ids and rho values
+
Generate the domains list of type ids and check for invalid type_ids and rho values
in preperation of compiling the simulation files.
- Raises
-DomainError – If a type_id is not set or rh for a particle is 0.
+DomainError – If a type_id is not set or rho=0 for a particle.
Submodules
Parameters
-xlim (tuple(float, float)) – highest and lowest coordinate in the x dimension
ylim (tuple(float, float)) – highest and lowest coordinate in the y dimension
xlim (float(2)) – highest and lowest coordinate in the x dimension
ylim (float(2)) – highest and lowest coordinate in the y dimension
nx (int) – number of particle spacing in the x dimension
ny (int) – number of particle spacing in the y dimension
type_id (int) – default type ID of particles to be created. Defaults to 1
mass (float) – default mass of particles to be created. Defaults to 1.0
nu (float) – default viscosity of particles to be created. Defaults to 1.0
c (float) – default artificial speed of sound of particles to be created. Defaults to 0.0.
rho – default density of particles to be created.
rho (float) – default density of particles to be created.
fixed (bool) – spatially fixed flag of particles to be created. Defaults to false.
rho0 (float) – background density for the system. Defaults to 1.0
c0 (float) – speed of sound for the system. Defaults to 10
P0 (float) – background pressure for the system. Defaults to 10
**kwargs – Additional keyword arguments passed to Domain.
Returns
Uniform 2D SpatialPy Domain object.
Return type
-spatialpy.Domain.Domain
+
Submodules
Parameters
-xlim (tuple(float, float)) – highest and lowest coordinate in the x dimension
ylim (tuple(float, float)) – highest and lowest coordinate in the y dimension
zlim (tuple(float, float)) – highest and lowest coordinate in the z dimension
xlim (float(2)) – highest and lowest coordinate in the x dimension
ylim (float(2)) – highest and lowest coordinate in the y dimension
zlim (float(2)) – highest and lowest coordinate in the z dimension
nx (int) – number of particle spacing in the x dimension
ny (int) – number of particle spacing in the y dimension
nz (int) – number of particle spacing in the z dimension
SubmodulesDomain.
Returns
Uniform 3D SpatialPy Domain object.
Return type
-spatialpy.Domain.Domain
+
Submodules
Parameters
-start (tuple(float, float, float) or tuple(float, float)) – Starting point
end (tuple(float, float, float) or tuple(float, float)) – Ending point
start (float(3)) – Starting point
end (float(2)) – Ending point
Returns
@@ -478,7 +463,7 @@ Submodules
Parameters
-geometry_ivar (spatialpy.geometry.Geometry) – an instance of a ‘spatialpy.Geometry’ subclass. The ‘inside()’ method
+
geometry_ivar (spatialpy.core.geometry.Geometry) – an instance of a spatialpy.core.geometry.Geometry subclass. The ‘inside()’ method
of this object will be used to create add the particles.
deltax (float) – Distance between particles on the x-axis.
deltay (float) – Distance between particles on the y-axis (defaults to deltax).
SubmodulesDomain.add_point().
Returns
@@ -619,7 +604,7 @@ SubmodulesSpatialPy Domain object created from the meshio object
Return type
-spatialpy.Domain.Domain
+
SubmodulesSpatialPy Domain object created from the mesh file.
Return type
-spatialpy.Domain.Domain
+
SubmodulesSpatialPy Domain object created from StochSS domain.
Return type
-spatialpy.Domain.Domain
+
SubmodulesSpatialPy Domain object created from xml mesh.
Return type
-spatialpy.Domain.Domain
+
Submodules
Parameters
-geometry_ivar (spatialpy.Geometry.Geometry) – an instance of a ‘spatialpy.Geometry’ subclass. The ‘inside()’ method
+
geometry_ivar (spatialpy.core.geometry.Geometry) – an instance of a spatialpy.core.geometry.Geometry subclass. The ‘inside()’ method
of this object will be used to assign properties to points.
type_id (str | int) – The identifier for this type.
vol (float) – The volume of each particle in the type.
Submodulesclass spatialpy.core.geometry.GeometryExterior[source]¶
Bases: spatialpy.core.geometry.Geometry
Mark particles that are on the edge of the domain.
-only works for meshes that define triangles and tetrahedrons.
+only works for domains that define triangles and tetrahedrons.
-
inside(point, on_boundary)[source]¶
@@ -849,7 +834,7 @@ Submodulesclass spatialpy.core.geometry.GeometryInterior[source]¶
Bases: spatialpy.core.geometry.Geometry
Mark particles that are not on the edge of the domain.
-Only works for meshes that define triangles and tetrahedrons.
+Only works for domains that define triangles and tetrahedrons.
-
inside(point, on_boundary)[source]¶
@@ -892,11 +877,16 @@ Submodulesobject
Class used to defined initial conditions in SpatialPy.
SubClasses must implement the ‘apply(model)’ method, which
-direction modifies the model.u0[species,voxel] matrix.
+direction modifies the model.u0[species, voxel] matrix.
-
apply(model)[source]¶
Set the initial condition of the species to the count.
+
+- Parameters
+model (spatialpy.core.model.Model) – Model contianing the target species.
+
@@ -909,7 +899,7 @@ Submodules
- Parameters
-species (spayialpy.species.Species) – The species to set the initial condition.
species (spatialpy.core.species.Species) – The species to set the initial condition.
count (int) – The initial condition for the target species.
location (float[3]) – X, Y, Z coordinates to place the initial condition.
@@ -921,7 +911,7 @@ Submodules
- Parameters
-model (spatialpy.model.Model) – Model contianing the target species.
+model (spatialpy.core.model.Model) – Model contianing the target species.
Submodules
- Parameters
-species (spayialpy.species.Species) – The species to set the initial condition.
species (spatialpy.core.species.Species) – The species to set the initial condition.
count (int) – The initial condition for the target species.
types (list) – Types of the particles to place the initial condition.
@@ -948,7 +938,7 @@ Submodules
- Parameters
-model (spatialpy.model.Model) – Model contianing the target species.
+model (spatialpy.core.model.Model) – Model contianing the target species.
Submodules
- Parameters
-species (spayialpy.species.Species) – The species to set the initial condition.
species (spatialpy.core.species.Species) – The species to set the initial condition.
count (int) – The initial condition for the target species.
types (list) – Types of the particles to place the initial condition.
@@ -975,7 +965,7 @@ Submodules
- Parameters
-model (spatialpy.model.Model) – Model contianing the target species.
+model (spatialpy.core.model.Model) – Model contianing the target species.
Submodules
-
add_boundary_condition(bound_cond)[source]¶
-Add an BoundaryCondition object to the model.
+Add an boundary condition object to the model.
- Parameters
-bound_cond (spatialpy.BoundaryCondition) – Boundary condition to be added
+bound_cond (spatialpy.core.boundarycondition.BoundaryCondition) – Boundary condition to be added
Submodules
add_data_function(data_function)[source]¶
Add a scalar spatial function to the simulation. This is useful if you have a
-spatially varying in put to your model. Argument is a instances of subclass of the
-spatialpy.DataFunction class. It must implement a function ‘map(x)’ which takes a
-the spatial positon ‘x’ as an array, and it returns a float value.
+spatially varying input to your model. Argument is a instances of subclass of the
+spatialpy.DataFunction class. It must implement a function ‘map(point)’ which takes a
+the spatial positon ‘point’ as an array, and it returns a float value.
- Parameters
data_function (spatialpy.DataFunction) – Data function to be added.
@@ -1033,7 +1023,7 @@ SubmodulesDataFunction object(s) added tothe model.
- Return type
-spatialpy.DataFunction | list(spatialpy.DataFunction)
+spatialpy.core.datafunction.DataFunction | list(spatialpy.core.datafunction.DataFunction)
- Raises
ModelError – Invalid DataFunction
@@ -1047,7 +1037,7 @@ Submodules
- Parameters
-domain (spatialpy.Domain.Domain) – The Domain object to be added to the model
+domain (spatialpy.core.domain.Domain) – The Domain object to be added to the model
- Raises
ModelError – Invalid Domain object
@@ -1061,7 +1051,7 @@ Submodules
- Parameters
-init_cond (spatialpy.InitialCondition.InitialCondition) – Initial condition to be added
+init_cond (spatialpy.core.initialcondition.InitialCondition) – Initial condition to be added
Submodules
- Parameters
-params (spatialpy.Model.Parameter | list(spatialpy.Model.Parameter)) – Parameter object or list of Parameters to be added.
+params (spatialpy.core.parameter.Parameter | list(spatialpy.core.parameter.Parameter)) – Parameter object or list of Parameters to be added.
- Returns
Parameter object which has been added to the model.
- Return type
-spatialpy.Parameter | list(spatialpy.Parameter)
+spatialpy.core.parameter.Parameter | list(spatialpy.core.parameter.Parameter)
- Raises
-ModelError – if obj is not a spatialpy.Parameter
+ModelError – if obj is not a spatialpy.core.parameter.Parameter
Submodules
- Parameters
-reacs (spatialpy.Model.Reaction | list(spatialpy.Model.Reaction)) – Reaction or list of Reactions to be added.
+reacs (spatialpy.core.reaction.Reaction | list(spatialpy.core.reaction.Reaction)) – Reaction or list of Reactions to be added.
- Returns
The Reaction object(s) added to the model
- Return type
-spatialpy.Model.Reaction
+spatialpy.core.reaction.Reaction | list(spatialpy.core.reaction.Reaction)
- Raises
-ModelError – Invalid input/reaction to add_reaction()
+ModelError – if obj is not a spatialpy.core.reaction.Reaction
Submodules
- Parameters
-obj (spatialpy.Model.Species | list(spatialpy.Model.Species) – The species or list of species to be added to the model object.
+obj (spatialpy.core.species.Species | list(spatialpy.core.species.Species) – The species or list of species to be added to the model object.
- Returns
Species object which was added to the model.
- Return type
-spatialpy.Species | list(spatialpy.Species)
+spatialpy.core.species.Species | list(spatialpy.core.species.Species)
- Raises
-ModelError – If obj is not a spatialpy.Species
+ModelError – If obj is not a spatialpy.core.species.Species
Submodules
- Parameters
-obj (spatialpy.Model.Parameter) – Parameter object to be removed
+obj (spatialpy.core.parameter.Parameter) – Parameter object to be removed
Submodules
- Parameters
-obj (spatialpy.Model.Reaction) – Reaction to be removed.
+obj (spatialpy.core.reaction.Reaction) – Reaction to be removed.
Submodules
- Parameters
-obj (spatialpy.Model.Species) – Species object to be removed
+obj (spatialpy.core.species.Species) – Species object to be removed
Submodules
- Parameters
-pname (spatialpy.Model.Parameter) – Name of parameter to be removed
+pname (str) – Name of parameter to be returned
- Returns
The Parameter object represented in the model by ‘pname’
- Return type
-Spatialpy.Model.Parameter
+Spatialpy.core.parameter.Parameter
- Raises
ModelError – No parameter named {pname}
@@ -1294,13 +1284,13 @@ Submodules
- Parameters
-rname (str) – name of Reaction to retrieve
+rname (str) – name of the reaction to be returned
- Returns
The Reaction Object in the model represented by ‘rname’
- Return type
-spatialpy.Model.Reaction
+-
- Raises
ModelError – Could not find reaction
@@ -1320,7 +1310,7 @@ SubmodulesThe Species objected represented by given ‘sname’
- Return type
-spatialpy.Model.Species
+-
- Raises
ModelError – if the model does not contain the requested species
@@ -1354,7 +1344,7 @@ SubmodulesA SpatialPy Result object containing simulation data.
- Return type
-spatialpy.Result.Result
+-
Submodules
-
set_timesteps(output_interval, num_steps, timestep_size=None)[source]¶
-”
-Set the simlation time span parameters.
+Set the simlation time span parameters.
- Parameters
@@ -1461,7 +1450,7 @@ Submodules
- Parameters
-spatailpy_model – SpatialPy model to be converted to StochSS
spatialpy_model (spatialpy.core.model.Model) – SpatialPy model to be converted to StochSS
filename (str) – Path to the exported stochss model
return_stochss_model (bool) – Whether or not to return the model
@@ -1535,7 +1524,7 @@ Submodulesspatialpy.core.parameter.Parameter) – if mass action, rate is a reference to a parameter instance.
annotation (str) – Description of the reaction (meta)
restrict_to (int, str, list of ints or list of strs) – Restrict reaction execution to a type or list of types within the domain.
@@ -1548,7 +1537,7 @@ Submodules
- Parameters
-S (spatialpy.Model.Species) – Species object to be produced by the reaction
species (spatialpy.core.species.Species) – Species object to be produced by the reaction
stoichiometry (int) – Stoichiometry of this product.
Submodules
- Parameters
-species (spatialpy.Model.Species) – reactant Species object
species (spatialpy.core.species.Species) – reactant Species object
stoichiometry (int) – Stoichiometry of this participant reactant
Submodules
- Parameters
-model (spatialpy.Model) – Target SpatialPy Model for annotation.
+model (spatialpy.core.model.Model) – Target SpatialPy Model for annotation.
Submodules
- Parameters
-folder_name (str (default current working directory)) – A path where the vtk files will be written, created if non-existant.
+folder_name (str) – A path where the vtk files will be written, created if non-existant. Defaults current working directory
If no path is provided current working directory is used.
-
--
-export_to_vtk(timespan, folder_name=None)[source]¶
-Write the trajectory to a collection of vtk files.
-The exported data is #molecules/volume, where the volume unit is implicit from the mesh dimension.
-Not currently implemented.
@@ -1643,7 +1623,14 @@ Submodules
- Parameters
-property_name (str) – A string describing the property to be returned.
property_name (str) – A string describing the property to be returned. Can be one of: {
+‘v’ : velocity,
+‘rho’: density,
+‘mass’: mass,
+‘id’: type_id,
+‘type’: type as str,
+‘bvf_phi’: boundary volume fraction,
+‘nu’: viscosity}
timepoints (int) – timespan index to be returned. Default is None
Submodulesnumpy.ndarray
- Raises
-ResultsError – Could not get data for given timepoints.
+ResultError – Could not get data for given timepoints.
Submodules
- Parameters
-species (str | dict) – A species in string or dictionary form to retreive information about
timepoints (int (default None)) – A time point where the information should be retreived from.
+
species (str | spatialpy.core.species.Species) – A species in string or dictionary form to retreive information about
timepoints (int) – A time point where the information should be retreived from.
If ‘timepoints’ is None (default), a matrix of dimension:
(number of timepoints) x (number of voxels) is returned.
If an integer value is given, that value is used to index into the timespan, and that time point is returned
-as a 1D array with size (number of voxel).
concentration (bool (default False)) – Whether or not the species is a concentration (True) or population (False)
+as a 1D array with size (number of voxel). Defaults to None
concentration (bool) – Whether or not the species is a concentration (True) or population (False)
If concentration is False (default), the integer, raw, trajectory data is returned.
-If set to True, the concentration (=copy_number/volume) is returned.
deterministic (bool (default False)) – Whether or not the species is deterministic (True) or stochastic (False)
debug (bool (default False)) – Whether or not debug information should be printed
deterministic (bool) – Whether or not the species is deterministic (True) or stochastic (False). Defaults to False
debug (bool) – Whether or not debug information should be printed. Defaults to False
- Returns
@@ -1718,8 +1705,8 @@ Submodulesdict
- Raises
-ResultsError – unable to plot species for given time
+ResultError – unable to plot species for given time
Submodules
name (str) – Name of the Species
diffusion_coefficient (float) – Non-constant coefficient of diffusion for Species.
restrict_to – Set the diffusion coefficient to zero for ‘species’ in all types not in ‘listOfTypes’.
restrict_to (int, str, list of ints or list of strs) – Set the diffusion coefficient to zero for ‘species’ in all types not in ‘listOfTypes’. This effectively restricts the movement of ‘species’ to the types specified in ‘listOfTypes’.
This effectively restricts the movement of ‘species’ to the types specified in ‘listOfTypes’.
-:type restrict_to: int, str, list of ints or list of strs
-
set_diffusion_coefficient(diffusion_coefficient)[source]¶
@@ -1974,7 +1959,7 @@ Submodulesdiffusion_coefficient (float) – Non-constant coefficient of diffusion for Species.
- Raises
-SpeciesError – If diffusion_coefficient is negative.
+SpeciesError – If diffusion_coefficient is negative or not a valid type.
Submodulesobject
Set spatial regions of the domain where a property of
particles are held constant (updated each simulation step)
-
+
- Conditions (one or more of the following must be set):
xmin, xmax: (float) min or max value in the x dimension
ymin, ymax: (float) min or max value in the y dimension
Submodules
@@ -2140,17 +2122,9 @@ Submodules
-- Parameters
-
+target (str) – Set target to properties, can be ‘nu’ ‘rho’ or ‘v’ or species name If species name, determinstic must also be set to True/False.
value (float or float[3]) – Value property will take in region defined by the conditions
model (spatialpy.Model.Model) – Target model of boundary condition
model (spatialpy.core.model.Model) – Target model of boundary condition
@@ -2186,18 +2160,18 @@ SubmodulesParameters
name (str) – Name of the Data Function.
- Raises
+DataFunctionError – If a name is not provided.
+
-
map(point)[source]¶
This method must be overridden by the DataFunction subclass.
-
-- NOTE: The spatial location is evaulated at t=0 and is not
reevaluated as the fluid domain moves over time.
-
+NOTE: The spatial location is evaulated at t=0 and is not re-evaluated as the fluid domain moves over time.
- Parameters
-point (vector of 3 doubles) – The x,y,z position
+point (float[3]) – The x, y, z position.
- Returns
Value of function at this spatial location.
@@ -2226,13 +2200,13 @@ SubmodulesParameters
numpoints (int) – Total number of spatial domain points
xlim (tuple(float)) – Range of domain along x-axis
ylim (tuple(float)) – Range of domain along y-axis
zlim (tuple(float)) – Range of domain along z-axis
xlim (float(2)) – Range of domain along x-axis
ylim (float(2)) – Range of domain along y-axis
zlim (float(2)) – Range of domain along z-axis
rho (float) – Background density for the system
c0 (float) – Speed of sound for the system
P0 (float) – Background pressure for the system
gravity – Acceleration of gravity for the system.
gravity (float[3]) – Acceleration of gravity for the system.
@@ -2243,14 +2217,14 @@ Submodules
- Parameters
-point (tuple(float, float, float) or tuple(float, float)) – Spatial coordinate vertices of point to be added
point (float(3)) – Spatial coordinate vertices of point to be added
vol (float) – Default volume of particle to be added
mass (float) – Default mass of particle to be added
type_id (str | int) – Particle type ID of particle to be created
nu (float) – Default viscosity of particle to be created
type_id (str | int) – Particle type ID of particle to be craddedeated
nu (float) – Default viscosity of particle to be added
fixed (bool) – True if particle is spatially fixed, else False
c (float) – Default artificial speed of sound of particle to be created
rho (float) – Default density of particle to be created
c (float) – Default artificial speed of sound of particle to be added
rho (float) – Default density of particle to be added
- Raises
@@ -2271,13 +2245,13 @@ Submodules
- Parameters
-point (tuple(float, float, float) or tuple(float, float)) – Target source point
+point (float(3)) – Target source point
- Returns
The coordinates of the nearest vertex to the source point.
- Return type
-tuple(float, float, float) or tuple(float, float)
+float(3)
Submodules
-
compile_prep()[source]¶
-Generate the domain list of type ids and check for invalid type_ids and rho values
+
Generate the domains list of type ids and check for invalid type_ids and rho values
in preperation of compiling the simulation files.
- Raises
-DomainError – If a type_id is not set or rh for a particle is 0.
+DomainError – If a type_id is not set or rho=0 for a particle.
Submodules
- Parameters
-xlim (tuple(float, float)) – highest and lowest coordinate in the x dimension
ylim (tuple(float, float)) – highest and lowest coordinate in the y dimension
xlim (float(2)) – highest and lowest coordinate in the x dimension
ylim (float(2)) – highest and lowest coordinate in the y dimension
nx (int) – number of particle spacing in the x dimension
ny (int) – number of particle spacing in the y dimension
type_id (int) – default type ID of particles to be created. Defaults to 1
mass (float) – default mass of particles to be created. Defaults to 1.0
nu (float) – default viscosity of particles to be created. Defaults to 1.0
c (float) – default artificial speed of sound of particles to be created. Defaults to 0.0.
rho – default density of particles to be created.
rho (float) – default density of particles to be created.
fixed (bool) – spatially fixed flag of particles to be created. Defaults to false.
rho0 (float) – background density for the system. Defaults to 1.0
c0 (float) – speed of sound for the system. Defaults to 10
P0 (float) – background pressure for the system. Defaults to 10
**kwargs – Additional keyword arguments passed to Domain.
- Returns
Uniform 2D SpatialPy Domain object.
- Return type
-spatialpy.Domain.Domain
+-
Submodules
- Parameters
-xlim (tuple(float, float)) – highest and lowest coordinate in the x dimension
ylim (tuple(float, float)) – highest and lowest coordinate in the y dimension
zlim (tuple(float, float)) – highest and lowest coordinate in the z dimension
xlim (float(2)) – highest and lowest coordinate in the x dimension
ylim (float(2)) – highest and lowest coordinate in the y dimension
zlim (float(2)) – highest and lowest coordinate in the z dimension
nx (int) – number of particle spacing in the x dimension
ny (int) – number of particle spacing in the y dimension
nz (int) – number of particle spacing in the z dimension
SubmodulesDomain.
- Returns
Uniform 3D SpatialPy Domain object.
- Return type
-spatialpy.Domain.Domain
+-
Submodules
- Parameters
-start (tuple(float, float, float) or tuple(float, float)) – Starting point
end (tuple(float, float, float) or tuple(float, float)) – Ending point
start (float(3)) – Starting point
end (float(2)) – Ending point
- Returns
@@ -2399,7 +2369,7 @@ Submodules
- Parameters
-geometry_ivar (spatialpy.geometry.Geometry) – an instance of a ‘spatialpy.Geometry’ subclass. The ‘inside()’ method
+
geometry_ivar (spatialpy.core.geometry.Geometry) – an instance of a spatialpy.core.geometry.Geometry subclass. The ‘inside()’ method
of this object will be used to create add the particles.
deltax (float) – Distance between particles on the x-axis.
deltay (float) – Distance between particles on the y-axis (defaults to deltax).
SubmodulesDomain.add_point().
- Returns
@@ -2540,7 +2510,7 @@ SubmodulesSpatialPy Domain object created from the meshio object
- Return type
-spatialpy.Domain.Domain
+-
SubmodulesSpatialPy Domain object created from the mesh file.
- Return type
-spatialpy.Domain.Domain
+-
SubmodulesSpatialPy Domain object created from StochSS domain.
- Return type
-spatialpy.Domain.Domain
+-
SubmodulesSpatialPy Domain object created from xml mesh.
Return type
-spatialpy.Domain.Domain
+
Submodules
Parameters
-geometry_ivar (spatialpy.Geometry.Geometry) – an instance of a ‘spatialpy.Geometry’ subclass. The ‘inside()’ method
+
geometry_ivar (spatialpy.core.geometry.Geometry) – an instance of a spatialpy.core.geometry.Geometry subclass. The ‘inside()’ method
of this object will be used to assign properties to points.
type_id (str | int) – The identifier for this type.
vol (float) – The volume of each particle in the type.
Submodulesclass spatialpy.core.GeometryExterior[source]¶
Bases: spatialpy.core.geometry.Geometry
Mark particles that are on the edge of the domain.
-only works for meshes that define triangles and tetrahedrons.
+only works for domains that define triangles and tetrahedrons.
-
inside(point, on_boundary)[source]¶
@@ -2769,7 +2739,7 @@ Submodulesclass spatialpy.core.GeometryInterior[source]¶
Bases: spatialpy.core.geometry.Geometry
Mark particles that are not on the edge of the domain.
-Only works for meshes that define triangles and tetrahedrons.
+Only works for domains that define triangles and tetrahedrons.
-
inside(point, on_boundary)[source]¶
@@ -2797,11 +2767,16 @@ Submodulesobject
Class used to defined initial conditions in SpatialPy.
SubClasses must implement the ‘apply(model)’ method, which
-direction modifies the model.u0[species,voxel] matrix.
+direction modifies the model.u0[species, voxel] matrix.
-
apply(model)[source]¶
Set the initial condition of the species to the count.
+
+- Parameters
+model (spatialpy.core.model.Model) – Model contianing the target species.
+
@@ -3136,10 +3111,10 @@ Submodules
-
add_boundary_condition(bound_cond)[source]¶
-Add an BoundaryCondition object to the model.
+Add an boundary condition object to the model.
- Parameters
-bound_cond (spatialpy.BoundaryCondition) – Boundary condition to be added
+bound_cond (spatialpy.core.boundarycondition.BoundaryCondition) – Boundary condition to be added
Submodules
add_data_function(data_function)[source]¶
Add a scalar spatial function to the simulation. This is useful if you have a
-spatially varying in put to your model. Argument is a instances of subclass of the
-spatialpy.DataFunction class. It must implement a function ‘map(x)’ which takes a
-the spatial positon ‘x’ as an array, and it returns a float value.
+spatially varying input to your model. Argument is a instances of subclass of the
+spatialpy.DataFunction class. It must implement a function ‘map(point)’ which takes a
+the spatial positon ‘point’ as an array, and it returns a float value.
- Parameters
data_function (spatialpy.DataFunction) – Data function to be added.
@@ -3159,7 +3134,7 @@ SubmodulesDataFunction object(s) added tothe model.
- Return type
-spatialpy.DataFunction | list(spatialpy.DataFunction)
+spatialpy.core.datafunction.DataFunction | list(spatialpy.core.datafunction.DataFunction)
- Raises
ModelError – Invalid DataFunction
@@ -3173,7 +3148,7 @@ Submodules
- Parameters
-domain (spatialpy.Domain.Domain) – The Domain object to be added to the model
+domain (spatialpy.core.domain.Domain) – The Domain object to be added to the model
- Raises
ModelError – Invalid Domain object
@@ -3187,7 +3162,7 @@ Submodules
- Parameters
-init_cond (spatialpy.InitialCondition.InitialCondition) – Initial condition to be added
+init_cond (spatialpy.core.initialcondition.InitialCondition) – Initial condition to be added
Submodules
- Parameters
-params (spatialpy.Model.Parameter | list(spatialpy.Model.Parameter)) – Parameter object or list of Parameters to be added.
+params (spatialpy.core.parameter.Parameter | list(spatialpy.core.parameter.Parameter)) – Parameter object or list of Parameters to be added.
- Returns
Parameter object which has been added to the model.
- Return type
-spatialpy.Parameter | list(spatialpy.Parameter)
+spatialpy.core.parameter.Parameter | list(spatialpy.core.parameter.Parameter)
- Raises
-ModelError – if obj is not a spatialpy.Parameter
+ModelError – if obj is not a spatialpy.core.parameter.Parameter
Submodules
- Parameters
-reacs (spatialpy.Model.Reaction | list(spatialpy.Model.Reaction)) – Reaction or list of Reactions to be added.
+reacs (spatialpy.core.reaction.Reaction | list(spatialpy.core.reaction.Reaction)) – Reaction or list of Reactions to be added.
- Returns
The Reaction object(s) added to the model
- Return type
-spatialpy.Model.Reaction
+spatialpy.core.reaction.Reaction | list(spatialpy.core.reaction.Reaction)
- Raises
-ModelError – Invalid input/reaction to add_reaction()
+ModelError – if obj is not a spatialpy.core.reaction.Reaction
Submodules
- Parameters
-obj (spatialpy.Model.Species | list(spatialpy.Model.Species) – The species or list of species to be added to the model object.
+obj (spatialpy.core.species.Species | list(spatialpy.core.species.Species) – The species or list of species to be added to the model object.
- Returns
Species object which was added to the model.
- Return type
-spatialpy.Species | list(spatialpy.Species)
+spatialpy.core.species.Species | list(spatialpy.core.species.Species)
- Raises
-ModelError – If obj is not a spatialpy.Species
+ModelError – If obj is not a spatialpy.core.species.Species
Submodules
- Parameters
-obj (spatialpy.Model.Parameter) – Parameter object to be removed
+obj (spatialpy.core.parameter.Parameter) – Parameter object to be removed
Submodules
- Parameters
-obj (spatialpy.Model.Reaction) – Reaction to be removed.
+obj (spatialpy.core.reaction.Reaction) – Reaction to be removed.
Submodules
- Parameters
-obj (spatialpy.Model.Species) – Species object to be removed
+obj (spatialpy.core.species.Species) – Species object to be removed
Submodules
- Parameters
-pname (spatialpy.Model.Parameter) – Name of parameter to be removed
+pname (str) – Name of parameter to be returned
- Returns
The Parameter object represented in the model by ‘pname’
- Return type
-Spatialpy.Model.Parameter
+Spatialpy.core.parameter.Parameter
- Raises
ModelError – No parameter named {pname}
@@ -3420,13 +3395,13 @@ Submodules
- Parameters
-rname (str) – name of Reaction to retrieve
+rname (str) – name of the reaction to be returned
- Returns
The Reaction Object in the model represented by ‘rname’
- Return type
-spatialpy.Model.Reaction
+-
- Raises
ModelError – Could not find reaction
@@ -3446,7 +3421,7 @@ SubmodulesThe Species objected represented by given ‘sname’
- Return type
-spatialpy.Model.Species
+-
- Raises
ModelError – if the model does not contain the requested species
@@ -3480,7 +3455,7 @@ SubmodulesA SpatialPy Result object containing simulation data.
- Return type
-spatialpy.Result.Result
+-
Submodules
-
set_timesteps(output_interval, num_steps, timestep_size=None)[source]¶
-”
-Set the simlation time span parameters.
+Set the simlation time span parameters.
- Parameters
@@ -3694,7 +3668,7 @@ Submodules
- Parameters
-species (spayialpy.species.Species) – The species to set the initial condition.
species (spatialpy.core.species.Species) – The species to set the initial condition.
count (int) – The initial condition for the target species.
location (float[3]) – X, Y, Z coordinates to place the initial condition.
@@ -3706,7 +3680,7 @@ Submodules
- Parameters
-model (spatialpy.model.Model) – Model contianing the target species.
+model (spatialpy.core.model.Model) – Model contianing the target species.
Submodulesspatialpy.core.parameter.Parameter) – if mass action, rate is a reference to a parameter instance.
annotation (str) – Description of the reaction (meta)
restrict_to (int, str, list of ints or list of strs) – Restrict reaction execution to a type or list of types within the domain.
@@ -3738,7 +3712,7 @@ Submodules
Parameters
-S (spatialpy.Model.Species) – Species object to be produced by the reaction
species (spatialpy.core.species.Species) – Species object to be produced by the reaction
stoichiometry (int) – Stoichiometry of this product.
Submodules
Parameters
-species (spatialpy.Model.Species) – reactant Species object
species (spatialpy.core.species.Species) – reactant Species object
stoichiometry (int) – Stoichiometry of this participant reactant
Submodules
Parameters
-model (spatialpy.Model) – Target SpatialPy Model for annotation.
+model (spatialpy.core.model.Model) – Target SpatialPy Model for annotation.
Submodules
Parameters
-folder_name (str (default current working directory)) – A path where the vtk files will be written, created if non-existant.
+folder_name (str) – A path where the vtk files will be written, created if non-existant. Defaults current working directory
If no path is provided current working directory is used.
-
--
-export_to_vtk(timespan, folder_name=None)[source]¶
-Write the trajectory to a collection of vtk files.
-The exported data is #molecules/volume, where the volume unit is implicit from the mesh dimension.
-Not currently implemented.
@@ -3825,7 +3790,14 @@ Submodules
- Parameters
-property_name (str) – A string describing the property to be returned.
property_name (str) – A string describing the property to be returned. Can be one of: {
+‘v’ : velocity,
+‘rho’: density,
+‘mass’: mass,
+‘id’: type_id,
+‘type’: type as str,
+‘bvf_phi’: boundary volume fraction,
+‘nu’: viscosity}
timepoints (int) – timespan index to be returned. Default is None
Submodulesnumpy.ndarray
Raises
-ResultsError – Could not get data for given timepoints.
+ResultError – Could not get data for given timepoints.
Submodules
Parameters
-species (str | dict) – A species in string or dictionary form to retreive information about
timepoints (int (default None)) – A time point where the information should be retreived from.
+
species (str | spatialpy.core.species.Species) – A species in string or dictionary form to retreive information about
timepoints (int) – A time point where the information should be retreived from.
If ‘timepoints’ is None (default), a matrix of dimension:
(number of timepoints) x (number of voxels) is returned.
If an integer value is given, that value is used to index into the timespan, and that time point is returned
-as a 1D array with size (number of voxel).
concentration (bool (default False)) – Whether or not the species is a concentration (True) or population (False)
+as a 1D array with size (number of voxel). Defaults to None
concentration (bool) – Whether or not the species is a concentration (True) or population (False)
If concentration is False (default), the integer, raw, trajectory data is returned.
-If set to True, the concentration (=copy_number/volume) is returned.
deterministic (bool (default False)) – Whether or not the species is deterministic (True) or stochastic (False)
debug (bool (default False)) – Whether or not debug information should be printed
deterministic (bool) – Whether or not the species is deterministic (True) or stochastic (False). Defaults to False
debug (bool) – Whether or not debug information should be printed. Defaults to False
Returns
@@ -3900,8 +3872,8 @@ Submodulesdict
Raises
-ResultsError – unable to plot species for given time
+ResultError – unable to plot species for given time
Submodules
Parameters
-species (spayialpy.species.Species) – The species to set the initial condition.
species (spatialpy.core.species.Species) – The species to set the initial condition.
count (int) – The initial condition for the target species.
types (list) – Types of the particles to place the initial condition.
@@ -4030,7 +4002,7 @@ Submodules
Parameters
-model (spatialpy.model.Model) – Model contianing the target species.
+model (spatialpy.core.model.Model) – Model contianing the target species.
Submodules
name (str) – Name of the Species
diffusion_coefficient (float) – Non-constant coefficient of diffusion for Species.
restrict_to – Set the diffusion coefficient to zero for ‘species’ in all types not in ‘listOfTypes’.
restrict_to (int, str, list of ints or list of strs) – Set the diffusion coefficient to zero for ‘species’ in all types not in ‘listOfTypes’. This effectively restricts the movement of ‘species’ to the types specified in ‘listOfTypes’.
This effectively restricts the movement of ‘species’ to the types specified in ‘listOfTypes’.
-:type restrict_to: int, str, list of ints or list of strs
-
set_diffusion_coefficient(diffusion_coefficient)[source]¶
@@ -4076,7 +4046,7 @@ Submodulesdiffusion_coefficient (float) – Non-constant coefficient of diffusion for Species.
- Raises
-SpeciesError – If diffusion_coefficient is negative.
+SpeciesError – If diffusion_coefficient is negative or not a valid type.
@@ -4098,7 +4068,7 @@ Submodules
Parameters
-species (spayialpy.species.Species) – The species to set the initial condition.
species (spatialpy.core.species.Species) – The species to set the initial condition.
count (int) – The initial condition for the target species.
types (list) – Types of the particles to place the initial condition.
@@ -4110,7 +4080,7 @@ Submodules
Parameters
-model (spatialpy.model.Model) – Model contianing the target species.
+model (spatialpy.core.model.Model) – Model contianing the target species.
Submodules
Parameters
-model (spatialpy.Model.Model) – Target model of solver simulation.
model (spatialpy.core.model.Model) – Target model of solver simulation.
debug_level (int) – Target level of debugging.
Submodules
Parameters
-spatialpy_model – spatialpy.Model
-SpatialPy model to be converted to StochSS
filename – str
-Path to the exported stochss model
return_stochss_model – bool
-Whether or not to return the model
model (spatialpy.core.model.Model) – SpatialPy model to be converted to StochSS.
filename (str) – Path to the exported stochss model.
return_stochss_model (bool) – Whether or not to return the model.
Returns
+StochSS model dict if return_stochss_model is True else path to StochSS model file.
+Return type
+dict | str
+
E
- export_to_vtk() (spatialpy.core.Result method)
-
-
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index e6a60f46..dfb90b68 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -100,7 +100,7 @@ Getting a copy of SpatialPyPlease register as a user! SpatialPy's development is funded by NIH grant 2R01EB014877, and to continue support, we need to prove SpatialPy has users. Please fill out our short registration form!
Examples¶
-See our Example Notebook - Getting Started for more information on how to build and simulate your models with SpatialPy. For an example of how to use SpatialPy to simulate a spatial stochastic reaction-diffusion system, see the 3D Cylinder Demo. We also provide examples of how to use SpatialPy to simulate physics (Gravity Demo) and fluid flow (Weir Model).
+See our Example Notebook - Start Here for more information on how to build and simulate your models with SpatialPy. For an example of how to use SpatialPy to simulate a spatial stochastic reaction-diffusion system, see the 3D Cylinder Demo. We also provide examples of how to use SpatialPy to simulate physics (Gravity Demo) and fluid flow (Weir Model).
Reporting Issues¶
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index 8e7baf8f..df1b09ba 100644
Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 4a0be063..70ef50ba 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/index.rst b/docs/index.rst
index ef9b1b78..33060207 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -20,7 +20,7 @@ The latest version of SpatialPy can be found on `PyPI `_ for more information on how to build and simulate your models with SpatialPy. For an example of how to use SpatialPy to simulate a spatial stochastic reaction-diffusion system, see the `3D Cylinder Demo `_. We also provide examples of how to use SpatialPy to simulate physics (`Gravity Demo `_) and fluid flow (`Weir Model `_).
+See our `Example Notebook - Start Here `_ for more information on how to build and simulate your models with SpatialPy. For an example of how to use SpatialPy to simulate a spatial stochastic reaction-diffusion system, see the `3D Cylinder Demo `_. We also provide examples of how to use SpatialPy to simulate physics (`Gravity Demo `_) and fluid flow (`Weir Model `_).
Reporting Issues
diff --git a/spatialpy/core/boundarycondition.py b/spatialpy/core/boundarycondition.py
index 55fb0bd0..c66579d2 100644
--- a/spatialpy/core/boundarycondition.py
+++ b/spatialpy/core/boundarycondition.py
@@ -31,7 +31,7 @@ class BoundaryCondition():
- type_id: type (subdomain) of the partciles
Targets (one of the following must be set):
property: (str), 'nu', 'rho','v'
- species: (str) name of a chemical species.
+ species: (str) name of a chemical species. \
Must also set deterministic=True/False flag.
:param xmin: x-axis coordinate lower bound of **condition**
@@ -59,7 +59,7 @@ class BoundaryCondition():
and applies to deterministic simulation. **BoundaryCondition not yet implemeneted for Stochastic Species**.
:type deterministic: bool
- :param target: Set **target** to properties, can be 'nu' 'rho' or 'v' or species name
+ :param target: Set **target** to properties, can be 'nu' 'rho' or 'v' or species name \
If species name, determinstic must also be set to True/False.
:type target: str
@@ -67,7 +67,7 @@ class BoundaryCondition():
:type value: float or float[3]
:param model: Target model of boundary condition
- :type model: spatialpy.Model.Model
+ :type model: spatialpy.core.model.Model
"""
def __init__(self, xmin=None, xmax=None, ymin=None, ymax=None, zmin=None, zmax=None,
diff --git a/spatialpy/core/datafunction.py b/spatialpy/core/datafunction.py
index f63b375f..a926fc5d 100644
--- a/spatialpy/core/datafunction.py
+++ b/spatialpy/core/datafunction.py
@@ -23,6 +23,8 @@ class DataFunction():
:param name: Name of the Data Function.
:type name: str
+
+ :raises DataFunctionError: If a name is not provided.
"""
def __init__(self, name=None):
@@ -35,11 +37,11 @@ def map(self, point):
"""
This method must be overridden by the DataFunction subclass.
- NOTE: The spatial location is evaulated at t=0 and is not
- reevaluated as the fluid domain moves over time.
+ NOTE: The spatial location is evaulated at t=0 and is not \
+ re-evaluated as the fluid domain moves over time.
- :param point: The x,y,z position
- :type point: vector of 3 doubles
+ :param point: The x, y, z position.
+ :type point: float[3]
:returns: Value of function at this spatial location.
:rtype: float
diff --git a/spatialpy/core/domain.py b/spatialpy/core/domain.py
index 27e6445a..b6c763de 100644
--- a/spatialpy/core/domain.py
+++ b/spatialpy/core/domain.py
@@ -37,13 +37,13 @@ class Domain():
:type numpoints: int
:param xlim: Range of domain along x-axis
- :type xlim: tuple(float)
+ :type xlim: float(2)
:param ylim: Range of domain along y-axis
- :type ylim: tuple(float)
+ :type ylim: float(2)
:param zlim: Range of domain along z-axis
- :type zlim: tuple(float)
+ :type zlim: float(2)
:param rho: Background density for the system
:type rho: float
@@ -55,7 +55,7 @@ class Domain():
:type P0: float
:param gravity: Acceleration of gravity for the system.
- :type species: float
+ :type gravity: float[3]
"""
def __init__(self, numpoints, xlim, ylim, zlim, rho0=1.0, c0=10, P0=None, gravity=None):
self.vertices = numpy.zeros((numpoints, 3), dtype=float)
@@ -132,10 +132,10 @@ def get_type_def(self, type_id):
def compile_prep(self):
"""
- Generate the domain list of type ids and check for invalid type_ids and rho values
+ Generate the domains list of type ids and check for invalid type_ids and rho values
in preperation of compiling the simulation files.
- :raises DomainError: If a type_id is not set or rh for a particle is 0.
+ :raises DomainError: If a type_id is not set or rho=0 for a particle.
"""
if self.type_id.tolist().count(None) > 0:
raise DomainError(f"Particles must be assigned a type_id.")
@@ -150,7 +150,7 @@ def add_point(self, point, vol=0, mass=0, type_id=1, nu=0, fixed=False, rho=None
Add a single point particle to the domain space.
:param point: Spatial coordinate vertices of point to be added
- :type point: tuple(float, float, float) or tuple(float, float)
+ :type point: float(3)
:param vol: Default volume of particle to be added
:type vol: float
@@ -158,19 +158,19 @@ def add_point(self, point, vol=0, mass=0, type_id=1, nu=0, fixed=False, rho=None
:param mass: Default mass of particle to be added
:type mass: float
- :param type_id: Particle type ID of particle to be created
+ :param type_id: Particle type ID of particle to be craddedeated
:type type_id: str | int
- :param nu: Default viscosity of particle to be created
+ :param nu: Default viscosity of particle to be added
:type nu: float
:param fixed: True if particle is spatially fixed, else False
:type fixed: bool
- :param c: Default artificial speed of sound of particle to be created
+ :param c: Default artificial speed of sound of particle to be added
:type c: float
- :param rho: Default density of particle to be created
+ :param rho: Default density of particle to be added
:type rho: float
:raises DomainError: Type_id is 0 or type_id contains an invalid character.
@@ -204,9 +204,9 @@ def set_properties(self, geometry_ivar, type_id, vol=None, mass=None, nu=None, r
"""
Add a type definition to the domain. By default, all regions are set to type 0.
- :param geometry_ivar: an instance of a 'spatialpy.Geometry' subclass. The 'inside()' method
+ :param geometry_ivar: an instance of a :py:class:`spatialpy.core.geometry.Geometry` subclass. The 'inside()' method
of this object will be used to assign properties to points.
- :type geometry_ivar: spatialpy.Geometry.Geometry
+ :type geometry_ivar: spatialpy.core.geometry.Geometry
:param type_id: The identifier for this type.
:type type_id: str | int
@@ -270,9 +270,9 @@ def fill_with_particles(self, geometry_ivar, deltax, deltay=None, deltaz=None, x
"""
Fill a geometric shape with particles.
- :param geometry_ivar: an instance of a 'spatialpy.Geometry' subclass. The 'inside()' method
+ :param geometry_ivar: an instance of a :py:class:`spatialpy.core.geometry.Geometry` subclass. The 'inside()' method
of this object will be used to create add the particles.
- :type geometry_ivar: spatialpy.geometry.Geometry
+ :type geometry_ivar: spatialpy.core.geometry.Geometry
:param deltax: Distance between particles on the x-axis.
:type deltax: float
@@ -301,8 +301,7 @@ def fill_with_particles(self, geometry_ivar, deltax, deltay=None, deltaz=None, x
:param zmax: Maximum z value of the bounding box (defaults to Domain.zlim[1]).
:type zmax: float
- :param kwargs: Key word arguments for Domain.add_point.
- :type kwargs: dict
+ :param \**kwargs: Additional keyword arguments passed to :py:meth:`Domain.add_point`.
:returns: The number of particles that were created within this geometry.
:rtype: int
@@ -416,10 +415,10 @@ def distance_between_2_vertices(self, start, end):
Get distance between 2 domain vertices.
:param start: Starting point
- :type start: tuple(float, float, float) or tuple(float, float)
+ :type start: float(3)
:param end: Ending point
- :type end: tuple(float, float, float) or tuple(float, float)
+ :type end: float(2)
:returns: a distance measurement between start and end point
:rtype: float
@@ -431,10 +430,10 @@ def closest_vertex(self, point):
Find the nearest vertex of a given point in the domain.
:param point: Target source point
- :type point: tuple(float, float, float) or tuple(float, float)
+ :type point: float(3)
:returns: The coordinates of the nearest vertex to the source point.
- :rtype: tuple(float, float, float) or tuple(float, float)
+ :rtype: float(3)
"""
min_dist = None
min_vtx = None
@@ -652,7 +651,7 @@ def read_xml_mesh(cls, filename):
:type filename: str
:returns: SpatialPy Domain object created from xml mesh.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
root = ET.parse(filename).getroot()
if not root.tag == 'dolfin':
@@ -705,7 +704,7 @@ def import_meshio_object(cls, mesh_obj):
:type mesh_obj: meshio.Mesh
:returns: SpatialPy Domain object created from the meshio object
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
# create domain object
xlim = (min(mesh_obj.points[:, 0]), max(mesh_obj.points[:, 0]))
@@ -742,7 +741,7 @@ def read_msh_file(cls, filename):
:type filename: str
:returns: SpatialPy Domain object created from the mesh file.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
try:
import meshio # pylint: disable=import-outside-toplevel
@@ -789,7 +788,7 @@ def read_stochss_domain(cls, filename):
:type filename: str
:returns: SpatialPy Domain object created from StochSS domain.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
try:
with open(filename, "r", encoding="utf-8") as domain_file:
@@ -825,13 +824,13 @@ def create_3D_domain(cls, xlim, ylim, zlim, nx, ny, nz, type_id=1, mass=1.0,
Create a filled 3D domain
:param xlim: highest and lowest coordinate in the x dimension
- :type xlim: tuple(float, float)
+ :type xlim: float(2)
:param ylim: highest and lowest coordinate in the y dimension
- :type ylim: tuple(float, float)
+ :type ylim: float(2)
:param zlim: highest and lowest coordinate in the z dimension
- :type zlim: tuple(float, float)
+ :type zlim: float(2)
:param nx: number of particle spacing in the x dimension
:type nx: int
@@ -855,22 +854,15 @@ def create_3D_domain(cls, xlim, ylim, zlim, nx, ny, nz, type_id=1, mass=1.0,
:type c: float
:param rho: default density of particles to be created.
- :type rho:
+ :type rho: float
:param fixed: spatially fixed flag of particles to be created. Defaults to false.
:type fixed: bool
- :param rho0: background density for the system. Defaults to 1.0
- :type rho0: float
-
- :param c0: speed of sound for the system. Defaults to 10
- :type c0: float
-
- :param P0: background pressure for the system. Defaults to 10
- :type P0: float
-
+ :param \**kwargs: Additional keyword arguments passed to :py:class:`Domain`.
+
:returns: Uniform 3D SpatialPy Domain object.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
# Create domain object
numberparticles = nx * ny * nz
@@ -897,10 +889,10 @@ def create_2D_domain(cls, xlim, ylim, nx, ny, type_id=1, mass=1.0,
Create a filled 2D domain
:param xlim: highest and lowest coordinate in the x dimension
- :type xlim: tuple(float, float)
+ :type xlim: float(2)
:param ylim: highest and lowest coordinate in the y dimension
- :type ylim: tuple(float, float)
+ :type ylim: float(2)
:param nx: number of particle spacing in the x dimension
:type nx: int
@@ -921,22 +913,15 @@ def create_2D_domain(cls, xlim, ylim, nx, ny, type_id=1, mass=1.0,
:type c: float
:param rho: default density of particles to be created.
- :type rho:
+ :type rho: float
:param fixed: spatially fixed flag of particles to be created. Defaults to false.
:type fixed: bool
- :param rho0: background density for the system. Defaults to 1.0
- :type rho0: float
-
- :param c0: speed of sound for the system. Defaults to 10
- :type c0: float
-
- :param P0: background pressure for the system. Defaults to 10
- :type P0: float
+ :param \**kwargs: Additional keyword arguments passed to :py:class:`Domain`.
:returns: Uniform 2D SpatialPy Domain object.
- :rtype: spatialpy.Domain.Domain
+ :rtype: spatialpy.core.domain.Domain
"""
# Create domain object
numberparticles = nx * ny
diff --git a/spatialpy/core/geometry.py b/spatialpy/core/geometry.py
index b94a9ace..ee3e7aa5 100644
--- a/spatialpy/core/geometry.py
+++ b/spatialpy/core/geometry.py
@@ -57,7 +57,7 @@ def inside(self, point, on_boundary):
class GeometryExterior(Geometry):
"""
Mark particles that are on the edge of the domain.
- only works for meshes that define triangles and tetrahedrons.
+ only works for domains that define triangles and tetrahedrons.
"""
def inside(self, point, on_boundary):
"""
@@ -75,7 +75,7 @@ def inside(self, point, on_boundary):
class GeometryInterior(Geometry):
"""
Mark particles that are not on the edge of the domain.
- Only works for meshes that define triangles and tetrahedrons.
+ Only works for domains that define triangles and tetrahedrons.
"""
def inside(self, point, on_boundary):
"""
diff --git a/spatialpy/core/initialcondition.py b/spatialpy/core/initialcondition.py
index 40b1cc67..f3cb505d 100644
--- a/spatialpy/core/initialcondition.py
+++ b/spatialpy/core/initialcondition.py
@@ -23,11 +23,14 @@ class InitialCondition():
"""
Class used to defined initial conditions in SpatialPy.
SubClasses must implement the 'apply(model)' method, which
- direction modifies the model.u0[species,voxel] matrix.
+ direction modifies the model.u0[species, voxel] matrix.
"""
def apply(self, model):
"""
Set the initial condition of the species to the count.
+
+ :param model: Model contianing the target species.
+ :type model: spatialpy.core.model.Model
"""
raise InitialConditionError("spatialpy.InitialCondition subclasses must implement apply()")
@@ -36,7 +39,7 @@ class PlaceInitialCondition(InitialCondition):
Class used to defined the place initial condition in SpatialPy.
:param species: The species to set the initial condition.
- :type species: spayialpy.species.Species
+ :type species: spatialpy.core.species.Species
:param count: The initial condition for the target species.
:type count: int
@@ -58,7 +61,7 @@ def apply(self, model):
Set the initial condition of the species to the count at the location.
:param model: Model contianing the target species.
- :type model: spatialpy.model.Model
+ :type model: spatialpy.core.model.Model
"""
spec_name = self.species.name
spec_ndx = None
@@ -74,7 +77,7 @@ class UniformInitialCondition(InitialCondition):
Class used to defined the uniform initial condition in SpatialPy.
:param species: The species to set the initial condition.
- :type species: spayialpy.species.Species
+ :type species: spatialpy.core.species.Species
:param count: The initial condition for the target species.
:type count: int
@@ -101,7 +104,7 @@ def apply(self, model):
Set 'count' of 'species' in over the list of types (all types if None).
:param model: Model contianing the target species.
- :type model: spatialpy.model.Model
+ :type model: spatialpy.core.model.Model
"""
spec_name = self.species.name
spec_ndx = None
@@ -126,7 +129,7 @@ class ScatterInitialCondition(InitialCondition):
Class used to defined the scatter initial condition in SpatialPy.
:param species: The species to set the initial condition.
- :type species: spayialpy.species.Species
+ :type species: spatialpy.core.species.Species
:param count: The initial condition for the target species.
:type count: int
@@ -153,7 +156,7 @@ def apply(self, model):
Scatter 'count' of 'species' randomly over the list of types (all types if None).
:param model: Model contianing the target species.
- :type model: spatialpy.model.Model
+ :type model: spatialpy.core.model.Model
"""
spec_name = self.species.name
spec_ndx = None
diff --git a/spatialpy/core/model.py b/spatialpy/core/model.py
index f605dcd9..68b74b03 100644
--- a/spatialpy/core/model.py
+++ b/spatialpy/core/model.py
@@ -32,8 +32,8 @@ def export_StochSS(spatialpy_model, filename=None, return_stochss_model=False):
"""
SpatialPy model to StochSS converter
- :param spatailpy_model: SpatialPy model to be converted to StochSS
- :type spatialpy_model: spatialpy.Model
+ :param spatialpy_model: SpatialPy model to be converted to StochSS
+ :type spatialpy_model: spatialpy.core.model.Model
:param filename: Path to the exported stochss model
:type filename: str
@@ -329,12 +329,12 @@ def add_species(self, obj):
Adds a species, or list of species to the model. Will return the added object upon success.
:param obj: The species or list of species to be added to the model object.
- :type obj: spatialpy.Model.Species | list(spatialpy.Model.Species
+ :type obj: spatialpy.core.species.Species | list(spatialpy.core.species.Species
:returns: Species object which was added to the model.
- :rtype: spatialpy.Species | list(spatialpy.Species)
+ :rtype: spatialpy.core.species.Species | list(spatialpy.core.species.Species)
- :raises ModelError: If obj is not a spatialpy.Species
+ :raises ModelError: If obj is not a spatialpy.core.species.Species
"""
from spatialpy.core.species import Species # pylint: disable=import-outside-toplevel
if isinstance(obj, list):
@@ -359,7 +359,7 @@ def delete_species(self, obj):
Remove a Species from model.listOfSpecies.
:param obj: Species object to be removed
- :type obj: spatialpy.Model.Species
+ :type obj: spatialpy.core.species.Species
"""
self.listOfSpecies.pop(obj) # raises key error if param is missing
@@ -389,7 +389,7 @@ def get_species(self, sname):
:type sname: str
:returns: The Species objected represented by given 'sname'
- :rtype: spatialpy.Model.Species
+ :rtype: spatialpy.core.species.Species
:raises ModelError: if the model does not contain the requested species
"""
@@ -417,12 +417,12 @@ def add_parameter(self,params):
Parameter object or a list of Parameter objects.
:param params: Parameter object or list of Parameters to be added.
- :type params: spatialpy.Model.Parameter | list(spatialpy.Model.Parameter)
+ :type params: spatialpy.core.parameter.Parameter | list(spatialpy.core.parameter.Parameter)
:returns: Parameter object which has been added to the model.
- :rtype: spatialpy.Parameter | list(spatialpy.Parameter)
+ :rtype: spatialpy.core.parameter.Parameter | list(spatialpy.core.parameter.Parameter)
- :raises ModelError: if obj is not a spatialpy.Parameter
+ :raises ModelError: if obj is not a spatialpy.core.parameter.Parameter
"""
from spatialpy.core.parameter import Parameter # pylint: disable=import-outside-toplevel
if isinstance(params,list):
@@ -449,7 +449,7 @@ def delete_parameter(self, obj):
Remove a Parameter from model.listOfParameters.
:param obj: Parameter object to be removed
- :type obj: spatialpy.Model.Parameter
+ :type obj: spatialpy.core.parameter.Parameter
"""
self.listOfParameters.pop(obj)
@@ -466,11 +466,11 @@ def get_parameter(self, pname):
"""
Return the Parameter object from model associated with 'pname'
- :param pname: Name of parameter to be removed
- :type pname: spatialpy.Model.Parameter
+ :param pname: Name of parameter to be returned
+ :type pname: str
:returns: The Parameter object represented in the model by 'pname'
- :rtype: Spatialpy.Model.Parameter
+ :rtype: Spatialpy.core.parameter.Parameter
:raises ModelError: No parameter named {pname}
"""
@@ -499,12 +499,12 @@ def add_reaction(self, reacs):
or a dict with name, instance pairs.
:param reacs: Reaction or list of Reactions to be added.
- :type reacs: spatialpy.Model.Reaction | list(spatialpy.Model.Reaction)
+ :type reacs: spatialpy.core.reaction.Reaction | list(spatialpy.core.reaction.Reaction)
:returns: The Reaction object(s) added to the model
- :rtype: spatialpy.Model.Reaction
+ :rtype: spatialpy.core.reaction.Reaction | list(spatialpy.core.reaction.Reaction)
- :raises ModelError: Invalid input/reaction to add_reaction()
+ :raises ModelError: if obj is not a spatialpy.core.reaction.Reaction
"""
from spatialpy.core.reaction import Reaction # pylint: disable=import-outside-toplevel
if isinstance(reacs, list):
@@ -529,7 +529,7 @@ def delete_reaction(self, obj):
Remove reaction from model.listOfReactions
:param obj: Reaction to be removed.
- :type obj: spatialpy.Model.Reaction
+ :type obj: spatialpy.core.reaction.Reaction
"""
self.listOfReactions.pop(obj)
@@ -555,11 +555,11 @@ def get_reaction(self, rname):
"""
Retrieve a reaction object from the model by name
- :param rname: name of Reaction to retrieve
+ :param rname: name of the reaction to be returned
:type rname: str
:returns: The Reaction Object in the model represented by 'rname'
- :rtype: spatialpy.Model.Reaction
+ :rtype: spatialpy.core.reaction.Reaction
:raises ModelError: Could not find reaction
"""
@@ -596,7 +596,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None,
:type profile: bool
:returns: A SpatialPy Result object containing simulation data.
- :rtype: spatialpy.Result.Result
+ :rtype: spatialpy.core.result.Result
"""
from spatialpy.solvers.solver import Solver # pylint: disable=import-outside-toplevel
@@ -608,7 +608,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None,
def set_timesteps(self, output_interval, num_steps, timestep_size=None):
- """"
+ """
Set the simlation time span parameters.
:param output_interval: size of each output timestep in seconds
@@ -668,7 +668,7 @@ def add_domain(self, domain):
Add a spatial domain to the model
:param domain: The Domain object to be added to the model
- :type domain: spatialpy.Domain.Domain
+ :type domain: spatialpy.core.domain.Domain
:raises ModelError: Invalid Domain object
"""
@@ -681,15 +681,15 @@ def add_domain(self, domain):
def add_data_function(self, data_function):
"""
Add a scalar spatial function to the simulation. This is useful if you have a
- spatially varying in put to your model. Argument is a instances of subclass of the
- spatialpy.DataFunction class. It must implement a function 'map(x)' which takes a
- the spatial positon 'x' as an array, and it returns a float value.
+ spatially varying input to your model. Argument is a instances of subclass of the
+ spatialpy.DataFunction class. It must implement a function 'map(point)' which takes a
+ the spatial positon 'point' as an array, and it returns a float value.
:param data_function: Data function to be added.
:type data_function: spatialpy.DataFunction
:returns: DataFunction object(s) added tothe model.
- :rtype: spatialpy.DataFunction | list(spatialpy.DataFunction)
+ :rtype: spatialpy.core.datafunction.DataFunction | list(spatialpy.core.datafunction.DataFunction)
:raises ModelError: Invalid DataFunction
"""
@@ -711,16 +711,16 @@ def add_initial_condition(self, init_cond):
Add an initial condition object to the initialization of the model.
:param init_cond: Initial condition to be added
- :type init_cond: spatialpy.InitialCondition.InitialCondition
+ :type init_cond: spatialpy.core.initialcondition.InitialCondition
"""
self.listOfInitialConditions.append(init_cond)
def add_boundary_condition(self, bound_cond):
"""
- Add an BoundaryCondition object to the model.
+ Add an boundary condition object to the model.
:param bound_cond: Boundary condition to be added
- :type bound_cond: spatialpy.BoundaryCondition
+ :type bound_cond: spatialpy.core.boundarycondition.BoundaryCondition
"""
bound_cond.model = self
self.listOfBoundaryConditions.append(bound_cond)
diff --git a/spatialpy/core/reaction.py b/spatialpy/core/reaction.py
index f72c4054..988f0823 100644
--- a/spatialpy/core/reaction.py
+++ b/spatialpy/core/reaction.py
@@ -42,7 +42,7 @@ class Reaction():
:type propensity_function: str
:param rate: if mass action, rate is a reference to a parameter instance.
- :type rate: spatialpy.model.Parameter
+ :type rate: spatialpy.core.parameter.Parameter
:param annotation: Description of the reaction (meta)
:type annotation: str
@@ -177,8 +177,8 @@ def add_product(self, species, stoichiometry):
"""
Add a product to this reaction
- :param S: Species object to be produced by the reaction
- :type S: spatialpy.Model.Species
+ :param species: Species object to be produced by the reaction
+ :type species: spatialpy.core.species.Species
:param stoichiometry: Stoichiometry of this product.
:type stoichiometry: int
@@ -195,7 +195,7 @@ def add_reactant(self, species, stoichiometry):
Add a reactant to this reaction
:param species: reactant Species object
- :type species: spatialpy.Model.Species
+ :type species: spatialpy.core.species.Species
:param stoichiometry: Stoichiometry of this participant reactant
:type stoichiometry: int
@@ -223,7 +223,7 @@ def initialize(self, model):
Deferred object initialization, called by model.add_reaction().
:param model: Target SpatialPy Model for annotation.
- :type model: spatialpy.Model
+ :type model: spatialpy.core.model.Model
"""
self.ode_propensity_function = self.propensity_function
diff --git a/spatialpy/core/result.py b/spatialpy/core/result.py
index fbc06f5f..a8408d8f 100644
--- a/spatialpy/core/result.py
+++ b/spatialpy/core/result.py
@@ -312,25 +312,25 @@ def get_species(self, species, timepoints=None, concentration=False, determinist
one or all timepoints. Returns a numpy array containing the species population/concentration values.
:param species: A species in string or dictionary form to retreive information about
- :type species: str | dict
+ :type species: str | spatialpy.core.species.Species
:param timepoints: A time point where the information should be retreived from.
If 'timepoints' is None (default), a matrix of dimension:
(number of timepoints) x (number of voxels) is returned.
If an integer value is given, that value is used to index into the timespan, and that time point is returned
- as a 1D array with size (number of voxel).
- :type timepoints: int (default None)
+ as a 1D array with size (number of voxel). Defaults to None
+ :type timepoints: int
:param concentration: Whether or not the species is a concentration (True) or population (False)
If concentration is False (default), the integer, raw, trajectory data is returned.
- If set to True, the concentration (=copy_number/volume) is returned.
- :type concentration: bool (default False)
+ If set to True, the concentration (=copy_number/volume) is returned. Defaults to False
+ :type concentration: bool
- :param deterministic: Whether or not the species is deterministic (True) or stochastic (False)
- :type deterministic: bool (default False)
+ :param deterministic: Whether or not the species is deterministic (True) or stochastic (False). Defaults to False
+ :type deterministic: bool
- :param debug: Whether or not debug information should be printed
- :type debug: bool (default False)
+ :param debug: Whether or not debug information should be printed. Defaults to False
+ :type debug: bool
:returns: A numpy array containing population/concentration values for target species across specified
timepoints. Defaults to all timepoints.
@@ -340,7 +340,7 @@ def get_species(self, species, timepoints=None, concentration=False, determinist
"""
num_voxel = self.model.domain.get_num_voxels()
- if isinstance(species,str):
+ if isinstance(species, str):
spec_name = species
else:
spec_name = species.name
@@ -404,11 +404,13 @@ def plot_species(self, species, t_ndx=None, t_val=None, concentration=False,
:param deterministic: Whether or not to plot the data as deterministic
:type deterministic: bool
- :param width: Width in pixels of output plot box
- :type width: int (default 500)
+ :param width: Width in pixels of output plot box or for matplotlib inches of output plot box. \
+ Defaults to 500 (Plotly) or 6.4 (MatPlotLib)
+ :type width: int
- :param height: Height in pixels of output plot box
- :type height: int (default 500)
+ :param height: Height in pixels of output plot box or for matplotlib inches of output plot box. \
+ Defaults to 500 (Plotly) or 4.8 (MatPlotLib)
+ :type height: int
:param colormap: colormap to use. Plotly specification, valid values: "Plotly3","Jet","Blues","YlOrRd",
"PuRd","BuGn","YlOrBr","PuBuGn","BuPu","YlGnBu", "PuBu","GnBu","YlGn","Greens","Reds",
@@ -450,7 +452,7 @@ def plot_species(self, species, t_ndx=None, t_val=None, concentration=False,
:returns: A dictionary containing data for a plotly figure of species output trajectory
:rtype: dict
- :raises ResultsError: unable to plot species for given time
+ :raises ResultError: unable to plot species for given time
"""
time_index_list = self.get_timespan()
@@ -578,7 +580,14 @@ def get_property(self, property_name, timepoints=None):
given, that value is used to index into the timespan, and that time point is returned \
as a 1D array with size (number of voxel).
- :param property_name: A string describing the property to be returned.
+ :param property_name: A string describing the property to be returned. Can be one of: {
+ 'v' : velocity,
+ 'rho': density,
+ 'mass': mass,
+ 'id': type_id,
+ 'type': type as str,
+ 'bvf_phi': boundary volume fraction,
+ 'nu': viscosity}
:type property_name: str
:param timepoints: timespan index to be returned. Default is None
@@ -587,7 +596,7 @@ def get_property(self, property_name, timepoints=None):
:returns: a numpy array of target property values across timepoints, defaults to all timepoints.
:rtype: numpy.ndarray
- :raises ResultsError: Could not get data for given timepoints.
+ :raises ResultError: Could not get data for given timepoints.
"""
l_time = len(self.get_timespan()) - 1
@@ -639,11 +648,13 @@ def plot_property(self, property_name, t_ndx=None, t_val=None, p_ndx=0, width=No
:param p_ndx: The property index of the results to be plotted
:type p_ndx: int
- :param width: Width in pixels of output plot box or for matplotlib inches of output plot box
- :type width: int (default 500)
+ :param width: Width in pixels of output plot box or for matplotlib inches of output plot box. \
+ Defaults to 500 (Plotly) or 6.4 (MatPlotLib)
+ :type width: int
- :param height: Height in pixels of output plot box or for matplotlib inches of output plot box
- :type height: int (default 500)
+ :param height: Height in pixels of output plot box or for matplotlib inches of output plot box. \
+ Defaults to 500 (Plotly) or 4.8 (MatPlotLib)
+ :type height: int
:param colormap: colormap to use. Plotly specification, valid values: "Plotly3","Jet","Blues","YlOrRd",
"PuRd","BuGn","YlOrBr","PuBuGn","BuPu","YlGnBu", "PuBu","GnBu","YlGn","Greens","Reds",
@@ -835,9 +846,9 @@ def export_to_csv(self, folder_name=None):
The columns of modelname_mesh.csv are: 'Voxel ID', 'X', 'Y', 'Z', 'Type', 'Volume', 'Mass', 'Viscosity'
The columns of modelname_species_S.csv: 'Time', 'Voxel 0', Voxel 1', ... 'Voxel N'.
- :type folder_name: str (default current working directory)
- :param folder_name: A path where the vtk files will be written, created if non-existant.
- If no path is provided current working directory is used.
+ :type folder_name: str
+ :param folder_name: A path where the vtk files will be written, created if non-existant. \
+ Defaults current working directory
"""
if not folder_name:
folder_name = os.path.abspath(os.getcwd())
@@ -866,7 +877,7 @@ def export_to_csv(self, folder_name=None):
for voxel in range(num_vox):
writer.writerow([voxel] + data[:,voxel].tolist())
- def export_to_vtk(self, timespan, folder_name=None):
+ def __export_to_vtk(self, timespan, folder_name=None):
"""
Write the trajectory to a collection of vtk files.
The exported data is #molecules/volume, where the volume unit is implicit from the mesh dimension.
diff --git a/spatialpy/core/species.py b/spatialpy/core/species.py
index 11a63b53..c1f03142 100644
--- a/spatialpy/core/species.py
+++ b/spatialpy/core/species.py
@@ -28,7 +28,7 @@ class Species():
:param diffusion_coefficient: Non-constant coefficient of diffusion for Species.
:type diffusion_coefficient: float
- :param restrict_to: Set the diffusion coefficient to zero for 'species' in all types not in 'listOfTypes'.
+ :param restrict_to: Set the diffusion coefficient to zero for 'species' in all types not in 'listOfTypes'. \
This effectively restricts the movement of 'species' to the types specified in 'listOfTypes'.
:type restrict_to: int, str, list of ints or list of strs
"""
@@ -71,7 +71,7 @@ def set_diffusion_coefficient(self, diffusion_coefficient):
:param diffusion_coefficient: Non-constant coefficient of diffusion for Species.
:type diffusion_coefficient: float
- :raises SpeciesError: If diffusion_coefficient is negative.
+ :raises SpeciesError: If diffusion_coefficient is negative or not a valid type.
"""
if not (isinstance(diffusion_coefficient, (Parameter, float, int)) or \
type(diffusion_coefficient).__name__ == 'Parameter'):
diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py
index 6f30f0c6..0387165f 100644
--- a/spatialpy/solvers/solver.py
+++ b/spatialpy/solvers/solver.py
@@ -49,7 +49,7 @@ class Solver:
SpatialPy solver object.
:param model: Target model of solver simulation.
- :type model: spatialpy.Model.Model
+ :type model: spatialpy.core.model.Model
:param debug_level: Target level of debugging.
:type debug_level: int
diff --git a/spatialpy/stochss/stochss_export.py b/spatialpy/stochss/stochss_export.py
index 3bd47f6c..02ecc484 100644
--- a/spatialpy/stochss/stochss_export.py
+++ b/spatialpy/stochss/stochss_export.py
@@ -200,13 +200,17 @@ def export(model, path=None, return_stochss_model=False):
"""
SpatialPy model to StochSS converter
- Args:
- spatialpy_model : spatialpy.Model
- SpatialPy model to be converted to StochSS
- filename : str
- Path to the exported stochss model
- return_stochss_model : bool
- Whether or not to return the model
+ :param model: SpatialPy model to be converted to StochSS.
+ :type model: spatialpy.core.model.Model
+
+ :param filename: Path to the exported stochss model.
+ :type filename: str
+
+ :param return_stochss_model: Whether or not to return the model.
+ :type return_stochss_model: bool
+
+ :returns: StochSS model dict if return_stochss_model is True else path to StochSS model file.
+ :rtype: dict | str
"""
_ = model.compile_prep()
if path is None: