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Source code for tvb.dsl.NeuroML.lems.model.component

"""
Parameter, ComponentType and Component class definitions.

@author: Gautham Ganapathy
@organization: LEMS (http://neuroml.org/lems/, https://github.com/organizations/LEMS)
@contact: gautham@lisphacker.org

MAvdVlag: altered attributes for constants and exposures. Added type 'function for CUDA generation'
"""

from ..base.base import LEMSBase
from ..base.map import Map
from ..base.errors import ModelError,ParseError

from .dynamics import Dynamics
from .structure import Structure
from .simulation import Simulation

from ..parser.expr import ExprParser

[docs]class Parameter(LEMSBase): """ Stores a parameter declaration. """ def __init__(self, name, dimension, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the parameter. @type: str """ self.dimension = dimension """ Physical dimension of the parameter. @type: str """ self.fixed = False """ Whether the parameter has been fixed or not. @type: bool """ self.fixed_value = None """ Value if fixed. @type: str """ self.value = None """ Value of the parameter. @type: str """ self.numeric_value = None """ Resolved numeric value. @type: float """ self.description = description """ Description of this parameter. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<{0} name="{1}" dimension="{2}"'.format('Fixed' if self.fixed else 'Parameter', self.name, self.dimension) +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
def __str__(self): return '{0}: name="{1}" dimension="{2}"'.format('Fixed' if self.fixed else 'Parameter', self.name, self.dimension) +\ (' description = "{0}"'.format(self.description) if self.description else '') def __repr__(self): return self.__str__()
[docs]class Fixed(Parameter): """ Stores a fixed parameter specification. """ def __init__(self, parameter, value, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ Parameter.__init__(self, parameter, '__dimension_inherited__', description) self.fixed = True self.fixed_value = value
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Fixed parameter="{0}"'.format(self.name) + ' value="{0}"'.format(self.fixed_value)+'/>'
[docs]class Property(LEMSBase): """ Store the specification of a property. """ def __init__(self, name, dimension = None, default_value = None, description = ''): """ Constructor. """ self.name = name """ Name of the property. @type: str """ self.dimension = dimension """ Physical dimensions of the property. @type: str """ self.description = description """ Description of the property. @type: str """ self.default_value = default_value """ Default value of the property. @type: float """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Property name="{0}"'.format(self.name) +\ (' dimension="{0}"'.format(self.dimension) if self.dimension else 'none') +\ (' defaultValue = "{0}"'.format(self.default_value) if self.default_value else '') +\ '/>'
[docs]class IndexParameter(LEMSBase): """ Stores a parameter which is an index (integer > 0). """ def __init__(self, name, description = ''): """ Constructor. """ self.name = name """ Name of the parameter. @type: str """ self.description = description """ Description of this parameter. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<IndexParameter name="{0}"'.format(self.name) + '' + \ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class DerivedParameter(LEMSBase): """ Store the specification of a derived parameter. """ def __init__(self, name, value, dimension = None, description = ''): """ Constructor. See instance variable documentation for more info on derived parameters. """ self.name = name """ Name of the derived parameter. @type: str """ self.dimension = dimension """ Physical dimensions of the derived parameter. @type: str """ self.value = value """ Value of the derived parameter. @type: str """ self.description = description """ Description of the derived parameter. @type: str """ try: ep = ExprParser(self.value) self.expression_tree = ep.parse() except: raise ParseError("Parse error when parsing value expression " "'{0}' for derived parameter {1}", self.value, self.name)
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<DerivedParameter name="{0}"'.format(self.name) +\ (' dimension="{0}"'.format(self.dimension) if self.dimension else '') +\ (' value="{0}"'.format(self.value) if self.value else '') +\ '/>'
[docs]class Constant(LEMSBase): """ Stores a constant specification. """ def __init__(self, name, default, domain = None, symbol = None, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the constant. @type: str """ self.symbol = symbol """ Symbol of the constant. @type: str """ self.default = default """ Value of the constant. @type: str """ self.domain = domain """ Physical dimensions of the constant. @type: str """ self.description = description """ Description of the constant. @type: str """ self.numeric_value = None """ Numeric value of the constant. @type: float """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Constant' +\ (' name = "{0}"'.format(self.name) if self.name else '') +\ (' symbol = "{0}"'.format(self.symbol) if self.symbol else '') +\ (' value = "{0}"'.format(self.value) if self.value else '') +\ (' dimension = "{0}"'.format(self.dimension) if self.dimension else '') +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class Function(LEMSBase): """ Stores a constant specification. """ def __init__(self, name, value, dimension=None, symbol=None, description=''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the constant. @type: str """ self.symbol = symbol """ Symbol of the constant. @type: str """ self.value = value """ Value of the constant. @type: str """ self.dimension = dimension """ Physical dimensions of the constant. @type: str """ self.description = description """ Description of the constant. @type: str """ self.numeric_value = None """ Numeric value of the constant. @type: float """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Constant' + \ (' name = "{0}"'.format(self.name) if self.name else '') + \ (' symbol = "{0}"'.format(self.symbol) if self.symbol else '') + \ (' value = "{0}"'.format(self.value) if self.value else '') + \ (' dimension = "{0}"'.format(self.dimension) if self.dimension else '') + \ (' description = "{0}"'.format(self.description) if self.description else '') + \ '/>'
[docs]class Exposure(LEMSBase): """ Stores a exposure specification. """ def __init__(self, name, choices, default, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the exposure. @type: str """ self.choices = list(choices.split(", ")) """ Choices of the exposure. @type: str """ self.default = list(default.split(", ")) """ Default option of the exposure. @type: str """ self.description = description """ Description of this exposure. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Exposure name="{0}" dimension="{1}"'.format(self.name, self.choices) +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class Requirement(LEMSBase): """ Stores a requirement specification. """ def __init__(self, name, dimension, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the requirement. @type: str """ self.dimension = dimension """ Physical dimension of the requirement. @type: str """ self.description = description """ Description of this requirement. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Requirement name="{0}" dimension="{1}"'.format(self.name, self.dimension) +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class ComponentRequirement(LEMSBase): """ Specifies a component that is required """ def __init__(self, name, description = ''): """ Constructor. """ self.name = name """ Name of the Component required. @type: str """ self.description = description """ Description of this ComponentRequirement. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<ComponentRequirement name="{0}"'.format(self.name) + '' + \ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class InstanceRequirement(LEMSBase): """ Stores an instance requirement specification. """ def __init__(self, name, type, description = ''): """ Constructor. """ self.name = name """ Name of the instance requirement. @type: str """ self.type = type """ Type of the instance required. @type: str """ self.description = description """ Description of this InstanceRequirement. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<InstanceRequirement name="{0}" type="{1}"'.format(self.name, self.dimension) +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class Children(LEMSBase): """ Stores children specification. """ def __init__(self, name, type_, multiple = False): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the children. @type: str """ self.type = type_ """ Component type of the children. @type: str """ self.multiple = multiple """ Single child / multiple children. @type: bool """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<{2} name="{0}" type="{1}"/>'.format(self.name, self.type, 'Children' if self.multiple else 'Child')
[docs]class Text(LEMSBase): """ Stores a text entry specification. """ def __init__(self, name, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the text entry. @type: str """ self.description = description """ Description of the text entry. @type: str """ self.value = None """ Value of the text entry. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Text name="{0}"'.format(self.name) +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
def __str__(self): return 'Text, name: {0}'.format(self.name)+\ (', description = "{0}"'.format(self.description) if self.description else '') +\ (', value = "{0}"'.format(self.value) if self.value else '') def __repr__(self): return self.__str__()
[docs]class Path(LEMSBase): """ Stores a path entry specification. """ def __init__(self, name, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the path entry. @type: str """ self.description = description """ Description of the path entry. @type: str """ self.value = None """ Value of the path entry. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Path name="{0}"'.format(self.name) +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class EventPort(LEMSBase): """ Stores an event port specification. """ def __init__(self, name, direction, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the event port. @type: str """ d = direction.lower() if d != 'in' and d != 'out': raise ModelError("Invalid direction '{0}' in event port '{1}'".format(direction, name)) self.direction = direction """ Direction - IN/OUT . @type: str """ self.description = description """ Description of the event port. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<EventPort name="{0}" direction="{1}"'.format(self.name, self.direction) +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class ComponentReference(LEMSBase): """ Stores a component reference. """ def __init__(self, name, type_, local=None): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the component reference. @type: str """ self.type = type_ """ Type of the component reference. @type: str """ self.local = local """ ??? @type: str """ self.referenced_component = None """ Component being referenced. @type: FatComponent """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<ComponentReference name="{0}" type="{1}"'.format(self.name, self.type) + \ (' local = "{0}"'.format(self.local) if self.local else '') + \ '/>'
[docs]class Attachments(LEMSBase): """ Stores an attachment type specification. """ def __init__(self, name, type_, description = ''): """ Constructor. See instance variable documentation for more details on parameters. """ self.name = name """ Name of the attachment collection. @type: str """ self.type = type_ """ Type of attachment. @type: str """ self.description = description """ Description about the attachment. @type: str """
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ return '<Attachments name="{0}" type="{1}"'.format(self.name, self.type) +\ (' description = "{0}"'.format(self.description) if self.description else '') +\ '/>'
[docs]class Fat(LEMSBase): """ Stores common elements for a component type / fat component. """ def __init__(self): """ Constructor. See instance variable documentation for more details on parameters. """ self.parameters = Map() """ Map of parameters in this component type. @type: Map(str -> lems.model.component.Parameter) """ self.properties = Map() """ Map of properties in this component type. @type: Map(str -> lems.model.component.Property) """ self.derived_parameters = Map() """ Map of derived_parameters in this component type. @type: Map(str -> lems.model.component.Parameter) """ self.index_parameters = Map() """ Map of index_parameters in this component type. @type: Map(str -> lems.model.component.IndexParameter) """ self.constants = Map() """ Map of constants in this component type. @type: Map(str -> lems.model.component.Constant) """ self.functions = Map() self.exposures = Map() """ Map of exposures in this component type. @type: Map(str -> lems.model.component.Exposure) """ self.requirements = Map() """ Map of requirements. @type: Map(str -> lems.model.component.Requirement) """ self.component_requirements = Map() """ Map of component requirements. @type: Map(str -> lems.model.component.ComponentRequirement) """ self.instance_requirements = Map() """ Map of instance requirements. @type: Map(str -> lems.model.component.InstanceRequirement) """ self.children = Map() """ Map of children. @type: Map(str -> lems.model.component.Children) """ self.texts = Map() """ Map of text entries. @type: Map(str -> lems.model.component.Text) """ self.links = Map() """ Map of links. @type: Map(str -> lems.model.component.Link) """ self.paths = Map() """ Map of path entries. @type: Map(str -> lems.model.component.Path) """ self.event_ports = Map() """ Map of event ports. @type: Map(str -> lems.model.component.EventPort """ self.component_references = Map() """ Map of component references. @type: Map(str -> lems.model.component.ComponentReference) """ self.attachments = Map() """ Map of attachment type specifications. @type: Map(str -> lems.model.component.Attachments) """ self.dynamics = Dynamics() """ Behavioural dynamics object. @type: lems.model.dynamics.Dynamics """ self.structure = Structure() """ Structural properties object. @type: lems.model.structure.Structure """ self.simulation = Simulation() """ Simulation attributes. @type: lems.model.simulation.Simulation """ self.types = set() """ Set of compatible component types. @type: set(str) """
[docs] def add_parameter(self, parameter): """ Adds a paramter to this component type. @param parameter: Parameter to be added. @type parameter: lems.model.component.Parameter """ self.parameters[parameter.name] = parameter
[docs] def add_property(self, property): """ Adds a property to this component type. @param property: Property to be added. @type property: lems.model.component.Property """ self.properties[property.name] = property
[docs] def add_derived_parameter(self, derived_parameter): """ Adds a derived_parameter to this component type. @param derived_parameter: Derived Parameter to be added. @type derived_parameter: lems.model.component.DerivedParameter """ self.derived_parameters[derived_parameter.name] = derived_parameter
[docs] def add_index_parameter(self, index_parameter): """ Adds an index_parameter to this component type. @param index_parameter: Index Parameter to be added. @type index_parameter: lems.model.component.IndexParameter """ self.index_parameters[index_parameter.name] = index_parameter
[docs] def add_constant(self, constant): """ Adds a paramter to this component type. @param constant: Constant to be added. @type constant: lems.model.component.Constant """ self.constants[constant.name] = constant
[docs] def add_function(self, function): """ Adds a paramter to this component type. @param constant: Constant to be added. @type constant: lems.model.component.Constant """ self.functions[function.name] = function
[docs] def add_exposure(self, exposure): """ Adds a exposure to this component type. @param exposure: Exposure to be added. @type exposure: lems.model.component.Exposure """ self.exposures[exposure.name] = exposure
[docs] def add_requirement(self, requirement): """ Adds a requirement to this component type. @param requirement: Requirement to be added. @type requirement: lems.model.component.Requirement """ self.requirements[requirement.name] = requirement
[docs] def add_component_requirement(self, component_requirement): """ Adds a component requirement to this component type. @param component_requirement: ComponentRequirement to be added. @type component_requirement: lems.model.component.ComponentRequirement """ self.component_requirements[component_requirement.name] = component_requirement
[docs] def add_instance_requirement(self, instance_requirement): """ Adds an instance requirement to this component type. @param instance_requirement: InstanceRequirement to be added. @type instance_requirement: lems.model.component.InstanceRequirement """ self.instance_requirements[instance_requirement.name] = instance_requirement
[docs] def add_children(self, children): """ Adds children to this component type. @param children: Children to be added. @type children: lems.model.component.Children """ self.children[children.name] = children
[docs] def add_text(self, text): """ Adds a text to this component type. @param text: Text to be added. @type text: lems.model.component.Text """ self.texts[text.name] = text
[docs] def add_path(self, path): """ Adds a path to this component type. @param path: Path to be added. @type path: lems.model.component.Path """ self.paths[path.name] = path
[docs] def add_event_port(self, event_port): """ Adds a event port to this component type. @param event_port: Event port to be added. @type event_port: lems.model.component.EventPort """ self.event_ports[event_port.name] = event_port
[docs] def add_component_reference(self, component_reference): """ Adds a component reference to this component type. @param component_reference: Component reference to be added. @type component_reference: lems.model.component.ComponentReference """ self.component_references[component_reference.name] = component_reference
[docs] def add_attachments(self, attachments): """ Adds an attachments type specification to this component type. @param attachments: Attachments specification to be added. @type attachments: lems.model.component.Attachments """ self.attachments[attachments.name] = attachments
[docs] def add(self, child): """ Adds a typed child object to the component type. @param child: Child object to be added. """ if isinstance(child, Parameter): self.add_parameter(child) elif isinstance(child, Property): self.add_property(child) elif isinstance(child, DerivedParameter): self.add_derived_parameter(child) elif isinstance(child, IndexParameter): self.add_index_parameter(child) elif isinstance(child, Constant): self.add_constant(child) elif isinstance(child, Exposure): self.add_exposure(child) elif isinstance(child, Requirement): self.add_requirement(child) elif isinstance(child, ComponentRequirement): self.add_component_requirement(child) elif isinstance(child, InstanceRequirement): self.add_instance_requirement(child) elif isinstance(child, Children): self.add_children(child) elif isinstance(child, Text): self.add_text(child) elif isinstance(child, Link): self.add_link(child) elif isinstance(child, Path): self.add_path(child) elif isinstance(child, EventPort): self.add_event_port(child) elif isinstance(child, ComponentReference): self.add_component_reference(child) elif isinstance(child, Attachments): self.add_attachments(child) else: raise ModelError('Unsupported child element')
[docs]class ComponentType(Fat): """ Stores a component type declaration. """ def __init__(self, name, description = '', extends = None): """ Constructor. See instance variable documentation for more details on parameters. """ Fat.__init__(self) self.name = name """ Name of the component type. @type: str """ self.extends = extends """ Base component type. @type: str """ self.description = description """ Description of this component type. @type: str """ self.types.add(name) def __str__(self): return 'ComponentType, name: {0}'.format(self.name)
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ xmlstr = '<ComponentType name="{0}"'.format(self.name) +\ (' extends="{0}"'.format(self.extends) if self.extends else '') +\ (' description="{0}"'.format(self.description) if self.description else '') chxmlstr = '' for property in self.properties: chxmlstr += property.toxml() for parameter in self.parameters: chxmlstr += parameter.toxml() for derived_parameter in self.derived_parameters: chxmlstr += derived_parameter.toxml() for index_parameter in self.index_parameters: chxmlstr += index_parameter.toxml() for constant in self.constants: chxmlstr += constant.toxml() childxml = '' childrenxml = '' for children in self.children: if children.multiple: childrenxml += children.toxml() else: childxml += children.toxml() chxmlstr += childxml chxmlstr += childrenxml for link in self.links: chxmlstr += link.toxml() for component_reference in self.component_references: chxmlstr += component_reference.toxml() for attachment in self.attachments: chxmlstr += attachment.toxml() for event_port in self.event_ports: chxmlstr += event_port.toxml() for exposure in self.exposures: chxmlstr += exposure.toxml() for requirement in self.requirements: chxmlstr += requirement.toxml() for component_requirement in self.component_requirements: chxmlstr += component_requirement.toxml() for instance_requirement in self.instance_requirements: chxmlstr += instance_requirement.toxml() for path in self.paths: chxmlstr += path.toxml() for text in self.texts: chxmlstr += text.toxml() chxmlstr += self.dynamics.toxml() chxmlstr += self.structure.toxml() chxmlstr += self.simulation.toxml() if chxmlstr: xmlstr += '>' + chxmlstr + '</ComponentType>' else: xmlstr += '/>' return xmlstr
[docs]class Component(LEMSBase): """ Stores a component instantiation. """ def __init__(self, id_, type_, **params): """ Constructor. See instance variable documentation for more details on parameters. """ self.id = id_ """ ID of the component. @type: str """ self.type = type_ """ Type of the component. @type: str """ self.parameters = dict() """ Dictionary of parameter values. @type: str """ for key in params.keys(): self.parameters[key] = params[key] self.children = list() """ List of child components. @type: list(lems.model.component.Component) """ self.parent_id = None """ Optional id of parent @type: str """ def __str__(self): return 'Component, id: {0}, type: {1},\n parameters: {2}\n parent: {3}\n'.format(self.id, self.type, self.parameters, self.parent_id) def __repr__(self): return self.__str__()
[docs] def set_parameter(self, parameter, value): """ Set a parameter. @param parameter: Parameter to be set. @type parameter: str @param value: Value to be set to. @type value: str """ self.parameters[parameter] = value
[docs] def add_child(self, child): """ Adds a child component. @param child: Child component to be added. @type child: lems.model.component.Component """ self.children.append(child)
[docs] def add(self, child): """ Adds a typed child object to the component. @param child: Child object to be added. """ if isinstance(child, Component): self.add_child(child) else: raise ModelError('Unsupported child element')
[docs] def set_parent_id(self, parent_id): """ Sets the id of the parent Component @param parent_id: id of the parent Component @type parent_id: str """ self.parent_id = parent_id
[docs] def toxml(self): """ Exports this object into a LEMS XML object """ xmlstr = '<Component id="{0}" type="{1}"'.format(self.id, self.type) for (k, v) in self.parameters.items(): xmlstr += ' {0}="{1}"'.format(k, v) if self.children: xmlstr += '>' for child in self.children: xmlstr += child.toxml() xmlstr += '</Component>' else: xmlstr += '/>' return xmlstr
[docs]class FatComponent(Fat): """ Stores a resolved component. """ def __init__(self, id_, type_): """ Constructor. See instance variable documentation for more details on parameters. """ Fat.__init__(self) self.id = id_ """ ID of the component. @type: str """ self.type = type_ """ Type of the component. @type: str """ self.child_components = list() """ List of child components. @type: lems.model.component.FatComponent """ self.parent_id = None """ Optional id of parent @type: str """ def __str__(self): return 'FatComponent, id: {0}, type: {1}, parent:{2}'.format(self.id, self.type, self.parent_id)+\ (', num children: {0}'.format(len(self.child_components)) if len(self.child_components)>0 else '')
[docs] def add_child_component(self, child_component): """ Adds a child component to this fat component. @param child_component: Child component to be added. @type child_component: lems.model.component.FatComponent """ self.child_components.append(child_component)
[docs] def add(self, child): """ Adds a typed child object to the component type. @param child: Child object to be added. """ if isinstance(child, FatComponent): self.add_child_component(child) else: Fat.add(self, child)
[docs] def set_parent_id(self, parent_id): """ Sets the id of the parent Component @param parent_id: id of the parent Component @type parent_id: str """ self.parent_id = parent_id